Atlantic Salmon Recovery Framework

 Atlantic Salmon Recovery Framework: 2011 Annual Report A summary of the collaborative actions under taken by the State of Maine, US Government, Penobscot Nation, and non‐governmental organizations to recover the Gulf of Maine Distinct Population Segment of Atlantic salmon in calendar year 2011. Prepared by Maine Department of Marine Resources US Fish and Wildlife Service and National Marine Fisheries Service Atlantic Salmon Recovery Plan 2011 Annual Report Page 1 Executive Summary Estimated total adult Atlantic salmon returns to rivers in the geographic area of the Gulf of Maine Distinct Population Segment (GOM DPS) in 2011 were 3,556. Most of the returns were to rivers in the Penobscot Bay Salmon Habitat Recovery Unit (SHRU). The number of potential spawners in rivers during autumn, known as escapement, was 3,815. Escapement of all ages to the GOM DPS area was not evenly distributed among the SHRU. Escapement was 56% of the estimated 2SW Conservation Spawner Escapement (CSE) for rivers in the Downeast Coastal SHRU; 37%of CSE for rivers in the Penobscot Bay SHRU, and 7% of CSE for the rivers in the Merrymeeting Bay SHRU. The current ten‐year geometric mean replacement rate, calculated from naturally reared returns with a five year time lag, exceeded 1.0 only for the Merrymeeting Bay SHRU. Marine survival (smolt to adult) for the 2009 cohort was higher for naturally reared smolt (2.03%) than for hatchery smolt on the Penobscot (0.38%) or Narraguagus (0.17%). In 2011, the Conservation Hatchery Action Team worked collaboratively to implement programs to prevent extinction and to maintain effective population size and genetic diversity of river specific Atlantic salmon populations in Maine. Approximately 3,316,000 salmon fry, 329,500 parr, 691,000 smolts, 994 pre‐spawn adults, and 2,552 post‐spawn adults were stocked into 12 rivers in Maine throughout the year. The USFWS provided eggs to the Downeast Salmon Federation hatchery facilities on the Pleasant and East Machias rivers. Both Green Lake and Craig Brook National Fish Hatcheries conducted fish health inspections and screenings to ensure high quality, healthy fish for salmon stocking efforts in Maine. Photoperiod was manipulated at Craig Brook to delay spawning of the 556 Penobscot River sea‐run broodstock, shift incubation at the hatchery to optimal water temperatures, and improve synchrony of fry development and environmental conditions at the time of released. The team, in collaboration with other Action Teams, reviewed proposals for new actions focused on new stocking strategies, determining fish passage effectiveness at hydropower dams in the Penobscot River watershed, and potential behavioral differences inadvertently created by handling and tagging of hatchery salmon. Maintaining genetic diversity and preserving the genetic structure present in Atlantic salmon is a critical component of recovery of Atlantic salmon in Maine. The Genetic Diversity Action Team has identified 27 actions in three primary focus areas: monitoring genetic diversity, evaluating hatchery practices and products, and monitoring to detect aquaculture Atlantic salmon. These actions are consistent with current broodstock management and include monitoring and evaluating hatchery management practices, and performance (survival) of hatchery products in the wild. Estimates of genetic diversity within each broodstock, broodstock screening, and genetic parentage assessments of broodstock that are basis for GDAT actions are provided. Marine ecology of Atlantic salmon has often been equated to a black box, however, new research tools and integrated oceanography and bioenergetics models are providing new insights in the ecology of salmon at sea. For 2011 the Marine and Estuarine Action Team took an interdisciplinary and multiagency approach to increase understanding of the structure and function of estuarine and marine communities and migration ecology of Atlantic salmon. A working paper summarizing the 2008‐2010 Maine Sea Grant ‐ NOAA Fisheries Workshops that reframed existing North American Atlantic salmon marine mortality hypotheses and presented new perspectives was completed in 2011. The document emphasized identifying parameters relevant to Gulf of Maine Atlantic salmon that could be managed at local or regional scales. Rather than a single, high‐profile species approach, the interdisciplinary group determined that integrating climate, environmental, fisheries, and community ecology studies was a Atlantic Salmon Recovery Plan 2011 Annual Report Page 2 better approach for understanding and managing a functioning and sustainable salmonid ecosystem. The document identified six primary hypotheses; five are priority for team actions. The team held a meeting in August to exchange information, coordinate research, and increase public awareness of the team’s activities. US scientists and managers, team members, and partners participated in NASCO‐ICES symposium entitled 'Salmon at Sea: Scientific Advances and their Implications for Management' in October, presenting posters and talks and preparing manuscripts for the symposium publication. The Freshwater Action Team is working to increase adult spawners through the freshwater production of smolts. The team had several metric to evaluate the abundance and distribution of Atlantic salmon, including juvenile abundance, smolt production, adult returns, and the number and distribution of redds. The highlight for the 2011 assessment was implementing a Generalized Random ‐ Tessellated Stratified sampling design (Stevens and Olsen 2004) for the 2011 sampling season. This new sampling design will allow us to monitor changes in abundance and distribution over time. A variety of habitat restorations were implemented by state and federal agencies and NGOs in 2011. Project SHARE was instrumental in implementing additions of large woody debris on the Narragugus River and the removal of ruminant log drive dams. Maine DEP and Project SHARE collaborated on a project to increase the buffering capacity of Dead Stream by adding clam shells. USFWS and NGOs continued efforts to identify areas for habitat restoration and protection. Modeling efforts included the USFWS’ Salmon Rearing Habitat Model, TNC’s Northeast Aquatic Resilience Project, Active River Area Prioritization, and Project SHARE’s Atlantic salmon Decision Support System. Ultimately the team expects to use the modeling information to generate a list of habitat restoration projects and locations for protection within each SHRU. The Connectivity Action Team focused on reconnecting headwater areas that are important for salmon spawning and rearing with the Gulf of Maine, highlighting three categories of actions in 2011: 1) Developing a list of barrier priorities for the GOM DPS and implementing connectivity restoration projects in a strategic fashion; 2) Monitoring and reporting on the effectiveness of connectivity restoration projects; 3) Minimizing the effects of existing fish passage barriers (such as dams) and providing incidental take authorization where appropriate. For 2011, the team estimated that between 38,000 and 39,000 suitable habitat units were probably accessible across the geographic range of the Gulf of Maine Distinct Population Segment, with approximately 68% of that in the Downeast Coastal Salmon Habitat Recovery Unit. The Education and Outreach Team worked with each Action Team to determine what messages and products were needed. The Team managed http://www.maine.gov/dmr/searunfish/salmonframework.shtml, which contains information about the Atlantic Salmon Framework and links to: Framework documents; news items related to Atlantic salmon recovery; meeting announcements; related agency websites; and the names of agency outreach contacts. They are working to complete an overall Education and Outreach Plan that provides a new direction for outreach, communication and stakeholder engagement. As the new draft recovery plan nears completion, they propose to use it as a focal point for transforming outreach, communication, and stakeholder engagement associated with the shared mission to recover Atlantic salmon. Atlantic Salmon Recovery Plan 2011 Annual Report Page 3 Table of Contents Executive Summary .................................................................................................................................. 2
Stock Assessment Action Team .............................................................................................................. 5
Conservation Hatchery Action Team .................................................................................................. 15
Genetic Diversity Action Team ............................................................................................................. 18
Marine and Estuarine Action Team ..................................................................................................... 27
Freshwater Action Team ....................................................................................................................... 36
Connectivity Action Team ..................................................................................................................... 44
Education and Outreach Action Team ................................................................................................ 52
Atlantic Salmon Recovery Plan 2011 Annual Report Page 4 Stock Assessment Action Team Michael Bailey, US Fish and Wildlife Service John Kocik, NOAA’s National Marine Fisheries Service John Sweka, US Fish and Wildlife Service Joan Trial, Maine Department of Marine Resources Strategy Assess the status and trends of the stocks that comprise the GOM DPS. Adult Returns Estimated total adult Atlantic salmon returns to rivers in the geographic area of the Gulf of Maine DPS (73 FR 51415‐51436) in 2011 were 3,556. Most of the returns were to the Penobscot Bay Salmon Habitat Recovery Unit (SHRU) (Figure 1.1). Returns were the sum of counts at fishways and weirs (3,438) and estimates from redd surveys. Counts were obtained at fishway trapping facilities on the Androscoggin, Narraguagus, Penobscot, Kennebec, and Union rivers, and at a semi‐permanent weir on the Dennys River. Fall conditions were suitable for adult dispersal throughout the rivers, and conditions allowed redd counting. The origin of the returns (hatchery or naturally reared) varied among the SHRU (Figure 1.2), with the lowest percentage of naturally reared salmon in the population occurring in the Penobscot Bay SHRU. In 2011 the numbers of potential spawners in rivers during autumn, known as escapement, was 3,815. Escapement of all ages to the GOM DPS area was not evenly distributed among the SHRU and was at most 56% of the estimated 2SW Conservation Spawner Escapement for rivers within a SHRU (Table 1.1). The differences in escapement were influenced by broodstock removal, and the distribution and number of smolt (Penobscot and Narraguagus rivers) and pre‐spawn captive broodstock stocked (Table 1.1). Table 1.1. Estimated 2011 spawner escapement into rivers within the three geographic areas defined as Salmon Habitat Recovery Units (SHRU) for the GOM DPS. Escapement = Returns – Losses + Stocked pre‐spawn adults. Returns = includes sea run returns and captive reared repeat spawners. Losses = broodstock and documented mortalities. Stocked = number of mature captive reared adults released to spawn naturally. CSE = Conservation spawner escapement for rivers within each SHRU (Beland 1984 and Colligan et al. 1999). SHRU
Returns
Losses
Stocked
Escapement
Downeast Coastal
304
737
1,041
1
Penobscot Bay
3,128
570
2,558
2
Merrymeeting Bay
127
1
90
216
Total
3,559
571
827
3,815
1
sea run returns + 3 captive reared repeat spawners, Broodstock to CBNFH
2
Illegal harvest
Atlantic Salmon Recovery Plan 2011 Annual Report CSE
1,865
6,942
3,280
12,087
% CSE
56%
37%
7%
32%
Page 5 For this report replacement rates were estimated based on naturally reared returns, however, the team is working to integrate estimates of escapement into the calculations. Estimated (adult to adult) replacement rate for returns to the GOM DPS as a whole has not exceeded one since the mid 1990’s (Figure 3). Most of the adults were 2SW salmon that emigrated as 2 year old smolt, thus, cohort replacement rates were calculated assuming a five year lag. These rates were used to calculate the geometric mean for the previous ten years (e.g. for 2000: 1991 to 2000) for the naturally reared component of returns to the GOM DPS overall and in each of three Salmon Habitat Recovery Units (SHRU). The current ten‐year geometric mean replacement rate exceeded 1.0 only for the Merrymeeting Bay SHRU. We also calculated apparent sub‐basin redd to redd replacement (2006 to 2011) rates for stocked adults. On Mopang Stream the apparent adult to adult replacement rate of 0.22. The replacement rate for captive reared adults on the Sheepscot River was 0.25. No redds and/or test pits were documented during a 2011 activity survey in Hobart Stream. In 2012, data on redd to redd replacement for sea run returns will be available for Old Stream. 6000
Numbers
5000
Merrymeeting Bay
Penobscot Bay
Downeast Coastal
4000
3000
2000
1000
0
1967 1972 1977 1982 1987 1992 1997 2002 2007
Year
Figure 1.1. Documented returns of Atlantic salmon to the GOM DPS by Salmon Habitat Recovery Units (SHRU). Numbers include angler harvests (up to 1986 on the Pleasant and 1995 on other rivers), trap and weir counts, and redd based estimates (1991 to 2011). Downeast Coastal SHRU Sea Run Spawners. Returns in 2011 were based on adult captures at the Dennys River weir, Cherryfield fishway trap, and fishway trap operated by Black Bear Hydro Partners, LLC on the Union River in Ellsworth below Graham Lake. On the Dennys River a total of nine sea run salmon were captured. The weir also captured three (3) aquaculture escapes and six (6) male captive reared adults released as part of the Dennys River pre‐spawn adult release experiment. These nine (9) salmon are not included in the season sea run return total. Staff documented 196 sea‐run salmon in the Narraguagus River ascending the Stillwater Dam in Cherryfield, Maine. Sea run spawners included 179 adults captured in the fishway trap and 17 adult salmon observed ascending the spillway (recorded on video). No salmon were captured in the trap on the Union River. Atlantic Salmon Recovery Plan 2011 Annual Report Page 6 100%
90%
Naturally Reared
80%
70%
60%
50%
40%
30%
20%
10%
0%
1967
1972
1977
Downeast Coastal
1982
1987
Year
1992
1997
Merrmeeting Bay
2002
2007
Penobscot Bay
Figure 1.2. Estimated percentage of returns that were naturally reared Atlantic salmon in the three Salmon Habitat Recovery Units (SHRU) defined for the GOM DPS. 10 year geometric mean replacement rate (naturally reared)
8
GOM DPS
7
Merrymeeting Bay
6
Penobscot Bay
5
Downeast Coastal
4
3
2
1
0
1990
1995
2000
Year
2005
2010
2015
Figure 1.3. Ten‐year geometric mean of replacement rate for returning naturally reared Atlantic salmon in the GOM DPS and in the three Salmon Habitat Recovery Units (SHRU). Estimated returns were extrapolated from redd count data using a return‐redd regression [ln (returns) = 0.559 ln (redd count) + 1.289] based on redd and adult counts from 1991‐2009 on the Narraguagus River, Dennys River and Pleasant River (USASAC 2010). Twenty six (26) redds attributed to wild returns were counted during 2011 redd surveys in the East Machias River that included approximately 98% of known spawning habitat area. A total of 188 redds were counted in approximately 87% of the spawning habitat area in the Machias drainage. Twenty three (23) redds were found in the Pleasant River in 2011 during surveys of about 85% of spawning habitat area. Captive Reared Spawners. A total of 737 CBNFH captive reared spawners were stocked into rivers in the Downeast Coastal SHRU in 2011. Most stockings were river specific: Dennys River (299), East Machias River [Northern Stream] (41), and Machias River [West Branch Machias River] (109). Releases of 288 mixed river origin salmon occurred in the Union River: East Machias (22), Machias (39), Narraguagus (108), and Pleasant (119). Spawning activity was observed in all rivers where this fish were stocked. One hundred and three (103) redds were counted during the 2011 redd surveys on the Dennys River that included approximately 89% of known spawning habitat area. On the East Machias 54 redds Atlantic Salmon Recovery Plan 2011 Annual Report Page 7 were located in Northern Stream. Ninety one (91) redds were documented in the West Branch of the Machias watershed where adults were stocked. Penobscot Bay SHRU Sea Run Spawners. Adult returns to the SHRU were dominated by captures at the Veazie Dam fishway trap on the Penobscot River. A total of 3,125 sea run Atlantic salmon were captures during 2011 and additional three captive reared adults released post‐spawn from Green Lake National Fish Hatchery were captured as repeat spawners. Of these 855 were released directly into the Penobscot River upstream of the Veazie Trap and an additional 1,537 salmon were trucked upstream to boat launches in Costigan and Old Town for release. A total of 736 salmon were transported to CBNFH, 570 were retained as broodstock and 166 salmon (109 females, 57 males) were subsequently released prior to spawning habitat in the Piscataquis River. Thus, total escapement to the Penobscot River above the Veazie Dam in 2011 was 2,558 Atlantic salmon. Based on trap counts at Weldon Dam 194 of these entered the East Branch. Estimated escapement to the Ducktrap River and Cove Brook was zero (0) based on redd counts. The survey on the Ducktrap River encompassed 73% of the spawning habitat area in the watershed and on Cove Brook 100% of identified Atlantic salmon spawning habitat was surveyed. Merrymeeting Bay SHRU Sea Run Spawners. Adult returns were counted at traps on the Androscoggin and Kennebec Rivers. The total trap catch at the Brunswick fishway trap on the Androscoggin River was 44 adult sea run Atlantic salmon. One salmon was illegally harvested by an angler. On the Kennebec River the sea‐run Atlantic salmon catch at the Lockwood fish lift was 64 adult; all were trucked and released to the Sandy River. No adult Atlantic salmon were captured or observed at the Benton Falls fish lift on the Sebasticook River, a Kennebec River tributary during 2011. Redd surveys conducted on the Sheepscot River focused on spawning habitat in the upper portion of the mainstem and West Branch and documented a total of 19 redds. Captive Reared Spawners. The Sheepscot River origin captive reared adults stocked in Togus Stream, a tributary to the Kennebec River estuary, produced 21 redds. Juvenile Population Status A Generalized Random ‐ Tessellated Stratified (GRTS) design (Stevens and Olsen 2004) was implemented for the 2011 sampling season. A total of 259 sites were developed for the Downeast SHRU, the Penobscot Bay SHRU, and the Merrymeeting Bay SHRU. Selection criteria included stream width and drainage. The sampling frame was selected using either the NHD Flow line feature from USGS or the Habitat Model developed by Wright et al. (2011) (see Freshwater Action Team for details). DMR conducted electrofishing surveys to monitor spatial and temporal abundance of Atlantic salmon juveniles at 346 sites in 2011. Two hundred and thirty five (235) of the sites were randomly selected (GRTS). The other sites were selected to document juvenile production from adult stocking and egg planting. Two sampling methods were used; the first estimated total abundance at sites on each river with data presented as fish/unit, where one unit equals 100 m2. The second method was based on standardized wand sweeping protocols for 300 seconds of wand time (catch per unit effort (CPUE) and produced relative abundance in fish/minute. At 24 (10.2%) of the randomly selected sites, CPUE sampling was done inside a total abundance site. These randomly chosen “double method” sites were Atlantic Salmon Recovery Plan 2011 Annual Report Page 8 done to maintain a record of catchability for gear and methods and to calibrate CPUE data among years. Data aggregated by Salmon Habitat Recovery Unit (Table 1.2) document the relative low juvenile Atlantic salmon populations throughout the geographic range of the Gulf of Maine DPS in the last six years. An index of juvenile abundance, calculated using annual densities (log + 0.01 transformed) at sites with more than ten years of data, confirms the relative low densities (Figure 1.5). A mixed random effects general linear model was used to analyze the data, with years specified as fixed effects; sites within 10 digit HUCs and 10 digit HUCs within years considered random effects. A "no intercept" model was specified. The index is the estimated annual least square means (and 95% CI) back transformed from logarithms to density. The index is sensitive to sample size, evidenced by the large confidence intervals and mean for 2011 (Figure 1.5), which had the lowest number of estimates since 2006 (Table 1.2). A similar index will be produced for relative abundances, when more years of data are available. Table 1.2. Minimum (min), median, and maximum (max) density (fish/100m2) and relative abundance (fish/minute) of Atlantic salmon juveniles. Data from sampled rivers were aggregated by Salmon Habitat Recovery Unit (SHRU), 2006 to 2011. SHRU
Downeast Coastal
Penobscot Bay
Merrymeeting Bay
Year
2006
2007
2008
2009
2010
2011
2006
2007
2008
2009
2010
2011
2006
2007
2008
2009
2010
2011
N
76
55
43
56
29
19
74
49
11
10
7
5
42
33
26
17
22
17
9
CPUE fish / minute
N
73
53
43
56
29
19
48
25
11
10
8
5
41
33
27
17
21
17
YOY
Min
Median
0.00
2.84
0.42
7.33
7.02
0.00
7.66
0.00
0.00
8.03
3.41
0.00
0.00
0.00
0.00
0.00
0.00
19.94
29.80
4.07
0.00
0.74
0.00
4.06
0.28
0.00
4.03
0.00
0.00
2.17
3.12
0.00
3.03
0.00
0.00
1.89
Max
51.53
58.85
73.83
36.54
89.09
65.74
67.16
66.78
47.08
39.74
29.54
49.80
25.28
69.76
38.85
28.07
109.94
43.26
N
139
133
18
49
91
173
24
41
82
161
86
87
12
37
38
46
110
45
Parr
Min
Median
0.00
1.01
0.00
0.56
0.00
0.00
0.79
0.00
0.00
1.00
0.80
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.20
Max
3.46
5.05
1.00
20.39
8.84
8.74
1.60
2.51
1.49
2.93
3.91
3.82
0.63
2.60
0.77
3.27
2.94
4.37
N
155
141
18
54
96
173
34
53
88
163
95
87
11
33
39
48
112
45
YOY
Min
Median
0.00
1.40
0.00
1.58
0.35
0.00
1.59
0.00
0.00
1.40
0.60
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.00
0.75
0.00
0.00
0.00
0.00
0.20
0.00
0.00
0.00
0.20
0.00
0.80
0.00
0.00
0.20
Max
4.33
15.31
8.75
15.37
15.54
6.32
2.20
1.80
6.75
4.48
15.95
5.72
3.95
5.03
1.40
9.35
29.40
9.80
Gulf of Maine
8
Density (parr per unit)
Density fish / unit
Parr
Min
Median
Max
0.00
2.85
35.21
0.00
2.88
22.32
3.55
0.00
20.15
3.75
0.00
32.53
0.54
5.17
28.00
2.83
0.00
94.58
0.19
0.00
26.88
0.00
0.00
33.73
0.00
6.69
17.75
7.89
0.00
20.39
0.00
17.03
22.07
0.00
6.99
14.90
1.34
0.00
23.38
0.28
0.00
50.27
0.00
1.65
21.65
6.01
0.00
21.74
2.14
0.00
16.57
0.00
8.65
44.45
7
6
5
4
3
2
1
0
1980
1985
1990
1995
2000
2005
2010
Year
2015
Figure 1.5. Index of parr abundance in the Gulf of Maine DPS, based on juvenile salmon assessments conducted from 1984 to 2011. Smolt Abundance NOAA‐National Marine Fisheries Service (NOAA) and the Maine Bureau of Sea Run Fisheries and Habitat (BSRFH), conducted seasonal field activities enumerating smolt populations using Rotary Screw Traps Atlantic Salmon Recovery Plan 2011 Annual Report Page 9 (RSTs) in one river in each SHRU. Scientists generated population estimates using program DARR 2.0.2 for R (Bjorkstedt 2005; Bjorkstedt 2010). Beginning in 2009, estimates for all years in the time series were recalculated using DARR 2.0, which differs from the program used in the past (SPAS; Arnason et al. 1996) in that DARR pools strata based on several predetermined factors and ensures a more rigorous and repeatable analysis. Downeast Coastal SHRU On the Narraguagus River 4,044 smolts were handled, 131 (3.2%) of which were recaptures. During the first week of May, ~ 63,000 age 1+ salmon smolts were stocked, and therefore most (93%) of the smolts captured were hatchery origin. The total estimate and standard error (STDER) of smolts (naturally reared, fall parr and hatchery stocked smolts) exiting the Narraguagus system was 27,737 ± 2,508. Similar to 2010, the overall estimate was much lower than the known number of 1+ hatchery smolts that were stocked into the system. The population estimate (STDER) for naturally‐reared smolts was 1,404 ± 381 smolts (Figure 1.6), considerably less than that of the previous year (2,170 ± 228) and slightly higher than the estimates from 2007‐2009. Penobscot Bay SHRU We collected 573 naturally reared smolts in the Piscataquis River RSTs, 393 of which were marked and released 3.2 km upstream. Of these marked smolts, 64 were recaptured (16.4%). The population estimate (STDER) of migrating smolts was 5,209 ± 1,312 (Figure 1.6). Merrymeeting Bay SHRU We captured 462 smolts at the Sheepscot River site, 206 of which were marked with an adipose clip, indicating they were stocked as 0+ parr in 2009 or 2010. The population estimate (STDER) of naturally‐
reared smolts was 1,702 ± 370 (1.1 smolts/habitat unit) and about 40% of the 2010 estimate (3,936 ± 370) (Figure 1.6). The estimate of hatchery origin smolts (stocked as fall parr in 2009 and 2010) in 2011 was 1,720 ± 399 (STDER). Atlantic Salmon Recovery Plan 2011 Annual Report Page 10 Figure 1.6. Population Estimates (± Std. Error) of emigrating smolts in the Narraguagus River (Downeast Coastal SHRU), Piscataquis River (Penobscot Bay SHRU), and Sheepscot River (Merrymeeting Bay SHRU), Maine from 1997 to 2010 using DARR 2.0.2. Survival Estimates Estuarine and Marine Atlantic salmon survival rates were calculated for marked hatchery stocks and naturally reared stocks for the Narraguagus, Penobscot, and Sheepscot rivers (Table 1.3). Calculations were based on known numbers of stocked salmon, smolt estimates, and adult returns. Smolt‐to‐adult (SAR) survival rates, the available proxy for marine survival, varied by origin. Hatchery parr stocked on the Narraguagus River had the highest average SAR survival, followed by naturally reared salmon and hatchery smolts, respectively. Hatchery parr‐to‐adult survival (PAR), which may include from 8 months to two years in freshwater, was similar between the Narraguagus hatchery parr and the accelerated growth parr stocked in the Penobscot River. Atlantic Salmon Recovery Plan 2011 Annual Report Page 11 Freshwater Over the last eight years survival rates of juvenile Atlantic salmon in freshwater were calculated based on stocking numbers and/or estimates of eggs deposited, 0+ and 1+ parr, and smolt populations for reaches or sub‐watersheds. We estimated the survival rate for each freshwater residence period as: where is the lifestage specific survival, is the estimated number or number stocked at lifestage i and is the estimated number at the following lifestage . To be able to use these rates in population models over varying periods of freshwater residence survival rates were converted to monthly survival based on the number of months encompassed by the transition from one stage to the next (Table 1.4). This is the first document where these survival rates have been compiled and we are identifying more opportunities to estimate survival. Research Projects An inventory of recently completed, ongoing, and supported projects is being maintained by the team (Appendix 1). Literature Cited Arnason, A. N. K. C. W., Schwarz, C. J., and Irvine, J. R. 1996. Computer Analysis of Data from Stratified Mark‐Recovery Experiments For Estimation of Salmon Escapements and Other Populations. Canadian Technical Report of Fisheries and Aquatic Sciences 2106: 37 pp. Beland, K.F. 1984. Strategic plan for management of Atlantic salmon in the state of Maine. Atlantic Sea Run Salmon Commission, Bangor, Maine. 92 pp. Bjorkstedt, E.P. 2010. DARR 2.0.2: DARR for R. http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3346 Bjorkstedt, E. P. 2005. DARR 2.0: updated software for estimating abundance from stratified mark‐
recapture data. NOAA Technical Memorandum NMFS‐SWFSC‐368. 13 p. Colligan, M.A., J.F. Kocik, D.C. Kimball, J. Marancik, J.F. McKeon, and P.R. Nickerson. 1999. Review of the status of anadromous Atlantic salmon (Salmo salar L.) under the U.S. Endangered Species Act. NMFS/USFWS Joint Publication. Gloucester, Massachusetts. 230 pp. Stevens, D. L. Jr. and A. R. Olsen. 2004. Spatially balanced sampling of natural resources. J. of the Amer. Stat. Assoc. 99(465): 262‐278. Atlantic Salmon Recovery Plan 2011 Annual Report Page 12 Table 1.3. Summary table of Atlantic salmon survival rates that include estuarine and marine lifestages. All rates for hatchery origin stocks were based on marked groups. Data represent cohorts were all 2 sea‐winter adult returns have been accounted for. Therefore, in some cases some 3 sea‐winter adults may still be at large. Cohort
Year
2008
2009
2008
2009
2006
2007
2008
2009
2006
2007
2008
2009
2006
2007
2002
2003
2004
2005
2006
2007
Salmon Habitat
Recovery Unit
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Downeast Coastal
Downeast Coastal
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Drainage
Narraguagus
Narraguagus
Narraguagus
Narraguagus
Narraguagus
Narraguagus
Narraguagus
Narraguagus
Penobscot
Penobscot
Penobscot
Penobscot
Narraguagus
Narraguagus
Penobscot
Penobscot
Penobscot
Penobscot
Penobscot
Penobscot
Source
Hatchery Smolts
Hatchery Smolts
Hatchery Parr
Hatchery Parr
Naturally Reared
Naturally Reared
Naturally Reared
Naturally Reared
Hatchery Smolts
Hatchery Smolts
Hatchery Smolts
Hatchery Smolts
Hatchery Parr
Hatchery Parr
Hatchery Accelerated Parr
Hatchery Accelerated Parr
Hatchery Accelerated Parr
Hatchery Accelerated Parr
Hatchery Accelerated Parr
Hatchery Accelerated Parr
Survival
From
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Smolt
Parr
Parr
Parr
Parr
Parr
Parr
Parr
Parr
Survival
To
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Adult
Number
Stocked or
Estimated
54116
52829
414
231
2300
1210
962
1180
169066
147619
147789
178034
17476
15687
50249
72835
69719
96320
100541
105577
Number of
survivors
21
88
5
9
19
9
7
24
409
529
241
673
5
9
27
26
34
41
54
23
%
Survival
0.0388
0.1666
1.2077
3.8961
0.8261
0.7438
0.7277
2.0339
0.2419
0.3584
0.1631
0.3780
0.0286
0.0574
0.0537
0.0357
0.0488
0.0426
0.0537
0.0218
Table 1.4. Summary table of Atlantic salmon freshwater survival rates (period and monthly) based on number of hatchery product stocked or estimates of juvenile life stages or eggs spawned. Initial
Lifestage
Cohort
Year
Survival
From
Survival
To
Number
Stocked
or
Estimated
Number
of
survivors
Approx.
Months
Period
%
Survival
Monthly
%
Survival
2010
2010
2010
2011
2011
2011
2010
2010
2010
2006
2007
2008
2008
SHRU
Drainage
Source
Downeast Coastal
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Naturally Reared
East Machias
Hatchery
Narraguagus
Both
Narraguagus
Both
Narraguagus
Both
Egg
Egg
Egg
Egg
Egg
Egg
YOY
YOY
YOY
YOY
Parr
Parr
Parr
YOY
YOY
YOY
YOY
YOY
YOY
Parr
Parr
Parr
Parr
Smolt
Smolt
Smolt
30,055
30,055
15,028
26,607
35,476
79,821
1,397
370
1,356
1,670
10,213
12,959
8,245
1,397
370
1,356
86
17
4,177
410
244
1,042
1,077
1,020
750
1,082
10
10
10
10
10
10
12
12
12
12
8
8
8
4.6
1.2
9.0
0.3
0.05
5.2
29.3
65.9
76.8
64.5
10.0
5.8
13.1
73.6
64.4
78.6
56.4
46.6
74.5
90.3
96.6
97.8
96.4
75.0
70.0
77.6
2009
2009
2010
2010
2010
2010
2010
2010
2010
2010
2004
2005
2006
2007
2008
Merrymeeting Bay
Sheepscot
Naturally Reared
Sheepscot
Naturally Reared
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sandy
Hatchery
Sheepscot
Hatchery
Sheepscot
Hatchery
Sheepscot
Hatchery
Sheepscot
Hatchery
Sheepscot
Hatchery
Egg
Egg
Egg
Egg
Egg
Egg
Egg
Egg
Egg
Egg
0 Parr
0 Parr
0 Parr
Fry
0 Parr
YOY
Parr
YOY
YOY
YOY
YOY
YOY
YOY
YOY
YOY
Parr
Parr
Parr
Parr
Parr
75,000
75,000
46,160
42,500
55,930
192,920
47,940
104,130
5,825
47,940
15,600
15,882
16,600
29,900
13,048
3,540
4,959
8,833
5,857
38,518
49,703
24,581
31,301
2,002
32,219
3,565
1,206
7,743
409
4,677
10
31
8
8
8
8
8
8
8
8
11
11
11
16
11
4.7
6.6
19.1
13.8
68.9
25.8
51.3
30.1
34.4
67.2
22.9
7.6
46.6
1.4
35.8
73.7
91.6
81.3
78.1
95.4
84.4
92.0
86.0
87.5
95.2
87.4
79.1
93.3
76.5
91.1
Conservation Hatchery Action Team Ernie Atkinson, Maine Department of Marine Resources Paul Christman, Maine Department of Marine Resources Chris Domina, US Fish and Wildlife Service Anitra Firmenich, US Fish and Wildlife Service Peter Lamothe, CHAIR, US Fish and Wildlife Service Christine Lipsky, NOAA’s National Marine Fisheries Service Joe Zydlewski, USGS Co‐operative Fisheries and Wildlife Unit Strategy Increase Adult Spawners through the Conservation Hatchery Program Strategy Metric Adult return per egg equivalent, reported by SHRU Background: The Conservation Hatchery Action Team (C.H.A.T) addresses the threat of declining populations and the eventual extirpation of river specific populations and/or the entire Gulf of Maine Distinct Population Segment. C.H.A.T. also addresses the loss of population diversity (genetic, morphological, physiological, and behavioral), catastrophic disease contraction and transmission, and catastrophic cohort loss in the wild. Accomplishments The conservation hatchery program currently implements the following: •
•
•
Brood stock management: Penobscot River sea‐run and domestic brood programs, and the captive brood program for the Sheepscot, Narraguagus, Pleasant, Machias, East Machias, and Dennys Rivers, with both pre‐and post spawn adults stocked (Table 2.1) Juvenile Production: various life stage and stocking strategies for each population held in the conservation hatchery program (Table 2.2) Fish health management: fish health inspections, screening, diagnostics and treatment and surveillance Members of the C.H.A.T. are working with the Stock Assessment Team to develop a performance metric for adult salmon returns per egg equivalent that can be used to explore the lifetime contributions of hatchery and naturally reared adult salmon to rivers within each salmon habitat recovery unit. Additional performance metrics that use estimated survival rates of different life‐stages of salmon being stocked in the GOM DPS and the relationship of survival of these fish to habitat quality are also being considered. Atlantic Salmon Recovery Plan 2011 Annual Report Page 15 Table 2.1. Number of adult Atlantic salmon stocked in Maine during 2011. Captive/Domestic
Sea Run
Pre-Spawn Post-Spawn Pre-Spawn Post-Spawn
Dennys
299
0
0
0
East Machias
41
123
0
0
Kennebec
90
0
0
0
Machias
109
222
0
0
Narraguagus
0
285
0
0
Penobscot
0
1,166
167
556
Pleasant
0
58
0
0
Sheepscot
0
142
0
0
Union
288
0
0
0
Total for Maine Program
Drainage
Total
299
164
90
331
285
1,889
58
142
288
3,546
Pre‐spawn refers to adults that are stocked prior to spawning of that year. Post‐spawn refers to fish that are stocked after they have been spawned in the hatchery. **The 167 pre‐spawn sea run fish stocked in the Penobscot River were sea run fish that were temporarily held in the hatchery prior to release to the river Table 2.2. Summary of juvenile Atlantic salmon stocking in Maine for 2011. Drainage
Fry
Dennys
539,000
East Machias
180,000
Machias
347,000
Narraguagus
465,000
Pleasant
124,000
Union
19,000
Downeast Coastal SHRU
Penobscot
952,000
Penobscot Bay SHRU
Kennebec
85,000
Sheepscot
129,000
Androscoggin
1,000
Merrymeeting Bay SHRU
Aroostook
237,000
Saco
238,000
Non DPS stocks
Total for Maine Program
0 Parr
1 Parr
1 Smolt
0
0
0
0
0
0
0
0
500
0
0
0
0
0
0
64,000
61,000
0
298,000
0
554,000
0
15,000
0
0
0
0
0
0
0
0
16,000
0
0
0
12,000
Total
539,000
180,000
347,500
529,000
185,000
19,000
1,799,500
1,804,000
1,804,000
85,000
144,000
1,000
230,000
237,000
266,000
503,000
4,336,500
These programs have been effective in preventing river specific populations from becoming extirpated, and have also maintained river specific effective population size, ensured healthy and disease free hatchery populations, maintained a sustainable source of parr for the captive brood program, and returned sufficient numbers of Penobscot River adults to sustain the sea‐run brood program (Table 2.3). General accomplishments and activities for 2011 and plans for 2012‐2015 are highlighted in Appendix 2. Based on DMR and USFWS freshwater assessments, adaptive management updates to the 5 year implementation activities are highlighted in grey. Atlantic Salmon Recovery Plan 2011 Annual Report Page 16 Table 2.3. Documented Atlantic salmon returns to Maine rivers in 2011 (returns to traps and weirs only), with totals for those identified as being stocked as parr and smolt. Drainage
Dennys
Narraguagus
Penobscot
Androscoggin
Kennebec
Total GOM DPS
Saco
Total Maine Program
I SW
2 SW
3 SW
Repeat
Hatchery
Wild
Hatchery
Wild
Hatchery
Wild
Hatchery
Wild
0
2
1
5
0
1
0
55
20
96
21
2
0
1
696
45
2,167
201
3
1
12
2
1
27
14
0
0
0
0
2
21
41
0
0
0
753
70
2,312
282
5
2
13
30
11
36
17
0
0
0
783
81
2,348
299
5
2
13
0
1
0
0
0
1
0
1
Total
Hatchery
1
154
2,878
29
21
3,083
66
3,149
In this 5 year implementation plan, the conservation hatchery program continues to provide fish health, broodstock management, and juvenile production programs but begins work towards improving integration of life stage specific assessment and stocking programs to increase adaptive management capacity. C.H.A.T also proposes new projects that move production projects towards realizing greater natural spawning occurrence in the wild. An example for 2011‐2012 includes ceasing fry stocking (2012) in the Denny’s River and instead releasing pre‐spawn captive adults into quality habitat (Fall 2011). 2011 Project Proposals Supported The C.H.A.T along with the other action teams reviewed a number of proposals for new actions (research and management) from both internal (agencies) and external partners and collaborators. All of the teams reviewed the proposals for consistency with the framework, lent technical advice, and made recommendations on implementing actions. A summary for each proposal received and reviewed by C.H.A.T that used hatchery products in 2011 and/or will use them in subsequent years are in Appendix 1. Atlantic Salmon Recovery Plan 2011 Annual Report Page 17 Genetic Diversity Action Team Meredith Bartron CHAIR, US Fish and Wildlife Service Denise Buckley, US Fish and Wildlife Service Paul Christman, Maine Department of Marine Resources Mike Kinnison, University of Maine (adjunct) Strategy Maintain the genetic diversity of Atlantic salmon populations in over time Strategy Metric Estimates of genetic diversity (e.g., allelic variation, heterozygosity) based on comparable suites of molecular markers will be assessed and monitored over time. Background: Maintenance of genetic diversity and the preservation of the genetic structure present in Atlantic salmon is a critical component to the restoration and recovery of Atlantic salmon in Maine. The Genetic Diversity Action Team (GDAT) has identified a variety of actions important to include as part of the broader management efforts for Atlantic salmon in Maine. Actions identified by the GDAT relate to three primary focus areas: monitoring genetic diversity, evaluating hatchery practices and products, and monitoring to detect aquaculture Atlantic salmon. Actions identified are consistent with the Broodstock Management Plan (Bartron et al. 2006), and expand to include additional research needs, monitoring of weirs for aquaculture‐origin salmon, and to monitor the effectiveness of the Aquaculture Biological Opinion. In total, 27 actions have been identified by the GDAT to be implemented and assessed for Atlantic salmon recovery and restoration in Maine. Many of the GDAT actions identified are specified in the Broodstock Management Plan (Bartron et al. 2006). Therefore, most actions are currently undertaken to maintain genetic diversity within the Atlantic salmon program and reduce risks associated with captive breeding programs and are critical to the recovery process. Actions identified by the GDAT provide additional monitoring and evaluation of hatchery management practices, including improving abilities to evaluate performance (survival) of hatchery products in the wild. Many of the GDAT actions identified are specified in the Broodstock Management Plan (Bartron et al. 2006). Therefore, most actions are currently undertaken to maintain genetic diversity within the Atlantic salmon program and reduce risks associated with captive breeding programs and are critical to the recovery process. Actions identified by the GDAT provide additional monitoring and evaluation of hatchery management practices, including improving abilities to evaluate performance (survival) of hatchery products in the wild. Actions added will increase evaluations of fitness and performance which will help determine how hatchery production is contributing to restoration activities. For example, genetic parentage analysis is be used to assess the composition of hatchery versus natural origin individuals within adult and parr broodstock collections. Other actions added to the GDAT collate all monitoring activities of aquaculture permits, genetic screening of broodstock for stray aquaculture‐
Atlantic Salmon Recovery Plan 2011 Annual Report Page 18 origin individuals, and operating weirs on the Dennys River, or in emergency situations in response to an escape event (Appendix 2). The strategy used to assess the overall outcome of the actions identified by the GDAT is the maintenance of genetic diversity over time. The metrics used to measure the effectiveness of the strategy are estimates of genetic diversity, including allelic variability (i.e. number of alleles per locus, allelic diversity), and heterozygosity. These estimates are obtained through the use of a comparable suite of molecular markers that are consistently used to monitor diversity over time. Loss of genetic diversity could be due to inbreeding, small population sizes, or artificial selection. Assessment and reporting schedules for most of the GDAT actions are specified as part of the Broodstock Management Plan (Bartron et al. 2006), or are part of the Aquaculture Biological Opinion. Although many actions are identified to be initiated in 2011, many are already part of Atlantic salmon restoration and recovery activities. Because the actions identified by the GDAT provide information and strategies to manage against loss of genetic diversity, implementation of these actions should help to maintain genetic diversity of Atlantic salmon populations in Maine over time. The GDAT works closely with the other action teams to evaluate and implement management practices that are consistent with maintenance of genetic diversity. Although the GDAT focuses evaluation efforts at the hatchery facilities, genetic methods can be utilized to evaluate of hatchery products in the wild, monitor contribution of natural reproduction by hatchery and wild Atlantic salmon, and as a marking tool to evaluate management practices and habitat utilization. Monitoring Genetic Diversity Genetic monitoring activities involve baseline characterization of potential broodstock to assess estimates of genetic diversity over time. In addition to monitoring genetic diversity over time, information obtained from genetic characterization is used to guide spawning activities, identify individuals for culling, and to track reproduction and recapture of stocked hatchery Atlantic salmon. Parr collected in 2009 for broodstock purposes were PIT tagged and fin clipped to collect tissue samples prior to transfer to the broodstock building at Craig Brook National Fish Hatchery (CBNFH) in 2010. Fin clip were sent by CBNFH to the USFWS Northeast Fishery Center Conservation Genetics Lab for genetic analysis, with results available prior to the first spawn of the 2009 year class in 2011. Sea‐run returning adults to the Penobscot River were trapped at Veazie Dam, PIT tagged, and fin clipped, and individuals identified to be used as broodstock were transported to CBNFH in the summer of 2011. All individuals (parr and sea‐run returning adults) were genotyped at a suite of 18 variable microsatellite loci. Loci analyzed include: Ssa197, Ssa171, Ssa202, Ssa85 (O’Reilly et al. 1996), Ssa14, Ssa289 (McConnell et al. 1995), SSOSL25, SSOSL85, SSOSL311, SSOSL438 (Slettan et al. 1995, 1996), and SSLEEN82 (GenBank accession number U86706), SsaA86, SsaD157, SsaD237, SsaD486, (King et al 2005), Sp2201, Sp2216, and SsspG7 (Paterson et al. 2004). Following PCR using conditions described in the primer descriptions, genotypes were visualized using an ABI 3100 (Applied Biosystems, Foster City, CA). Genescan and Genotyper software from Applied Biosystems (Foster City, CA) was used to identify alleles at each of the 18 loci. Genetic characteristics such as allele frequency, number of alleles per locus, observed and expected heterozygosity, within population variability, and allelic richness to standardize the number of alleles per locus per collection for differences in sample size (Table 3.1) were estimated using FSTAT (Goudet 1995) and GDA (Lewis and Zaykin 2001). Effective population sizes and 95% jackknife‐based confidence intervals were estimated using LDNe (Waples 2006). Atlantic Salmon Recovery Plan 2011 Annual Report Page 19 Estimates of genetic diversity are used to monitor if genetic diversity within each individual broodstock is being maintained over time. Maintenance of genetic diversity is one of the primary goals of the hatchery program: to maintain the genetic characteristics of each individual broodstock, to allow for the diversity to persist for natural selection and adaptation to occur, and to ensure that genetic diversity is not being lost inadvertently due to management practices. Estimates of heterozygosity (observed and expected) compared over time within a broodstock and between broodstocks indicate that similar levels of diversity are present in each broodstock, however for some broodstocks such as the Pleasant River broodstock, has slightly decreased estimates of allelic diversity (Na=10.3, Table 3.1), likely a result of decreased broodstock number in the early and mid 1990’s. Estimates of effective population size (Ne) vary between broodstocks. The largest estimate of effective population size is found in the Penobscot River broodstock (Ne=303.3, 95% CI=278.2‐331.2, Table 3.1), due to the larger total broodstock number and overall population size of the Penobscot River population being the largest in Maine. Table 3.1. Summary results for estimates of genetic diversity from the 2002 to 2009 collection years for broodstock. Estimates include the number of individuals sampled (N), the number of alleles per locus (Na), the expected (He) and observed (Ho) heterozygosity, inbreeding (f), estimated effective population size (Ne) and the 95% confidence interval, and the number of locus used for the analysis. Broodstock
Dennys
East Machias
Machias
Narraguagus
Penobscot
Pleasant
Sheepscot
Sample
Year
2009
2009
2009
2009
2009
2009
2009
n
151
148
239
243
677
109
159
Na
12.4
11.5
12.4
12.4
13.7
10.3
11.4
He
0.684
0.672
0.679
0.692
0.69
0.663
0.697
Ho
0.679
0.689
0.693
0.704
0.695
0.694
0.693
f
-0.012
-0.026
-0.020
-0.016
-0.007
-0.048
0.005
Ne
62.2
70.4
109.5
96.5
303.3
64.1
79.6
95% CI
57.7 - 67.1
65.0 - 76.4
101.5 - 118.4
90.7 - 102.9
278.2 - 331.2
58.7 - 70.3
73.3 - 86.7
# loci
18
18
18
18
18
18
18
Evaluating Hatchery Practices and Products Information regarding genetic characterization of potential broodstock along with genetic principles is used to guide hatchery practices at Craig Brook National Fish Hatchery and Green Lake National Fish Hatchery. Genetic data on relatedness is used to inform mate selection and determine if spawning between capture years is necessary (Hardy and Vekemans 2002) to reduce the potential for mating related individuals, in combination with using the genetic‐based spawning optimization software. Information about the number of families created is used to guide mixing of fry prior to stocking, stocking practices, and recapture of parr. Genetic determination of parentage is used to determine the hatchery family composition to assess recapture of hatchery produced families (Table 3.2). Understanding of the percentage of hatchery produced families is critical to efforts to maintain genetic diversity. Stocking protocols have been implemented to distribute representatives of hatchery families throughout their river‐specific habitats, to maximize the potential for recapture of each individual family during subsequent broodstock collection efforts. Broad distribution of families throughout their river‐
specific habitats should allow for natural selection to be the primary driver for variance in recapture rates opposed to stocking practices or habitat quality. Monitoring the recapture of hatchery families allows for evaluation of both the stocking and broodstock recapture practices. Atlantic Salmon Recovery Plan 2011 Annual Report Page 20 Individuals not assigned to hatchery families are considered of unknown origin. These individuals could represent offspring of natural reproduction from wild adults, or from spawning of precious parr (hatchery or wild) spawning with wild females. Although incorporating offspring from natural reproduction is important to capture the total genetic diversity of the population, these spawning events are likely from a limited number of reproducing individuals compared to the number of adults spawned in the hatchery. Disproportionate use of unknown origin individuals from limited number of parental pairs in future broodstock may limit the maintenance of the total genetic diversity (including that being maintained in the hatchery) of each Atlantic salmon population. Parentage results indicate that the highest proportions of hatchery fish being recaptured are from the Dennys, East Machias, Machias, and Narraguagus Rivers (Table 3.3). Although a goal of the stocking and parr broodstock program is to incorporate offspring of natural reproduction into the hatchery broodstock program, lower proportion of recapture of hatchery fish such as in the Pleasant and Sheepscot rivers (Table 3.3) may result in less of the total genetic diversity being stocked into these rivers that is being maintained in the hatchery could be recaptured. Evaluation of the age structure of the parr being recaptured indicates that for most populations, the greatest proportion of fish are age 1+ parr, with some contribution of 2+ parr. For the 2009 parr recapture year, no 0+ parr were indicated to be recaptured based on parentage analysis to spawn year (Table 3.3). Table 3.2. Hatchery spawn years that would be used to identify parr broodstock captured in 2009 based on potential age at recapture. Life Stage
Spawn year
Fry stocked
Parr (0+)
Parr (1+)
Parr (2+)
2006
2007
2007
2008
2009
Year
2007
2008
2008
2009
2010
2008
2009
2009
2010
2011
Table 3.3. Parentage results for the 2009 capture year parr, including the allocation of parentage analysis to the spawn year they were assigned (2008, 2007, or 2006). Broodstock
Dennys
East Machias
Machias
Narraguagus
Pleasant
Sheepscot
Samples
151
148
239
243
109
159
Assigned
Proportion
Hatchery
Assigned
Parents
121
0.80
104
0.70
184
0.77
198
0.82
64
0.59
110
0.69
Number recaptured
age 0+
age 1+
age 2+
2008
2007
2006
0
113
8
0
94
10
0
162
22
0
183
15
0
64
0
0
100
10
age 0+
2008
Proportion
age 1+
age 2+
2007
2006
0
0.93
0.07
0
0.90
0.10
0
0.88
0.12
0
0.92
0.08
0
1.00
0.00
0
0.91
0.09
Evaluating the proportion of the families spawned in 2007 and recaptured in 2009 indicated that overall, less than half of the families spawned were recaptured for most broodstock populations (Table 3.4). Long term implications of the reduced recapture of the offspring of parental broodstock include a reduction in the maintenance of genetic diversity and increased inbreeding in future generations. Additional families spawned in 2007 may be recaptured in the 2008 or 2010 parr broodstock collections, however based on parentage analysis for the 2008 parr broodstock collection, the only broodstock with 2007 spawn year origin individuals were from the East Machias, which included individuals from a total of four families, of which only two families were not present in the 2009 parr collection year. Given the Atlantic Salmon Recovery Plan 2011 Annual Report Page 21 parr sampling, tagging, and fin clipping schedule, parr broodstock collections from 2010 are currently being genotyped and results will be available prior to spawning in the fall of 2012. Table 3.4. The proportion of families recaptured in the 2009 parr broodstock collection from the 2007 spawn year. Broodstock
Dennys
East Machias
Machias
Narraguagus
Pleasant
Sheepscot
Spawn
Year
2007
2007
2007
2007
2007
2007
Families
Created
84
78
150
186
77
81
Capture
Families
P
Year
Recaptured Recaptured
2009
41
0.49
2009
37
0.47
2009
67
0.45
2009
91
0.49
2009
32
0.42
2009
53
0.65
Monitoring to Detect Aquaculture Atlantic salmon To screen potential escapees from aquaculture facilities, or strays from outside the region, a two‐phased hierarchical screening process has been established for potential broodstock Craig Brook National Fish Hatchery (Bartron et al. 2006). The first phase screens to determine continent‐of‐origin due to the use of non‐North American origin Atlantic salmon for aquaculture purposes, and based on the large differences in allele frequencies between populations from different continents (King et al. 2001). The second screening phase is based on identifying individuals from the river of origin, or region of origin (Maine), and to allow for natural straying among populations by excluding individuals with low assignment probability to either the population of origin or to other Maine rivers. Individuals may be identified to be excluded from spawning through either procedure (Table 3.5). A two‐step hierarchical criterion based on probability of assignment to population of origin was used to classify individuals. First, an individual would be identified for additional analysis if there was a less than 1% probability of assignment to the population an individual putatively originated. For individuals identified for potential removal with the first criteria, only individuals that had a less than 5% probability of assignment to any other Maine population (Narraguagus, East Machias, Dennys, Ducktrap, Penobscot, Kennebec, Machias, Pleasant, and Sheepscot) would be removed from the broodstock. This method was developed to increase the likelihood of correctly identifying individuals belonging to a specific population, while still allowing for the possibility of straying between neighboring drainages. Because other source populations not included in the baseline may have contributed to the unknown group of individuals, the use of the 2‐step process and low probability of assignment thresholds would aid in identification to any of the baseline populations used. Therefore, probability of assignment to river or to other Maine populations would identify individuals of unknown origin due to low assignment probabilities. Other Projects Hobart Stream Study To increase natural reproduction of Atlantic salmon in Maine rivers, and to evaluate the potential of hatchery adults to successfully spawn in the natural environment, gravid adult Atlantic salmon from Craig Brook National Fish Hatchery have been stocked prior to spawning. In general, these adult hatchery salmon are returned to their population of origin; however Hobart Stream has been experimentally stocked with adults from multiple hatchery broodstocks. Prior to this study, no Atlantic Atlantic Salmon Recovery Plan 2011 Annual Report Page 22 salmon or natural reproduction by Atlantic salmon had been detected in Hobart Stream for over 15 years. Table 3.5. Results from the screening for aquaculture origin individuals conducted on the 2009 capture year parr broodstock and 2011 sea‐run adult Penobscot broodstock. Capture
Year
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2009
2011
Broodstock
Dennys
Dennys
Dennys
Dennys
Dennys
Dennys
Dennys
Dennys
Dennys
East Machias
Machias
Machias
Machias
Machias
Machias
Narraguagus
Narraguagus
Sheepscot
Penobscot
CG Lab ID
CBDE-09-098
CBDE-09-134
CBDE-09-017
CBDE-09-135
CBDE-09-007
CBDE-09-003
CBDE-09-008
CBDE-09-126
CBDE-09-143
CBEM-09-038
CBMA-09-057
CBMA-09-085
CBMA-09-190
CBMA-09-107
CBMA-09-095
CBNA-09-070
CBNA-09-061
CBSH-09-119
CBPN-11-187
PIT ID
486A3B435C
48774A510C
486B241A1E
4876622D70
486A5C457B
48770B7F12
48761B2C0A
487561452C
4875721968
487656341C
47086C6F6C
470620245F
4702646968
4706494E62
4705201B7A
4877075F4A
48683B5C1E
48664F1238
1C2D66EEE5
Reason Excluded
River/Region
River/Region & Continent of origin
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
River/Region
Continent of origin
A total of 18 variable microsatellite loci were used to genotype all stocked hatchery adults and sampled juveniles, and genetic parentage analysis to assess the reproductive ability of the hatchery adults and determine mate choice patterns for hatchery adults in Hobart Stream. We assessed natural reproduction for two release years (2006 and 2007), through captures of parr and smolts in 2008, 2009, and 2010. In 2006, adults from three different broodstock populations were stocked into Hobart Stream, and in 2007, adults from two different broodstock populations were stocked (Table 3.6). Of the 90 juvenile Atlantic salmon sampled and genotyped, 84 were assigned to parental spawning pairs (Table 3.7), indicating that hatchery‐raised Atlantic salmon can successfully reproduce in streams (Table 3.8) and produce offspring that survive through the juvenile life stages. Based on assignment of sampled juveniles to parental broodstock, observed spawning pair combinations significantly deviated from expected proportions based on numbers stocked (Table 3.9), indicating either non‐random selection of mates or differential survival of offspring occurred, both for the 2006 release year (X2=40.36, p<0.001) and 2007 release year (X2=9.17 p=0.03). Determination of reproductive capabilities of hatchery reared Atlantic salmon, and their mating strategies following stocking in the wild will provide important information to guide restoration activities and stocking practices of hatchery Atlantic salmon. The results from this study are useful to understanding natural reproduction of hatchery adults in Maine rivers, and suggest that including pre‐spawn adults into stocking strategies can result in natural reproduction, which would help to maximize natural selection and local adaptation to the wild. Continued monitoring of natural reproduction through juvenile sampling to assess maintenance of genetic diversity from these pre‐spawn adult stocking events is important to understand the reproductive contribution of these pre‐spawn adults. Atlantic Salmon Recovery Plan 2011 Annual Report Page 23 Table 3.6. The number of adult pre‐spawn Atlantic salmon broodstock from CBNFH stocked into Hobart Stream, Maine in 2006 and 2007. Year
River Stock
2006
Dennys
Narraguagus
Pleasant
Dennys
Narraguagus
2007
Number
Stocked
28
93
49
31
49
Proportion
of Total
0.17
0.55
0.29
0.39
0.61
Sum
170
80
Table 3.7. Parentage assignment results from the 2008 and 2009 sample years, including both parr and smolt samples. Sample
year
2008
2009
2009
2010
Sum
Life
stage
parr
parr
smolts
smolts
Number Number
P
sampled assigned Assigned
59
57
0.97
3
3
1.00
14
13
0.93
14
11
0.79
90
84
0.93
Table 3.8. Spawning success (P =proportion spawning) of stocked pre‐spawn adults, based on assigning captured juveniles to river stock and parental sex for the 2008 and 2009 parr and smolt samples. Year
2006
2007
River Stock
Stocked
12
36
28
12
22
Dennys
Narraguagus
Pleasant
Dennys
Narraguagus
Females
With
Offspring
P
Recaptured Reproducing
5
0.42
18
0.50
6
0.21
1
0.08
5
0.23
Stocked
15
57
18
7
13
Males
With
Offspring
P
Recaptured Reproducing
9
0.60
23
0.40
3
0.17
2
0.29
6
0.46
Atlantic Salmon Recovery Plan 2011 Annual Report Page 24 Table 3.9. For the 2008 and 2009 parr and smolt collections from Hobart Stream, the observed and expected number of offspring per cross from the 2006 and 2007 release years. NA means that the parent could not be assigned to a river stock. Release
Year
2006
2006
2006
2006
2006
2006
2006
2006
2006
2007
2007
2007
2007
Female River
Dennys
Dennys
Dennys
Narraguagus
Narraguagus
Narraguagus
Pleasant
Pleasant
Pleasant
Dennys
Dennys
Narraguagus
Narraguagus
Male River
Dennys
Narraguagus
Pleasant
Dennys
Narraguagus
Pleasant
Dennys
Narraguagus
Pleasant
Dennys
Narraguagus
Dennys
Narraguagus
Observed
Number Proportion
3
0.04
7
0.10
0
0.00
15
0.21
35
0.50
3
0.04
2
0.03
5
0.07
0
0.00
2
0.14
0
0.00
1
0.07
11
0.79
Expected
Number Proportion
1.8
0.03
5.5
0.08
4.3
0.06
7.0
0.10
21.0
0.30
16.3
0.23
2.2
0.03
6.6
0.10
5.2
0.07
1.7
0.12
3.2
0.23
3.2
0.23
5.9
0.42
Investigators: Meredith Bartron, USFWS Northeast Fishery Center; Denise Buckley, USFWS Craig Brook National Fish Hatchery; Ernie Atkinson, Maine Department of Marine Resources Literature Cited Bartron, M.L., D. Buckley, T.L. King, T. King, M. Kinnison, G. Mackey, and T. Sheehan. 2006. Captive Broodstock Management Plan for Atlantic salmon at Craig Brook National Fish Hatchery. Report to Maine Technical Advisory Committee. Goudet, J. 1995. F‐STAT v. 1.2: A computer program to calculate F‐Statistics. Journal of Heredity 86:485‐
486. Hardy, O.J. and X. Vekemans. 2002. SPAGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Molecular Ecology Notes 2: 618‐620. King, T.L., M.S. Eackles, B.H. Letcher. 2005. Microsatellite DNA markers for the study of Atlantic salmon (Salmo salar) kinship, population structure, and mixed‐fishery analyses. Molecular Ecology Notes 5:130‐132. Lewis, P.O. and D. Zaykin. 2001. Genetic Data Analysis: Computer program for the analysis of alleleic data, version 1.0 (d.16c). Available from http://lweis.eebuconnedu/lewishome/software.html McConnell, S.K., P.T. O'Reilly, L. Hamilton, J.M. Wright, and P. Bentzen. 1995. Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Canadian Jouranl of Fisheries and Aquatic Sciences 52: 1863‐1872. O'Reilly, P.T., L. C. Hamilton, S.K. McConnell, and J.M. Wright. 1996. Rapid detection of genetic variation in Atlantic salmon (Salmo salar) by PCR multiplexing of dinucelotide and tetranucleotide microsatellites. Canadian Journal of Fisheries and Aquatic Sciences 53: 2292‐2298. Atlantic Salmon Recovery Plan 2011 Annual Report Page 25 Paterson, S., S.B. Piertney, D. Knox, J. Gilbey, and E. Verspoor. 2004. Characterization and PCR multiplexing of novel highly variable tetranucleotide Atlantic salmon (Salmo salar L.) microsatellites. Molecular Ecology Notes 4:160‐162. Slettan, A., I. Olsaker, and O. Lie. 1995. Atlantic salmon, Salmo salar, microsatellites at the loci SSOSL25, SSOSL85, SSOSL311, SSOSL417 loci. Animal Genetics 26:281‐282. Slettan, A., I. Olsaker, and O. Lie. 1996. Polymorphic Atlantic salmon, Salmo salar L., microsatellites at the SSOSL438, SSOSL429, and SSOSL444 loci. Animal Genetics 27:57‐58. Raymond, M. and F. Rousset. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248‐249. Rice, W.R. 1989. Analyzing tables of statistical tests. Evolution 43: 223‐225. Waples, R.S. 2006. A bias correction method for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetics 7: 167‐184. Atlantic Salmon Recovery Plan 2011 Annual Report Page 26 Marine and Estuarine Action Team Graham Goulette, NOAA’s National Marine Fisheries Service John Kocik, CHAIR, NOAA’s National Marine Fisheries Service James Manning, NOAA’s National Marine Fisheries Service Michael O’ Malley, Integrated Statistics Mark Renkawitz, NOAA’s National Marine Fisheries Service Tim Sheehan, NOAA’s National Marine Fisheries Service Linda Welch, US Fish and Wildlife Service Strategy Increase marine and estuary survival by increased understanding of these ecosystems and the location and timing of constraints to the marine productivity of salmon Strategy Objective To document factors limiting marine and estuarine survival of Atlantic salmon to facilitate informed ecosystem management of these stocks Strategy Metrics ƒ
Monitor marine survival of hatchery smolts in Penobscot Bay SHRU and decrease uncertainty in estimates ƒ
Monitor marine survival of naturally‐reared smolts in Downeast and Merrymeeting Bay SHRU and decrease uncertainty in estimates ƒ
Monitor estuarine and coastal marine survival and identify location and time of mortality events at a population scale using telemetry and pelagic monitoring techniques in Penobscot Bay SHRU ƒ
Increase understanding of Atlantic salmon transition ecology in estuaries, and coastal migrations in US waters and distant waters through active research and cooperatives through partners including universities, marine research institutes, ICES and NASCO resulting in peer‐reviewed products Background: Significant increase (8x) in estuarine and marine survival are needed to increase the number of adult returns (particularly those from wild origin), to achieve self‐sustaining populations, maintain genetic diversity, and to maintain and increase the geographic distribution of salmon within the GOM DPS. While, NOAA Fisheries has a role in many activities within the scope of the Marine and Estuarine Action Team (M.E.A.T.), an interdisciplinary and multiagency approach is needed to understand salmon marine ecosystems more fully. This year activities were primarily research and assessment projects that sought Atlantic Salmon Recovery Plan 2011 Annual Report Page 27 to understand the estuarine and marine ecology and migration of Atlantic salmon. This work was focused on understanding the structure and function of these communities and working towards identifying the factors that may be contributing to the current low survival. With increased knowledge, we intend to implement management actions with the goal of increasing survival of emigrating smolts, post smolts and ultimately increasing adult returns. Accomplishments General accomplishments and activities are highlighted in Appendix 2. While the marine ecology of Atlantic salmon has often been equated to a black box, new research tools and integrating models from oceanography and bioenergetics are providing new insights in many aspects of salmon at sea. Many of the projects described and cited below were discussed at our Action Team Meeting in August, 2011. That meeting provided a forum for information exchange and research coordination. International Research and Assessment The work of the M.E.A.T. and the Stock Assessment Team provided essential inputs to international management of Atlantic salmon through International Council for the Exploration of the Sea (ICES) Working Group on North Atlantic Salmon (WGNAS) and North Atlantic Salmon Conservation Organization (NASCO). Active engagement in international science and management both helps to protect these stocks from fisheries at sea and understand marine ecology of Atlantic salmon. The output of much of the GOM DPS marine assessment work was vetted through the US Atlantic Salmon Assessment Committee. The results of 2011 studies and assessments were published in May 2012 as Annual Report 24: 2011 Activities. These data are then brought forward to international managers through both the North American Commission and West Greenland Commission through the leadership of M.E.A.T. member Tim Sheehan. Additionally, the US has a key role in West Greenland monitoring and sampling as Tim Sheehan coordinates this international sampling program. The results of 2010 studies and assessments were folded into North American scale summaries and published in July 2011 in the Report of North Atlantic Salmon Working Group. In addition to core international work, T. Sheehan participates in NASCO’s International Atlantic Salmon Research Board (IASRB). The IASRB was initiated in 2008 with the goal of implementing a major integrated program of marine surveys in the Northeast and Northwest Atlantic, together with enhanced sampling of the fishery at West Greenland under the SALSEA Program and there have been other major research initiatives. This was a watershed year for this effort with the 'Salmon Summit', an international symposium Co‐Convened by NASCO and ICES entitled 'Salmon at Sea: Scientific Advances and their Implications for Management' in October 2011. The objectives of the Symposium were: to review recent advances in our understanding of the migration, distribution and survival of salmon at sea and the factors influencing them; to consider the management implications of recent advances in understanding of the salmon’s marine life; to identify gaps in current understanding and future research priorities; to increase awareness of recent research efforts to improve understanding of salmon at sea and to encourage support for future research. US scientists and managers, and M.E.A.T. members and partners played a major role in this event with multiple presentations and papers (see presentation section). Maine Sea Grant – NOAA Fisheries Workshop Summary Cairns (2001) reported four leading hypotheses of declining abundance of Atlantic salmon in estuarine‐
marine environments: 1) Post‐fishery marine mortality is higher than presumed by fishery models. Atlantic Salmon Recovery Plan 2011 Annual Report Page 28 2) Smolt survival is reduced due to fish predation in estuaries. 3) Bird and mammal predation reduces survival at sea. 4) Salmon have changed migration routes due to altered oceanographic conditions. The 2008‐2010 Maine Sea Grant ‐ NOAA Fisheries Workshops were designed to reframe these existing North American Atlantic salmon mortality hypotheses and gain new perspectives. The deliberations focused on the migration and estuarine and coastal ecology of Atlantic salmon in the Gulf of Maine and did not address the freshwater life stages, except where effects may have affected marine phases. Conveners placed emphasis on identifying parameters that could be managed at local or regional scales, and those with particular relevance to Gulf of Maine Atlantic salmon. Rather than a single, high‐profile species approach, the interdisciplinary group felt that integration of climate, environmental, fisheries, and community ecology studies will foster an approach aimed at understanding and managing for the functional aspects and flexibility of the salmonid ecosystem. The workshop proceedings have been edited and are in the final editorial stages and will be available at the workshop website (http://www.seagrant.umaine.edu/program/nmfs‐nearshore‐salmon‐ecology) in early 2012. However, it is important to note that work on the six primary hypotheses developed in this process is underway as M.E.A.T. members took action on these items while document was being developed. The six hypotheses emerged from the Workshops as priority areas for research from these workshops ‐ •
Climate altered ocean habitat (temperature, productivity physical oceanography) affect survival •
Climate altered oceanographic conditions (current intensity and direction) led to changing migration routes that affect survival •
Human activities have changed Northeast Shelf communities (fish, birds, mammals) altering food webs •
Human activities have reduced abundance of co‐evolved diadromous complex resulting in reduced marine survival •
Climatic disruption in historic correspondence between freshwater and saltwater conditions •
Salmon declines linked to loss of genetic diversity – life history diversity including variable run‐
timing and migration routes Select Research Highlights Important insights into salmon marine ecology published this year that added new information to our understanding of marine ecology of salmon in US waters. M.E.A.T members authored and co‐authored 3 articles of note. Sheehan et al. (2011) published a thorough analysis of the first targeted at‐sea capture of Gulf of Maine Atlantic salmon using a surface trawl survey in Penobscot Bay and the nearshore Gulf of Maine waters. They found significant differences in early migration success among different stocking groups, but subsequent marine survival was independent of stocking group. While the post‐smolt population was primarily composed of hatchery origin smolt‐stocked fish, parr stocked fish represented a higher proportion of the population than previously assumed. Catch distribution suggests evidence of an initial Atlantic Salmon Recovery Plan 2011 Annual Report Page 29 marine migratory pathway of south to southeast out of the dynamic Penobscot Bay in the study years. Sheehan et al. (2011) also found that the hypothesized benefits of a predator refuge based on the co‐
occurring species complex (Saunders et al. 2006) was likely minimal in the postsmolt trawl study area. They found a mismatch in the size overlap among other species and smolts and documented generally low abundance of other co‐occurring diadromous populations. Expanding diadromous populations could still have an impact on smolt survival as diadromous populations recover both greater abundance and more complex age (size) structure. However, the Bay and coastal ecosystems seem less likely candidates for this prey‐buffering interaction based on these findings. Renkawitz and Sheehan (2011) also examined diet of Atlantic salmon post‐smolt stomachs collected from 2001 to 2005 in Penobscot Bay during the trawling. This study provides our first modern insights into the feeding ecology of early marine phase post‐smolts from different rearing origins. Renkawitz and Sheehan (2011) found that stomachs contained only one or two prey types, suggesting active prey selection or patchy distribution of prey. Post‐smolts that lived in the river longer, naturally‐reared or parr‐stocked origins, were smaller but consumed more fish than invertebrates. The larger, smolt‐
stocked origin post‐smolts that emigrated immediately post‐stocking consumed 48% fish and 40% crustaceans. The naturally‐reared smolts consumed 84% fish and 16% crustaceans and parr‐stocked were intermediate. This information suggests that stocking stage and exposure to natural forage leads to differences in the type and quantity of prey consumed. Further understanding these behavioral differences among rearing origins could be used to optimize post‐smolt survival and potentially increase the contributions of stocked fish to recovery. Friedland et al. (2011) published a comprehensive analysis of the North American stock complex of Atlantic salmon, Salmo salar L., suggesting that marine mortality is influenced most by variation in predation pressure affecting post‐smolts during the first months at sea. They tested this hypothesis for Gulf of Maine (GOM) stocks (Penobscot River) by examining: 1) wind pseudostress and 2) distribution of piscivorous predator fields. They correlated declining marine survival over recent decades with a change in the direction of spring winds. They hypothesize that this extends postsmolt migration by favoring routes using the western GOM. In addition, they found that higher spring sea surface temperatures have been associated with shifting distributions of a range of fish species – including important pelagic piscivores that may prey upon salmon post‐smolts. They found abundance of these predators is higher in the areas that serve as migration corridors for post‐smolts. Predators of particular concern highlighted were: silver hake, Merluccius bilinearis (Mitchell), red hake, Urophycis chuss (Walbaum), and spiny dogfish, Squalus acanthias L. They concluded that climate variation and shifting predator distributions in the GOM are consistent with a predator hypothesis of recruitment control for the stock complex. NOAA and USGS partner in ultrasonic telemetry studies in the Penobscot River, Estuary, and Bay to gain insights into Atlantic salmon smolt and post smolt coastal and nearshore marine ecology. Evaluating survival and emigration dynamics of smolt stocked and river‐reared fish has provided a better understanding of migration behavior, migration corridors, bottlenecks and survival through Penobscot estuary and to the Gulf of Maine. Data collected thus far indicate both smolt origins (smolt stocked and naturally‐reared) rapidly emigrate Penobscot estuary and bay (~4.5 days) while partitioning habitat use in the bay in a similar manner (i.e. using similar routes). Despite the rapid emigration time, survival for both origins is around 40% leaving questions as to what factors are causing the high mortality. Coupling telemetry efforts with ongoing avian and marine mammal surveys will provide the opportunity to learn more about some predator/prey interactions and what role species such as double crested cormorants and harbor seals play in the Atlantic salmon’s coastal and nearshore ecosystem. In addition, Link et al. (2011) looked at diet of coastal fish to look for diadromous forage. Extending beyond the Gulf of Maine, Atlantic Salmon Recovery Plan 2011 Annual Report Page 30 NEFSC has partnered with the Ocean Tracking Network (OTN) to share telemetry data benefiting multiple research efforts. With the existence of OTN’s Halifax array, NEFSC has gained important spatial and temporal data for post smolt arrival to this region. The Penobscot Estuarine Fish Community and Ecosystem Survey is a pilot project to evaluate optimal data platforms for ecosystem monitoring and hypothesis testing. 2011 was the first full year of testing the proposed sampling methods, with promising results. The work integrates several fish capture techniques with hydroacoustics to monitor changes in species composition by location and season (Figure 5.1). Pelagic trawling, fyke netting and beach seining in 2011 unexpectedly revealed multiple size classes of alosines suggesting extensive habitat use. Investigators found contemporary evidence of natural reproduction of American shad (Alosa sapidissima). We also tested using multi‐frequency split‐
beam techniques to evaluate the spatial and temporal variability of fish and zooplankton distributions (Figure 5.2). Using Sv dB differencing techniques to distinguish fish and zooplankton in echograms of mobile transects, we produced biomass and single target fish estimates over large spatial and volumetric scales. Surface transects of environmental parameters (temp., salinity, etc.) were collected concurrently. Transects also provided the platform for estuarine bird and marine mammal monitoring, to investigate the relationships between the estuarine use by these species and fish biomass distribution. Knowledge gained from this study will improve our ability to: 1) manage estuaries in the future; 2) conduct vital research on the habitats and ecosystem services they provide; and 3) investigate ecosystem‐wide influences on smolt mortality in the estuary. The design specifics should also be transferable to multiple systems to develop a regional perspective. Selected 2011 Publications, Presentations, and Reports Journal Publications 1)
Renkawitz, M.D., and Sheehan, T.F. 2011. Feeding ecology of early marine phase Atlantic salmon Salmo salar postsmolts. Journal of Fish Biology, 79:356‐373. 2)
Sheehan, T.F., Renkawitz, M.D., and Brown, R.W. 2011. Surface trawl survey for U.S. origin Atlantic salmon Salmo salar. Journal of Fish Biology, 79: 374‐398. 3)
Friedland, K. D., Manning, J. P., Link, J. S., Gilbert, J. R., Gilbert, A. T. and O’connell, A. F. 2011, Variation in wind and piscivorous predator fields affecting the survival of Atlantic salmon, Salmo salar, in the Gulf of Maine. Fisheries Management and Ecology. 1365‐2400. Presentations 4)
Hawkes, J. P., Sheehan, T. F., and Atkinson, E. 2011. Assessing Estuarine and Coastal Migration and Survival of Age‐1 Hatchery Atlantic Salmon Smolts from the Dennys River, Maine (USA) Using Acoustic Telemetry. American Fisheries Society 2011 Annual Meeting. Seattle, WA. 5)
Hawkes, J.P., J.F. Kocik and R.W. Dudley. Climate Impacts on Diadromous Fisheries. Inland Climate Change Workshop. Ithica, New York. 6)
Hawkes, J.P., T.F. Sheehan, P.A. Music, D. Stich and E. Atkinson. Assessing estuarine and coastal migration and survival of Age‐1 hatchery Atlantic salmon smolts from the Dennys River, Maine (USA) using acoustic telemetry. 141st Meeting of the American Fisheries Society. Seattle, Washington. Atlantic Salmon Recovery Plan 2011 Annual Report Page 31 7)
Kocik, J. F., Hawkes, J. P., Goulette, G. S., Music, P. A., and Sheehan, T. F. 2011. Estimating Atlantic salmon survival in estuaries and bays of Maine. American Fisheries Society 2011 Annual Meeting. Seattle, WA. 8)
Kocik, J.F., J.P. Hawkes, G.S.Goulette, P. A. Music and T.F.Sheehan. Estimating Atlantic Salmon Survival in Estuaries and Bays of Maine. 141st Meeting of the American Fisheries Society. Seattle, Washington. 9)
Lipsky, C.A., J.P. Hawkes, J.F. Kocik. Mark‐Recapture Estimates of Atlantic Salmon Smolts In Maine Rivers: Habitat and Trapping‐ Location, Location, Location. 141st Meeting of the American Fisheries Society. Seattle, Washington. 10)
Lipsky, C., Stevens, J., O’Malley, M., Saunders, R. and J. Kocik. The Penobscot Estuarine Fish and Ecosystem Survey– Overview and Preliminary Results. School of Marine Sciences Autumn Seminar Series, November 28th, 2011. University of Maine, Orono, Maine. 11)
Miller, A. S., Sheehan, T. F., Renkawitz, M. D., Spencer, R. C., and Miller, T. J. 2011. Retrospective Analysis of Atlantic Salmon Marine Growth Parameters in the Northwest Atlantic Based on Tag‐Recovery Data. American Fisheries Society 2011 Annual Meeting. Seattle, WA. 12)
Miller, A., Sheehan, T.F., Renkawitz, M.D., Spencer, R., and Miller, T. 2011 Retrospective analysis of Atlantic salmon marine growth parameters in the northwest Atlantic based on tag‐recovery data. NASCO/ICES Salmon Summit, October 11‐13, 2011. La Rochelle, France. 13)
Nieland, J. L., Sheehan, T. F., Saunders, R., Murphy, J. S., and Trinko Lake, T. 2011. Dam Impact Analysis on Atlantic Salmon Recovery in the Penobscot River, Maine. American Fisheries Society 2011 Annual Meeting. Seattle, WA. 14)
O’Malley, M., Stevens, J., Lipsky, C., Saunders, R. and J. Kocik. The Penobscot Estuarine Fish and Ecosystem Survey – Overview of Fish Capture Methods and Split‐Beam Hydroacoustics. Marine and Estuarine Action Team Annual Meeting, August 10th 2011. Brunswick, Maine. 15)
O’Malley, M., Stevens, J., Lipsky, C., Saunders, R. and J. Kocik. The Penobscot Estuarine Fish and Ecosystem Survey– Overview and Preliminary Results (Poster). Maine Water Conference, March 16th 2011. Augusta, Maine. 16)
Renkawitz, M.D., Sheehan, T.F., Reddin, D.G., Chaput, G. 2011. Atlantic salmon foraging ecology in the Northwest Atlantic. ‐ NASCO/ICES Salmon Summit, October 11‐13, 2011. La Rochelle, France. 17)
Rikardsen, A.H., Chittenden, C.M., Righton, D., Økland, F., Næsje, T.F., Gargan, P., Renkawitz, M.D., Sheehan, T.F., Ådlandsvik, B., Pedersen, O., ThorstadE.B., Davidsen, J.G., Halttunen, E., McKinley, R.S., Finstad, B., and Aarestrup, K. 2011. Tracking Atlantic salmon migration at sea by use of pop‐up satellite tags. 1st International Conference on Fish Telemetry. June 12‐18, 2011. Hokkaido University, Sapporo, Japan. 18)
Saunders, R., Coghlan, S. M. Jr., Zydlewski, J., and Sheehan, T. F. 2011. Dam removal allows re‐
colonization of historic habitat by three species of anadromous fish in Sedgeunkedunk. American Fisheries Society 2011 Annual Meeting. Seattle, WA. Atlantic Salmon Recovery Plan 2011 Annual Report Page 32 19)
Saunders, R., Collins, M., Sheehan, T. F., Royte, J., and Baeder, C. 2011. Evaluating the Ecological Effects of the Penobscot River Restoration Project. American Fisheries Society 2011 Annual Meeting. Seattle, WA. 20)
Sheehan, T.F., Reddin, D.G., Chaput, G., and Renkawitz, M.D. 2011. SALSEA North America: A pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic. NASCO/ICES Salmon Summit, October 11‐13, 2011. La Rochelle, France. 21)
Stevens, J., Lipsky, C., O’Malley, M., Saunders, R. and J. Kocik. The Penobscot Estuarine Fish and Ecosystem Survey – An Overview with Rainbow Smelt Monitoring Components (Poster). Fourth North American Workshop on Rainbow Smelt, January 24‐25th 2011. Portland, Maine. 22)
Stevens, J., Lipsky, C., O’Malley, M., Saunders, R. and J. Kocik. The Penobscot Estuarine Fish and Ecosystem Survey. Coastal and Estuarine Research Federation, 6th‐10th November 2011. Daytona Beach, Florida. 23)
Saunders, R and M. Colligan. 2011. Ramifications of persistent low marine survival to Atlantic salmon management in the United States. Salmon at Sea: Scientific advances and their implications for management. L’ Aquarium, La Rochelle, France; 11 – 13 October, 2011. Reports and Working Papers 24)
Lipsky, C.A., J.P. Hawkes, R. Hass‐Castro, O. Cox, M. P. Ruksznis, M. Simpson, R. Spencer, J. Stevens and J. Trial. Update on Maine River Atlantic Salmon Smolt Studies: 2010. Working Paper #2010/##. U.S. Atlantic Salmon Assessment Committee Meeting. Portland, ME. 11 pp. 25)
Hawkes, J.P., G.S. Goulette, J.F. Kocik and P.A. Music. Update on NOAA Fisheries Service Coastal Maine River Atlantic Salmon Smolt Telemetry Studies: 2010. Working Paper #2010/##. U.S. Atlantic Salmon Assessment Committee Meeting. Portland, ME. 19 pp. 26)
Goulette, G.S., J.P. Hawkes. Overview of NOAA‐Fisheries Service Atlantic Salmon Water Quality Report: 2010. Working Paper #2010/##. U.S. Atlantic Salmon Assessment Committee Meeting. Portland, ME. 14 pp. 27)
Sheehan, T. F., D. G., Reddin, R. Nygaard and T. L. King. 2011. The International Sampling Program, Continent of Origin and Biological Characteristics of Atlantic Salmon Collected at West Greenland in 2010. Working Paper 01. International Council for the Exploration of the Seas Working Group on North Atlantic Salmon Annual Meeting. Copenhagen, Denmark. 28)
Sheehan, T. F. 2011. Tag recaptures at Greenland (2003‐2010). Working Paper 02. International Council for the Exploration of the Seas Working Group on North Atlantic Salmon Annual Meeting. Copenhagen, Denmark. 29)
Trial, J., Sweka, J., Kocik, J. and Sheehan, T. F. 2011. National Report for the United States, 2010. Working Paper 4. International Council for the Exploration of the Seas Working Group on North Atlantic Salmon Annual Meeting. Copenhagen, Denmark. Atlantic Salmon Recovery Plan 2011 Annual Report Page 33 Papers in Advanced Development 1)
Lacroix, G.L., Knox, D., Sheehan, T.F., Renkawitz, M.D., Bartron, M.L. 2011. Distribution of Emigrating Atlantic Salmon Post‐smolts of Maine Hatchery Origin in the Northeastern Gulf of Maine. Transactions of the American Fisheries Society. SUBMITTED. 2)
Renkawitz, M.D., Sheehan, T.F., Goulette, G.S. 2012. Swimming depth, behavior and survival of Atlantic salmon postsmolts Salmo salar L. in Penobscot Bay, Maine USA. Transactions of the American Fisheries Society. Accepted 3)
Sheehan, T.F., Reddin, D.G., Chaput, G., and Renkawitz, M.D. 2011. SALSEA North America: A pelagic ecosystem survey targeting Atlantic salmon in the Northwest Atlantic. NASCO/ICES Salmon Summit Symposium Proceedings, October 11‐13, 2011. La Rochelle, France. 4)
Miller, A., Sheehan, T.F., Renkawitz, M.D., Spencer, R., and Miller, T. 2011 Retrospective analysis of Atlantic salmon marine growth parameters in the northwest Atlantic based on tag‐
recovery data. NASCO/ICES Salmon Summit Symposium Proceedings, October 11‐13, 2011. La Rochelle, France. Figure 4.1. Conducting downward looking mobile hydroacoustic transects using RV Silver Smolt on 07/01/2011. The two split‐beam transducers (38 and 120 kHz) are held in place 0.5m below the surface from the port side with an aluminum frame. Atlantic Salmon Recovery Plan 2011 Annual Report Page 34 Figure 4.2. Echograms of the water column from an area close to the Verona Bridges, 11/08/2011; individual fish distribution (top echogram) and zooplankton aggregations (bottom echogram). Atlantic Salmon Recovery Plan 2011 Annual Report Page 35 Freshwater Action Team Colby Bruchs, Maine Department of Marine Resources Oliver Cox, CHAIR, Maine Department of Marine Resources Scott Craig, US Fish and Wildlife Service Dan Kirchies, NOAA’s National Marine Fisheries Service Strategy Increase adult spawners through the freshwater production of smolts Strategic Objectives •
Increase juvenile Atlantic salmon survival by 10% •
Increase our understanding of factors that limit juvenile Atlantic salmon survival •
Develop a process and infrastructure to identify and implement habitat restoration projects •
Protect and conserve productive Atlantic salmon Habitat Strategic Metrics •
Population estimates of smolt production at index rivers •
Catch‐per‐unit‐effort of large parr based on a stratified random sampling design •
Distribution and abundance of redds (Stock Assessment action) •
Counts of wild adult returns at index rivers (Stock Assessment action) Background: The objective of the Freshwater Action Team is to increase adult spawners through the freshwater production of smolts. Our goal is to increase freshwater survival for juveniles from an estimate of <1% to 3%. This can be accomplished be reducing the threats to Atlantic salmon in freshwater and improving habitat. It is also important to maximize the production potential of each returning adult Atlantic salmon. There are three additional objectives in support of our primary objective; 1) increase our knowledge and understanding of factors that limit juvenile production; 2) develop a structured system to identify habitat restoration projects; and 3) protect known productive Atlantic salmon habitat. Accomplishments Updates on each action are provided in Appendix 2. Not every action proposed by the Freshwater Action Team was intended to be address in year one. Some actions are sequential and others were being phased in. Our overall impression of this first year was positive. Increasing freshwater production is an ongoing process and our intention is to refine actions as necessary to best match our strategic Atlantic Salmon Recovery Plan 2011 Annual Report Page 36 objectives and build upon the work of the Atlantic salmon community. There were three actions under policy and permitting listed as ongoing that did not get implemented this year. Juvenile Assessment Stream residents FWAT action 1 was to design and implement a state‐wide juvenile salmon sampling plan based on statistically valid sampling methodology. Ernie Atkinson, Maine DMR, implemented a Generalized Random ‐ Tessellated Stratified (GRTS) design (Stevens and Olsen 2004) for the 2011 sampling season. A total of 259 sites were developed for the Downeast Coastal, Penobscot Bay, and Merrymeeting Bay Salmon Habitat Recovery Unit (SHRU). Selection criteria included stream width and drainage. The sampling frame was selected using the NHD Flow line feature for the DE SHRU and the Habitat Model developed by Wright et al. (2011) for the Penobscot and Sandy Rivers (Figure 5.1). Analyses based on this sampling design will be provided in DMR’s July Atlantic Salmon Freshwater Assessments and Research of Mutual Interest to Maine BSRFH and NOAA Report. Figure 5.1. Locations of sites (magenta dots) selected using the Generalized Random ‐ Tessellated Stratified design during 2011. Atlantic Salmon Recovery Plan 2011 Annual Report Page 37 GRTS data, aggregated by HUC 12 and SHRU, document the relative low juvenile Atlantic salmon populations throughout the geographic range of the Gulf of Maine DPS. Atlantic salmon occupied 65% of the 72 HUC 12s sampled in the GoM DPS. Eighty‐three percent of the sites sampled in the Downeast Coastal SHRU were occupied by Atlantic salmon parr or young‐of‐year (YOY); 38% of the sites in the Penobscot Bay SHRU had parr and 35% had YOY; and 70% in the Merrymeeting Bay SHRU had parr and 50% had YOY (Figure 5.2). Abundance of YOY ranged from 0 to 6.32 per minute (Figure 5.2). The median CPUE of YOY at occupied sites ranged from 0.79 to 1.19 YOY per minute. Abundance of parr ranged from 0 to 8.74 per minute (Figure 5.2). The median CPUE of parr at occupied sites ranged from 0.39 to 1 parr per minute. Additional juvenile abundance and density data are presented in the Stock Assessment section (Table 1.2). Figure 5.2. Summary of juvenile Atlantic salmon surveys and redd locations in the Gulf of Maine Distinct Population Segment, Salmon Habitat Conservation Units (SHRU) by HUC 12. Smolt Assessment Smolt traps were successfully deployed at three locations (Table 5.2). These were sites that have all been sampled for several years. One change was a shift by NOAA to utilize DMR crews at the Narraguagus and Sheepscot rivers. NOAA provided the populations analyses for the Narraguagus and Sheepscot rivers, while DMR produced the population estimate for the Upper Piscataquis site (Table 5.3). Both agencies used a standard method that produces a ML estimate based on mark‐recapture Atlantic Salmon Recovery Plan 2011 Annual Report Page 38 data. Local data was entered and audited this fall and the 2011 data was appended to the archive database in December 2011. These estimates are reported in the US Atlantic Salmon Assessment Committee report on 2011 activities and the Stock Assessment section of the report (Figure 1.6). Table 5.2. Total captures of Atlantic salmon smolts, by origin, and dates of rotary screw trap operations for three drainages in Maine. Drainage
Dates Deployed
Narraguagus
23-Apr
4-Jun
Upper Piscataquis
1-May
3-Jun
Sheepscot
26-Apr
9-Jun
Hobart
12-Apr
25-May
Total
First
Captures Capture
Wild
277
27-Apr
Hatchery
3,636
27-Apr
Wild
573
3-May
Wild
244
27-Apr
Hatchery
215
26-Apr
Wild
20
27-Apr
Origin
Last
Capture
30-May
27-May
27-May
5-Jun
1-Jun
8-May
Median
Capture
10-May
11-May
14-May
9-May
13-May
3-May
Table 5.3. 2011 naturally reared Atlantic salmon smolt population estimates and standard error (se) from rivers in gulf of Maine DPS. SHRU
Downeast Coastal
Penobscot Bay
Merrymeeting Bay
Drainage
Narraguagus River
Upper Piscataquis River
Sheepscot River
Estimate
1,404
5,209
1,702
SE
381
1,312
370
Adult Assessment A full adult assessment will be completed by the Stock Assessment Action Team. Results will also follow the 2012 USASAC meeting. Adult Atlantic salmon were trapped at several locations in the State of Maine (Table 5.4). Regional data was entered through the trapping seasons audited and appended to the archive database on December 23, 2011. Sea‐run Atlantic salmon captures increased at every trap location with the exception of the Dennys River. Trap catches at the Veazie Dam double from 1,315 in 2010 to 3,125 in 2011. With the exception of the Penobscot River, all adult returns are released upstream to spawn. In the Penobscot River, Maine DMR crews collected 559 broodstock and released 2,559. In 2011, 11% of sea‐run returns were of naturally reared (wild spawning and fry stocking) origin (Figure 5.3). Atlantic Salmon Recovery Plan 2011 Annual Report Page 39 Table 5.4. Total captures of Atlantic salmon adults, by origin, and dates of trap operations for six drainages in Maine. Dates of Operations
SHRU Drainage
Total
First
Captures Capture
Origin
Last
Capture
Median
Capture
Downeast Coastal SHRU
Dennys
a
23-Apr
Narraguagus
Wild
4-Jun
23-Apr
4-Jun
23-Apr
4-Jun
Androscoggin
23-Apr
4-Jun
Kennebec
23-Apr
4-Jun
23-Apr
4-Jun
8
4-Jun
2-Sep
22-Jun
Hatchery
Wild
Hatchery
1
42
154
26-Jun
9-Jun
5-May
26-Jun
30-May
18-Oct
26-Jun
30-Jun
29-Jun
Wild
Hatchery
247
2878
4-May
8-May
12-Oct
20-Oct
9-Jun
15-Jun
Wild
Hatchery
Wild
Hatchery
15
29
43
21
7-Jun
27-May
4-Jun
6-Jun
12-Jul
20-Sep
18-Oct
12-Jul
13-Jun
15-Jun
30-Jun
2-Jul
Wild
Hatchery
28
66
9-May
26-May
19-Aug
19-Aug
10-Jun
14-Jun
b
Penobscot Bay SHRU
Penobscot
Merrymeeting Bay SHRU
Not - GOM DPS
Saco
a
also trapped on the Dennys River: 3 aquaculture suspects and 6 captive reared salmon Hatchery origin returns were from smolts stocked in the Narraguagus River b
Percent of Wild Returns
25%
20%
15%
10%
5%
11
10
20
20
09
20
08
20
06
07
20
05
20
20
04
20
03
20
02
00
01
20
20
20
99
19
19
98
0%
Year
Figure 5.3. Percentage of wild Atlantic salmon returns to Maine since 1998. Atlantic Salmon Recovery Plan 2011 Annual Report Page 40 Redd Surveys Atlantic salmon spawning surveys were performed in waters of the Gulf of Maine Distinct Population Segment (GOM DPS) known to containing adults. Redd surveys starting on 12 October and continued into December. Maine DMR surveyed the spawning habitat within each SHRU (Figure 4). DMR document redd in each SHRU (Table 5.5). Many of the redds in the Downeast Coastal SHRU were created by out planted captive reared adult salmon (e.g. Dennys) or as a result of smolt stocking (e.g. Narraguagus River); however, wild origin sea‐run adults also contributed to increase redd production. Old Stream, a tributary to the Machias River contained 58 redds which was 1.6 times greater than CSE. The East Machias contained 26 redds in addition to the out‐planted origin redds. It is hard to determine the spawner success in the Penobscot because of the size and inability to survey the drainage effectively. However, 2011 saw one of the highest returns to Veazie in twenty years. Spawning escapement and redds increased on the Machias, Narraguagus, and Pleasant rivers compared to previous years (Figure 5.5). Figure 5.4. Extent of spanner surveys by SHRU showing location of redds and sub‐reaches surveyed. Atlantic Salmon Recovery Plan 2011 Annual Report Page 41 Table 5.5. Summary of total redd documented and the proportion of habitat surveyed by drainages within Salmon Habitat Recovery Unit (SHRU), Gulf of Maine DPS, fall of 2011. Downeast Coastal
Downeast Coastal
Dennys*
East Machias*
% Spawning
Habitat Surveyed
103
89.46
80
98.15
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Downeast Coastal
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Penobscot Bay
Merrymeeting Bay
Merrymeeting Bay
Hobart
Machias*
Narraguagus
Pleasant
Union*
Ducktrap
East Branch Penobscot
Mattawamkeag
Passagassawakeag
Penobscot
Piscataquis
Lower Kennebec*
Sheepscot
0
188
263
23
204
0
0
9
0
65
253
79
16
SHRU
Drainage
Redds
53.53
86.97
91.1
85.38
90.35
73.16
20.14
1.49
81.34
9.74
42.58
9.49
80.65
* redds from captive reared stocked adults included in total Dennys
Machias
Ducktrap
Narraguagus
East Machias
Pleasant
Hobart Stream
Sheepscot
300
250
200
150
100
50
0
2000
2001
2002
2003
2004
2005
2006
2007
2008
2009
2010
2011
Figure 5.5. Total number of redds by drainage for years 2000 – 2011 within the original GOM DPS (pre 2009). All redds were from sea‐run escapement with the exceptions of redds in 2000, 2001, 2004, and 2011 in the Dennys River, which include redds produced by stocked captive reared adults. Atlantic Salmon Recovery Plan 2011 Annual Report Page 42 2012 Implementation As FWAT moves into is second year of implementation there will be a strong emphasis to work with NGOs that are currently modeling habitat to identify areas for protection and restoration. In 2012, FWAT will continue to develop it’s method for identifying habitat restoration needs. One deviation from our original proposal of identifying and prioritizing a list of projects is to identify project target areas. Within target areas a more extensive list of projects will be identified. FWAT metrics will also be refined to include metrics to monitor the distribution of Juvenile Atlantic salmon. References Stevens, D. L. Jr. and A. R. Olsen. 2004. Spatially balanced sampling of natural resources. J. of the Amer. Stat. Assoc. 99(465):262‐278. Wright, J., J. Sweka, A. Abbott, and T. Trinko, 2011. Update of GIS –Based Atlantic Salmon Habitat Model, 2008. US Fish and Wildlife Service, Gulf of Maine Coastal Program, Northeast Fishery Center and NOAA Fisheries Service. Atlantic Salmon Recovery Plan 2011 Annual Report Page 43 Connectivity Action Team Scott Craig, US Fish and Wildlife Service Richard Dill, Maine Department of Marine Resources Dan Kircheis, NOAA’s National Marine Fisheries Service Dan McCaw, Penobscot Indian Nation Rory Saunders, CHAIR, NOAA’s National Marine Fisheries Service Tara Trinko Lake, NOAA’s National Marine Fisheries Service Jed Wright, US Fish and Wildlife Service Strategy
Enhanced connectivity between the ocean and freshwater habitats important for salmon recovery Strategy Objectives
•
Provide full access to 30,000 habitat units with a habitat quality score of 2 or 3 in the Merrymeeting Bay SHRU; •
Provide full access to 30,000 habitat units with a habitat quality score of 2 or 3 in the Penobscot Bay SHRU; •
Provide full access to 30,000 habitat units with a habitat quality score of 2 or 3 in the Downeast SHRU. Strategy Metrics
•
Number of fully accessible habitat units in Merrymeeting Bay SHRU; •
Number of fully accessible habitat units in Penobscot Bay SHRU; •
Number of fully accessible habitat units in Downeast SHRU; Background: Atlantic salmon require a diverse array of well‐connected habitat types in order to complete their life cycle. Historically, the upstream extent of anadromy extended well into the mountainous headwaters of even the largest watersheds of Maine including the West Branch of the Penobscot River, the Carrabasset River in the Kennebec drainage and the Swift River in the Androscoggin basin as well as all the smaller coastal rivers. Today, the upstream migrations are substantially limited by dams and road crossings. Unfortunately, many of the most productive areas for spawning and rearing are not well connected; either completely or partially inaccessible because of mainstem hydroelectric dams, smaller non‐FERC licensed dams, and road crossings. Atlantic Salmon Recovery Plan 2011 Annual Report Page 44 Accessible Habitat For 2011, we estimate that fewer than 39,000 suitable habitat units are available across the DPS (Figure 6.1). These estimates are imprecise and optimistic because they do not include the effects of culverts even from the limited number of road‐stream crossing surveys conducted in portions of the freshwater range of the GOM DPS. However as a result of a number of survey efforts, we have inventories of ongoing connectivity remediation projects, and results of dam and road/stream crossing surveys that will be used to refine these estimates. Figure 6.1. Estimated number of habitat units for the entire GOM DPS. Note these estimates to not fully include the effect of culverts and is therefore an over‐estimate of the total amount of habitat currently available. Acessibility also varies greatly in each SHRU (Table 6.1). The Downeast SHRU is more connected than either the Penobscot or Merrymeeting Bay SHRU, largely because there are fewer intact dams in Downeast Maine. Atlantic Salmon Recovery Plan 2011 Annual Report Page 45 Table 6.1. Amount and accessibility of salmon habitat (100m2 units) estimated by Salmon Habitat Recovery Unit (SHRU). Habitat ratings 2 and 3 are described fully in NMFS’ critical habitat designation (74 Fed. Reg. 29300; June 19, 2009). SHRU
Penobscot
Merrymeeting Bay
Downeast
Totals
Suitable Units (2 or 3 rating)
Total
Suitable
with
impeded
likely
Habitat
Habitat Units
access
accessible*
(2 or 3 rating)
Units
315,574
221,859
89,831
8,432
339,182
220,213
10,713
7,035
59,066
35,629
9,082
23,316
713,822
447,701
109,626
38,783
* based on a recent dam survey; does not include known road‐stream crossings passage barriers. Within the Merrymeeting Bay SHRU, 248 dams block or impair access to the vast majority of salmon habitat. Those dams include 35 FERC regulated dams; 2 FERC‐exempt dams; and 211 non‐regulated dams. Of the FERC dams, five are equipped with upstream passage facilities (DMR and DEP, 2008). Of the 211 known non‐regulated dams, 16 are equipped with upstream fish passage facilities. Of the remaining 29,000 units of fully accessible habitat, approximately 7,000 units are in areas considered suitable for spawning and rearing, while the remaining 22,000 are in areas considered marginally suitable for spawning and rearing. Within the Penobscot SHRU, 142 dams block or impair access to the vast majority of salmon habitat. Those dams include 25 dams regulated by the Federal Energy Regulatory Commission (FERC); 6 FERC exempt dams; and 111 non‐regulated dams. Of the FERC dams, 13 have upstream anadromous fish passage, and 10 have a structure or measures for downstream passage (DMR and DEP, 2008). Of the 111 non‐regulated dams, 16 have upstream fish passage. Of the 21,000 units of fully accessible habitat, all are located below Veazie Dam. Approximately 8,500 units are in areas considered suitable for spawning and rearing while approximately 12,500 units are in areas considered marginally suitable for spawning and rearing. These marginal habitats are mostly in mainstem areas that include habitats with abundant predators and competitors, and habitats with water quality and substrate conditions that often impair Atlantic salmon survival. Within the Downeast SHRU, 77 dams block or impair access to considerable amounts of habitat. Of those dams, there are three FERC‐regulated dams and 74 non‐regulated dams. Of the three FERC dams, one is equipped with an upstream passage facility. Of the 74 non‐regulated dams, sixteen are equipped with upstream passage facilities. Of the remaining 37,500 units of habitat unimpacted by dams, approximately 23,300 units are in areas considered suitable for Atlantic salmon spawning and rearing while 14,200 units are in areas considered marginally suitable for spawning and rearing. Thus, there is much work to be done to meet the goal of connecting 30,000 units of suitable habitat in each SHRU. Fortunately, there is considerable effort on the part of each agency and many partner agencies, non‐governmental organizations, and private industry. Following is a brief synopsis of several efforts that are ongoing to address these high priority recovery actions. Connectivity Projects A wide variety of efforts are currently underway throughout the Gulf of Maine DPS to improve connectivity for Atlantic salmon and other aquatic organisms. These range from large public‐private partnerships to improve awareness, coordination and project management to smaller‐scale individual projects with municipal or private landowners. The following is a brief summary of some of the Atlantic Salmon Recovery Plan 2011 Annual Report Page 46 organizations and efforts. It is important to note that the four agencies represented on the Atlantic salmon connectivity team have involvement in nearly each of the following efforts. Stream‐Smart Road Crossing Workshops ‐ A statewide effort is underway in Maine to educate professionals responsible for road‐stream crossings on how to improve stream habitat by creating better crossings. The workshops will cover road‐stream crossing projects from site assessment to permitting and installation. Maine Audubon, and other partners, including U.S. Fish and Wildlife Service, Maine Forest Service and Maine Department of Inland Fisheries and Wildlife, Maine Department of Environmental Protection, Maine Forest Products Council, Maine Coastal Program, USDA Natural Resources Conservation Service, National Marine Fisheries Service, and Project SHARE will develop and present the workshops this winter. The group is hosting these Stream‐Smart Road Crossing Workshops in four regions of the state to inform public and private road owners about opportunities to replace aging and undersized culverts with designs that last longer, improve stream habitat, save money on maintenance, and can reduce flooding. Among those registering for these workshops are town road commissioners, public works directors, contractors, forest landowners, foresters, loggers, engineers, conservation commissions, watershed groups and land trusts. Aquatic Resource Management Strategy (ARMS) – Maine Department of Transportation is leading an effort to develop a statewide Aquatic Resource Management Strategy. The ARMS goal is to develop networks of properly functioning watersheds that support populations of fish and other aquatic and riparian dependent organisms across Maine. The strategy will focus on maintenance and restoration of ecological processes responsible for creating and sustaining habitats over broad landscapes as opposed to individual projects or small watershed scales. This plan will consist of four components: broad scale passive restoration via standards and guidance; active restoration strategically focused on watershed analysis; partnerships; and education and outreach. Atlantic Salmon Federation – Atlantic Salmon Federation (ASF) has played a critical role in improving developing local support for fish passage projects, fundraising, and through undertaking project management roles. In 2011, the Atlantic Salmon Federation and its Maine Council continued its work to provide fish passage in key salmon watersheds. They initiated engineering work at four dams and expect this work to continue in 2012. The following is a brief summary of key efforts supported by ASF. Mill Street Dam Feasibility Study: The Mill Street Dam is on the Sabattus River, a tributary of the Androscoggin River, in the Town of Lisbon, Maine. It is the lowermost of five dams on the Sabattus River, and was originally constructed in 1850 to supply water to a fabric mill. The dam is owned by Miller Industries, but no longer serves any hydraulic purpose and completely blocks all fish passage. A feasibility study has been contracted to look at fish passage options including dam removal. This project represents the beginning of the Atlantic Salmon Federation’s effort to restore free swim to alewives, sea lampreys and American eel in the Sabattus River. The NOAA Restoration Center and USFWS are partners in the project. Hawkes’ Mill Dam Fish Passage Feasibility Study: The Hawkes’ Mill Dam is on Mill Stream, a tributary of the Sebasticook River, in the Town of Albion, Maine. The dam, owned by Jim Hawkes and originally constructed in 1833 to power a sawmill, holds back an impoundment of approximately 2 acres. The feasibility study seeks to assess various alternatives for fish passage at the dam site for diadromous and resident species, including alewife (Alosa pseudoharengus), American eel (Anguilla rostrata), Atlantic salmon (Salmo salar) and brook trout (Salvelinus fontinalis). It is the goal of the dam owner and project partners to complete the feasibility study by March 1, 2012 to ensure that we can move ahead with final Atlantic Salmon Recovery Plan 2011 Annual Report Page 47 design, permitting, and construction in the 2012 field season. The NOAA Restoration Center is a partner in the project. Pushaw Lake Fishway: Pushaw Lake is 11 miles from the main stem of the Penobscot River in the lower central portion of the Penobscot watershed. At 5,051 acres, Pushaw Lake has been identified as a high priority for sea‐run alewife restoration in the Penobscot watershed. The location, size and depth of the lake make the potential for alewife production at over 1 million fish. The final design for the fishway was completed in January, 2012. Pending final negotiations with the dam owner, the fishway is expected to be constructed in the summer of 2012. The USFWS, MEDMR, and NOAA Fisheries are key partners. Davis/Holbrook Fishway: This project is a continuation of ASF’s decade long effort to restore fish passage for migratory fish in Blackman Stream. Previous efforts have removed or provided passage at three downstream blockages. Currently, ASF is working with the dam association to build a fishway at the outlet of Davis Pond which would also provide passage in to Holbrook Pond. This project is a partnership with the USFWS and MEDMR. USFWS engineers will be developing the preliminary design for a fishway in the winter of 2012. Penobscot River Restoration Project: As a founding member of the Penobscot River Restoration Trust, ASF continues to invest significant time in this project as the project is a top international priority for the organization. The removal of the Great Works Dam is scheduled to begin in June 2012. Project SHARE – Project SHARE continues to be a leader in the identification and removal of fish passage barriers in the Downeast Coastal SHRU. Since 2005, the group has replaced 100 traditional round culverts with open‐bottom structures designed to accommodate natural stream processes, and removed a number remnant log drive dams. Project SHARE will continue to serve as project manager for barrier removal projects and implement habitat restoration projects in 2012. Penobscot River Restoration Trust ‐ The Penobscot River Restoration Trust (PRRT) is the non‐profit organization charged with implementing the core aspects of the restoration effort, including purchase and removal of the two lowermost dams on the Penobscot River, Veazie and Great Works, and purchase and decommissioning of a third dam, Howland Dam, where a fish bypass will be constructed. Members of the Trust include the Penobscot Indian Nation, American Rivers, Atlantic Salmon Federation, Maine Audubon, Natural Resources Council of Maine, Trout Unlimited, and The Nature Conservancy. The tribe and each conservation organization are represented on the board of directors, along with three additional board members. Northeast Aquatic Connectivity Project – The Nature Conservancy has led an effort to undertake an ecoregional assessment of fish passage barriers through the development of a regional database and specific tools and analysis. The work is being developed by the Northeast states to reconnect fragmented river, stream, coastal, reservoir, lake, and estuarine habitat by removing or bypassing key barriers to fish passage thereby enhancing fish populations. Maine Forest Service – The Maine Forest Service (MFS), in partnership with numerous state and federal agencies and nongovernmental organizations, has surveyed thousands of culverts at road‐stream crossings throughout Maine. In addition, MFS provides extensive outreach and education efforts to private landowners on the importance of fish‐friendly stream crossings. MFS also initiates and serves as project manager on many culvert replacement and removal projects throughout the Gulf of Maine DPS. Maine Forest Products Council – In Maine, the Sustainable Forestry Initiative represents 7 million acres of certified forest lands and the American Tree Farm represents in excess of 800,000 acres of certified Atlantic Salmon Recovery Plan 2011 Annual Report Page 48 family forests. In addition under the SFI umbrella, nearly all of the largest forest products manufacturers have SFI certified procurement programs which have extensive responsibilities for wood sourced from lands outside of the SFI and Tree Farm systems. Nearly every harvest that takes place in Maine provides some wood to an SFI facility which in turns creates an opportunity to back feed information through that relationship. SFI has, and will continue to make use of this networking apparatus to educate forest resource professionals on fish passage and stream connectivity issues. The SFI Implementation Committee is also committed to work with state and federal agencies, and other relevant interest, to establish the Fisheries Improvement Network (FIN). FIN will facilitate a non‐
regulatory approach in providing landowners tools, training, and other assistance that is currently available through agency programs and projects to improve long‐term stream connectivity while being flexible and adaptable to various landowner capabilities and approaches. Natural Resource Conservation Service – Natural Resource Conservation Service (NRCS) provides extensive technical and financial support to barrier removal efforts within the Gulf of Maine DPS. In 2011, a fisheries biologist was hired with support from Maine Department of Inland Fisheries and Wildlife and Maine Department of Marine Resources, to work directly with private landowners in the Penobscot River watershed. The work is focused on fish passage barriers identified through watershed scale surveys. In 2011, the program removed a number of culverts in the Pleasant River watershed. In 2012, the program will continue to work with private landowners to educate and to implement barrier removal projects. Keeping Maine’s Forest ‐ Keeping Maine's Forests is an effort to maintain the state’s land base as forest. The initiative’s focus is on helping landowners find practical solutions for keeping their lands undeveloped, open, and productive. KMF is interested in protecting biodiversity (such as rare, threatened, and endangered species recognized at the federal, state, and tribal level, unique and exemplary natural areas, late successional forest features in working forests, and others similar, as well as maintaining, and where practicable, restoring viable populations of game and non‐game wildlife). In addition their goals include maintaining or enhancing existing public access for the full spectrum of existing recreational uses, and attracting an increased number of recreational users by selective investments in improved recreation facilities and facilitating the adaptation of forest systems to a changing climate particularly by maintaining large contiguous and interconnected areas of forest. KMF has identified restoring aquatic habitat connectivity as a primary initial focus for the organization. A variety of partners are contributing to this effort by assisting with identifying biological priorities, providing datasets on potential barrier removals, identifying funding mechanisms and through technical assistance for specific barrier removal projects. Maine Stream Connectivity Work Group ‐ The Maine Stream Connectivity Work Group was convened in 2009 as an informal effort to grapple with the practical and technical challenges that hinder the re‐
establishment of aquatic connectivity in Maine. The Work Group is currently coordinated by the Maine Coastal Program (State Planning Office) with oversight from the Coastal Program and Maine Department of Marine Resources Bureau of Sea‐Run Fisheries. Populated by restoration practitioners affiliated with state, federal and tribal agencies, non‐government organizations, forest products companies, and engineering firms, the Work Group has evolved to act as a forum and increasingly as a mechanism for coordination. The group is concentrating much of its work on the development of prioritization tools and online barrier data access. The Work Group is focused on completing the following objectives: •
Identify alternatives for a dedicated ecological restoration program that focuses on improving aquatic connectivity statewide. Atlantic Salmon Recovery Plan 2011 Annual Report Page 49 •
•
•
•
•
•
•
Increase resources to support priority, on‐the‐ground barrier removal needs at specific sites and regions throughout Maine. Provide incentives and tools for owners of dams and roads to integrate ecological considerations into the operation and maintenance of infrastructure. Provide technical support for the development of stream crossing regulatory rules that compliment statewide aquatic restoration and conservation efforts. Support development of objective, ecologically‐based prioritization approaches that allow a starting point for sequencing restorative action. Provide the restoration community and other users relevant to restoration with efficient access to barrier data. Continue barrier inventories in priority watersheds throughout Maine. Identify alternatives for streamlining regulatory requirements that apply to restoration projects. Mainstem Dams There is considerable progress in relation to mainstem hydroelectric dams. First, a model is under development by the Northeast Fisheries Science Center (see presentation by Nieland et al. at the 2012 Atlantic salmon forum) to quantify the demographic effects of dams in relation to prospects of recovery of the GOM DPS. This model will be used to set performance standards for upstream and downstream passage. There is also direct progress on developing species protection plans and/or habitat conservation plans at many existing hydro dams owned by Black Bear Hydro, NextEra Energy, Brookfield Power, and Miller Hydro. These planning efforts are crucial to the successful recovery of the GOM DPS. Finally, there has been considerable progress on the development of fish passage guidelines by NMFS, USFWS, and PIN. Several regional and national experts have been brought together to develop these guidelines. A report of the committee is expected in the spring of 2012. Emerging Science There has been good progress on the scientific underpinnings of the connectivity action team’s strategy. Ongoing and recently published findings support the general assumptions of increased connectivity leading to enhanced opportunities for diadromous fish restoration and salmon recovery specifically. In addition, there were two peer‐reviewed publications in 2011 that directly address issues of importance to connectivity of the GOM DPS in the context of recovery: Holbrook, CM., MT Kinnison, and J Zydlewski. 2011. Survival of migrating Atlantic salmon smolts through the Penobscot River, Maine: a pre‐restoration assessment. Transactions of the American Fisheries Society 140:1255–1268. Gardner, C, SM Coghlan, J Zydlewski, and R Saunders. 2011. Distribution and abundance of stream fishes in relation to barriers: implications for monitoring stream recovery after barrier removal. River Research and Applications doi 10:1002/rra. 1572 In addition, there are several ongoing research studies made possible by large grants through the NOAA Restoration Center (guided by several members of the connectivity action team) to Project SHARE and the Penobscot River Restoration Trust. These grants have funded several graduate projects and smaller scale evaluations of the ecological effects of dam removals. Many graduate students and other investigators presented these recent findings at the 2012 Atlantic salmon research forum. Theses, dissertations, and peer‐reviewed publications will begin emerging in 2012 along with other contributions from members of the connectivity action team. Atlantic Salmon Recovery Plan 2011 Annual Report Page 50 Finally, accumulating evidence suggests that salmon recovery is likely dependent upon the concurrent recovery of the full suite of diadromous fish, many of which are nearly as imperiled as the Atlantic salmon. These concepts are under scientific scrutiny by several investigators. Preliminary findings are being presented at regional and national science meetings as they become available. At the American Fisheries Society meeting in Seattle 2011, Margaret Guyette and collaborators presented strong evidence of increased growth of juvenile salmon following additions of marine‐derived nutrients and Steve Coghlan and collaborators documented the beneficial effects of “habitat conditioning” attributable to sea lamprey spawning. Peer‐reviewed publications are forthcoming. Financial support and indirect assistance (field crews) from the Atlantic salmon recovery program made these studies possible. Atlantic Salmon Recovery Plan 2011 Annual Report Page 51 Education and Outreach Action Team Peter Steenstra, CHAIR, US Fish and Wildlife Service Don Sprangers, Washington Academy Josh Platt, Kennebec Soil and Water Conservation District Katrina Mueller, Project SHARE Jacob Van de Sande, Downeast Salmon Federation Kathy Libby, NOAA’s National Marine Fisheries Service Strategy Provide coordinated education and outreach for framework activities. Background: The Framework agencies and those stakeholders participating in this team have viewed the “outreach and education action team” as unique from the beginning. It was formed about six years ago, and has been composed of both agency staff and stakeholders from outside the agencies that have an interest in Atlantic salmon outreach and natural science education for the public. The team has involved about a dozen members from among our strongest supporters in the community, including the Atlantic Salmon Federation, the Down east Salmon Federation and the Penobscot River Restoration Trust. We have now realized that a larger view of outreach and stakeholder engagement is warranted. We see value in a focus on not only communicating about meetings, species biology, and special events; but about research, agency proposed actions, and the results of agency actions. We intend to develop a strategy for engaging stakeholders, not just a strategy for a one way flow of information. Accomplishments The Education and Outreach Team worked with each Action Team to determine what messages and products were needed and are working to complete an overall Education and Outreach Plan. The Team identified diverse outreach and education needs: increasing awareness of the agencies activities; changing the behavior of an individual or industry to minimize impacts on salmon and their habitat; and encouraging collaboration among agencies, academia, conservation organizations, and other interested parties. The Team manages http://www.maine.gov/dmr/searunfish/salmonframework.shtml, which contains information about the Atlantic Salmon Framework, links to Framework documents, news items related to Atlantic salmon recovery, meeting announcements, related agency websites, and the names of agency outreach contacts. Atlantic Salmon Recovery Plan 2011 Annual Report Page 52 During the Atlantic Salmon Framework Meeting in January, comments were solicited from those attending following the Education and Outreach Team presentation regarding outreach, communication and stakeholder engagement in Atlantic salmon recovery. These included: A well‐known consultant stated they had not been contacted directly and believed outreach had been selective rather than effective, noting that that many clients of consultants, municipalities, NGOs, watershed protection councils, are not being attended to; A representative of Maine Department of Marine Resources addressed the status of the website, which is not housed where it was supposed to be and needs to be improved; A representative of the Downeast Salmon Federation believes that while agency staff was accessible, there needs to be a clear structure for communication, and plan was needed. They also stated that the website needs financial support. A representative from the Atlantic Salmon Federation stated that ASF and DSF feel a need for inclusion. People have tried to include individuals, but the agencies need to remember that NGOs can reach thousands of people. A free flow of information is essential. The ASF representative gave one objective of the original outreach committee as an example ‐‐ production of interpretive signs on the River. In the end, ASF raised the money for the signs. The original team identified a bunch of needed things that never happened; A representative from Project SHARE said that in that room, we are speaking to choir members. People who own the land are totally disconnected. Busy commercial foresters are not going to take the time to look us up. They are looking for the information and this group needs to reach out to them. Most of the state is in private ownership but not a single large landowner was present; A representative from the National Marine Fisheries Service (NMFS) noted that the Science Center had hired a contractor to do an outreach survey. She found that ATS are not on the radar of 99% of the people of Maine. People do care about clean water, and healthy ecosystems, and a vibrant commercial fishing community, but do not make the ecosystem link between commercial fisheries and declining of populations of all anadromous fish. A representative of the U.S. Fish and Wildlife Service noted that in‐reach is important too – in‐reach, outreach to that inner circle and those very active, engaged NGOs and then also to the greater public; DSF asked what would be the messages – for example, what is the definition of success? Losing no ground? Stakeholders need a forum for dialogue. Decisions on stocking versus no stocking and genetic strains used seem to be internal. DSF believes that we also need to consider engaging people, watershed by watershed in appropriate forums; A representative from The Nature Conservancy noted that engagement is not just telling others what is going on, but networking with lots of little partners. Sharing a common agenda, being part of preparing agendas, developing common metrics for measuring progress are examples. Development of activities Atlantic Salmon Recovery Plan 2011 Annual Report Page 53 to allow for mutual participation would be another example with merit. The NGOs are a strong backbone of support. The little watershed groups are struggling. The group also discussed the need to translate the scientific findings into management decision‐making and discussed a need to determine how to make those decisions transparent in part by explaining things in plain English. We need to seek a way of keeping principal investigators engaged but transferring assessments into practical tools for use by restoration practitioners. 2012 Implementation A new direction for outreach, communication and stakeholder engagement is warranted. An outreach, communication and stakeholder engagement strategy needs to be developed. As the new draft recovery plan nears completion, we propose to use it as a focal point for transforming the outreach, communications and stakeholder engagement associated with our shared mission to recover Atlantic salmon. The first step will be to contact the original outreach team and use them as a core group to develop ideas for outreach on the release of the recovery plan, and also to develop an overarching strategy to engage stakeholders in a meaningful way (while being mindful of the limitations imposed by rules such as the Federal Advisory Committee Act). The release of the draft recovery plan will likely involve Public Informational Meetings held across the DPS; this core group of advocates for the species (the original outreach team) would be of great value in making those informational meetings useful and appropriately geared to the audiences of interested publics. During these informational meetings we can invite other interested stakeholders to participate in stakeholder meetings, into the future, whether as part of an outreach and stakeholder engagement group, or as a party interested in one or more of the three yearly meetings of the Framework committees. Atlantic Salmon Recovery Plan 2011 Annual Report Page 54 Appendix 1 RESEARCH and ASSESSMENT Inventory of completed and ongoing assessment and research projects supported during TAC or Framework review, 2001 ‐ 2012. Contact
J. Zydlewski
J. Zydlewski
J. Zydlewski
J. Zydlewski
Project short title
Smolt acoustictag lab study
Smolt migration
Smolt salinity lab study
Penobscot PIT Tagging
J. Zydlewski
Al & pH smolt physiology
M. Brown
J. Burrows
J. van de Sande
P. Ruksznis
Androscoggin River adults
Marsh Stream parr
East Machias Parr
Cove Brook egg planting
M. Guyette
Marine Derived Nutrients
R. Wathen
Bass salmon interactions
W. Ashe
Conectivity and productivity
Smolt timing from stocked Green Lake
parr
Smolt (alternate rearing) stocking
Smolt (alternate rearing) stocking
0+ parr stocking
0+ parr stocking
Captive reared pre-spawn adult stocking
Single strategy - Captive reared prespawn adult stocking
P. Ruksznis
O. Cox
J. Trial
P. Christman
O. Cox
E. Atkinson
E. Atkinson
Data
UM Thesis
2011
2012 -2016
2014-2023
2015-2020
Data
Data
Rearing
Pending
interim updates
interim updates
interim updates
interim updates
2009-2011
2009-2012
NA
Ongoing
UM Thesis
2008-2009
2008-2009
NA
Completed
2010, 2011
NA
2009-2010
NA
Ongoing
UM Thesis
Pleasant River, Penobscot
2002-2011
2003-2012
2003-2013
Completed
Narraguagus
Pleasant River
Sheepscot
Narraguagus
Hobart
2008-2012
2011-2013
2004-2005
2008-2010
2006-2010
2008-2012
2011-2013
2005-2007
2008-2011
2007-2012
2009-2014
2012-2015
2006-2011
2010-2014
2009-2014
Analysis
Data
Complete
Analysis
Data
interim updates
interim updates
2008
2011
interim updates
Dennys
2011 - 2015
2012-2017
2014-2021
Captive reared pre-spawn adult stocking Sheepscot
C. Bruchs
Captive reared pre-spawn adult stocking Machias
P. Christman
Streamside incubation
B. Naumann
LWD additions
O. Cox
M. Simpson
E. Atkinson
Wild Veazie returns genetics
Upper drainage smolt assessment
Whole River Point stocking
G. Mackey
Point stocking, range of sites
R. Spencer
R. Spencer
R. Spencer
R. Dill
C. Lipsky
T. Lindley
J. Sweka
J. Kocik
G. Mackey
Sea run, captive reared comparison
Upper Piscataquis fry growth
Upper Piscataquis adult transfer
Smolt stocking - sites, timing
Smolt stocking - sites, timing
Merical Penobscot
Fry stocking - habitat & genetics
Fry stocking - Smolt & Adult genetics
Alewife abundance and smolt survival
J. Trial
Stocking density
J. Trial
D Macaw
M. Bailey
Stocked fry upstream movements
Translocated adults
Size selective mortality
J. Trial
Riverine index sites; monitoring juvenile
populations
J. Trial
Adult trap counts
J. Trial
Redd Counts
J. Kocik/Joan Trial
Smolt population estimates and indices
NA
2011-2014
2012-2017
2012 -2016
Reports
NA
NA
2012-2019
2012-2018
P Christman
Upstream stocking post-spawn Captive
broodstock
Egg planting
Egg planting
2012 - 2015
Adult
Return years
NA
2013 - 2016
NA
2012 - 2014
2012 - 2014 2013 -2016
Captive reared pre-spawn adult stocking East Machias
P. Christman
P. Christman
Juvenile
Field years
2012
2012 - 2014
2012 - 2014
NA
UM Thesis
UM Thesis
UM Thesis
UM Thesis
C. Bruchs
E. Atkinson
Study
Stocking years
NA
2012 - 2014
NA
NA
Status
Data
Data
Data
Data
Watersheds
Penobscot
Penobscot
Penobscot
Penobscot
Narraguagus, Penobscot,
Sheepscot
Androscoggin River
Marsh Stream
East Machias
Cove Brook
Piacataquis; Kingsburry
Stream
Penobscot; Pollard, Great
Works, Hemlock, Hoyt
Machias
2005 - 2008 &
2009 - 2014
2006-2010
2006-2010 &
2011 -2013
2011
Stocking
interim updates
2006 - 2015 2009-2019
Data
interim updates
2007-2012
2009-2014
Data
interim updates
2007-2012
2009-2014
Data
interim updates
Data
interim updates
Narraguagus
2007- ?
NA
2008 - ?
Sheepscot, Kennebec
Kennebec
2003-2007
2009-strategy
2004-2009
2010-
2007-20012 Data
2014Data
Sheepscot, Kennebec
2002-2006
2003-2008
2006-2011
Complete
interim updates
interim updates
Sheepscot 2008
Kennebec 2006
2006-2010
2007-2014
NA
Data
interim updates
NA
2003-2008
2007-2010
2005-2010
2008-2012
2005-2012
NA
NA
Data
Data
Data
interim updates
interim updates
interim updates
2005-2007
2006-2009
NA
Analysis
2009
2003-2008
2006-2008
2009-2011
2001-2006
2002-2006
2003-2005
2004
ongoing
Historic data
2004-2010
2006-2009
2010-2013
2001-2006
2002-2006
2003-2005
NA
NA
2013-2016
2002-2008
2003-2007
2004-2007
ongoing
ongoing
Complete
Data
Data
Complete
Complete
Completed?
Completed
Analysis
Completed
2007
interim updates
interim updates
2010
2011
2008
2008, 2012
interim updates
2009
2002-2006
2002-2007
NA
Completed
2007, 2008
2007
NA
2005-2007
2007-2008
NA
2005-2007
NA
2006-2009
NA
Completed
Completed
Completed
2008, 2009
2008, 2009
UM Thesis, 2008
NA
NA
NA
Ongoing
Annual reporting
USASAC, ICES
NA
NA
NA
Ongoing
Annual reporting
USASAC, ICES
NA
NA
NA
Ongoing
Annual reporting
USASAC, ICES
NA
NA
NA
Ongoing
Annual reporting
USASAC, ICES
Machias, East Machias,
Narraguagus
Penobscot
Narraguagus
Dennys
Machias, East Machias,
Narraguagus, Kennebec
Aroostook
Penobscot
Penobscot
Dennys
Penobscot
Penobscot
Sheepscot
Narraguagus
Narraguagus
Narraguagus, East Machias,
Saco
Machias, East Machias
Kennebec
Narraguagus, Penobscot
Narraguagus, Dennys,
Machias, East Machias,
Pleasant, Saco, Kennebec,
Lower Penobscot tributaries,
Penobscot
Penobscot, Kennebec,
Narraguagus, Dennys,
Androscoggin, Saco,
Aroostook, East Branch
Penobscot, St. Croix, Union,
Pleasant
Narraguagus, Dennys,
Machias, East Machias,
Pleasant, Sheepscot, Lower
Penobscot tributaries
Narraguagus, Sheepscot
Proposals Supported During Reviews by Action Teams Marsh Stream Atlantic Salmon Stocking Proposal The Atlantic Salmon Federation, U.S. Fish and Wildlife Service, and Maine Department of Marine Resources requested that 30,000 large parr be stocked in North Branch of Marsh Stream for four years (2011 to 2014). The objective of this pilot project is to evaluate the potential of using a parr stocking program to re‐establish the salmon run in Marsh Stream following the removal of the West Winterport Dam in 2010, which restored access to Atlantic salmon and other diadromous fish to more than 85 miles of mainstem and tributaries. Assessment will consist of monitoring adult fish at the Denil fishway exit at the Frankfort Dam using an underwater video camera during the upstream migration period. Principle Investigators: John Burrows, Atlantic Salmon Federation; Fred Seavey, U.S. Fish & Wildlife Service; Norm Dube, Maine Department of Marine Resources Planting Atlantic Salmon Ova in the Sheepscot River The Maine Department of Marine Resources requested 9,000 Sheepscot origin eyed eggs to assess planting of ova in artificial redds as a restoration strategy in the West Branch of the Sheepscot River. Assessment will consist of fry trapping. Principle Investigator: Paul Christman, Maine Department of Marine Resources Sheepscot River Streamside Incubation Project In 2007 a streamside incubation project was completed in the Sheepscot River comparing survival of streamside incubated to hatchery incubated Atlantic salmon juveniles. The results of this study indicated that survival to the smolt stage was significantly higher for the streamside incubated groups (Christman et al. 2009). The results obtained in this study indicate that non‐conventional methods of incubation, with respect to more natural rearing, seem to have substantial benefits. Given the desire to boost adult returns, as soon as possible, we propose to begin a multi year project in the Sheepscot River where by we utilize streamside incubators to incubate 100,000 eyed eggs. This effort is a short term adaptive management actions specifically aimed at boosting the adult population while new projects are developed to further our understanding of natural rearing. Principle Investigator: Paul Christman, Maine Department of Marine Resources Smolt field studies The Penobscot River hosts the largest returning run of adult Atlantic salmon in the United States. Nonetheless, populations in this and neighboring systems have experienced precipitous declines (USASAC 2005, Fay et al., 2007). The National Academy of Sciences (2004) identified dams as one of the greatest and most acute impediments to Atlantic salmon restoration; dams are known sites of impact through direct injury, and migratory delay (Nettles and Gloss 1987). There are currently five dams in the main stem of the Penobscot River, all of which generate hydropower. There are three dams in the Stillwater Branch. As part of the Penobscot River Restoration Project, Pennsylvania Power and Light (PPL) has agreed to sell three of these dams (Veazie, Great Works, Howland) for eventual removal and/or decommissioning. Work was conducted in 2005 and 2006 (Holbrook, 2007 thesis) to characterize movements of both hatchery‐ and naturally‐reared smolts in order to quantify 1) routes of passage 2) speeds of migration and 3) loss to the system (mortality). The work entailed the use of an acoustic array to monitor tagged fish moving downstream, providing the most rigorous assessment of survival through the Penobscot system directly applicable to the current restoration efforts. Most striking from this work were the observations of poor survival at the Milford Dam, a dam that will remain intact through the Restoration Project. The work proposed for this objective will build on the 2005‐2006 study, collecting up to three additional years of smolt survival data. This work has been completed for the 2009 and 2010 smolt runs. In 2011, emphasis will continue to be placed on movements near Milford Dam (using radio equipment). Recent changes to Milford operations associated with smolt passage have not been evaluated in detail (USASAC 2005). It is also likely that hydroelectric generation will be increased at this location as well as other dams in the lower Penobscot River. There remains the opportunity to inform PRRP planning as to the current condition of downstream passage. Opportunities to optimize hydroelectric facility operations or downstream bypass structures may be informed by detailed information about smolt behavior and passage success through the Milford head pond. Therefore the period of time prior to implementation of the PRRP represents a critical window of opportunity to provide agencies and dam operators with detailed information as to the migratory paths of smolts near this hydroelectric facility. Principal Investigator: Joseph Zydlewski, Assistant Leader‐Fisheries, USGS Maine Cooperative Fish and Wildlife Research Unit, University of Maine Smolt Laboratory studies An assumption of tagging is that metrics of behavior are representative of untagged fish (the population). Survival after tagging is often used as an assessment of long term performance (Collis et al. 2001). Few studies have probed post tagging performance by measuring physiological parameters (e.g Jepsen et al. 2001). In order to assess behavioral response, a large (17’) annular tank has been constructed in the Aquaculture Resource Center at the University of Maine (Figure 3). Multiple pumps circulate water around the tank Figure 3‐ Image of annular tank to be used for behavioral assessment.
simulating natural stream flow. Multiple PIT antennas are installed so that the movement and direction of tagged fish can be determined remotely with this monitoring technique. Such an approach has been used successfully to quantify migratory urge related to smolt development (Zydlewski 2005; Spencer et al. 2010). The importance of directly evaluating behavior in concert with physiological indicators has been clearly demonstrated. Previously such integration of approach relied on field data that are correlative and subject to sampling bias (Zaugg and Wagner 1973; Solomon 1978; Muir et al. 1994a&b). This methodology allows direct assessment of behavioral differences between treatment groups in a controlled situation. Principal Investigator: Joseph Zydlewski, Assistant Leader‐Fisheries, USGS Maine Cooperative Fish and Wildlife Research Unit, University of Maine Smolt imprinting study Hatchery supplementation has been a critical component of Atlantic salmon restoration, and has likely prevented extinction in Maine rivers (NRC 2004). The majority of adult salmon returning to the Penobscot are of smolt‐stocked origin. The smolt‐to‐adult return rate (SAR), however, has declined steadily over the past 30 years indicating increased mortality in the river or at sea (Moring et al. 1995; USASAC 2005). During migration, smolts can incur significant direct or indirect mortality from dams (Ruggles 1980; Coutant and Whitney 2000) and predation (Larsson 1985; Jepsen et al. 1998). Hatchery‐
reared salmon have been shown to incur higher mortality than their wild counterparts in many systems (Collis et al. 2001; Fresh et al. 2003; Johnsson et al. 2003; Metcalf et al. 2003). Differential performance at seawater entry may also be partly responsible for these differences (Alvarez and Nicieza 2003; Fuss and Byrne 2002; Hockett 1994; Shrimpton et al. 1994). Studies have shown that survival of hatchery smolts may be maximized if hatchery releases coincide with the emigration of wild smolts (Hvidsten and Johnsen 1993; Heinimaa 2003). Survival at seawater entry has been shown to be highest in cohorts that enter the estuary in an evening outgoing tide (Clemens et al., 2009) presumably minimizing predation risk. The parr‐smolt transition is a critical transitional stage in the life history of Atlantic salmon. A territorial, stream‐dwelling parr transforms undergoes a complex suite of behavioral, morphological and physiological changes resulting in a migratory smolt (McCormick and Saunders 1987). Both endogenous and environmental patterns (e.g. photoperiod, temperature, turbidity, and flow) contribute to the timing of these shifts (Hoar 1976; Eriksson and Lundqvist 1982; McCormick et al. 1998). Successful transition into the marine environment is thought to occur during a “window of opportunity,” when physiological condition is optimal for survival (McCormick and Saunders 1987). Poor synchrony can result in high mortality in the estuary (McCormick et al. 1999) or at sea (Virtanen et al. 1991; Staurnes et al. 1993). In addition to the obvious advantage of surviving emigration, ability of anadromous salmon to return to a natal stream successfully is pivotal to their reproductive success (McDowall, 2001). Effective homing allows adaptation to local habitats, enhancing the performance of individuals from the local population (Quinn and Dittman, 1990). Straying can be considered an alternate strategy to homing or simply a failure to home effectively. In natural populations, this alternative behavior may be beneficial to the overall persistence of a metapopulation by reducing inbreeding (Heggberget et al. 1988; Quinn, 1993). For hatchery product, straying is an unintended outcome. Salmon species home to natal rivers via a suite of cues and clues, olfaction being the primary mechanism. During the parr‐smolt transformation, enhanced olfactory sensitivity has been documented in Atlantic salmon (Morin et al., 1989a, b). Wild fish may imprint at multiple life stages following cues from the variable environment (Scholtz et al. 1976; Kudo et al., 1994; Dittman and Quinn, 1996), whereas hatchery fish are held in a more constant environment do not experience such cues. For salmon that typically live in their natal stream for years prior to seaward migration, imprinting can also occur during a brief period during the parr‐smolt transformation before the initiation of migration (Scholz et al., 1976). Where smolts are imprinted to is clearly important for natural recruitment for broodstock collection. Smolts stocked in the lower river tend to home to the lower river (Power and McCleave 1980; Gorsky 2005), where successful spawning is improbable (or capture as broodstock may be impractical). A successful stocking strategy balances risks of mortality during migration, with straying risks and the timing of seawater entry such that adult returns are maximized. Gunnerod et al. (1988) stocked Atlantic salmon in the River Surna, its estuary and offshore. Consistent with the hypothesis that in river mortality was a significant factor, SAR’s for salmon stocked in the ocean were more than double the returns for in river stocking. Estuary stocking returns were intermediate. Interestingly, stray rates increase with distance downstream; at sea stocking had the highest stray rates, while in river stocking had no known strays. We propose to assess a smolt stocking protocol that would a) allow a period of imprinting in order to minimize straying, b) avoid in river mortality by releasing smolts into the estuary and 3) maximize the probability of rapid seaward migration by stocking at night on an outgoing tide. This proposal represents the first phase of a longer term vision to optimize smolt stocking methodologies. Figure 3‐ Image of West Enfield Dam, the three imprinting pools are indicated with the black arrow. Beginning in 2009, a three year study to asses this methodology was initiated. Approximately 29,000 smolts are marked using an unambiguous VIE tag (as part of NOAA’s ongoing marking program) and transferred to the West Enfield holding ponds (Figure 4) in order to imprint to the upper Penobscot River for 10 days. Imprinted smolts will be removed from the imprinting pools and transported to the Verona Island boat ramp for direct release into seawater. In order to minimize the risk of predation (a goal of this stocking scenario), the smolts will be released at the start of the outgoing tide, after dark. Such timing had been shown to reduce the risk of mortality in migrating salmonids (Clemens et al. 2009). Some of these fish (~50) will be tagged using acoustic tags in a joint NOAA‐Maine Coop Unit‐USFWS cooperative assessment for the purpose of assessing survival through Penobscot Bay. Principal Investigators: Joseph Zydlewski, Assistant Leader‐Fisheries, USGS Maine Cooperative Fish and Wildlife Research Unit, University of Maine, Anitra Firmenich USFWS Adult field studies In recent decades, efforts to restore Atlantic salmon (Salmo salar) to a number of Maine rivers have been coordinated through the Maine Atlantic Salmon Commission (ASC; now Department of Marine Resources, DMR) and the U. S. Fish and Wildlife Service (USFWS). Efforts targeting the Penobscot River included the installation and improvement of upstream fish passage facilities (Everhart and Cutting 1967). Significant hatchery supplementation was intended to restore large self‐sustaining runs of anadromous Atlantic salmon to the river. Over all, natural reproduction has failed despite these extensive enhancement efforts. Dams have been identified as one of the most acute impediments to restoration of Atlantic salmon in the USA (NRC 2004). The Penobscot River watershed is approximately 22,000 km², and 563 km long, Maine’s largest watershed. The river widens into Penobscot Bay near the town of Bucksport and is tidal from the Veazie Dam to where the bay empties into the Gulf of Maine. The Penobscot River has five hydroelectric dams on the main‐stem, and four located on a major tributary, the Piscataquis River. While the Penobscot River hosts the largest remaining run of adult Atlantic salmon in the USA (USASAC 2005), all high quality spawning and rearing habitats are located upstream of at least four hydroelectric dams (Fay et al. 2006). Three of these dams (Veazie, Great Works and Milford dams) are located within 15 km from the head of tide. Plans are currently underway to remove the two downstream‐most dams (Veazie and Great Works dams) as part of the Penobscot River Restoration Project. Ultimately, benefits of dam removal for Atlantic salmon restoration will depend in large part on the degree and fashion by which these dams currently affect salmon passage success and behavior. In 2000, the Maine Atlantic Salmon Commission Technical Advisory Committee (TAC) identified “Terms of Reference” that needed investigation with respect to the long‐term unified agency goal of restoring self‐sustaining Atlantic salmon populations to their historic range in the Penobscot River (TAC 2000). Goals included evaluating fish passage facilities and characterization of movement in the watershed with respect to reproductive success. This, in turn, spurred the initiation of a collaborative study to track adult Atlantic salmon in the Penobscot River using PIT tag detection in the major fishways in 2002, 2003 and 2004. PIT tagged adults were subsequently monitored using data‐logging receiver/computers at the entrance and exit of each fish way upstream of the Veazie Dam in addition to the entrance and exit of the Veazie fishway. This work was able to demonstrate that hatchery smolts planted in major tributaries of the Penobscot demonstrated fidelity in path choice, homing towards the stocking site (Gorsky 2005; Gorsky et al. 2009) and contributed to an estimate of fish passage efficiency (Holbrook et al. 2009). In 2005, the infrastructure for this work was removed due to lack of funding. These telemetry studies have suggested that migrating adults are delayed at dams throughout the Penobscot River, despite the presence of fishways at all main stem dams (Shepard 1995; Power and McCleave 1980; Dimitry Gorsky, University of Maine Thesis, 2005). PIT technology to quantify passage success and first entry into a fishway. This approach, however, is limited by small detection ranges (less than 1 m). Thus, while the study revealed substantial time lapses between the exit of one fishway and the entrance of the next, it was unable to localize delays to dams, other obstructions, or slow movement rates and holding behavior within free‐flowing reaches. Radio telemetry studies have utilized extensive mobile tracking to provide valuable information on movement patterns and disposition of adult salmon. With a limited number of repeated individual observations and continuously‐running stationary receivers, these studies have limited accuracy in the estimation of movement rates, particularly within free‐flowing reaches. By using the extensive acoustic array (Figure 1) together with an extensive PIT array system, the proposed study will provide a detailed assessment of adult movement rates between many fixed sites to accurately assess the extent of delays at Penobscot River dams. Principal Investigator: Joseph Zydlewski, Assistant Leader‐Fisheries, USGS Maine Cooperative Fish and Wildlife Research Unit, University of Maine Union Salmon Association Fry Request The Union Salmon Association (USA) requested that 20,000 Atlantic salmon F2 eggs be incubated at Green Lake NFH (GLNFH) and allocated for fry stocking activities in the Silsby Plain area of the West Branch Union River in May of 2011. The requested allocation of 20,000 eggs is less than 2% of the Penobscot F2 egg production (total 2010=1,268,630) at GLNFH and would have minimal/no impact on recovery efforts in other watersheds currently stocked with F2 hatchery products. The Union River Atlantic salmon population is considered extirpated and river‐specific broodstock (wild or domestic) are unavailable for the Union. However the Union and Penobscot River are within the same GOM DPS and Penobscot strain eggs are suitable for recovery of extirpated populations within the GOM DPS The lack of adult salmon returns to the Union River in recent years has resulted in an absence of natural reproduction. The requested allocation of eggs represents the only current source of juvenile salmon recruitment for Union River salmon populations. Although natural fish passage on the Union River is blocked by the Ellsworth dam, Black Bear Hydro traps fish below the dam and transports them in tank trucks to upriver release sites. The trap serves as a tool for assessing the stocking program and spawning escapement in the Union River without cost to the Services. Principal Investigators: Barb Witham, Union Salmon Association; Anitra Firmenich, United States Fish & Wildlife Service; Randy Spencer, Maine Dept. of Marine Resources On river hatchery rearing of 0+ fall parr to increase adult Atlantic salmon returns to the East Machias River Over the past ten or fifteen years fry stocking has been the primary stocking strategy for the Downeast Rivers and has been the primary focus of our hatchery production as well. While fry stocking has stabilized these populations it has not increased smolt production to desired levels and has not produced desired adult returns. In recent years a portion of rearing capacity has been focused on smolt production in hopes of increasing adult returns with mixed results. One technique that has not been utilized on the Downeast rivers is the rearing and stocking of fall parr. We believe that a collaboration between the DSF and the USFWS to rear a significant number of fall parr at our facility for the East Machias River has the potential to increase smolt production, adult returns and the potential to assess efficacy of fall parr stocking as an alternate stocking strategy for the Downeast Rivers. For 2011 we propose to retain 2,000 fry from the 50,000 eggs we are incubating currently at EMARC to rear through the summer to be stocked into the East Machias in October at the direction of DMR BSFH. Concurrently we would begin planning with USFWS and BSFH for a larger scale fall parr stocking program including rigorous assessment. Our goal would be to rear enough parr to stock the entire drainage or some portion depending on the study design. BSFH staff have suggested stocking densities of 10 to 25 parr/ unit, so basin wide stocking would require the rearing of 20,000 to 50,000 fall parr at our facility. Principal Investigator: Downeast Salmon Federation Penobscot Broodstock Photoperiod Treatment In 2010, Craig Brook National Fish Hatchery (CBNFH) began administering a photoperiod treatment on Penobscot sea run broodstock in an attempt to delay the onset of broodstock maturation. Since 2000 the onset of Penobscot broodstock spawning at CBNFH has steadily advanced from the 2nd of November to as early as October 24th. As CBNFH relies solely on ambient water sources, eggs taken in October are typically exposed to water temperatures above optimal levels for spawning and egg incubation [6 – 10 °C]. Above‐
optimal water temperatures during early egg development affect both egg and fry survival, and may increase the potential for embryonic deformities. In addition, accelerated early egg development results in fry that biologically require feeding, but are unable to do so due to cold ambient process water. Attempts were made in 2008 and 2009 to delay the egg take of Penobscot broodstock by not spawning fish until early November [2008] and by reducing handling of broodstock [in 2009]. Both these attempts were unsuccessful as they did not delay the maturation of the broodstock, just the collection of eggs. Therefore both attempts led to incomplete egg takes in 2008 and 2009. A photoperiod treatment was first implemented in 2010 to extend the light available during the summer solstice [June 21] for several weeks following the solstice. The extension of light is applied to ‘re‐set’ the biological clock in the sea‐run broodstock, thus delaying maturation as well as the onset of spawning. Filtered ambient light is still available; extra light is administered in both a disease screening facility and three Swedish pools via existing overhead lighting using a predetermined schedule [below] and simple time clocks. The broodstock are returned to ambient light on November 1st. The broodstock are separated by gender within each Swedish Pool on October 19th; during this sort, the broodstock are examined to determine maturation level. Additional examinations are performed on October 28th, November 1st, and November 8th. Penobscot broodstock are spawned beginning on November 9th and all eggs are collected by November 22nd. The photoperiod treatment results in a delay in spawning by ten days over the ten year average. The delay of egg take into mid‐November allows eggs to begin incubation in optimal water temperatures. Chart 1. Photoperiod treatment applied to Penobscot broodstock at Craig Brook National Fish Hatchery in 2010. Chart 2. Average number of Penobscot broodstock spawned at Craig Brook National Fish Hatchery during specific weeks. ^ In 2008 an attempt was made to delay spawning without a photoperiod adjustment resulting in an incomplete egg take. * In 2009 all female broodstock were spawned on a single day – an unprecedented occurrence at the facility. Purpose The purpose of continuing the photoperiod treatment in 2011 is achieve a slight delay in broodstock maturation leading to a favorable developmental regime for eggs destined for both fry and smolt production. Outplanting and evaluation of gravid adults from the Denny’s
broodstock line reared at Craig Brook National Fish Hatchery into the
Denny’s River:
C.H.A.T. Action Item 34: The use of outplanted adults in smaller scale systems like Northern Stream (Bruchs 2011) and other small tributaries (Mackey et al. 2009) has provided insight and knowledge into behavior of outplanted adults. The next step is to evaluate this management strategy on a larger geographic scale. We propose to outplant a minimum of 218 gravid adult salmon into the Dennys River watershed at a sex ratio of 1:1 in the fall of 2011 and for four subsequent years. This management action would replace the need to spawn adults at Craig Brook from 2011 through 2015. Adults from both the parr to adult and pedigree lines would be used at an equal rate. No fry stocking would occur in the Dennys River during this time. Monitoring and evaluation will include: spawner surveys during each fall, redd trapping during two selected springs, and juvenile abundance and distribution surveys during the late summer and early fall and possibly spring smolt trapping. ME ‐ DMR Bureau of Sea‐run Fisheries and Habitat (BSRFH) have planted gravid adults into several streams within the Downeast SHRU. The resulting juveniles were as successful as hatchery reared salmon, and there were indications that these stream reared fish had better fitness. This may be due to lifelong acclimation to ambient water chemistry or development in synch with stream temperatures. Objectives (bulleted list): 1. Replace stocked hatchery fry with outplanted adults. 2. Stock a minimum of 218 gravid adults late September early October 2011. Continue fall outplanting for four additional years (2015) or one Atlantic salmon lifecycle. 3. Monitor spawning activity to document timing and amount of spawning that occurs until river conditions prevent further activity. 4. Use this information to determine the rate of distribution with in the Dennys River. 5. Trap redds to record timing and duration of emergence. 6. Conduct assessment work to determine distribution and abundance of juvenile salmon. In addition, data will be collected on length and weight to estimate condition. 7. Deploy a rotary screw smolt trap in the lower Dennys River Drainage to assess outmigration timing and abundance. 8. Produce an annual report each December providing updates on the project. 9. Publish a summary of findings and results. Principal Investigator: Ernest Atkinson Appendix 2 Tables of Actions in 2011. Bold indicates activity; grey shading indicates change from Operational Plan Conservation Hatchery Actions
Current Program: review and implement biosecurity plan
Current Program: Provide therapeutic and prophylactic
treatment recommendations for optimum fish health
Current Program: conduct USFWS annual Fish Health
Inspections
Current Program: fish health diagnostics
Current Program: screen all non-fry mortality for pathogens
at Craig Brook NFH
Current Program: screen all gametic fluids taken during
broodstock spawning
Current Program: produce Penobscot F2 eggs as backup
source
Current Program: maintain captive brood for Machias
Current Program: maintain captive brood for Narraguagus
Current Program: maintain captive brood for Dennys
Current Program: maintain captive brood for Sheepscot
Current Program: maintain captive brood for East Machias
Current Program: maintain captive brood for Pleasant
Current Program: maintain Penobscot domestic brood
Current Program: conducts surveillance of Infectious
Salmon Anemia Virus in sea-run brood
Current Program: maintain use of Penobscot sea-run brood
Current Program: release spent broodstock into river of
origin
Current Program: 50,000 1+ smolt / 1+ parr into the
Narraguagus
Current Program: 50,000 1+ smolt / 1+ parr into the
Machias
Current Program: 550,000 1+ smolt into the Penobscot
Current Program: 350,000 0+ parr into the Penobscot
Culture & Stocking: 50,000 1+ smolt / 1+ parr into the
Pleasant
Current Program: stock 15K parr in Sheepscot
Current Program: stock 1 million fry in Penobscot
Culture & Stocking: stock 750K fry in Penobscot; balance of
searun adult spawn naturally
Current Program: stock 500K fry in Machias
Current Program: stock 500K fry in Narraguagus
Current Program: stock 400K fry in Dennys
Culture & Stocking: stock gravid adults (no fry) in Dennys
Current Program: stock 200K fry in Sheepscot
Current Program: stock 100K fry in East Machias
Current Program: supply eggs to East Machias Aquatic
Research Center (EMARC) to stock 50k parr in East
Machias
Current Program: stock 100K fry in Pleasant
Tools & Assess: mark significant number of parr releases
Culture & Stocking: smolt release utilizing imprinting and
seawater acclimation
Culture & Stocking: artificial redd / egg stocking in
Kennebec (Sandy River)
Tools & Assess: develop and implement in-hatchery product
assessment program
Tools & Assess: in-stream fry and parr assessment
program
Tools & Assess: smolt migration / production assessment
program
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Genetic Diversity Actions
Evaluation of hatchery practices and products
Optimize practices to reduce risks of inadvertent selection
that might reduce fitness in the wild
Utilize broodstock database to track spawning history for all
salmon held for broodstock purposes and implement
spawning protocols described in the Broodstock
Management Plan
Implement stocking practices that broadly distribute genetic
groups (families) throughout the stocking sites
Implement pedigree lines if demographic, family recovery,
aquaculture escape event, or other parameter limits the
potential collection of a broodstock year class
Maintain and enhance as applicable the genetic viability of
river-specific broodstocks for supplementation according to
the Broodstock Management Plan
Link hatchery production parameters (i.e.. Changes in
fecundity, broodstock reproducing, etc.) to genetic
characteristics of the broodstocks to assist in monitoring of
fitness
Implement collection practices that obtain representative
genetic variation (i.e. majority of artificial and wild spawned
families), including widespread field collection-Juveniles for
DPS parr collections for current parr program
Evaluate the genetic implications of collecting adult fish for
captive propagation versus wild reproduction
Evaluate and optimize grading practices to reduce genetic
selection (initial emphasis on grading for smolt production)
Implement collection practices that obtain representative
genetic variation (i.e. majority of artificial and wild spawned
families), including widespread field collection-Adults for
collection of adult returns to the Penobscot for broodstock
Experimental genetic analyses and projects for increased
hatchery evaluation
Consider options to evaluate, improve, and enhance the
hatchery product and broodstock management practices in
experimental environments outside of hatchery production
requirements
Monitoring of genetic diversity
Monitor broodstocks for evidence of genetic diseases or
deleterious genetic traits
Genetically assess consequences of alternate stocking
strategies for multiple life history stages
Prioritize current genetic data analysis needs with respect to
current and long-term management goals
Evaluate if certain program components are missing (gap
analysis) in regards to genetic goals of the program.
Monitor estimates of genetic diversity of the wild or naturally
reproducing Atlantic salmon (for currently defined hatchery
program/DPS and Penobscot)
Use genetic determination of parentage to identify
percentage of families recovered from stocking events, and
monitor yearly to evaluate broodstock collection practices
Improve management of data resulting from production,
stocking, and genetic evaluation to facilitate program
assessment and monitoring
Continually monitor critical trait variation (quantitative,
morphometric, other physical trait) to assess risks of
inadvertent selection
Fundamental: Use genetic methods to annually characterize
parr and sea-run adults
Use 2-phased criteria to assess if spawning optimization
program effectively reduces potential for inbreeding
Use 3-phased criteria (relatedness, inbreeding, and limited
population size) to determine if spawning populations within
or between capture years is needed
Monitoring for aquaculture
Screen incoming parr and adults for aquaculture escapees
Monitor effectiveness of Aquaculture Biological Opinion
(including site inspections, audits, etc)
Prevent aquaculture adults from entering rivers with existing
trapping facilities and using emergency methods when large
escapes occur and trapping is possible.
Operate the Denny's weir for the preemptive purpose of
excluding aquaculture Atlantic salmon
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Marine Estuarine Actions
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Domestic and International Assessment & Management
Participation in ICES WGNAS
Participation in NASCO
Participate in NASCO’s International Atlantic Salmon
Research Board
Participation and oversight of NASCO’s West Greenland
Sampling
Conduct analysis and document findings of SALSEA WG
sampling in 2009 - 2011
Seek opportunities to integrate SALSEA WG, MERGE and
NA research findings
Continue to archive and data mine historical high seas tag
recaptures
Continue to support the development of amendments to the
NEFMC FMP for Atlantic salmon prohibiting possession and
any directed or incidental commercial fishery in federal
waters
Continue to condition permits for activities within the
estuaries of DPS rivers so as to minimize potential effects
on migration of juveniles and adults
Continue to enhance protection of estuarine riparian areas
where necessary through expanded enforcement and
modifications to the Natural Resource Protection Act, Forest
Practices Act, LURC Zoning standards, and/or Municipal
Shoreland Zoning
Initiate a comprehensive evaluation of existing marine
related data for correlations with trends in salmon
population abundance at USA, North America and North
Atlantic scales
Research Scoping
Continued Participation in NOAA Fisheries Service-Sea
Grant Nearshore Workshop
Active Estuarine and Marine Sampling and Research
Continue to build large scale tracking infrastructure at
domestic and international level and participate in such a
program through initiation of tracking studies
Continue to monitor the occurrence of marine mammal
scars on returning adults to the adult trap in the Penobscot
River
Initiate smolt radio tag project to further investigate when
and where smolts are dying in the estuary
Initiate a new study to evaluate whether river herring
populations reduce predation risks to emigrating smolts
Initiate a new study on bioenergetic modeling/analysis of
marine salmon to evaluate cost/benefits of future scenarios
of ocean conditions, forage fish dynamics, predatory
dynamics
Initiate adaptive management studies based on Nearshore
survival workshop recommendations to synthesize
information and improve our understanding of factors
affecting the estuarine and nearshore mortality of Atlantic
salmon.
Manuscript
in Review
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Freshwater Actions
Evaluation of Action
Timeline
Design and implement a state-wide juvenile salmon Review of sampling design and data quality (variance) of Ongoing
sampling plan based on statistical sampling with
the Parr Production Index (%CV ≤ 35)
fully standardized methods
Evaluate smolt production on selected rivers (i.e.
Narraguagus, Penobscot, and Sheepscot Rivers)
Calculated smolt estimates and evaluate smolt production Ongoing
in association with large parr production
Monitor reaches for natural re-colonization
Contrast tends in natural re-colonization to adult Atlantic
salmon abundance, distribution, and changes in
connectivity
Monitor water temperatures in selected salmon river Data will be used by manages when evaluating juvenile
systems
production and juvenile production potential
Develop habitat based productivity estimates and
identify key elements of productive salmon habitat
and limiting factors
Data used as inputs for the Atlantic salmon production
model
Ongoing
Ongoing
2012-2015
Status
Maine DMR developed and implemented a state-wide juvenile sampling plan. The sampling scheme
was used fall of 2011. Results are presented in the FWAT and SAAT sections of this report. In addition
a review of the sampling design and logistic will be conducted to determine ways of streamlining the
effort.
Atlantic salmon smolt production was estimated at three locations, Narraguagus River, Upper
Piscataquis River, and the Sheepscot River. Results are presented in the FWAT and SAAT sections of
this report.
Redd counts were conducted within each SHRU and results are presented in the FWAT and SAAT
sections of this report.
Water temperature was monitored at 40 locations by Maine DMR in the GoM DPS. DMR data is
currently being appended to their water temperature database. USFWS FRO monitored water
temperature on the Narraguagus River. Water temperature was also monitored on the Sheepscot River
by Keith Nislow.
Data on of fry density, juvenile density, and water temperature have been collected and are currently be
analyzed. There is limited data relating water quality and juvenile salmon densities. If staff and time are
available, this action will receive more attention in 2012.
Wesley Ashe, UMO has been evaluating growth and survival of fry stocked ATS in small headwater
streams with over 20 habitat variables. Water temperature, brook trout biomass, interstitial spaces, and
percent cobble correlate the strongest with growth and survival.
Following a review of USFWS and NGOs modeling efforts, this action will be reevaluated to better align
the action with the goal of focusing restoration efforts
Develop a GIS model to predict Atlantic salmon
production, based on abiotic and biotic parameters
Completion of the model is used to develop a model to
predict habitat suitability for Juvenile Atlantic salmon
2012-2015
Conduct surveys to validate GIS Atlantic salmon
production model (e.g. substrate quality, complexity
etc.)
Map riparian zones and activities (e.g., harvest
practices, ATVs, development etc.) that may impact
Atlantic salmon (sedimentation, flow, etc)
Identify areas for riparian forest improvement and
pursue resources for improvements
Support riparian zones management practices for
water quality and habitat
Prioritize and evaluate habitat restoration strategies
based on system connectivity, habitat quality, and
the expected Atlantic salmon production and pursue
resources for improvements
Model successfully predicts Atlantic salmon production
2014-2015
None
Completed map of riparian zones that can inform
restoration prioritization
2012-2013
Map of riparian areas that could be targeted for
restoration and number of grant applications filed
Number of consultation and acres of riparian zones in
conservation
The development of a list
2013-2014
While this action was to commence in 2012, TNC did conduct a modeling exercise looking at lateral
connectivity to the stream in its ARA model. It is our goal to discuss how their efforts and our actions
FWAT 8 and 9 can benefit from their work.
See action FWAT 8
Ongoing
None
2014-2015
This action is the culmination of this implantation plan building on current actions, FWAT will be ramping
up its effort on this task in 2012 as it has discussion with Project SHARE, TNC, and USFWS with the
goal of evaluating current habitat model efforts to accomplish a prioritization of focus areas. FWAT no
ling believes it is practical to prioritize habitat restorations on a project bases, but rather based on
drainage or sub-drainage.
Freshwater Actions
Increase escapement of adult salmon to the
Penobscot River
Evaluation of Action
Increasing % of wild origin trap catch
Trap and truck adult salmon from Lockwood Dam to A positive association between the number of female
the Sandy River drainage, Kennebec basin
Atlantic salmon transported upstream and redd counts
and juvenile CPUE is expected
Sample all Aquaculture suspects captured for
Review of pathogen reports and management SOPs as
disease
necessary
Investigate recruitment from natural spawning and Comparison of fry and large parr recruitment
various hatchery stocking strategies as tools to
repopulate vacant habitat with Atlantic salmon to
facilitate future adult returns
Evaluate the impacts of sedimentation and changes Data was used to inform habitat modeling efforts
to stream channel geomorphology on habitat
quality/quantity
Retain large woody debris in streams and rivers to Number of river kilometers where land owners have
support salmon habitat quality and quantity
made a committed to maintain LWD inputs
Implement habitat manipulations adding large wood Number of river kilometers treated and juvenile Atlantic
to streams
salmon response
Perform experimental habitat manipulations to
reduce sedimentation (i.e. embeddedness/armoring)
and evaluate the effect on the biological function of
streams
Assess avian, fish, and mammal predation in
freshwater-all life stages
Number of river kilometers treated and juvenile Atlantic
salmon response
Timeline
Ongoing
Ongoing
Ongoing
2012-2015
Status
At a meeting among DMR, Craig Brook staff, and GDAT ways of reducing the numbers of sea-run
broodstock were discussed. The outcome of that discussion was that GDAT, is not comfortable
reducing the number of broodstock because it would reduce the effective spawning population size. In
fact, GDAT would like to see the effective spawning population size increase. Given the large number
of adult returns to the Penobscot River in 2011, it is apparent that the resource agencies need to do a
better job of getting adults upstream into productive spawning areas. DMR documented 45 redds in
Great Works Stream. That happens to be were 1/3 of the GLNFH smolts are stocked. Additionally,
based on the PIT tag array, DMR noticed 1,000 adults that were released to the river were never
documented trying to pass upstream. Most likely they were not motivated to. An evaluation of smolt
stocking practices is recommended.
Adult returns were reported on Maine DMR’s adult trap catches web page weekly
64 Atlantic salmon were transported from Lockwood to the Sandy river. Subsequently 51 redds were
documented.
Two aquaculture suspects were lethally sampled from the Dennys’ weir. Both were confirmed
aquaculture escapes.
CHAT, GDAT, and FWAT approved egg planting 56,000 eyed eggs in Cove Brook Stream, Penobscot
Bay SHRU. This work will commence in January 2012.
2012-2015
None
Ongoing
There is a project on the Sheepscot River, monitoring movements of 17 trees from a natural blow down
and the bed-channel profile associated with those debris jams.
For three years, Project SHARE and DMR have collaborated on large woody debris additions to several
Downeast Coastal streams. In 2011, several trees were “dropped” below route 9 in the Narraguagus
river.
No in stream embeddedness assessments were conducted in 2011; however, sediment deposition was
monitor in associating with large woody debris.
2012-2015
2012-2015
Report on Atlantic salmon predation issues that leads to a 2012-2015
reduction in salmon predation
None
Freshwater Actions
Evaluation of Action
Report on nutrient additions
Evaluate the ecological role and importance of
diadromous fish (alewives, shad, smelt etc.)
contributions to the freshwater production of smolts
Timeline
2011-2015
Status
In addition to several monitoring efforts being conducted in the Kennebec and Penobscot estuaries,
DMR counted river herring, shad, and sea lamprey at many adult salmon trapping facilities.
Margaret Guyette, UMO, conducted a nutrient addition study on Kingsbury Stream, Upper Piscataquis
River looking at growth and condition of juvenile Atlantic salmon and uptake of MDN by primary and
secondary consumers.
Young-of-the-year Atlantic salmon were 22 – 56% larger and had 1.3 – 2.3 times greater fat reserves in
treatment reaches relative to control reaches for three months following nutrient additions
Salmon carcass analog uptake was evident in fish muscle tissue within one month and in some
macroinvertebrate taxa within two weeks following nutrient addition.
Investigate natural spawning performance of
translocated adult salmon
Transporting Atlantic salmon into novel habitat increased 2011-2013
juvenile production in the targeted habitat relative to other
strategies (e.g. stocking smolts or fry)
Capture and captive-rear, in sea-cages, wild and/or Increased adult escapement, juvenile production, and
“return” rates relative to treatment controls.
naturally-reared Penobscot smolts for release as
sexually mature adults in selected river reaches
Assess overwinter survival of juvenile salmon using
best available data initially, and design and
undertake further research as needed
Support and implement studies that provide
managers with information on abundance,
distribution, and habitat utilization of Atlantic salmon
Review existing water quality standards for salmon
rivers to determine adequacy to meet the needs of
Atlantic salmon
Ensure that water withdrawal permit requirements
protect stream flows required for the recovery and
conservation of Atlantic salmon. Enforce all
appropriate permits for water withdrawals
Evaluation of permit requests associated with
incidentally take of Atlantic salmon
Review existing stocking programs (various trout
spp, bass spp, or any other species) and assess the
potential impacts of these introductions on Atlantic
salmon populations
Minimize bycatch of Atlantic salmon through closure
of adult Atlantic salmon holding areas to fishing and
angler education
Report on overwinter survival in Maine
Ongoing
Increased knowledge of Atlantic salmon distribution and
habitat utilization that can be incorporated with passage
and juvenile production data
Ongoing
Report on the adequacy of water quality standards in
Maine to protect Atlantic salmon
Ongoing
None
Report on the adequacy of water withdrawal permits in
Maine to protect Atlantic salmon
Ongoing
Maine DMR reviewed LURC irrigation permits
Number of permit requests reviewed
Ongoing
At this time, FWAT does not know the number of permits reviewed.
No specific work was conducted on overwinter survival; however, FWS and NOAA have been working
on updating life history models. Both of those agency efforts are working to better understand how
passage inefficacies at FERC Hydro projects can influences population dynamics.
Mike Brown, Maine DMR, radio tagged adult Atlantic salmon returns to the Androscoggin River. Two of
the tagged salmon dropped out of the Androscoggin and were subsequently handled at Lockwood fish
lift.
Identification of stocking programs that have the potential Ongoing
to reduce Atlantic salmon survival.
None
Areas closed and/or posted
No new closures were enforced this year. Randy Spenser, Maine DMR did meet with Maine Warden
Service to discuss Atlantic salmon holding areas. Maine DMR biologists did contact various game
wardens to discuss the disposition of Atlantic salmon in the Penobscot River. There was one case of an
“illegal” gillnet known to have captured one Atlantic salmon reported my Maine DMR to USFWS and
State Wardens.
At this time, we do not have any documentation reporting bycatch of Atlantic salmon.
Continue to enforce commercial freshwater fisheries Reducing Atlantic salmon bycatch
regulations/permits where the potential for incidental
take of Atlantic salmon exists
Ongoing
Randy Spencer, Maine DMR, translocated 167 pre-spawn adults in Oct. of 2011. As part of this project
redds from 2010 were trapped to study fry emergence. In addition, juvenile surveys and smolt trapping
were also conducted. This is the third and final year of adult stocking. Juvenile and smolt production
will be assessed for through the 2010 spawning cohort.
This action needs to be reevaluated in light of recent staffing cuts
Ongoing
Ongoing