Appendices Appendix A1 - Otago University Research Archive

Transcription

Appendices
Table of Contents
Appendix A1 ............................................................................................ 3
Figure A1.1: .................................................................................................................... 3
Appendix A2 ............................................................................................ 9
Table A2.1: ..................................................................................................................... 9
Table A2.2: ................................................................................................................... 35
Appendix A3 .......................................................................................... 38
Table A3.1: ................................................................................................................... 38
Appendix B1 ........................................................................................... 40
Appendix B2 ........................................................................................... 64
Table B2.1: .................................................................................................................... 64
Table B2.2: .................................................................................................................... 67
Table B2.3: .................................................................................................................... 69
Table B2.4: .................................................................................................................... 72
Appendix B3 ........................................................................................... 74
Figure B3.1: .................................................................................................................. 74
Figure B3.2: .................................................................................................................. 75
Figure B3.3:................................................................................................................... 76
Figure B3.4: .................................................................................................................. 77
Figure B3.5: .................................................................................................................. 78
Figure B3.6: .................................................................................................................. 79
Appendix C1 .......................................................................................... 74
Figure C3.1: .................................................................................................................. 74
Appendix C2 .......................................................................................... 75
Table C2.1: .................................................................................................................... 75
Appendix D............................................................................................. 78
Table D1: ...................................................................................................................... 78
Table D2: ...................................................................................................................... 80
Table D3: ...................................................................................................................... 82
Appendix E ............................................................................................. 85
Table E1.1: .................................................................................................................... 85
Appendix F ........................................................................................... 100
Incidence of plastic fragments among burrow-nesting seabird colonies on offshore
islands in northern New Zealand ............................................................................................ 100
F.1 Abstract ................................................................................................................. 100
F.2 Introduction........................................................................................................... 100
F.3 Methods ................................................................................................................ 102
F.4 Results................................................................................................................... 105
F.5 Discussion ............................................................................................................. 110
References ............................................................................................ 112
Appendix A1
Site-specific growth
Metapopulation processes
+
rtNt(D+/D−)i + It
Nt = NAt + NPrt + NJt
NAt = (NAt-1 * SA) + NPrt = (NJt-AFR *
SJ[AFR]) * Pret
(NPrt-1 * SPr)
It
It α ft(D+/D−)e *Rt (D+/D−)i
NJt = NAt * Ft
ft = ΣNPrt/Ds
R=H*C
Ft = (1−Skipt) * BSt
Figure A1.1:
Generic model of seabird colony growth considering both site-specific parameters and
metapopulation processes.
rt – per capita growth rate, Nt – number of individuals in a colony, (D+/D−)i – intrinsic
density dependence, It – immigration, NAt – number of adults, NPrt – number of pre-breeding
birds, NJt – number of immature birds, SA – adult survival, SPr – pre-breeder survival, AFR – age
at first return, Pret – probability of return (philopatry), SJ[AFR] – immature survival until age at first
return, Ft – fecundity, Skipt – number of adults skipping breeding, BSt – breeding success per
breeding adult, ft – number of immature birds prospecting a new colony, (D+/D−)e – extrinsic
density dependence, R – probability of prospectors recruiting into a new colony, ΣNPrt – total
pool of pre-breeding birds in a metapopulation, Ds – distance to natal colony, H – habitat quality,
C – social cues.
Generic colony growth model
The rate of growth of a seabird colony depends on “intrinsic” or site-specific growth,
influenced by the per capita growth rate, rt, at any moment in time, t, the number of individuals
in the colony Nt, and positive or negative intrinsic (i) density-dependent effects (D+/D-)i; and
“extrinsic” metapopulation dynamics, or the number of immigrants recruiting from other
colonies It (Fig. A1).
Colony growth = rtNt(D+/D-)i + It
(1)
Per-capita growth rate, rt depends on an interaction between species-specific life history
strategies and environmental stochasticity moderated by density-dependence (D+/D-) i.
Although mechanisms associated with density dependence are not well understood in seabird
populations (Moller et al. 2009), negative density-dependence may occur as a result of
limitations in breeding sites and food (Croxall and Rothery 1991, Baker and Wise 2005, Sandvik
et al. 2012), while positive density dependence may be associated with coloniality (i.e. "safety in
numbers" from predators, Lyver et al. 2000, Jones 2003). Even less is understood about seabird
dispersal and immigration to new colonies (It), which are assumed to be regulated by negative
density-dependent factors; however, social behaviour may over-ride their importance (Hunter et
al. 2000, Kildaw et al. 2005, Kerbiriou et al. 2012). We predict that immigration will play a
disproportionately large role in colony growth, considering the effects of seabirds’ characteristic
long generation times and low rt values. To simplify the general model, we excluded dispersal
by adults , as site fidelity is common among seabirds once breeding has been established (Dubois
and Cézilly 2002).
Intrinsic growth
Seabird life histories are characterised by prolonged absences from breeding sites
following fledging, and a number of years of attendance as “pre-breeders” before pair bonding
and successful breeding. Thus, the number of individuals associated with a seabird colony in
any given season (Nt) is made up of the number of breeding-age adults (NAt), the number of prebreeders (NPrt), and the number of immature birds (NJt; Fig. 1).
Nt = NAt + NPrt + NJt
(2)
For most seabirds, as in other long-lived animals, the number of adults from the previous
season (NAt-1) that survive, at a rate SA, to breed has the greatest influence on intrinsic population
growth rate (Russell 1999, Saether and Bakke 2000, Igual et al. 2009). Variables affecting SA
include natural (e.g. disease) and anthropogenic (e.g. fisheries bycatch; Burger and Gochfeld
1994) factors. The number of adults in a season (NAt) will also depend on the number (NPrt-1) and
survival (SPrt-1) of pre-breeding birds from the previous season.
NAt = (NAt-1 * SA) + (NPrt-1 * SPr)
(3)
The number of pre-breeders (NPrt) that return to the natal colony will depend on
the number (NJt-AFR) and survival (SJ[AFR]) of immature birds until the species’ characteristic ‘age
at first return’ to the colony (AFR), and the probability of return (Pret) to the natal site (i.e.
philopatry). Although AFR can vary between individuals and with environmental stochasticity
and Pret is generally considered to be high in seabirds (Warham 1990, Milot et al. 2008); each
species is likely to have a characteristic values for these parameters (Ovenden et al. 1991,
Mougin 2001, Aubry et al. 2009). Factors that are thought to influence immature survival
include natural and anthropogenic variation in at sea conditions (e.g. sea surface temperature and
oil spills; Votier et al. 2008). Immature birds often represent a significant proportion of a
population and their dynamics can therefore potentially have large consequences for population
growth (Hunter et al. 2000, Votier et al. 2008, Votier et al. 2011). However, seabirds cannot be
easily monitored away from breeding areas, so the precise effects of factors affecting the survival
(SJ) of immature birds on population growth are not well understood (Oro et al. 2006).
NPrt = (NJt-AFR * SJ[AFR]) * Pret
(4)
The number of immature birds produced by a colony will depend on the number of
breeding adults (NAt) and their fecundity (Ft).
NJt = (NAt* Ft)
(5)
Short-term changes in fecundity (Ft) generally have little effect on long-term intrinsic
population growth trajectories. Variation in reproductive success can be high, which serves to
buffer populations from environmental stochasticity (Cairns 1989, Doherty et al. 2004).
However, long-term decreases or increases in fecundity will eventually translate to changes in
per capita population growth and one of the main causes of prolonged suppression of
reproductive success is predation by alien mammals or humans (Muñoz Del Viejo et al. 2004).
Fecundity is the product of breeding success (BSt; the number successfully reared fledglings per
individual breeding attempt) and the number of adults attempting breeding (1-Skipt; Baker and
Wise 2005, Pascoe et al. 2011). Intermittent breeding, or “skipping,” (Skipt) is a characteristic of
seabirds that produce one offspring per year (i.e.procellariiformes; Cubaynes et al. 2011) and is
considered to be a buffer against adverse environmental conditions (Erikstad et al. 1998).
Ft = (1-Skipt) * BSt
(6)
Extrinsic processes
Although seabirds exhibit high rates of philopatry, immigration of immature individuals
(It) has been shown to be a significant factor in the dynamics of metapopulations (Inchausti and
Weimerskirch 2002, Milot et al. 2008, Pascoe et al. 2011). We assume here that immigration
rate is influenced by density-dependent processes, both at the source, affecting the size of the
available pool of birds exploring a new colony (prospectors; NPrt), and locally, by the number of
birds already breeding at that colony (Nt; Oro et al. 2006).
It α ft(D+/D-)e * Rt (D+/D-)i
(7)
Where ft represents the number of immature birds available to prospect a new colony,
mediated by extrinsic (e) density-dependence (D+/D-)e, and R is the probability that these
prospectors recruit to the new colony, mediated by intrinsic density-dependence (D+/D-)i within
the new colony.
The number of birds prospecting a new colony depends on the size of the pool of prebreeding birds available to prospect (ΣNPrt) which, in turn, likely reflects density-dependence at
the source colony (e.g. availability of breeding sites); and the distance between the prospective
colony and the natal colony (Ds).
ft = ΣNPrt /Ds
(8)
The probability of recruitment to a new colony depends on the interaction between
habitat quality (H) at the new colony (Kildaw et al. 2005) and the strength of positively densitydependent social cues (C, i.e. social facilitation, Danchin et al. 2004, or Allee effects, Schippers
et al. 2011).
R=H*C
(9)
Appendix A2
Table A2.1:
List of islands in New Zealand with all non-native predators removed and pre- and post-eradication information regarding breeding
seabirds. Types of data include (N) none, (A) anecdotal, (O) observation of relative abundance, and (C) direct counts of birds or
burrows. (U) = Unknown
Island
Area
(ha)
Raoul
2938
Invasive
pred.
removed
Goat
Cat
Date
introd.
Date
erad.
1836
1984
1836
2004
1921
2004
c. 1250
2004
Seabird species
Wedge-tailed
shearwater
Kermadec little
shearwater
Norway
rat
Pacific rat
Black-winged
petrel
White-naped
petrel
Kermadec petrel
Red-tailed
tropicbird
Masked booby
Sooty tern
Colony size Type of Response
pre-erad.
data
post-erad.
1 burrow in
1980s
A 1 new colony
Type of
data
Suspected
Burrows
found in 1910,
none in 80s
A
None
O
Sources
C. Gaskin pers.
comm.
(Veitch et al.
2004)
A
3 new
colonies
C
(Veitch et al.
2011)
Suspected
A
O
(Parkes 1984)
None
A
None
None
None
A
A
A
None
Small
numbers now
breeding
Recolonization
None
Re-
C
O
O
O
O
colonization
Macauley
236
Goat
Pacific rat
Manama Tawhi
(Great Island)
300
Goat
Pig
c. 1836
1970
c. 1788
2008
1643 and
1869
1946
1946
Kermadec stormpetrel
None
Wedge-tailed
shearwater
~40 000 pairs
Kermadec little
shearwater
numerous'
Black-winged
2–3 million
petrel
pairs
White-naped
petrel
~50 000
Kermadec petrel
<50 pairs
Kermadec stormpetrel
Suspected
White-bellied
storm-petrel
Suspected
Red-tailed
tropicbird
50–100 pairs
Masked booby
~100 pairs
Fluttering
shearwater
Common
Common diving
petrel
Grey-faced petrel
Red-billed gull
Sooty shearwater
Black-winged
petrel
Southern blackbacked gull
A
None
O
O
U
N
A
U
N
O
U
N
O
O
U
U
N
N
A
U
N
A
U
N
O
O
U
U
N
N
O
Rare
Common
Common
Rare
O
O
O
O
Unown, rare
O
None
Increase in
relative
abundance
U
U
U
Breeding,
now
moderately
common
Breeding
O
U
O
N
A
N
N
N
A
(Tennyson et al.
1998)
(Tennyson et al.
2003)
(Veitch et al.
2004)
(Tennyson and
Taylor 1990)
(Ramsay and
Watt 1971)
(Powlesland
1990)
(Richie 1998)
Motuopao
Aorangi
Taranga
30
110
718
Pacific rat
Pig
Pacific rat
1879
c. 1820
U
Generally
1989 Little blue penguin distributed
Sooty shearwater <20 burrows
Fluttering
shearwater
1 burrow
Small
Common diving
scattered
petrel
colonies
Small number
Grey-faced petrel of burrrows
Black-winged
~800-1000
petrel
pairs
White-faced
storm-petrel
~20
Small
scattered
1936 Buller's shearwater colonies
Fluttering
shearwater
Common
A. Booth pers.
comm.
(Pierce and
Parrish 1993)
O
U
N
O
U
N
O
N
O
U
Increase in %
cover of
island
O
U
N
O
U
Increase in
numbers
200 000
breeding
pairs
N
None
Increase in
numbers
after
eradication,
decrease
recently
None
A
G. Taylor pers.
comm.
(Hamilton
1925)
A
A
(Buddle 1941)
(Harper 1983)
None
None
Too soon
after
eradication
A
A
(Harper 1976)
O
O
O
Grey-faced petrel
Pycroft’s petrel
Common diving
petrel
Fairy prion
Common
Rare
O
O
Rare
Common
O
O
2011 Little blue penguin
Common
O
A
N
C
(Skegg 1964)
(Hen Island)
Coppermine
80
Pacific rat
U
Flesh-footed
Last seen in
shearwater
1954
Sooty shearwater 1–10 pairs
Fluttering
shearwater
Common
Little shearwater
~100s
Grey-faced petrel Common
Pycroft’s petrel
Common
3–4 pairs
White-fronted tern A few pairs
Pied shag
3–33 pairs
Moderate
1997 Little blue penguin numbers
Grey-faced petrel Scattered
Pycroft’s petrel
Flesh-footed
shearwater
Little shearwater
White-fronted tern
Lady Alice
155
Pacific rat
c. 1800
Grey-faced petrel
Pycroft’s petrel
O
O
O
O
O
O
O
O
O
O
O
U
U
Increase in
breeding
success
N
N
N
Moderate
numbers
Tens of
thousands
O
Rare
C
U
Increase in
breeding
success
One pair
Breeding
Moderate
numbers
Scattered
O
O
U
U
N
N
O
O
U
U
Increase in
breeding
success
C
N
Small
numbers
C
C
(McCallum et
al. 1984)
(Pierce 2002)
C
C
C
(McCallum et
al. 1984)
(Pierce 2002)
Flesh-footed
shearwater
Sooty shearwater
Whatupuke
Urupukapuka
102
102
Pacific rat
Stoat
U
Thousands
Hundreds
Little shearwater
Rare
Several pairs
White-fronted tern Breeding
Moderate
1997 Little blue penguin numbers
Grey-faced petrel Scattered
Small
Pycroft’s petrel
numbers
Flesh-footed
shearwater
U
Fluttering
shearwater
One only
Four pairs
U
2009
Pied shag
Common
U
2009
Little shag
Few
U
2009
O
O
N
N
C
U
U
Increase in
breeding
success
O
O
U
U
N
N
C
O
O
U
U
N
N
O
U
N
O
U
N
O
U
N
O
U
N
O
U
N
U
N
(McCallum et
al. 1984)
(Pierce 2002)
(Hitchmough
and McCallum
1980)
Norway
rat
Ship rat
Waewaetorea
52
Stoat
Norway
U
2009
U
2009
Southern blackbacked Gull
Few
O
U
N
(Hitchmough
and McCallum
1980)
rat
Ship rat
Okahu
21
Stoat
U
2009
U
2009
U
2009
U
2009
Southern blackbacked Gull
Few
O
U
N
(Hitchmough
and McCallum
1980)
N
(Hitchmough
and McCallum
1980)
N
(Hitchmough
and McCallum
1980)
N
(Hitchmough
and McCallum
1980)
Norway
rat
Ship rat
Motukiekie
29
Stoat
U
U
2009
U
2009
Breeding
O
U
Norway
rat
Ship rat
Moturua
135
Stoat
U
U
2009
U
2009
U
2009
Rare
O
U
Norway
rat
Ship rat
Pacific rat
Motuarohia
50
Stoat
U
2009
U
2009
Norway
rat
Red-billed gull
Breeding
Common
U
O
U
Ship rat
Stoat
Poroporo
U
U
2009
2009
Red-billed gull
Common
O
U
N
U
2009
Common
U
2009
U
breeding
O
A
none
A
U
Recolonization
U
2004
U
2004
U
2004
U
2004
U
2004
U
2004
U
O
U
N
U
1991
O
U
Population
increase
Recolonization
Re-
N
(Hitchmough
and McCallum
1980)
Norway
rat
Ship rat
Common
brushtail
Tawharanui
588
possum
Ship rat
Stoat
Cat
Grey-faced petrel
C. Gaskin pers.
comm.
(Lovegrove and
Ritchie 2005)
Norway
rat
Weasel
Ferret
Pokohinu
(Burgess)
56
Goat
Pacific rat
Breeding
Significant
Grey-faced petrel concentrations'
Common diving
petrel
Breeding
White-faced
storm-petrel
None
Little shearwater
None
O
A
A
A
A
A
C. Gaskin pers.
comm.
(McCallum
1980)
Lizard
Mokohinau islets
Atihau
1
10
16
Pacific rat
Pacific rat
Pacific rat
1970s
U
U
1978
Horomea
11
U
1991
1991
(Maori Bay)
Motukino
(Fanal)
79
Pacific rat
U
None
A
Black petrel
None
A
Cook’s petrel
Fluttering
shearwater
Breeding
A
Low numbers
O
Little shearwater Low numbers
White-faced
storm-petrel
Common
Common diving
petrel
Breeding
O
O
A
1997
A
A
A
U
Population
increase
N
None
Population
increase
A
1991
(Trig)
Pacific rat
Fluttering
shearwater
colonization
Recolonization
Recolonization
Colony
expansion
A
A
N
Fluttering
shearwater
Low numbers
Significant
Diving petrel
Breeding
Sooty shearwater
Breeding
Fluttering
shearwater
Low numbers
Significant
Diving petrel
Breeding
Significant
Diving petrel
Breeding
C. Gaskin pers.
comm.
(McCallum
1980)
O
U
N
O
A
U
U
N
N
A
U
N
O
U
N
O
A
U
U
N
N
O
U
N
A
U
N
(McCallum
1980)
C. Gaskin pers.
comm.
(McCallum
1980)
C. Gaskin pers.
comm.
(McCallum
1980)
C. Gaskin pers.
comm.
(McCallum
1980)
Hauturu
2817
Pacific rat
Cat
(Little Barrier)
U
<1870
1980
Common
O
U
Increase in
breeding
success
Population
increase
Recolonization
Increase in
breeding
success
Recolonization
N
Cook's petrel
Est. 50 000
pairs
O
Black petrel
Breeding
A
Diving petrel
None
A
Fluttering
shearwater
Breeding
A
Grey-faced petrel
None
A
Grey-faced petrel
~5–15
burrows
C
None
O
~5–15
burrows
C
None
O
Breeding
Breeding
Breeding
C
C
C
U
U
U
N
N
N
O
G. Taylor pers.
comm.
(McKenzie
1950)
(Imber et al.
2003b)
O
(Rayner et al.
2009)
O
O
A
House
Te Haupa
6
mouse
U
2010
(Tennyson and
Taylor 1999)
Norway
rat
Tiritiri Matangi
196
Cat
Pacific rat
<1981
<1984
U
Red-billed gull
White-fronted tern
1970s Little blue penguin
Breeding
A
1993
Breeding
A
None
A
Rare
A
Grey-faced petrel
Common diving
petrel
Fluttering
shearwater
U
Colony
expansion
Recolonization
Increase in
breeding
success
N
A
A
A
C. Gaskin pers.
comm.
Tiritiri Matangi
Project
(Tennyson and
Taylor 1999)
Red-billed gull
White-fronted tern
Breeding
Breeding
Breeding
A
A
A
U
U
U
N
N
N
Breeding
A
U
N
Norway
Motuihe
195
rat
1997
1997
(Stubbs 1996)
>1987
Breeding
A
U
N
(Veitch 2002b)
c. 1984
2004 White-fronted tern
Breeding
A
U
N
(Hawley 2005)
2005
Breeding
Breeding
Breeding
Breeding
None
A
A
A
A
A
U
U
U
U
None
N
N
N
N
O
None
A
None
O
None
A
None
O
None
U
N
None
U
N
House
mouse
Cat
European
rabbit
U
Caspian tern
Pied shag
Little shag
Red-billed gull
Grey-faced petrel
Common diving
petrel
Fluttering
shearwater
European
Motukorea
58
rabbit
c. 1975
1991
1980s
1995
U
1995
U
Norway
rat
(Browns)
House
mouse
Rangitoto-
2300–
Cat
U
P. Brown pers.
Motutapu
1500
Stoat
U
2009
U
2009
Red-billed gull
U
2009 White-fronted tern
U
2009
U
2009
U
2009
1868
1997
1868
2000
1920–
1972
2004
c. 1998
2002
Comm.
(Miller et al.
1994)
U
U
N
U
U
N
U
U
N
None
A
None
A
None
U
N
A
Population
increase
A
G. Taylor pers.
comm.
N
(Cameron et al.
2007)
Norway
rat
Ship rat
House
mouse
Hedgehog
Common diving
petrel
Fluttering
shearwater
European
rabbit
Common
brushtail
possum
Brushtailed rock
wallaby
Norway
Rakino
148
rat
Norway
Tarahiki
5
rat
Grey-faced petrel
~200 pairs
Norway
Pakatoa
29
rat
U
1997
None
U
Kauwahaia
0.7
Ship rat
U
1989
Sooty shearwater
Common
Flesh-footed
shearwater
Less common
Common diving
petrel
Less common
O
O
U
U
N
N
O
U
N
O
U
N
(Taylor and
Cameron 1990)
Norway
Otata
22
rat
Stoat
1956
1980–
1948
1955
U
1945
Breeding
Grey-faced petrel 150 burrows
A
U
N
O
New colonies
A
C
Recolonization
A
G. Taylor pers.
comm.
(Cunningham
and Moors
1985)
European
rabbit
Spotted shag
None
Norway
Maria
1
rat
1959
Grey-faced petrel
White-faced
storm-petrel
Breeding
A
U
N
U
A
N
Breeding
A
U
Population
increase
10 nests
C
U
N
A
Norway
Motuhoropapa
9
rat
<1962
1981–
Grey-faced petrel
David Rocks
1
Norway
1960
G. Taylor pers.
comm.
(Cunningham
and Moors
1985)
Breeding
O
U
N
75 burrows
C
None
O
Breeding
A
U
N
(Cunningham
and Moors
1985)
(MacKay et al.
2007)
(Cunningham
and Moors
1985)
rat
White-faced
storm-petrel
Cuvier
181
Goat
Cat
Pacific rat
O
U
N
O
C
U
U
N
N
c. 1889
Few burrows
50 birds in
Spotted shag
nests
White-fronted tern 12 nests
Little Blue
1960
penguin
few
Moderate
1964 Grey-faced petrel
numbers
<1827
1993
A
1890
Sooty shearwater
None
Pied shag
6 pairs
400 pairs on
Red-billed gull
monument
5-10 pairs on
White-fronted tern monument
Fluttering
shearwater
None
Common diving
petrel
None
Pycroft’s petrel
None
Little shearwater
None
Moturehu
(Double)
32
Pacific rat
c. 1900
1989
Common diving
petrel
Less common
Fluttering
shearwater
Less common
Sooty shearwater
Few
Flesh-footed
Few
O
O
C
O
O
A
A
A
A
U
Population
increase
Recolonization
Population
increase
Decrease in
numbers
N
U
Recolonization
Recolonization
None
None
N
A
A
G. Taylor pers.
comm.
(Blackburn
1967)
(Bellingham et
al. 1981)
O
O
A
A
N
N
A
None
A
A
U
N
A
A
A
U
U
U
N
N
N
G. Taylor pers.
Comm.
(McFadden
1992)
shearwater
Pycroft’s petrel
Korapuki
18
Pacific rat
c. 1900
Rare
A
Population
increase
Breeding
O
U
N
600–700
C
Population
increase
O
None
1 breeding
female
C
U
N
C
U
N
Common
Moderate
numbers
3 birds
O
U
N
O
C
N
N
Localized
O
U
U
Population
increase
O
U
N
Around
perimeter
O
N
Breeding
O
U
Population
increase
U
A
U
N
U
Breeding
A
O
U
U
N
N
None
8 nests
A
O
None
U
N
N
A
(Hicks et al.
1975)
European
rabbit
c. 1900
1987
Grey-faced petrel
Fluttering
shearwater
Sooty shearwater
Fluttering
shearwater
Little shearwater
Pycroft’s petrel
Common diving
petrel
Whakau
(Red Mercury)
225
Pacific rat
U
Grey-faced petrel
Pycroft’s petrel
Flesh-footed
shearwater
Fluttering
shearwater
Little shearwater
Common diving
petrel
Pied shag
(Towns 2002)
(Towns and
Atkinson 2004)
A
A
G. Taylor pers.
Comm.
(Fogarty and
Douglas 1972)
Kawhitu
100
Pacific rat
<1900
c1900
1991
Common
O
U
N
Rare
Common
O
O
None
A
breeding
4–28 nests
O
C
Population
increase
U
Recolonization
Population
increase
U
12 nests
C
U
N
Breeding
A
N
Breeding
O
U
Population
increase
Breeding
Small
numbers
Small
numbers
O
N
O
U
Population
increase
O
U
N
Breeding
O
U
N
Breeding
A
U
N
A
U
N
A
A
U
U
N
N
G. Taylor pers.
Comm.
European
rabbit
(Stanley)
Fluttering
shearwater
Grey-faced petrel
Common diving
Petrel
Pycroft’s petrel
Pied shag
A
N
A
(Edgar 1962)
(Skegg 1963)
(Thoresen
1967)
A
N
European
Ohinau
45
rabbit
Pacific rat
U
U
Flesh-footed
2005
shearwater
Fluttering
shearwater
Grey-faced petrel
Common diving
petrel
Middle Chain
23
Pacific rat
U
1994
Grey-faced petrel
Little blue penguin Breeding
Fluttering
Breeding in
shearwater
1920s
Common diving Breeding in
(Skegg 1963)
A
A
(Sladden and
Falla 1928)
(Fogarty and
Douglas 1973)
petrel
1920s
Norway
Whenuakura
3
rat
c. 1982
1984
c. 1980
1984
c. 1900
1915
None
U
N
(Moore 1976)
A
Population
increase
A
G. Taylor pers.
Comm.
Breeding
A
U
N
16 nests
C
N
none
A
U
Recolonization
None
U
N
House
mouse
(Donut)
Mahurangi
23
Goat
Grey-faced petrel A few burrows
Norway
rat
(Goat)
Tuhua
1311
Pig
Pacific rat
(Mayor)
Cat
Rurima
Moutohora
4
173
Pacific rat
Goat
U
U
<1993 Little blue penguin
White-throated
2002
shag
U
2002
U
2002
U
1984
Grey-faced petrel
c. 1890
c. 1920
1987
1968
1987
A
(Edwards 1954)
C
U
N
(Croxall and
Millener 1971)
C
Population
increase
C
(Butts and
Porter 1993)
~10 pairs
O
U
N
(Imber et al.
2000)
~10 pairs
Breeding
O
A
U
U
N
N
None
None
A
A
None
None
C
C
15 nests
Norway
(Whale)
rat
Several
Grey-faced petrel hundred pairs
European
rabbit
Pied shag
White-fronted tern
Fluttering
shearwater
Common diving
petrel
Pycroft’s petrel
Little shearwater
None
None
A
A
None
None
C
C
None
U
N
None
U
N
Norway
Mokoia
135
rat
<1839
1989 U
c. 1965
2001
1906
1968
U
1997
House
mouse
Whangaokena
13
Goat
Pacific rat
(East)
U
(Moors 1980)
Norway
Motu-o-Kura
14
rat
c. 1936
(Bare)
Kapiti
1970
Cattle
Goat
Cat
c. 1837
1906
c. 1830
1928
c. 1900
1934
1893
1987
<1850
1998
Common
brushtail
possum
Norway
Common
O
U
N
(Walls 1998)
Sooty shearwater
Fluttering
shearwater
Common diving
Petrel
~ 20 pairs
O
None
C
(Walls 1988)
None
A
None
C
None
A
C
Spotted shag
None
A
None
Recolonization
C
(Miskelly 2000)
rat
Pacific rat
Sheep
<1850
1998
1850s
1930
U
None
U
N
<1850
1998
U
None
U
N
<1850
1998
U
None
U
N
1800s
Breeding
None
U
N
Sooty shearwater
White-fronted tern
Breeding
Breeding
None
None
U
U
N
N
Red-billed gull
Breeding
None
Common diving
petrel
None
Fluttering
shearwater
None
Norway
Tahoramaurea
1
rat
Norway
Motungara
3
rat
House
Mana
Matiu/Somes
217
27
mouse
Ship rat
c. 1961
1990
Pied shag
Fairy prion
None
None
Breeding
Spotted shag
Breeding
U
Recolonization
after active
A
restoration
Recolonization
after active
A
restoration
ReA
colonization
A
None
Population
None
increase
Population
None
increase
N
(Miskelly and
Taylor 2004)
(Townsend
1994)
(Miskelly 1999)
(Miskelly et al.
2004)
C
C
C
C
A
A
S. Cotter pers.
comm.
Fluttering
shearwater
Mokopuna
(Leper)
0.5
Takapouera
150
Ship rat
1990
U
A
None
A
None
U
N
(Parrish 1984)
Cat
Sheep
(Stephens)
Cattle
Te Hoiere
c. 1961
None
309
Pig
Goat
(Maud)
1925
1984
Fairy prion
1 million pairs
O
None
A
U
U
Sooty shearwater
U
O
U
N
U
U
c1870
1970
c1870
1970s
<1955
1975
c1948
1953
U
None
U
A
A
(Harper 1985)
(Markwell
1997)
(Campbell 1967)
P. Gaze pers.
comm.
(Bell et al.
2005)
(Gaze and Cash
2008)
Norway
Titi
32
rat
Pig
Fluttering
shearwater
Common diving
petrel
Sooty shearwater
Flesh-footed
shearwater
Little blue penguin
Motuara
59
Pig
Pacific rat
Kokomohua
(Long)
142
Pacific rat
Breeding
None
U
N
(Gaze 2000)
Breeding
None
U
N
(Bell 1969)
Breeding
A
None
C
(Gaze 1982)
Breeding
Breeding
A
None
None
U
C
N
c1840
1950s Sooty shearwater
Breeding
A
U
N
U
U
A
U
N
U
1997
Sooty shearwater
Fluttering
Breeding
Breeding
A
A
U
Population
N
A
P. Gaze pers.
comm.
P. Gaze pers.
comm.
M. Bell pers.
shearwater
increase
comm.
House
Pickersgill
103
mouse
Pig
U
2007
U
None
U
N
c. 1840 1950s
House
Blumine
377
mouse
Pig
U
2007
c. 1840
1980
<1980
1982
c. 1900
1989
None
A
U
N
U
None
U
N
P. Gaze pers.
comm.
Common
brushtail
Allports
16
possum
House
mouse
Nukuwaiata
(Inner
Chetwode)
195
Pig
Goat
Pacific rat
Weka
Te Kakaho
(Outer
Chetwode)
83
Weka
c. 1900
1963
Fluttering
shearwater
U
1993
Sooty shearwater
U
None
None
A
U
1994
c. 1920
1994
c. 1920
1994
Sooty shearwater
Common diving
petrel
Breeding
A
U
N
U
A
U
N
Breeding
A
None
A
C. Miskelly
pers. Comm.
P. Gaze pers.
comm.
(Walls et al.
1984)
P. Gaze pers.
comm.
Norway
WhakaterePapanui
74
rat
Pacific rat
U
1999
Sooty shearwater
Breeding
A
None
A
(Millar and
Gaze 1997)
U
1999
Fluttering
U
None
None
A
(Markwell and
shearwater
Daugherty
2003)
P. Gaze pers.
comm.
Norway
Tinui
95
rat
U
1999
Sooty shearwater
U
A
U
N
P. Gaze pers.
comm.
U
1999
Sooty shearwater
Breeding
A
U
N
P. Gaze pers.
comm.
U
1989
U
2007
Sooty shearwater
5 active
burrows
A
None
A
U
2007
Sooty shearwater
None
A
None
A
(Taylor and
Tilley 1984)
1977
2003
Norway
Puangiangi
69
rat
House
Motutapu
2
mouse
None
N
House
Tonga
8
mouse
(Golding 2010)
C. Golding pers.
comm.
House
Adele
87
mouse
Stoat
House
Fisherman
4
mouse
U
2007
U
~1775
1988
Fiordland crested
penguin
~1775
1986
U
A
U
N
(Taylor and
Tilley 1984)
O
None
C
(McLean et al.
1993)
None
U
N
None
None
A
Norway
Breaksea
170
rat
Breeding
Norway
Hawea
9
Anchor
1130
rat
Stoat
U
2001 Broad-billed prion
U
G. Taylor pers.
Comm.
R. Moorhouse
pers. comm.
Red Deer
Chalky
Rarotoka
(Centre)
Pomona
514
88
262
Stoat
Pacific rat
Red deer
U
U
2004
2001
Fiordland crested
penguin
3 nests
A
None
A
Sooty shearwater
U
None
None
A
H. Edmonds
pers. comm.
(McLean et al.
1993)
U
1997
U
None
U
N
U
2007
U
None
U
N
U
2007
U
2007
U
2007
U
2007
U
2007
U
None
U
N
U
2007
U
1985
Near
extinction
C
Population
increase
C
G. Taylor pers.
Comm.
Breeding
colony on
north coast
A
U
N
(Dell 1950)
Common
Common
O
O
None
U
O
N
(West 1990)
(Imber 1996)
Common
brushtail
possum
Ship rat
Stoat
House
mouse
Rona
60
Stoat
House
mouse
Whenua Hou
1396
Weka
Cook's petrel
Common
brushtail
(Codfish)
possum
Pacific rat
<1925
U
Fiordland crested
penguin
Yellow-eyed
1997
penguin
Little blue penguin
1987
Common diving Small colony
petrel
(Sealers Bay)
South-Georgian
diving petrel
U
Small
Sooty shearwater
numbers
Mottled petrel
Breeding
Pied shag
3 nests
Red-billed gull
Breeding
Broad-billed prion
None
O
A
O
A
C
O
A
Population
increase
Population
increase
None
none
U
U
Recolonization
A
A
A
A
N
N
(Imber et al.
2003)
(Darby 2003)
(Scott et al.
2009)
A
Norway
Ulva
Mokinui
Putauhinu
270
86
141
rat
Pacific rat
30
Pukeweka
3
Taukihepa
939
(Big South Cape)
1997
Sooty shearwater
None
A
None
A
U
2006
Sooty shearwater
Common
A
U
N
(Flack 1976)
Breeding
C
None
A
U
Recolonization
A
U
1960s Sooty shearwater
Common diving
1997
petrel
Mottled petrel
U
None
None
(Flack 1976)
(Bragg et al.
2009)
(Moller et al.
2009)
(McClelland et
al. 2011)
(McClelland et
al. 2011)
Cat
Pacific rat
Rerewhakaupoko
(Solomon)
U
B. Masuda pers.
comm.
Ship rat
Ship rat
Ship rat
A
c. 1960
2006
Sooty shearwater
Breeding
C
U
N
c. 1960
2006
Sooty shearwater
Breeding
C
U
N
c. 1960
2006
Sooty shearwater
Breeding
C
None
A
(Bell 1962)
(Scott et al.
2005)
(Newman et al.
2008)
(Moller et al.
2009)
Campbell
11331
Cattle
Sheep
1902
1984
1895
1991
Yellow-eyed
penguin
Rock-hopper
penguin
490-600
breeding pairs
O
U
N
Breeding
O
U
N
P. McClelland
pers. comm.
(Westerskow
1960)
Breeding
O
U
N
(Kinsky 1969)
Rare
C
U
N
(Moore 1992)
~2300
C
U
N
~1000
A
U
N
Thousands
O
U
N
Common
Common
Thousands
O
O
O
N
N
A
U
O
U
Common
O
O
U
U
None
Recolonization
Recolonization
U
Common
O
U
N
Rare
Rare
O
O
N
N
O
G. Taylor pers.
comm.
N
(Bell 1955)
Norway
rat
Mangere
113
Sheep
Cattle
c1810
2001
Erect-crested
penguin
Wandering
albatross
Southern royal
albatross
Black-browed
albatross
Grey-headed
albatross
Light-mantled
albatross
Giant petrel
Sooty shearwater
Grey-backed
storm-petrel
White-chinned
petrel
Antarctic tern
Campbell Island
shag
Red-billed gull
<1892
1968
Sooty shearwater
Breeding
O
U
U
Population
increase
U
U
Fairy prion
Breeding
O
U
A
A
N
European
rabbit
Cat
<1892 ~1892 Broad-billed prion
Black-winged
~1892 1950
petrel
White-faced
storm-petrel
Breeding
O
Breeding
O
Breeding
O
Population
increase
Population
increase
Recolonization
Litlle blue penguin
Pied shag
Breeding
Breeding
O
O
U
U
Brown skua
Red-billed Gull
White-fronted tern
Rangatira
(South East)
218
Sheep
Cattle
Pig
Goat
1841
1961
1880
1961
1800
1839
Breeding
Breeding
Breeding
Sooty shearwater ~17 000 nests
C
C
C
N
N
(Dawson 1955)
(Tennyson
1991)
(Imber 1994)
(Bell and Bell
2003)
(Tennyson and
Millener 1994)
O
O
O
U
U
U
N
N
N
O
None
O
G. Taylor pers.
comm.
Common
A
None
O
(Bell 1955)
1961
Diving petrel
White-faced
storm-petrel
Common
A
None
O
(Dawson 1955)
1961
Fairy prion
U
A
O
Broad-billed prion
Black-winged
petrel
Yellow-eyed
penguin
Little blue penguin
Pied shag
Red-billed gull
Common
A
Breeding
A
U
Population
increase
Population
increase
(Imber 1994)
(Nilsson et al.
1994)
(Roberts et al.
2007)
U
Breeding
U
A
A
A
U
U
U
N
N
N
~30 pairs
Rare
O
A
U
U
N
N
O
O
Brown skua
Red-billed gull
White-fronted tern
Chatham Island
petrel
Grey-backed
storm-petrel
Chatham albatross
Little shearwater
Breeding
Breeding
Breeding
A
A
A
Rare
A
None
None
None
A
A
A
U
U
U
Population
increase
Recolonization
None
None
N
N
N
O
O
C
A
Table A2.2:
Common and scientific species names of seabirds and non-native predators presented in Table A2.1.
Seabird species
Scientific name
Non-native species
Scientific name
Antarctic tern
Sterna vittata
Brush-tailed rock wallaby Petrogale penicillata
Black petrel
Procellaria parkinsoni
Cat
Felis catus
Black-browed albatross
Thalassarche melanophrys
Cattle
Bos taurus
Black-winged petrel
Pterodroma nigripennis
Brushtail possum
Trichosurus vulpecula
Broad-billed prion
Pachyptila vittata
European rabbit
Oryctolagus cuniculus
Brown skua
Stercorarius antarcticus
Ferret
Mustela furo
Buller’s shearwater
Puffinus bulleri
Goat
Capra hircus
Campbell Island shag
Phalacrocorax campbelli
European hedgehog
Erinaceus europaeus
Caspian tern
Hydroprogne caspia
Mouse
Mus musculus
Chatham albatross
Thalassarche eremita
Norway rat
Rattus norvegicus
Chatham Island petrel
Pterodroma axillaris
Pacific rat
Rattus exulans
Common diving petrel
Pelecanoides urinatrix
Pig
Sus scrofa
Cook’s petrel
Pterodroma cookii
Red deer
Cervus elaphus scoticus
Erect-crested penguin
Eudyptes sclateri
Sheep
Ovis aries
Fairy prion
Pachyptila turtur
Ship rat
Rattus rattus
Fiordland crested penguin
Eudyptes pachyrhynchus
Stoat
Mustela erminea
Flesh-footed shearwater
Puffinus carneipes
Weasel
Mustela nivalis vulgaris
Fluttering shearwater
Puffinus gavia
Weka
Gallirallus australis
Grey-backed storm-petrel
Garrodia nereis
Grey-faced petrel
Pterodroma macroptera gouldii
Grey-headed albatross
Thalassarche chrysostoma
Puffinus assimilus
Kermadec little shearwater
kermadecensis
Kermadec petrel
Pterodroma neglecta
Kermadec storm-petrel
Pelagodroma marina albiclunis
Light-mantled albatross
Phoebetria palpebrata
Little blue penguin
Eudyptula minor
Little shag
Microcarbo melanoleucos
Little shearwater
Puffinus assimilus
Masked booby
Sula dactylatra
Mottled petrel
Pterodroma inexpectata
Pied shag
Phalacrocorax varius
Pycroft’s petrel
Pterodroma pycrofti
Red-billed gull
Chroicocephalus scopulinus
Red-tailed tropicbird
Phaethon rubricauda
Rock-hopper penguin
Eudyptes chrysocome
Sooty shearwater
Puffinus griseus
Sooty tern
Onychoprion fuscatus
Southern black-backed gull
Larus dominicanus
Southern giant petrel
Macronectes giganteus
Southern royal albatross
Diomedea epomophora
South-Georgian diving petrel
Pelecanoides georgicus
Spotted shag
Phalacrocorax punctatus
Wandering albatross
Diomedea exulans
Wedge-tailed shearwater
Puffinus pacificus
White-bellied storm-petrel
Fregetta grallaria
White-chinned petrel
Procellaria aequinoctialis
White-faced storm-petrel
Pelagodroma marina
White-fronted tern
Sterna striata
White-naped petrel
Pterodroma cervicalis
White-throated shag
Microcarbo melanoleucos brevirostris
Yellow-eyed penguin
Megadyptes antipodes
Appendix A3
Table A3.1:
Summary of top 5 candidate models investigating the effects of a range of key environmental variables on the probability of detecting
a seabird population response (all responses; colony growth; recolonization) after predator removal on islands, controlled for island
and species. Models were ranked by Akaike weights (wi) based on comparisons of AIC values corrected for small sample size (Δ
QAICc).
Model
ΔQAICc wi
All seabird responses (colony growth, re-colonization combined) n = 96
Distance to source
0.00
0.20
Population size + Distance to source + Population status
0.25
0.17
Population size + Distance to source + Population status + Number of other spp. breeding
0.88
0.13
Age at first breeding + Population size + Distance to source + Population status
1.00
0.12
Distance to source + Population status
1.26
0.11
Population size + Population status
0.00
0.13
Intercept
0.05
0.13
Distance to source
0.05
0.13
Colony growth n = 47
Population size + Population status + Years since eradication
0.43
0.11
Population size + Population status + Habitat modification
0.88
0.09
Years since eradication + Distance to source + Number of other spp. breeding
0.00
0.58
Years since eradication + Distance to source + Population status + Number of other spp. breeding
1.48
0.28
Years since eradication + Habitat modification + Number of other spp. breeding
5.77
0.03
Years since eradication + Distance to source + Competition + Age at first breeding + Population status
6.45
0.02
Distance to source + Habitat modification + Competition + Age at first breeding + Population status
7.32
0.01
Re-colonization n = 50
Appendix B1
Two-state zero-inflated Poisson Bayesian hierarchical model code for R version 2.14.2 (R
Development Core Team 2012)
library(MASS)
library(mvtnorm)
########### Functions
#################
logit <- function(x){log(x/(1-x))}
invlogit <- function(x){1/(1 + exp(-x))}
probY_FX <- function(y, phi, delta, lambda)
{
LogProbY <- log((phi*delta) + (1-phi)*(lambda^y)*exp(lambda)/(gamma(y+1)))
return(LogProbY)
}
dicFX <- function(y, delta, mu_phi, mu_lambda, gammaVect, Mu_gammaVect,
sigma_gammaVect,
betaVect, Mu_betaVect, sigma_betaVect, bigMuPriorMean, bigMuPriorVar)
{
dev <- sum(probY_FX(y, invlogit(mu_phi), delta, exp(mu_lambda))) +
sum(dnorm(gammaVect, Mu_gammaVect, sqrt(sigma_gammaVect), log = T)) +
sum(dnorm(betaVect, Mu_betaVect, sqrt(sigma_betaVect), log = T)) +
sum(dnorm(Mu_gammaVect, bigMuPriorMean, sqrt(bigMuPriorVar), log = T)) +
sum(dnorm(Mu_betaVect, bigMuPriorMean, sqrt(bigMuPriorVar), log = T))
dev <- -2*dev
return(dev)
}
residFX <- function(delta, Yjk, meanPhi, meanLambda)
{
residPhi <- (delta - invlogit(meanPhi)) / sqrt(invlogit(meanPhi) * (1 - invlogit(meanPhi)))
residLambda <- (Yjk - exp(meanLambda)) / sqrt(exp(meanLambda))
residList <- list(residPhi, residLambda)
return(residList)
}
dicCalcFX <- function(outpar, nGammaCov, nBetaCov, Wphi, Wlambda, nIslands, island,
nBigMuGamma, nBigMuBeta, ndat, keep, delta, Yjk)
{
muPhiPred <- rep(0,ndat)
muLambdaPred <- rep(0,ndat)
idGamma <- rep(1:nIslands, nBigMuGamma)
medGamma <- outpar[1:nGammaCov,1]
idBeta <- rep(1:nIslands, nBigMuBeta)
medBeta <- outpar[(nGammaCov + 1) : (nGammaCov + nBetaCov), 1]
for(i in 1:nIslands)
{
gammaIsland <- medGamma[idGamma == i]
wIslandPhi <- Wphi[island == i, ]
muPhiPred[island == i] <- wIslandPhi %*% gammaIsland
betaIsland <- medBeta[idBeta == i]
wIslandLambda <- Wlambda[island == i, ]
muLambdaPred[island == i] <- wIslandLambda %*% betaIsland
}
Mu_gammaVect <- rep(outpar[(nGammaCov + nBetaCov + 1) : (nGammaCov + nBetaCov +
nBigMuGamma), 1], each=nIslands)
Mu_betaVect <- rep(outpar[(nGammaCov + nBetaCov + nBigMuGamma +1) : (nGammaCov +
nBetaCov + nBigMuGamma + nBigMuBeta), 1], each=nIslands)
sigma_gammaVect <- rep(outpar[(dim(outpar)[1] + 1 - nBigMuGamma - nBigMuBeta) :
(dim(outpar)[1] - nBigMuBeta),1],each=nIslands)
sigma_betaVect <- rep(outpar[(dim(outpar)[1] + 1 - nBigMuBeta) : (dim(outpar)[1]),
1],each=nIslands)
postdev <- dicFX(Yjk, delta, muPhiPred, muLambdaPred, medGamma, Mu_gammaVect,
sigma_gammaVect, medBeta, Mu_betaVect, sigma_betaVect, bigMuPriorMean,bigMuPriorVar)
residList <- residFX(delta, Yjk, muPhiPred, muLambdaPred)
postdevList <- list(postdev, residList[[1]], residList[[2]], muPhiPred, muLambdaPred)
return(postdevList)
}
####
# updata gamma parameters#
gammaUpdate <- function(y, x, mu_phi, mu_lambda, priorMean, priorVar, nIslands, island,
gamma, delta)
{
nPara <- dim(x)[2]
{
x_s <- x[island==i,]
y_s <- y[island==i]
d_s <- delta[island==i]
IVmu_phiI <- invlogit(mu_phi[island == i])
Emu_lambdaI <- exp(mu_lambda[island==i])
for(j in 1:nPara)
{
g_s <- gamma[i,]
g_s[j] <- rnorm(1, gamma[i,j], 0.2)
IVmu_s <- invlogit(x_s %*% g_s)
pnow <- sum(probY_FX(y_s, IVmu_phiI, d_s, Emu_lambdaI)) + dnorm(gamma[i,j],
priorMean[j], sqrt(priorVar[j]), log = T)
pnew <- sum(probY_FX(y_s, IVmu_s, d_s, Emu_lambdaI)) + dnorm(g_s[j], priorMean[j],
sqrt(priorVar[j]), log = T)
r <- exp(pnew - pnow)
z <- runif(1,0,1)
if(r>z)
{
gamma[i,j] <- g_s[j]
IVmu_phiI <- IVmu_s
mu_phi[island == i] <- logit(IVmu_s)
}
}
}
gammaList <- list(gamma, mu_phi)
return(gammaList)
}
###########
# updata sigma_alpha, beta and gamma
####
# use full conditionals - conjugate priors #
sigmaParaUpdate <- function(ParaMat, bigMu, s1, s2, nIslands)
{
sigmaVector <- rep(0,dim(ParaMat)[2])
for(i in 1:length(sigmaVector))
{
diffPredict <- ParaMat[,i] - bigMu[i]
sx <- crossprod(diffPredict)
u1 <- s1 + .5*nIslands
u2 <- s2 + .5*sx
sigmaVector[i] <- (1/rgamma(1,u1,u2))
}
return(sigmaVector)
}
###########
####
# updata big Mu
# use full conditionals - conjugate priors
#
bigMuUpdate <- function(ParaMat, sigmaPara, bigMuPriorVar, bigMuPriorMean, nIslands)
{
nPara <- dim(ParaMat)[2]
xx <- rep(1,nIslands)
bigMuVector <- rep(0,nPara)
vinvert <- 1/bigMuPriorVar
ppart <- vinvert %*% bigMuPriorMean
for(i in 1:nPara)
{
sx <- crossprod(xx)/sigmaPara[i]
sy <- crossprod(xx,ParaMat[,i])/sigmaPara[i]
bigv <- solve(sx + vinvert) # solve means inverse
smallv <- sy + ppart
bigMuVector[i] <- t(rmvnorm(1,bigv%*%smallv,bigv))
}
return(bigMuVector)
}
############# # beta update using Metropolis algorithm#
betaUpdate <- function(y, x, mu_phi, mu_lambda, priorMean, priorVar, nIslands, island, beta,
delta)
{
nPara <- dim(x)[2]
{
x_s <- x[island==i,]
y_s <- y[island==i]
d_s <- delta[island==i]
IVmu_phiI <- invlogit(mu_phi[island == i])
Emu_lambdaI <- exp(mu_lambda[island==i])
for(j in 1:nPara)
{
g_s <- beta[i,]
g_s[j] <- rnorm(1, beta[i,j], 0.1)
Emu_s <- exp(x_s %*% g_s)
pnow <- sum(probY_FX(y_s, IVmu_phiI, d_s, Emu_lambdaI)) + dnorm(beta[i,j], priorMean[j],
pnew <- sum(probY_FX(y_s, IVmu_phiI, d_s, Emu_s)) + dnorm(g_s[j], priorMean[j],
r <- exp(pnew - pnow)
z <- runif(1,0,1)
if(r>z)
{
beta[i,j] <- g_s[j]
Emu_lambdaI <- Emu_s
mu_lambda[island == i] <- log(Emu_s)
}
}
}
betaList <- list(beta, mu_lambda)
return(betaList)
}
# read data
nest <- read.table("burrows.csv", sep=",", header=T)
island <- as.numeric(as.factor(nest$Island))
ndat <- dim(nest)[1]
# read in data
# id islands as numbers
# number of plots
nIslands <- 6
# inital values
Yjk <- nest$burrows
delta <- ifelse(nest$burrows_pa == 0, 1, 0)
#############################
# Presence initial values####
Wphi <- cbind(rep(1,ndat), scale(nest$W),
scale(nest$Slope), scale(nest$S_Depth), scale(nest$Rock),
scale(nest$MahoeS), scale(nest$KaramuS))
# covariates for presence
Mu_gamma <- c(.2, -.1, .2, -.1, .2, -.1, .2)
# big Mu gamma
nBigMuGamma <- length(Mu_gamma)
sigma_gamma <- rep(.1, nBigMuGamma)
# initial sigma_gamma:
gamma <- matrix(0, nIslands, nBigMuGamma)
# initial gamma for each island
gammaExpand <- matrix(0, ndat, nBigMuGamma)
for(i in 1:nBigMuGamma)
{
gamma[,i] <- rnorm(nIslands, Mu_gamma[i], .1) # initial gamma for each island
gammaExpand[,i] <- gamma[island, i]
# expand the gamma for each plot for
# the corresponding island
}
mu_phi <- apply(Wphi*gammaExpand,1,sum)
# initial mu_phi:
nGammaCov <- nBigMuGamma * nIslands
############################## Poisson lambda initial values####
Wlambda <- cbind(rep(1,ndat), scale(nest$S), scale(nest$W),
scale(nest$Slope), scale(nest$S_Depth), scale(nest$Rock),
scale(nest$Total_large_stem), scale(nest$MahoeS), scale(nest$KaramuS)) #covariates for
counts
Mu_beta <- c(-.1, .2, -.1, -.1, .2, -.1, .2, -.1, .2)
# big Mu lambda
nBigMuBeta <- length(Mu_beta)
sigma_beta <- rep(.1, nBigMuBeta)
# initial sigma_beta:
beta <- matrix(0, nIslands, nBigMuBeta)
# initial beta for each island
betaExpand <- matrix(0, ndat, nBigMuBeta)
for(i in 1:nBigMuBeta)
{
beta[,i] <- rnorm(nIslands, Mu_beta[i], .1) # initial beta for each island
betaExpand[,i] <- beta[island, i]
}
# expand the beta for each plot for the
# corresponding island
mu_lambda <- apply(Wlambda*betaExpand,1,sum)
# initial mu_lambda:
nBetaCov <- nBigMuBeta * nIslands
# Priors##
s1 <- .1
# variance inverse gamma prior
s2 <- .1
# variance inverse gamma prior
bigMuPriorVar <- 100
# variance prior for big Mu
bigMuPriorMean <- 0
# mean prior for big Mu
####
ngibbs <- 2500
# number of samples to keep
ggibbs <- matrix(0,ngibbs,nGammaCov)
# gamma regression parameters
bigMuGamma_gibbs <- matrix(0,ngibbs, nBigMuGamma)
# Big Mu parameters
sigGamma_gibbs <- matrix(0,ngibbs, nBigMuGamma)
bgibbs <- matrix(0,ngibbs,nBetaCov)
bigMuBeta_gibbs <- matrix(0,ngibbs, nBigMuBeta)
sigBeta_gibbs <- matrix(0,ngibbs, nBigMuBeta)
residPhi_gibbs <- rep(0,ndat)
dicgibbs <- 0
thinrate<- 40
# thin rate
burnin <- 10000
# number of burnin iterations
keepseq <- seq((burnin+1),ngibbs*thinrate + burnin,by=thinrate) # iteration numbers to keep
### MCMC###
cc <- 1
for(g in 1:(ngibbs*thinrate+burnin))
{
gammaList <- gammaUpdate(Yjk, Wphi, mu_phi, mu_lambda, Mu_gamma, sigma_gamma,
nIslands, island, gamma, delta)
gamma <- gammaList[[1]]
mu_phi <- gammaList[[2]]
Mu_gamma <- bigMuUpdate(gamma, sigma_gamma, bigMuPriorVar, bigMuPriorMean,
nIslands)
sigma_gamma <- sigmaParaUpdate(gamma, Mu_gamma, s1, s2, nIslands)
betaList <- betaUpdate(Yjk, Wlambda, mu_phi, mu_lambda, Mu_beta, sigma_beta, nIslands,
island, beta, delta)
beta <- betaList[[1]]
mu_lambda <- betaList[[2]]
Mu_beta <- bigMuUpdate(beta, sigma_beta, bigMuPriorVar, bigMuPriorMean, nIslands)
sigma_beta <- sigmaParaUpdate(beta, Mu_beta, s1, s2, nIslands)
if(g%in%keepseq)
{
gammaVect <- as.vector(gamma)
ggibbs[cc,] <- gammaVect
bigMuGamma_gibbs[cc,] <- Mu_gamma
sigGamma_gibbs[cc,] <- sigma_gamma
betaVect <- as.vector(beta)
bgibbs[cc,] <- betaVect
bigMuBeta_gibbs[cc,] <- Mu_beta
sigBeta_gibbs[cc,] <- sigma_beta
Mu_gammaVect <- rep(Mu_gamma, each=nIslands) # expected dic calculations
sigma_gammaVect <- rep(sigma_gamma, each=nIslands)
Mu_betaVect <- rep(Mu_beta, each=nIslands)
sigma_betaVect <- rep(sigma_beta, each=nIslands)
dicPre <- dicFX(Yjk, delta, mu_phi, mu_lambda, gammaVect, Mu_gammaVect,
sigma_gammaVect, betaVect, Mu_betaVect, sigma_betaVect, bigMuPriorMean,
bigMuPriorVar)
dicgibbs <- dicgibbs + dicPre
cc <- cc+1
}
}
##############
#####
End MCMC
keep <- seq(1,(cc-1),by=1)
#thin predictions
#meanResidPhi <- residPhi_gibbs/ngibbs
# Mean residual
### make results table
outpar <- matrix(NA,nrow = nGammaCov + nBetaCov + (nBigMuGamma*2) +
(nBigMuBeta*2), ncol=3)
for(i in 1:nGammaCov)
{
outpar[i,1:3]<-c(quantile(ggibbs[keep,i],c(0.5,.05,.95)))
}
for(i in 1:nBetaCov)
{
outpar[i + nGammaCov,1:3]<-c(quantile(bgibbs[keep,i],c(0.5,.05,.95)))
}
{
outpar[i+nGammaCov + nBetaCov,1:3]<c(quantile(bigMuGamma_gibbs[keep,i],c(0.5,.05,.95)))
}
{
outpar[i+nGammaCov + nBetaCov + nBigMuGamma,1:3]<c(quantile(bigMuBeta_gibbs[keep,i],c(0.5,.05,.95)))
}
{
outpar[i+nGammaCov + nBetaCov + nBigMuGamma + nBigMuBeta, 1:3]<c(quantile(sigGamma_gibbs[keep,i],c(0.5,.05,.95)))
}
{
outpar[i+nGammaCov + nBetaCov + (nBigMuGamma*2) + nBigMuBeta, 1:3]<c(quantile(sigBeta_gibbs[keep,i],c(0.5,.05,.95)))
}
dimnames(outpar)[2] <- list(c("Median","5%","95%"))
dimnames(outpar)[1] <list(c("pa0_Korapuki","pa0_Mauitaha","pa0_Ohinau","pa0_Stanley","pa0_Taranga", "pa0_Nui",
"paW_Korapuki","paW_Mauitaha","paW_Ohinau","paW_Stanley", "paW_Taranga",
"paW_Nui",
"paSlope_Korapuki","paSlope_Mauitaha","paSlope_Ohinau","paSlope_Stanley",
"paSlope_Taranga", "paSlope_Nui",
"paSDepth_Korapuki","paSDepth_Mauitaha","paSDepth_Ohinau","paSDepth_Stanley",
"paSDepth_Taranga", "paSDepth_Nui",
"paRock_Korapuki","paRock_Mauitaha","paRock_Ohinau","paRock_Stanley",
"paRock_Taranga", "paRock_Nui",
"paMahoeS_Korapuki","paMahoeS_Mauitaha","paMahoeS_Ohinau","paMahoeS_Stanley",
"paMahoeS_Taranga", "paMahoeS_Nui",
"paCopmacS_Korapuki","paCopmacS_Mauitaha","paCopmacS_Ohinau","paCopmacS_Stanley"
, "paCopmacS_Taranga", "paCopmacS_Nui",
"count0_Korapuki","count0_Mauitaha","count0_Ohinau","count0_Stanley","count0_Taranga",
"count0_Nui",
"countS_Korapuki","countS_Mauitaha","countS_Ohinau","countS_Stanley",
"countS_Taranga", "countS_Nui",
"countW_Korapuki","countW_Mauitaha","countW_Ohinau","countW_Stanley",
"countW_Taranga", "countW_Nui",
"countSlope_Korapuki","countSlope_Mauitaha","countSlope_Ohinau","countSlope_Stanley",
"countSlope_Taranga", "countSlope_Nui",
"countSDepth_Korapuki","countSDepth_Mauitaha","countSDepth_Ohinau","countSDepth_Stan
ley", "countSDepth_Taranga", "countSDepth_Nui",
"countRock_Korapuki","countRock_Mauitaha","countRock_Ohinau","countRock_Stanley",
"countRock_Taranga", "countRock_Nui",
"countTotallgstem_Korapuki","countTotallgstem_Mauitaha","countTotallgstem_Ohinau","count
Totallgstem_Stanley", "countTotalsmstem_Taranga", "countTotalsmstem_Nui",
"countMahoeS_Korapuki","countMahoeS_Mauitaha","countMahoeS_Ohinau","countMahoeS_S
tanley", "countMahoeS_Taranga", "countMahoeS_Nui",
"countCopmacS_Korapuki","countCopmacS_Mauitaha","countCopmacS_Ohinau","countCopm
acS_Stanley", "countCopmacS_Taranga", "countCopmacS_Nui",
"bigMuGamma0", "bigMuGamma1", "bigMuGamma2", "bigMuGamma3", "bigMuGamma4",
"bigMuGamma5", "bigMuGamma6",
"bigMuBeta0", "bigMuBeta1", "bigMuBeta2", "bigMuBeta3", "bigMuBeta4", "bigMuBeta5",
"bigMuBeta6", "bigMuBeta7", "bigMuBeta8",
"sigGamma0", "sigGamma1", "sigGamma2", "sigGamma3", "sigGamma4", "sigGamma5",
"sigGamma6",
"sigBeta0", "sigBeta1", "sigBeta2", "sigBeta3", "sigBeta4", "sigBeta5", "sigBeta6", "sigBeta7",
"sigBeta8"))
signif(outpar,3)
##########
64 – R. Buxton et al.
Appendix B2
Table B2.1:
Median values and 95% credible intervals from the posterior distribution of parameter estimates from univariate zero-inflated Poisson
models. Each model had two components: probability of a burrow being absent (
) and the zero-inflated burrow count (
). Each
habitat variable (Hab var) was run in a separate model; median results are displayed for each island and among islands (
and
), as well as a deviance information criterion (DIC) value for each model. † indicates a 95% credible interval that did not
overlap 0.
Burrow presence/absence (
)
Hab var
Mauitaha Taranga Ohinau Stanley Korapuki Nui
Mauitaha Taranga
Median −1.02†
−0.19 −0.8† −0.43 −0.55† −0.17 −0.63†
0.03
0.05
5% −2.00
−0.75 −1.47 −0.89
−1.12 −0.49 −1.27 −0.24 −0.10
Soil
depth
95% −0.36
0.28 −0.32
0.01
−0.02
0.15 −0.09
0.29
0.19
Median −0.66†
−0.35 −0.55† −0.29 −0.68† −0.23† −0.47†
0.04 −0.03
5% −1.58
−1.02 −0.98 −0.62
−1.21 −0.67 −0.91 −0.31 −0.29
Māhoe
stem
95% −0.06
0.26 −0.19
0.03
−0.30
0.22 −0.06
0.36
0.19
Median −0.81† −0.89† −0.82† −0.95† −0.50† −0.57† −0.76† −0.14
0.07
5% −1.41
−1.48 −1.34 −1.38
−0.90 −1.09 −1.17 −0.44 −0.09
Rock
95% −0.24
−0.45 −0.40 −0.59
−0.08 −0.04 −0.37
0.14
0.22
Median
0.05
5% −0.41
Karamū
stem
95% 0.48
0.27 −0.28
−0.14 −1.09
0.68 0.26
−0.24
−0.64
0.09
0.41†
0.01
0.77
−0.37
−1.19
0.16
−0.03
−0.55
0.39
0.00
−0.22
0.22
Burrow count (
Ohinau StanleyKorapuki
0.27†
0.09
0.39†
0.13 −0.04
0.24
0.40
0.21
0.54
−0.08 0.29†
−0.06
−0.22
0.19
−0.16
0.07
0.38
0.05
−0.03 −0.05
0.31†
−0.18 −0.16
0.20
0.12
0.06
0.42
0.06 0.15 −0.19†
−0.08 −0.03 −0.30
0.20 0.33 −0.08
−0.13
−0.28
0.01
)
Nui
0.08†
0.03
0.13
−0.31†
−0.39
−0.24
−0.04
−0.13
0.05
DIC
0.13 2522.0
−0.09
0.35
−0.03 2527.4
−0.27
0.22
0.02 2543.0
−0.21
0.25
0.32† 0.04 2548.0
0.24 −0.20
0.39 0.27
)
Hab var
Mauitaha Taranga
Median −0.58† −0.77† −0.78† −0.85† −0.49† −0.65† −0.72†
0.13
0.13
5% −1.11
−1.29 −1.28 −1.28
−0.91 −1.05 −1.14 −0.14 −0.02
Slope
95% −0.01
−0.33 −0.35 −0.48
−0.04 −0.24 −0.32
0.42
0.28
−0.09 0.53† 0.90†
−0.28
0.05
0.15 −0.23
0.05
Small Median −0.08
5% −0.69
−0.60 0.12
0.49
−0.95 −0.40 −0.36 −0.49 −0.07
stem
count
95% 0.45
0.30 0.95
1.36
0.20
0.45
0.62
0.02
0.14
Median
0.19
−0.16 −0.08 −0.17
0.00 −0.41 −0.12 −0.04 −0.14†
5% −0.28
−0.69 −0.56 −0.48
−0.48 −1.12 −0.54 −0.29 −0.28
S aspect
95% 0.69
0.21 0.33
0.13
0.43
0.06
0.25
0.20 −0.01
Median −0.73
−0.38 −0.64† −0.36† −0.74†
0.02 −0.47†
0.11
0.06
5% −1.74
−1.06 −1.11 −0.69
−1.20 −0.45 −0.97 −0.37 −0.12
Māhoe
canopy
95% 0.03
0.18 −0.25 −0.04
−0.36
0.58 −0.02
0.73
0.23
Median
0.29
−0.51 0.79† 0.53†
0.76†
0.69
0.43
0.04 −0.05
5% −0.13
−1.50 0.38
0.24
0.06 −0.41 −0.18 −0.18 −0.21
Māpou
stem
95% 0.70
0.12 1.21
0.82
1.36
2.06
1.05
0.24
0.10
Median
0.16
−0.01 0.66† 0.40†
0.21
0.49
0.32 −0.13
0.10
5% −1.86
−0.81 0.31
0.15
−0.77 −0.47 −0.46 −0.97 −0.06
Māpou
canopy
95% 1.06
0.46 1.03
0.64
0.74
1.82
0.84
0.92
0.25
Median −0.10
0.02 −0.16 −0.01
−0.31
0.06 −0.10
0.10
0.06
5% −0.54
−0.39 −0.64 −0.42
−0.81 −0.50 −0.46 −0.11 −0.06
N aspect
95% 0.28
0.36 0.20
0.36
0.06
0.61
0.25
0.32
0.19
Median −0.80
−0.44 −0.56† −0.53†
0.03
0.11
0.02
0.12
0.07
5% −2.18
−1.18 −1.31 −1.06
−0.30 −0.34 −0.20 −0.23 −0.07
W aspect 95% 0.04
0.06 −0.08 −0.16
0.39
0.58
0.22
0.46
0.20
Total
Median −0.21
0.16 −0.24 −0.34
0.00 −0.23 −0.16
0.31 −0.08
large
5% −1.04
−0.32 −0.96 −0.89
−0.41 −0.72 −0.61 −0.01 −0.27
stem
count
95% 0.30
0.63 0.23
0.10
0.41
0.12
0.21
0.59
0.09
Burrow count (
−0.03
0.13
0.23†
−0.21 −0.01
0.08
0.14
0.27
0.39
−0.05 −0.18† −0.18†
−0.22 −0.31
−0.33
0.11 −0.04
−0.02
0.08
0.06
−0.10
−0.08 −0.04
−0.26
0.24
0.16
0.05
0.04 0.16†
0.10
−0.10
0.06
−0.01
0.19
0.26
0.22
−0.05 −0.17† −0.31†
−0.30 −0.32
−0.74
0.15 −0.05
−0.01
0.01 −0.16† −0.35†
−0.19 −0.27
−0.67
0.19 −0.06
−0.09
−0.11 −0.12
0.14
−0.25 −0.28
0.04
0.03
0.04
0.24
0.04 −0.06
0.07
−0.09 −0.16
−0.03
0.17
0.04
0.17
−0.13 −0.02
−0.09
−0.32 −0.18
−0.23
0.06
0.15
0.05
)
Nui
−0.07
−0.14
0.01
−0.22†
−0.31
−0.13
0.28
0.21
0.36
−0.16†
−0.24
−0.08
−0.38
−1.79
0.27
−0.34
−2.02
0.34
−0.39†
−0.59
−0.22
−0.16†
−0.24
−0.08
−0.17†
−0.25
−0.09
DIC
0.09 2557.6
−0.12
0.31
−0.13 2561.4
−0.35
0.07
0.03 2562.4
−0.21
0.25
0.05 2566.5
−0.17
0.29
−0.16 2566.5
−0.57
0.14
−0.14 2579.7
−0.68
0.23
−0.05 2581.7
−0.32
0.19
0.30† 2583.6
0.07
1.71
−0.03 2584.0
−0.28
0.21
Hab var
Total
canopy
cover
Pōhutukawa
canopy
E aspect
Kanuka
canopy
Ridge
topography
)
Mauitaha Taranga
Median −0.12
−0.23 0.18 −0.27
−0.24
0.23 −0.07 −0.11
0.03
5% −0.63
−0.75 −0.29 −0.71
−0.73 −0.21 −0.47 −0.41 −0.13
95% 0.44
0.21 0.72
0.14
0.21
0.77
0.34
0.17
0.20
Median −0.45 −0.48† −0.37 −0.26
0.14 −0.41† −0.32 −0.04
0.00
5% −1.63
−1.31 −1.29 −0.64
−0.21 −0.94 −0.88 −0.33 −0.14
95% 0.14
−0.02 0.14
0.06
0.46 −0.01
0.06
0.23
0.14
Median −0.15
0.15 0.09
0.12
−0.11 −0.09 −0.01 −0.14 −0.08
5% −1.23
−0.50 −0.37 −0.14
−0.77 −0.61 −0.49 −0.44 −0.31
95% 0.37
0.62 0.43
0.37
0.27
0.31
0.33
0.12
0.13
Median 0.57†
0.33† 0.48
0.43
0.78
0.72
0.56
0.01 0.13†
5% 0.24
0.02 −1.08 −1.00
−0.28 −0.32 −0.25 −0.23
0.02
95% 0.94
0.62 1.84
1.66
2.35
2.76
1.50
0.19
0.24
Median −2.45†
−1.28 −1.22 −1.72 −1.27† −1.10 −1.40 −0.20 −0.06
5% −12.20 −10.90 −11.00 −11.00 −10.90 −10.40 −11.00 −0.41 −0.17
95% −0.04
0.12 0.14
0.05
−0.01
1.25
0.08
0.00
0.06
Burrow count (
−0.09 −0.05
−0.06
−0.27 −0.20
−0.20
0.10
0.09
0.10
−0.25 −0.03
−0.05
−0.46 −0.13
−0.15
−0.05
0.07
0.05
−0.11
0.09 −0.21†
−0.26 −0.01
−0.35
0.04
0.18
−0.08
−0.07 −0.18
−0.39
−2.12 −2.34
−2.81
1.23
1.18
0.97
−0.05 −0.27†
0.03
−0.17 −0.53
−0.06
0.09 −0.07
0.13
)
Nui
−0.22†
−0.31
−0.14
0.15†
0.08
0.21
−0.01
−0.09
0.07
−0.46
−4.88
0.73
−0.22
−1.02
0.35
DIC
−0.08 2587.9
−0.30
0.13
−0.03 2588.0
−0.26
0.18
−0.08 2596.5
−0.31
0.13
−0.15 2598.5
−1.86
0.57
−0.13 2611.7
−0.43
0.13
Table B2.2:
Median values and 95% credible intervals from the posterior distribution of parameter estimates
from observed burrow occupancy models (ψjk). Each habitat variable (Hab var) was run in a
separate model; median results are displayed for each island and among islands (
ψjk), as
well as a deviance information criterion (DIC) value for each model. † indicates a 95% credible
interval that did not overlap 0.
Hab mod
Mauitaha Taranga Ohinau Stanley Korapuki
Median
0.31
0.39†
0.03
0.40†
0.14
5%
−0.15
0.15
−0.28
0.18
−0.15
Soil depth
95%
0.78
0.65
0.34
0.62
0.41
Median
0.20 −0.53†
−0.36 −0.28†
0.50
5%
−0.09
−1.01
−1.33
−0.57
−0.02
Māpou stem
95%
0.50
−0.20
0.17
−0.03
1.16
Median
−0.01
−0.22
0.37
0.02 −0.25†
5%
−0.83
−0.56
−0.02
−0.18
−0.48
Māhoe canopy
95%
0.81
0.11
0.88
0.23
0.00
Median
−0.34
−0.21
−0.11
−0.15
−0.01
5%
−0.81
−0.50
−0.46
−0.42
−0.30
Total small stem
count
95%
0.06
0.02
0.23
0.11
0.29
Median
−0.03
0.08
−0.12 −0.32†
−0.01
5%
−0.59
−0.17
−0.49
−0.55
−0.22
W aspect
95%
0.56
0.33
0.23
−0.11
0.21
Median
0.08
−0.06
0.28
−0.09
0.10
5%
−0.27
−0.28
−0.04
−0.39
−0.13
N aspect
95%
0.42
0.15
0.61
0.20
0.32
Median
0.12
0.32†
−0.25
0.24†
0.06
5%
−0.27
0.01
−0.78
0.04
−0.37
Soil strength
95%
0.54
0.68
0.23
0.44
0.46
Median
0.22
−0.11
0.44†
0.18
0.13
5%
−0.21
−0.37
0.01
−0.08
−0.18
Total canopy
cover
95%
0.68
0.14
0.97
0.46
0.45
ψjk
0.25
−0.11
0.60
−0.11
−0.68
0.47
−0.02
−0.45
0.44
−0.17
−0.51
0.17
−0.08
−0.45
0.27
0.06
−0.25
0.38
0.10
−0.31
0.48
0.17
−0.21
0.57
DIC
733.77
735.69
737.61
737.65
738.27
739.06
739.84
741.08
Hab mod
Mauitaha Taranga Ohinau Stanley Korapuki
Median
−0.14
−0.02
−0.19
−0.14
0.01
5%
−0.50
−0.25
−0.67
−0.34
−0.26
Karamū stem
95%
0.19
0.21
0.21
0.05
0.28
Median
−0.01
−0.09
−0.18
0.17
−0.04
5%
−0.39
−0.31
−0.62
−0.02
−0.35
S aspect
95%
0.35
0.13
0.17
0.37
0.27
Median
−0.28
0.24
−0.23
0.16
−0.15
5%
−1.32
−0.11
−0.75
−0.01
−0.46
E aspect
95%
0.28
0.64
0.15
0.33
0.14
Median
−0.08
0.09
0.03
0.20
0.06
5%
−0.54
−0.12
−0.27
−0.19
−0.15
Ridge
topography
95%
0.29
0.30
0.29
0.69
0.27
Median
0.06
0.19
0.34
0.19
0.07
5%
−0.50
−0.22
−0.02
−0.01
−0.15
Māhoe stem
95%
0.56
0.60
0.81
0.39
0.31
Median
−0.04
−0.10
−0.38
0.06
0.34
5%
−1.19
−0.34
−1.41
−0.12
−0.06
Māpou canopy
95%
1.00
0.14
0.10
0.23
0.79
Median
0.14
−0.10
−0.14
0.13
−0.15
5%
−0.32
−0.34
−0.54
−0.10
−0.46
Slope
95%
0.68
0.11
0.22
0.34
0.15
Median
0.69
0.05
0.82
0.33
0.47
5%
−0.23
−0.14
−0.06
−0.18
−0.20
Elevation
95%
2.33
0.25
2.14
0.87
1.24
Median
−0.14
0.08
0.05
0.06
−0.23
5%
−0.58
−0.15
−0.30
−0.20
−0.52
Total large stem
count
95%
0.22
0.31
0.37
0.32
0.01
Median
−0.15
0.04 −0.40†
0.11
−0.11
5%
−0.64
−0.23
−0.90
−0.10
−0.35
Rock
95%
0.31
0.32
−0.03
0.31
0.13
Median
−0.14
0.20
−0.08
−0.12
0.14
5%
−0.69
−0.05
−0.60
−0.33
−0.06
Pōhutukawa
canopy
95%
0.30
0.46
0.33
0.06
0.35
Median
−0.10 −0.16†
0.01
−0.15
−0.04
5%
−0.44
−0.32
−1.34
−2.14
−1.63
Kanuka canopy
95%
0.15
−0.01
4.55
1.75
2.47
ψjk
−0.09
−0.42
0.22
−0.03
−0.38
0.29
−0.05
−0.58
0.36
0.06
−0.28
0.39
0.17
−0.17
0.55
−0.02
−0.64
0.53
−0.03
−0.35
0.32
0.45
−0.15
1.37
−0.04
−0.39
0.28
−0.10
−0.50
0.24
0.00
−0.40
0.33
−0.08
−1.09
1.73
DIC
742.11
742.42
743.11
743.55
743.71
743.84
744.14
745.08
745.72
745.83
746.06
747.21
Table B2.3:
Multivariate zero-inflated Poisson models constructed using habitat variables (Wkl) from univariate models with the smallest deviance
information criterion (DIC) and 95% credible intervals not overlapping 0. Each model had two components: probability of a burrow
being absent ( ) and the zero-inflated burrow count ( ). S indicates species categories from stem counts and C indicates species
categories from canopy cover. * indicates a variable whose 95% credible intervals overlapped 0. Italicized model indicates the final
multivariate model selected, based on the smallest DIC, best diagnostic plots, and no variables whose 95% credible intervals
overlapped 0. N, S, E, W indicates north, south, east, and west aspect respectively.
Wkl φ (parameters for burrow presence/absence model) Wkl λ (parameters for burrow count model)
Total variables
DIC
Slope + Soil depth
Slope + Soil depth
4
2607.61
W + Rock
W + Rock
4
2619.02
Soil depth + Rock + MāhoeS
W + Soil depth + Totalsmstem
6
2665.81
Slope + Soil depth + Rock
Slope + Soil depth + Rock
6
2671.35
Slope + Soil depth + Rock + MāhoeS
W + Slope* + Soil depth + Totalsmstem
8
2740.81
13
2900.29
13
2902.73
14
2913.90
S + Soil depth + Rock + MāhoeC + MāhoeS +
W + Slope + Soil depth + Rock + MāhoeS + KaramūS KaramūS + MāpouS
Slope + Soil depth + Rock + MāhoeC* +
W + Slope + Soil depth + Rock + MāhoeS + KaramūS MāhoeS + KaramūS + MāpouS
S + W + Slope + Soil depth + Rock +
W + Slope + Soil depth + Rock + MāhoeS + KaramūS Totallgstem + MāhoeS + KaramūS
Total variables
DIC
13
2913.97
14
2928.86
13
2944.91
14
2951.69
15
2957.21
15
2985.03
16
3007.29
20
3061.37
17
3137.59
20
3213.05
W* + Soil depth + Rock + MāhoeC + MāhoeS +
W + Slope + Soil depth + Rock + MāhoeS + KaramūS KaramūS + MāpouS
W + Slope + Soil depth + Rock + MāpouC + KaramūS S + Slope + Soil depth + Rock + MāhoeC +
+ MāpouS
MāhoeS + KaramūS
S + Slope + Soil depth + Rock + Totallgstem +
W + Slope + Soil depth + Rock + MāpouC + KaramūS MāhoeC + KaramūS
W + Slope + Soil depth + Rock + MāpouC + KaramūS S + Slope + Soil depth + Rock + Totalsmstem*
+ MāpouS
+ MāhoeC + KaramūS
W + Slope + Soil depth + Rock + MāhoeS + KaramūS Totallgstem + MāhoeC + MāhoeS + KaramūS
W + Slope + Soil depth + Rock + MāpouC + MāhoeS
S + Slope + Soil depth + Rock + MāhoeC +
* + KaramūS + MāpouS
MāhoeS + KaramūS
W + Slope + Soil depth + Rock + MāpouC + MāhoeS
+ KaramūS
Totallgstem + MāhoeC + MāhoeS + KaramūS
W + Slope + Soil depth + Rock + MāpouC +
MāhoeC* + MāhoeS + KaramūS*
Totallgstem + MāhoeC + MāhoeS + KaramūS
W + Slope + Soil depth + Rock + MāpouC * +
S + Slope + Soil depth + Rock + MāhoeC* +
MāhoeC * + MāhoeS* + KaramūS
MāhoeC + MāhoeS + KaramūS + MāpouS*
W + Slope + Soil depth + Rock + MāpouC + MāhoeC Canopycover* + Totallgstem + MāhoeC +
* + MāhoeS* + KaramūS* + MāpouS*
MāhoeS + KaramūS + MāpouS*
W + Slope + Soil depth + Rock + Totalsmstem* +
S + Slope + Soil depth + Rock + Totalsmstem*
MāpouC* + MāhoeC* + MāhoeS* + KaramūS* +
+ MāpouC + MāhoeC + MāhoeS + KaramūS +
MāpouS
MāpouS*
Total variables
DIC
20
3240.67
26
3560.20
N* + S + W + Slope + Soil depth + Rock +
W + Slope + Soil depth + Rock + Totalsmstem* +
Canopycover* + Totalsmstem* + Totallgstem +
PōhutukawaC* + MāpouC* + MāhoeC* + MāhoeS* + PōhutukawaC* + MāpouC* + MāhoeC* +
KaramūS + MāpouS*
MāhoeS + KaramūS + MāpouS*
Table B2.4:
Multivariate observed burrow occupancy Bernoulli models constructed using habitat variables
(Wkl) from univariate models with the smallest deviance information criterion (DIC) and 95%
credible intervals not overlapping 0. * indicates a variable whose 95% credible intervals
overlapped 0. S indicates species categories from stem counts and C indicates species categories
from canopy cover. Italicized model indicates the final multivariate model selected, based on the
smallest DIC, best diagnostic plots, and no variables whose 95% credible intervals overlapped 0.
N, S, W indicates north, south, and west aspect respectively.
Number of
Model variables:
variables
DIC
W + Soil depth
2
764.76
Soil depth + Soil strength*
2
767.05
W + Soil depth + Rock + MāpouS
4
839.73
Soil depth + Canopycover + MāhoeC + MāpouS
4
841.77
W + Soil depth + Rock + KanukaC + MāpouS
5
871.91
Soil depth + Rock + Canopycover*+ MāhoeC + MāpouS
5
879.55
W + Soil depth +Rock + MāhoeC + MāpouS
5
881.30
W + Soil depth + Rock + Totalsmstem* + MāpouS
5
883.85
W + Soil depth + Sstrength* + PōhutukawaC* + MāpouS
5
888.74
W + Soil depth + Rock +Totalcanopy* + MāhoeC* + MāpouS
6
912.75
W + Soil depth + Rock + KanukaC + MāhoeC + MāpouS
6
919.91
W + Soil depth + Sstrength* + Rock + MāhoeC* + MāpouS
6
920.30
W + Soil depth + Sstrength* +Totalcanopy* + MāhoeC + MāpouS
6
924.95
W + Soil depth + Sstrength* + Rock + MāhoeS* + MāpouS
6
929.06
W + Soil depth + Sstrength* + Rock + Canopycover* + MāhoeC* + MāpouS
7
961.34
10
1087.74
N* + S* + W* + Soil depth + Soil strength* + Canopycover + Totalsmstem* +
MāhoeC + KaramūS* + MāpouS
Appendix B3
Figure B3.1:
Semivariogram values versus lag distance for residual values of φ (probability of burrow absence in a plot), from the top multivariate
zero-inflated Poisson (ZIP) model. Mauitaha still has Pacific rats present, Ruamaahuanui never had rats introduced, and other islands
are arranged with increasing time since Pacific rat eradication.
Figure B3.2:
Moran’s I values versus neighborhood size for residual values of φ (probability of burrow absence in a plot), from the best
multivariate ZIP model. Black dots indicate Moran’s I values significantly different from 0. Mauitaha still has Pacific rats present,
Ruamaahuanui never had rats introduced, and other islands are arranged with increasing time since Pacific rat eradication.
Figure B3.3:
Semivariogram values versus lag distance for residual values of λ (zero-inflated burrow counts in a plot), from the best multivariate
ZIP model. Mauitaha still has Pacific rats present, Ruamaahuanui never had rats introduced, and other islands are arranged with
increasing time since Pacific rat eradication.
Figure B3.4:
Moran’s I values versus neighborhood size for residual values of λ (zero-inflated burrow counts in a plot), from the best multivariate
ZIP model. Black dots indicate Moran’s I values significantly different from 0. Mauitaha still has Pacific rats present, Ruamaahuanui
never had rats introduced, and other islands are arranged with increasing time since Pacific rat eradication.
Figure B3.5:
Semivariogram values versus lag distance for residual values of ψ (observed occupancy of a burrow in a plot), from the best
multivariate binomial model. Mauitaha still has Pacific rats present, Ruamaahuanui never had rats introduced, and other islands are
arranged with increasing time since Pacific rat eradication.
Figure B3.6:
Moran’s I values versus neighborhood size for residual values of ψ (observed occupancy of a burrow in a plot), from the best
multivariate binomial model. Black dots indicate Moran’s I values significantly different from 0. Mauitaha still has Pacific rats
present, Ruamaahuanui never had rats introduced, and other islands are arranged with increasing time since Pacific rat eradication.
Appendix C1
Figure C3.1:
Semivariogram values versus lag distance for residuals from top ranked habitat models (assessed using Akaike’s information criterion
for small sample sizes –AICc) for: FFSH – Flesh-footed shearwater; GFPE –Grey-faced petrel; FLSH – Fluttering shearwater; LISH –
Little shearwater; PYPE – Pycroft’s petrel; and CODI – Common diving petrel. I assumed if an asymptotes (sill) was reached at a
distance of ≤30 m, there was no statistically significant spatial autocorrelation.
Appendix C2
Table C2.1:
Observed (Obs) and unconstrained (Un) and constrained (Cn) simulated co-occurrence indices (C-scores) of each pair of six burrownesting petrel species on six islands off the north-east coast of New Zealand’s North Island with different time since Pacific rat
eradication. Mauitaha is still inhabited by Pacific rats; Ruamaahuanui never had mammals introduced and all other islands ordered
from bottom to top by increasing time since eradication. All values are normalized by *10-2.
FFSH
GFPE
Obs CScore
Un C- Cn CScore Score
FFSH
GFPE
n/a
n/a
n/a
n/a
FLSH
n/a
n/a
FLSH
Obs CScore
Un CScore
Cn CScore
n/a
n/a
n/a
n/a
n/a
0
n/a
2.49 ±
2.21
Obs
CUn CScore Score
Ruamaahuanui
n/a
n/a
n/a
9
LISH
n/a
n/a
n/a
11
3.95 ±
0.75
PYPE
n/a
n/a
n/a
0
0.91 ±
0.25
n/a
0
DIPE
n/a
n/a
n/a
0
4.07 ±
0.82
n/a
0
n/a
9.75
±
1.21
2.26
±
0.44
10.69
±
1.42
LISH
Cn CScore
PYPE
Obs CScore
Un CScore
Cn CScore
Obs CScore
Un CScore
Cn CScore
n/a
n/a
n/a
n/a
n/a
0
4.02 ±
1.42
n/a
n/a
n/a
n/a
n/a
6
16.95
± 2.11
n/a
0
4.22 ±
1.23
n/a
n/a
Korapuki
FFSH
GFPE
FLSH
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
LISH
n/a
n/a
n/a
7.32
PYPE
n/a
n/a
n/a
DIPE
n/a
n/a
FFSH
GFPE
FLSH
n/a
n/a
n/a
LISH
n/a
n/a
4.79 ±
0.32
n/a
n/a
n/a
n/a
n/a
n/a
n/a
3.26
n/a
n/a
4.78 ±
0.32
1.95 ±
0.21
n/a
n/a
n/a
n/a
n/a
2.09
1.92 ±
0.21
2.42 ±
0.27
n/a
n/a
Stanley
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
1.11
n/a
n/a
n/a
n/a
PYPE
n/a
n/a
n/a
4.11
n/a
n/a
n/a
0.21
DIPE
n/a
n/a
n/a
1.12
n/a
n/a
0.64 ±
0.12
4.22 ±
0.30
0.67 ±
0.12
n/a
n/a
n/a
n/a
0.61 ±
0.11
3.89 ±
0.27
0.60 ±
0.11
n/a
n/a
Ohinau
n/a
FFSH
n/a
1.93 ±
0.37
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
0.45 ±
0.31
n/a
1.43
n/a
1.26 ±
0.12
n/a
1.52 ±
0.15
n/a
n/a
n/a
n/a
n/a
n/a
n/a
GFPE
FLSH
LISH
PYPE
n/a
1.96
±
2.46 0.39
n/a
n/a
0.41
±
0.49 0.23
n/a
n/a
0.97
n/a
0.83 ±
0.40
n/a
0.84 ±
0.40
n/a
n/a
n/a
0.97
0.83 ±
0.40
0.81 ±
0.38
0.36
0.34 ±
0.56
0. 34
± 0.55
0. 029
n/a
0.19 ±
0.33
0. 028
± 0.07
n/a
0.19 ±
0.32
0.029
± 0.08
0.21
n/a
0.19 ±
0.32
n/a
0.19 ±
0.37
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
DIPE
n/a
Taranga
FFSH n/a
GFPE n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
FLSH
n/a
n/a
1.43
n/a
1.32 ±
0.13
n/a
1.64 ±
0.16
n/a
1.52 ±
0.15
n/a
n/a
0.12
±
0.13
0.52
0.065
±
0.066 0.78
n/a
n/a
Mauitaha
LISH
n/a
n/a
n/a
1.43
1.26 ±
0.12
PYPE
DIPE
n/a
n/a
n/a
n/a
n/a
n/a
0
n/a
0.63 ±
0.09
n/a
0.70 ±
0.09
n/a
FFSH
n/a
n/a
3.08
±
0.22
0.57
±
0.36
1.10
±
0.34
0.57
±
0.37
n/a
n/a
n/a
n/a
n/a
0.57 ±
0.35
2.15
1.57 ±
0.16
1.58 ±
0.16
n/a
1.12 ±
0.37
4.31
3.05 ±
0.22
3.04 ±
0.22
0.62
2.15
n/a
1.56 ±
0.16
n/a
1.62 ±
0.16
n/a
GFPE
4.31
FLSH
0.62
LISH
1.23
PYPE
DIPE
0.62
n/a
3.08 ±
0.22
0.57 ±
0.35
n/a
n/a
0.31
n/a
n/a
0.57
±
0.35
0.29
±
0.51
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
0.12 ±
0.42
n/a
n/a
n/a
0.064
± 0.53
n/a
0.066
n/a
0.065
± 0.57
n/a
0.063
± 0.49
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
0.56 ±
0.33
n/a
0.56 ±
0.33
n/a
0.62
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
n/a
0.57 ±
0.34
0.29 ±
0.42
n/a
78
Appendix D
Table D1:
Median effect sizes and 95% credibility intervals (CI) of habitat covariates and time since Pacific
rat eradication from a multivariate model predicting petrel burrow density on six islands in
northeastern New Zealand. Mauitaha is still inhabited by Pacific rats; Ruamaahuanui (Nui)
never had mammals introduced and all other islands are ordered from top to bottom by
increasing time since eradication. Habitat variables were selected based on Buxton et al. in
review. Italicized median values do not overlap 0.
Parameter
Island
Time since eradication
Median
5% CI
95% CI
0.063
0.047
0.079
Soil depth
Mauitaha
0.018
0.008
0.040
Soil depth
Taranga
0.009
0.008
0.025
Soil depth
Ohinau
0.024
-0.008
0.043
Soil depth
Kawhitu
0.015
-0.005
0.033
Soil depth
Korapuki
0.033
0.012
0.061
Soil depth
Nui
0.024
0.010
0.039
Slope
Mauitaha
0.010
0.012
0.033
Slope
Taranga
0.013
0.002
0.028
Slope
Ohinau
0.002
-0.021
0.022
Slope
Kawhitu
0.019
0.001
0.039
Slope
Korapuki
0.015
-0.004
0.037
Slope
Nui
-0.010
-0.035
1.251
Rock cover
Mauitaha
0.001
-0.027
0.022
Rock cover
Taranga
0.010
0.005
0.027
Rock cover
Ohinau
0.006
0.014
0.023
Rock cover
Kawhitu
0.007
-0.007
0.022
Rock cover
Korapuki
0.018
0.002
0.038
79
Rock cover
Nui
-0.007
-0.044
0.017
Southern aspect
Mauitaha
-0.004
-0.025
0.017
Southern aspect
Taranga
-0.005
-0.020
0.011
Southern aspect
Ohinau
0.008
-0.013
0.029
Southern aspect
Kawhitu
0.004
-0.013
0.021
Southern aspect
Korapuki
0.001
-0.022
0.024
Southern aspect
Nui
0.068
0.037
0.097
Western aspect
Mauitaha
0.008
-0.011
0.028
Western aspect
Taranga
0.008
-0.005
0.021
Western aspect
Ohinau
0.006
-0.009
0.019
Western aspect
Kawhitu
0.007
-0.005
0.020
Western aspect
Korapuki
0.006
-0.007
0.017
Western aspect
Nui
0.008
-0.006
0.026
Total small stem count
Mauitaha
-0.002
-0.015
0.020
Taranga
-0.006
-0.019
5.972
Ohinau
-0.005
-0.018
8.337
Kawhitu
-0.003
-0.017
0.014
Korapuki
-0.007
-0.023
5.884
Nui
-0.008
-0.021
2.339
Mahoe stem count
Mauitaha
0.007
-0.028
0.045
Mahoe stem count
Taranga
0.003
-0.022
0.028
Mahoe stem count
Ohinau
0.007
-0.010
0.024
Mahoe stem count
Kawhitu
0.028
0.009
0.047
Mahoe stem count
Korapuki
-0.006
-0.025
0.013
Mahoe stem count
Nui
-0.024
-0.055
4.751
Mahoe stem count
Mauitaha
0.006
-0.015
0.026
Karamu stem count
Taranga
-0.003
-0.020
0.014
Karamu stem count
Ohinau
0.019
-0.012
0.052
Karamu stem count
Kawhitu
0.005
-0.012
0.022
Karamu stem count
Korapuki
-0.015
-0.035
4.742
Karamu stem count
Nui
0.089
0.051
0.127
80
Table D2:
Multivariate varying intercept models investigating the effects of habitat covariates on the probability of petrel burrows being present
in plots among islands off the north-eastern coast of New Zealand’s North Island. The model with the best fit (largest AUC - area
under Receiver Operating Characteristic curves - and smallest DIC - deviance information criterion) is indicated in red.
Model
AUC ± SD
DIC
0.79 ± 0.02
1289.9
0.79 ± 0.02
1753.5
0.77 ± 0.02
1229.0
0.77 ± 0.02
1241.3
Slope +N + S + E + W + Elevation
0.76 ± 0.02
1028.3
Slope +N + S + E + W + Elevation + Slope*Elevation
0.76 ± 0.02
1068.8
0.76 ± 0.02
1351.2
0.73 ± 0.02
764.3
0.71 ± 0.02
1160.2
Slope + S + W + Elevation + Slope*Elevation + Slope*S +Slope*W + Elevation*S +Elevation*W +
Slope*Elevation*S + Slope*Elevation*W
Slope +N + S + E + W + Elevation + Slope*Elevation + Slope*N + Slope*S + Slope*E + Slope*W +
Elevation*N + Elevation*S + Elevation*E + Elevation*W + Slope*Elevation*N +Slope*Elevation*S +
Slope*Elevation*E + Slope*Elevation*W
Slope +N + S + E + W + Elevation + Slope*N + Slope*S + Slope*E + Slope*W
Slope +N + S + E + W + Elevation + Slope*Elevation*N +Slope*Elevation*S + Slope*Elevation*E +
Slope*Elevation*W
Slope +N + S + E + W + Elevation + Slope*Elevation + Elevation*N + Elevation*S + Elevation*E +
Elevation*W
Slope
Slope + N + E + Elevation + Slope*Elevation + Slope*N +Slope*E + Elevation*N +Elevation*E +
Slope*Elevation*N + Slope*Elevation*E
81
N
0.70 ± 0.02
785.4
Slope*Elevation*N +Slope*Elevation*S + Slope*Elevation*E + Slope*Elevation*W
0.70 ± 0.02
960.3
0.70 ± 0.02
1515.9
Elevation
0.67 ± 0.02
804
W
0.65 ± 0.02
798.3
E
0.65 ± 0.02
799.8
S
0.65 ± 0.02
800.4
Slope +N + S + E + W + Elevation + Slope*Elevation + Slope*N + Slope*S + Slope*E + Slope*W +
Elevation*N + Elevation*S + Elevation*E + Elevation*W
82
Table D3:
Median effect sizes and 95% credibility intervals (CI) from the top multivariate model predicting
petrel burrow presence/absence (Table D2). Median values among islands were generated from
varying intercept models, while median values for each island were generated from varying
slope, varying intercept models. Islands are off the northeastern coast of New Zealand’s North
Island. Mauitaha is still inhabited by Pacific rats; Ruamaahuanui (Nui) never had mammals
introduced and all other islands are ordered from top to bottom by increasing time since
eradication. Italicized median values do not overlap 0.
Parameter
Island
Intercept
Mauitaha
-0.103
-0.846
0.748
Intercept
Taranga
0.821
0.404
1.25
Intercept
Ohinau
4.12
2.04
8.52
Intercept
Kawhitu
1.08
0.421
1.77
Intercept
Korapuki
0.302
-1.29
1.29
Intercept
Ruammahuanui
0.356
-0.209
0.932
0.709
0.297
1.13
N
0.31
-4.5
5.07
S
0.338
-4.31
4.95
E
0.195
-3.49
3.84
W
0.639
-3.93
5.24
Elevation
-0.322
-1.26
0.369
Slope*N
-1.11
-7.88
5.96
Slope*S
-1.11
-7.67
5.77
Slope*E
-0.978
-6.15
4.36
Slope*W
-0.903
-7.38
5.85
All islands (see
Median 5% CI
95% CI
, Eq. 3 in text)
Slope
Individual islands (see
, Eq. 6 in text)
83
Slope
Mauitaha
0.665
0.0364
1.25
Slope
Taranga
0.772
0.372
1.2
Slope
Ohinau
0.815
0.155
1.64
Slope
Kawhitu
0.682
0.207
1.15
Slope
Korapuki
0.553
0.0571
1.02
Slope
Ruammahuanui
0.754
0.378
1.16
N
Mauitaha
0.153
-4.62
4.98
N
Taranga
0.28
-4.52
5.04
N
Ohinau
0.2
-4.58
5.05
N
Kawhitu
0.377
-4.45
5.11
N
Korapuki
0.481
-4.29
5.27
N
Ruammahuanui
0.283
-4.54
5.07
S
Mauitaha
0.139
-4.51
4.78
S
Taranga
0.415
-4.22
5.01
S
Ohinau
0.308
-4.32
5.01
S
Kawhitu
0.414
-4.25
5.04
S
Korapuki
0.247
-4.33
4.91
S
Ruammahuanui
0.357
-4.29
4.96
E
Mauitaha
0.357
-3.21
4.1
E
Taranga
0.138
-3.51
3.78
E
Ohinau
0.217
-3.46
3.94
E
Kawhitu
0.0659
-3.58
3.68
E
Korapuki
0.223
-3.41
3.86
E
Ruammahuanui
0.0259
-3.67
3.69
W
Mauitaha
0.875
-3.7
5.77
W
Taranga
0.598
-3.98
5.22
W
Ohinau
0.558
-3.96
5.3
W
Kawhitu
0.513
-4.1
5.1
W
Korapuki
0.351
-4.23
4.94
W
Ruammahuanui
0.81
-3.8
5.43
Elevation
Mauitaha
-0.167
-1.16
0.857
84
Elevation
Taranga
-0.509
-1.48
0.254
Elevation
Ohinau
-0.334
-2.02
0.889
Elevation
Kawhitu
-0.0875
-1.01
0.885
Elevation
Korapuki
-0.936
-2.81
0.0974
Elevation
Ruammahuanui
0.0951
-0.204
0.407
Slope*N
Mauitaha
-0.971
-7.8
6.05
Slope*N
Taranga
-1.3
-8.02
5.78
Slope*N
Ohinau
-1.11
-7.91
6.02
Slope*N
Kawhitu
-0.91
-7.68
6.18
Slope*N
Korapuki
-1.2
-7.98
5.87
Slope*N
Ruammahuanui
-1.14
-7.93
5.88
Slope*S
Mauitaha
-1.08
-7.7
5.73
Slope*S
Taranga
-1.03
-7.57
5.84
Slope*S
Ohinau
-1.13
-7.72
5.74
Slope*S
Kawhitu
-1.24
-7.82
5.66
Slope*S
Korapuki
-1.06
-7.65
5.8
Slope*S
Ruammahuanui
-1.03
-7.61
5.8
Slope*E
Mauitaha
-1.22
-6.48
4.12
Slope*E
Taranga
-0.76
-5.92
4.61
Slope*E
Ohinau
-0.907
-6.1
4.4
Slope*E
Kawhitu
-0.716
-5.87
4.66
Slope*E
Korapuki
-0.992
-6.18
4.36
Slope*E
Ruammahuanui
-1.3
-6.47
4.01
Slope*W
Mauitaha
-0.906
-7.44
5.82
Slope*W
Taranga
-1.01
-7.48
5.77
Slope*W
Ohinau
-0.921
-7.43
5.86
Slope*W
Kawhitu
-1.14
-7.65
5.64
Slope*W
Korapuki
-0.767
-7.27
5.99
Slope*W
Ruammahuanui
-0.672
-7.19
6.04
85
Appendix E
Table E1.1:
List of monitoring strategies on islands in New Zealand with all non-native predators removed. Monitoring programmes, the species
group targeted, and the institution performing the monitoring were identified the published or unpublished literature or by
interviewing island researchers. DOC = Department of Conservation and OSNZ = Ornithological Society of New Zealand.
Island
Raoul
Macauley
Manama Tawhi
(Great Island)
Motuopao
Date
Time
Area predators
Dates
Frequency spent on
(ha) eradicated
visited
of visits
island Survey activity
2938
2004
1967-2008 Annually
3 hrs
Point counts
General island
surveys,
presence/absence
noted during
2004-2006 Annually
weeding
236
2008
1946, 1951,
2 plots of 15 by 15,
300
1946
1963, 2003 Annually
1 plot 40 by 40
General mapping
surveys and 8
1995-1999,
random quadrats of
2001
Annually
10 m2
1.5 hr-34
1887-1989 Eight times days
Inventory
30
1989
Twice
annually
Wildlife
targeted
Birds
Institution
DOC
Source
(Veitch et al. 2011)
Seabirds
DOC
(Veitch et al. 2011)
Plants
DOC
(Bellingham et al.
2010)
Land snails
Birds and
lizards
DOC
(Brook 2002, 2003)
“Fauna monitoring” Flax Snail
DOC
(Powlesland 1990)
DOC and Te
Ahu Heritage
Museum
86
1981-1992
Aorangi
Taranga (Hen
Island)
Coppermine
110
1936
470
2011
80
1997
2011, 2013
1992-2000
1997-2010
Lady Alice
155
1994
2007-2014
1997-2010
Whatupuke
Urupukapuka
Waewaetorea
102
102
52
1997
2009
2009
1997-2010
2009-2014
2009-2014
Inventory/
distribution, 1
quadrat in Blackwinged Petrel
colony
Birds
Occupancy and
burrow counts,
30*10 m fixed plots
and 3 m radius
circular plots on
Bullers
transect lines
Shearwater
5 times
Annually
2-4 visits
annually
Twice
annually
1-4 visit
annually, 1
visit
annually
2012-2014
Twice
annually
Twice
annually
Weeding
every 2
weeks,
planting
annually
Weeding
DOC
(Pierce and Parrish
1993)
DOC
G. Taylor pers.
comm.
Pycroft's and
10-29 permanently little
marked burrows
shearwaters
DOC
Post-release
monitoring
Lizards
DOC
9-68 transect of 2 m
wide through
Te Papa
colonies, burrow
Tongarewa
density and
Flesh-footed museum and
4-10 days occupancy
shearwater
Latitude 42
Post-release
monitoring
Lizards
DOC
Post-release
monitoring
Lizards
DOC
1 day
1 day
Trap, tracking card,
and tracking tunnel
grids
Trap, tracking card,
Invasive
predators
and plants
Invasive
(Pierce 2002)
(Parrish 2010)
(Baker et al. 2010,
Waugh and Taylor
2012)
(Parrish 2010)
(Parrish 2010)
Project Island
Song (DOC
and local
www.project
Maori)
islandsong.co.nz/
Project Island www.project
87
every 2
weeks,
planting
annually
2009-2014
Okahu
Motukiekie
Moturua
Motuarohia
Poroporo
Pokohinu
(Burgess)
Lizard
21
29
135
50
56
1
2009
2009
2009
2009
2009
1991
1978
2009-2014
2009-2014
2009-2014
2009-2014
2009
Weeding
every 2
weeks,
planting
annually
Weeding
every 2
weeks,
planting
annually
Weeding
every 2
weeks,
planting
annually
Weeding
every 2
weeks,
planting
annually
and tracking tunnel predators
grids
and plants
Several plots
established
Plants
Song (DOC
and local
Maori)
DOC
islandsong.co.nz/
(Young 2009)
1 day
Trap, tracking card, Invasive
grids
and plants
Project Island
Song (DOC
and local
www.project
Maori)
islandsong.co.nz/
1 day
grids
and plants
Project Island
Song (DOC
and local
www.project
Maori)
islandsong.co.nz/
1 day
grids
and plants
Project Island
Song (DOC
and local
www.project
Maori)
islandsong.co.nz/
grids
and plants
Project Island
Song (DOC
and local
www.project
Maori)
islandsong.co.nz/
Transects, 50 by 50
m plots, 10 by 10 m
plots
Seabirds
Petrels
Sandager
Pokohinu
Research and
Conservation (Gaskin and HeissTrust
Dunlop 2010)
DOC
Taylor unpubl. Data
1 day
88
Mokohinau islets
Atihau (Trig)
Horomea (Maori
Bay)
10
16
1991
1991
11
1991
Motukino (Fanal)
79
1997
Kauwahaia Island 0.7
Hauturu (Little
Barrier)
2817
1994
1989
2004
9 days
Annually
1975-1989
Annually
Inventory, 3 semipermanent quadrats Vegetation
BurrowBurrow occupancy nesting
of entire island
seabirds
1 week
(each
transect
counted
8-12
500 m by 20 m
times) transects
Transects
Recommended: 75
random 3-mcircular plots 2-3
times annually
Te Haupa
(Saddle Island)
6
Tiritiri Matangi
196
Annually
2010
2004-2005
1987-1990,
1997
Annually
1 day
1993
1987-2010
Annually
2 days
194 circular plots of
3-m-radius
Entire island
searched
Point counts along
transects
(de Lange et al.
1995)
DOC
G. Taylor pers.
comm.
Birds
DOC
(Girardet et al. 2001)
Reptiles,
Little Barrier
invasive
Island
species,
Supporters www.little
birds, plants
Trust
barrierisland.org.nz/
Weta
Kakapo
Cook's
Petrel
Flora and
fauna
Birds
DOC
DOC, Forest
and Bird, NZ
Aluminium
Smelters Ltd.
Auckland
University
(Mckenzie 2003)
www.kakapo
recovery.org.nz/
DOC
(Rayner et al. 2007)
(Tennyson and
Taylor 1999)
OSNZ
(Graham et al. 2013)
89
1992-2013
Motuihe
Motukorea
(Browns)
RangitotoMotutapu
195
2004
58
1995
23001500
148
Tarahiki
5
Pakatoa
29
Otata
Maria
22
1
Motuhoropapa
David Rocks
Cuvier
9
1
181
Band resighting
2009
Invasive predators
1990-1991
Rakino
Robin and
hihi
Birds,
insects,
Monitoring stations plants
Invasive
Bait stations
predators
Annually
Every six
weeks
1 day
Bird counts along
main path
Birds
DOC,
Auckland
Regional
Council,
Graduate
students
(Armstrong and
Ewen 2013)
www.motuihe.org.nz
Motuihe Trust /
(Veitch 2002a)
Motutapu
Restoration
Trust
DOC,
University of
Auckland
www.motutapu.org.n
z/
(Miller and
Anderson 1992)
2004
1988, 1994,
2007
Annually 1-2 days
1-4 visits
1997
1996-2001 annually
Every six
1980-2002
months
1960
2002
1985, 2004,
1981-2002
2006
1964
1993
1968-1985
1974-1980
Opportunistic
surveys
Counts in 4 island
regions
Surveys
Survival estimates
Observations
Plants
North Island
weka
Invasive
predators
Birds
Saddlebacks
Birds
DOC
(Cameron et al.
2007)
(Beauchamp et al.
2009)
DOC
(Moors 1985b)
University of
Auckland,
Auckland
Botanical Club (MacKay et al. 2007)
DOC
Auckland
Jenkins et al. unpubl.
data
(Bellingham et al.
90
Moturehu
(Double)
Korapuki
Whakau (Red
Mercury)
32
18
1989
1986
225
1992
Kawhitu (Stanley) 100
1991
Ohinau
Middle Chain
Whenuakura
(Donut)
Mahurangi (Goat)
Tuhua (Mayor)
45
23
2005
1994
3
1984
23
1311
<1993
2002
(Waugh et al. 2013)
Lizards
DOC
Landcare
Research,
Otago
University
DOC and
Landcare
Research
Pycroft's
petrel
DOC
Taylor unpubl. Data
Petrels
DOC
Taylor unpubl. Data
14 plots of 10 by 10 Burrowm and 19 plots of 5- nesting
4-7 days m-radius
seabirds
2010, 2012,
2013
80 pitfall traps
1986-1995 Biannually
along 4 m transects
Banding, searching
all burrows in three
1998, 2009
colonies near camp
Burrow occupancy
1993, 1998,
in 3 plots 20 by 20
2003
m
wide through
colonies, burrow
2007-2010, 1-4 visit
density and
2012-2014 annually 4-10 days occupancy
1993-2012
1981)
Flesh-footed
Shearwater
1988-1990
2005-2011
University
10 transects of 25
by 5 m
Annually
Annually
two
weeks
Te Papa
Tongarewa
shearwater
Latitude 42
Fish and
lobster
Marine
fauna
Coastal and
Aquatic
systems Ltd.
And DOC
Lyver unpubl. data,
this study
(Monks et al. 2014)
(Baker et al. 2010,
Waugh and Taylor
2012)
(Haggitt 2011)
www.boppoly.
ac.nz/go/news/
Bay of Plenty reserve-monitoringPolytechnic tuhuawedand DOC
14032012-1200am
91
1996present
Rurima
Moutohora
(Whale)
4
1984
173
1987
Tuatara
1999-2002
2007-2010
1998-2000
Whangaokena
(East)
Motu-o-Kura
(Bare)
Kapiti
Tahoramaurea
Motungara
(Kapiti)
13
14
"Ad-hoc"
Translocation of
Orange-fronted
Fauna
Parakeet and
Recovery New
Brown Teal
Birds
Zealand
Post-release
Brown Teal, North Island
monitoring
Robin, Tuatara
"Walk through in
conjunction with
rodent inspections" Vegetation
DOC
Annually
Twice
annually
Annually
33 island sections
photographed from
15 photopoints
Burrow scoping 27
plots of 10 by 10
Burrow counts 78172 circular plots of
2 m radius per 16
island sections
1997
1991
1970
1
1998
1998
3
1998
vegetation
Grey-faced
petrel
Grey-faced
petrel
Grey-faced
petrel
1991-1992,
1995
1990-1991,
1994, 1995,
1998
1-3 visits 1-2 days
30 pitfall traps set
for 41-70 days
Invertebrates
2 plots of 20 by 5, 4
plots of 1 by 1m, 9
photopoints
Plants
1999, 2000,
2001
Searches using
dogs
Brown Teal
DOC
DOC
Landcare
Research
DOC
http://fauna
recovery.org.nz/
J. Heaphy pers.
comm.
(Shaw 2000)
(Towns 2005)
(Shaw et al. 2003)
(Whitehead et al.
2014)
(Imber et al. 2003a)
DOC
DOC
(Walls 1998)
DOC
(Walls 1998)
http://brown
teal.com/kapitiisland/
DOC
92
Mana
Matiu/Somes
217
27
1991
1999-2014
1-3 visits
annually
1986-1993
3-11 visits 2-4 nights
annually per visit Trap setting
1990
2002-2005
Mokopuna
(Leper)
Takapouera
(Stephens)
0.5
150
Te Hoiere (Maud) 309
3-5 visits
annually
2 day
surveys
Counts along 3
transects
Sooty
Shearwater,
Diving
Petrel and
Fairy Prion
McGregor's
Skink,
lizards
Tuatara,
fluttering
shearwater,
little blue
penguin
Birds
Te Papa
Tongarewa
museum and
DOC
DOC
(C. Miskelly pers.
comm., Miskelly
1999)
(Newman 1994)
Matiu/Somes
Island
Cheritable http://matiusomes
Trust
trust.weebly.com/
J. Greenman and E.
Dunning pers.
OSNZ
comm..
1990
1924
1993
1995, 2002,
16 pitfall traps in
2003
Annually 2-7 days each of 8 grids
1991-2014
Annually
1983-2014
Annually
*2013 mice
discovered
5 days
Re-survey 16 years
after release
2008-2010
Annually
Skinks
Hamilton's
Frog
Victoria
University
DOC
Transects, 12 by 12
m study grids,
occupancy
Victoria
modelling
Frogs
University
Cook
Post-release
Straight
monitoring
Giant Weta
DOC
Color
band
reading
Malherbe's
and
parakeet
(Stephens 2004)
P. Gaze pers. comm.
(Bell et al. 2004, Le
Roux 2008)
(Meads and Notman
1992)
Massey University
93
habitat use
in
transects
along
main track
2007-2013
1990spresent
Titi
32
1975
2007-2010,
2012-2014
Annually
Annually
1-4 visit
annually
1998, 2000,
2006
Annually
1987-1998
Motuara
59
Annually
1991
1994, 2001,
2002, 2005 Annually
Kokomohua
142
1997
1973-1999
2005-2007
5 minute bird
counts
Post-translocation
productivity
wide through
colonies, burrow
density and
4-10 days occupancy
185
person Post-release
hours monitoring
Burrow counts 10
plots of 100 m2
Post-release
monitoring
Post-release
monitoring
Nest boxes, no
formal monitoring
Reproductive
Twice
success
Annually ~13 days Post-release
Birds
Fluttering
shearwater
DOC
DOC
(Ortiz-Catedral)
C. Birmingham pers.
comm.
Te Papa
Tongarewa
Shearwater
Latitude 42
C. Birmingham pers.
comm.
Tuatara
Flesh-footed
shearwater
and Sooty
shearwater
(Miller et al. 2010)
Frogs
DOC
DOC
DOC and
University of
Saddlebacks Canterbury
Little blue
Otago
penguin
University
Lincoln
University and
South Island University of
Robin
Canterbury
Saddlebacks
DOC and
(Gaze 2000)
(Pledger 1999)
(Hale 2008)
www.penguin.net
(Byrne 1999)
94
(Long)
monitoring and
monitoring for
avian malaria and
avian pox
Size, density,
behaviour in
transects at 5
reserve sites and 4
1992-2001 Annually
control sites
Radio tagging and
demography of
2011-2013 Annually
entire population
All burrows
inspected with
2008-2009 One season 7-30 days burrow scope
Pickersgill
103
2007
2007-2014
Blumine
377
2007
2002-2013
Weekly
3 visits
annually
2007-2014
Allports
16
Nukuwaiata
(Inner Chetwode) 195
Trap checks
1989
1994
Trap checks
University of
Canterbury
DOC and
Davidson
Environmental
Blue Cod
Ltd.
Little
Victoria
Spotted
University and
Kiwi
Cougar Line
Victoria
Sooty
University and
Shearwater
DOC
Invasive
predators
DOC
Snail, birds,
weta
Invasive
predators
DOC
South Island University of
Saddleback
Canterbury
Annually
2001-2007
Mohua
Annually
2004-2010
Hamilton's
Frog
Annually
Gallery occupancy
1994-1998 4 nights in 4 plots of 625 m2 Tree Weta
1998
Kakapo
DOC
DOC and
University of
Otago
University of
Otago and
Canterbury
DOC
(Hale 2008)
(Davidson 2001,
Willis 2013)
H. Taylor unpubl.
data
(Geary et al. 2014)
P. Clarke pers.
comm
P. Clarke pers.
comm
(Byrne 1999)
(Gaze and Cash
2008)
(Bell et al. 2010)
(Merton 1999,
Rufaut and Gibbs
95
2003)
Te Kakaho (Outer
Chetwode)
83
1994
WhakaterePapanui
74
1999
Tinui
95
1999
Puangiangi
69
1999
Surveys
Post-release
monitoring
2002-2004
Monitoring plots
set up
2013
1 week per
2012-2013
month
Motutapu
Tonga
2
8
87
4
Vegetation
Monitoring of
shearwater burrows Petrels
1989
2007
2007
2007
Counts and size
measurements in 2
by 2 by 30 m
transects, benthic
quadrats
1993-2013
2007-2009
Adele
Fisherman
Weka
Green
geckos,
Cook
Straight
giant weta,
tuatara
2007-2009
2007-2009
Every 3
months
Every 3
months
Every 3
Marine
fauna
Invasive
Tracking tunnels,
House
chew tags, rat dogs Mouse
Fluttering
Social attraction
and sooty
with speakers
shearwater
Invasive
Tracking tunnels,
House
chew tags, rat dogs Mouse
Tracking tunnels,
Invasive
DOC
University of
Wellington,
DOC and Alan
Wilson Center
Beauchamp and
Butler 1999
(Beauchamp and
Butler 1999)
(Alan Wilson Center
report, Hoare 2006)
Fauna
Recovery NZ
Trust
Fauna
Recovery NZ
Trust
Walls Unpubl. data
P. Gaze pers. comm..
DOC and
Davidson
Environemental
Ltd.
DOC
DOC and
Project
Janszoon
DOC
DOC
(Davidson and
Richards 2013)
(Golding 2010)
http://www.janszoon
.org/
(Golding 2010)
96
months
Breaksea
170
1988
2011
1994-2014
1988-1993
Hawea
9
1986
Anchor
1130
2001
2005-2014
2001, 2005
2001-2014
Chalky
514
Rarotoka (Centre) 88
Whenua Hou
(Codfish)
1396
Annually
Twice
annually
3 days
chew tags, rat dogs House
Mouse
Territory
boundaries, nesting South Island University of
success
saddlebacks
Otago
South Island
Robin,
weevils,
Mohua,
Fiordland
Landcare
skink
Research
Fiordland
crested
penguin
DOC
Seedling counts
DOC and
in20 plots of 25 m2,
Landcare
19 plots of 100 m2 Vegetation
Research
Fiordland
Landcare
skink
Research
Radio transmitters
on each bird
Kakapo
DOC and
Post-release
University of
monitoring
Rock wren
Otago
5 minute counts
All birds
DOC
Stoats and
Trapping lines
Deer
DOC
2001
1997
1997
1996-97 to
2004-2005
Annually
Burrow occupancy
in 50 study burrows
Burrow density and
occupancy in 3
Cook's
Petrel
Sooty
Shearwater
(Golding 2010)
(Hooson and
Jamieson 2003)
(Thomas 2002)
(Allen et al. 1994)
(Thomas 2002)
http://kakapo
recovery.org.nz/
Weston pers. comm
A. Smart pers.
comm.
(Edmonds 2002)
University of
Otago
(Imber et al. 2003b)
97
plots of 513–2226
m2 and 15 transects
2m by "20
burrows"
Ulva
270
1997
2008-2014
>Once
Annually
Mokinui
86
2006
2011-2013
Annually
Putauhinu
141
1997
1996-97 to
2004-2005
1-3 times
annually
Rerewhakaupoko
(Solomon)
30
2006
2012-2014
Annually
Pukeweka
Taukihepa (Big
3
939
2006
2006
2011-2013
2011-2013
Annually
Annually
Reintroduced
birds:
saddleback,
Yellowhead,
Stewart
Island robin,
Riffleman
Plots
Burrow density and
occupancy in 70
transects 1m by "20
burrows"
Opportunistic
monitoring by
muttonbirders
(McKechnie et al.
2009)
Sooty
Shearwater
DOC
Oikonos
Ecosystem
Knowledge,
DOC, and
University of
Otago
Sooty
Shearwater
(McClelland et al.
University of 2011, Nevins and
Otago
Hester 2011)
DOC and
(McKechnie et al.
Saddlebacks Rakiura Maori 2009)
Oikonos
Ecosystem
Knowledge,
DOC,
Burrow density and Sooty
University of
occupancy in plots Shearwater
Otago
Burrow density and Sooty
Oikonos
(McClelland et al.
98
South Cape)
occupancy in plots
2006, 2008,
2010
Campbell
11331
2001
2004-2008
1985-1986
Mangere
Rangatira (South
East)
113
218
Bird counts in 35
1-3 days plots of 10 m radius
Nest mapping,
50-60 collecting banding
Annually
days
data
128 plots of 3 m
radius along
transect in 6
colonies, 45 plots
Annually
2.5 by 2.5 m
Anually
Shearwater
Birds
Southern
Royal
Albatross
Rockhopper
penguins
1950
1961
1999-2010
Annually
1990-2003
Twice
2000-2010
Twice
3 days
Ecosystem
Knowledge,
DOC, and
University of
Otago
Ka Mate Nga
Kiore
Incorporated
Society and
Command
Trustee
Council
2011, Nevins and
Hester 2011)
(McClelland et al.
2011, Nevins and
Hester 2011)
DOC
(Harper 2010)
DOC
(Moore et al. 2012)
(Moors 1985a,
Cunningham and
Moors 1994)
Chatham
Islands
Mollymawk
Nests counted
Vegetation surveys
and photo-points in
62-96 10 by 10 m
plots checked
Vegetation
Chatham
Island Taiko
(Robertson and
Scofield 2003)
(Urlich and Brown
2005) (Rayner et al.
2012)
99
OTHER
SEABIRD
MONITORING
PROGRAMS
Island
Punakaiki
20022005 Annually
19972009 Annually
Antipodes Island,
Archway
Island,Windward 1978Islands
2011 4 counts
Mount
Maunganui and
Motuotau Island
19912000 Annually
Great Barrier
Island
19952013 Annually
Dates
Time spent
Survey
visited Frequency of visits on island
activity
Wildlife targeted
0.5-40 search
Colony limits
hours per person
defined and
Westland
per colony
burrows counted
Petrel
DOC
(Wood and Otley 2013)
150 burrows
checked for
occupancy in
Westland
50*10m plot
Petrel
DOC
DOC Unpubl. Data
Erect-crested
and
16 days to survey
Repeatable nest Rockhoper
all islands
counts
Penguins
DOC
(Hiscock 2013)
Landcare Research,
Ornithological
8-34 nights of
Grey-faced
Society of New
banding per season
Banding
Petrel
Zealand
(Jones et al. 2011)
9 census grids
(40*40 m), 10-26
transects (400*4
m), nests
counted,
occupancy
assessed,
41-47 days over 3
banding,
trips
geolocators
Black Petrel
DOC
(Bell et al. 2013)
Appendix F
Incidence of plastic fragments among burrow-nesting seabird colonies on
offshore islands in northern New Zealand
Rachel T. Buxton, Caitlin A. Currey, Philip O’B. Lyver, and Christopher J. Jones
Published in Marine Pollution Bulletin
F.1 Abstract
Marine plastic pollution is ubiquitous throughout the world’s oceans, and has been found
in high concentrations in oceanic gyres of both the northern and southern hemispheres. The
number of studies demonstrating plastic debris at seabird colonies and plastic ingestion by adult
seabirds has increased over the past few decades. Despite the recent discovery of a large
aggregation of plastic debris in the South Pacific subtropical gyre, the incidence of plastics at
seabird colonies in New Zealand is unknown. Between 2011 and 2012 we surveyed six offshore
islands on the northeast coast of New Zealand’s North Island for burrow-nesting seabird colonies
and the presence of plastic fragments. We found non-research related plastic fragments (0.031
pieces/m2) on one island only, Ohinau, within dense flesh-footed shearwater (Puffinus carneipes)
colonies. On Ohinau, we found a linear relationship between burrow density and plastic density,
with 3.5 times more breeding burrows in areas with plastic fragments found. From these data we
conclude that plastic ingestion is a potentially a serious issue for flesh-footed shearwaters in New
Zealand. Although these results do not rule out plastic ingestion by other species, they suggest
the need for further research on the relationship between New Zealand’s pelagic seabirds and
marine plastic pollution.
F.2 Introduction
Rates of plastic production and pollution into marine systems have increased steadily
since the 1950s (Barnes et al. 2009). Plastics constitute the majority of anthropogenic debris
occurring throughout the global marine environment (Derraik 2002). Among the many negative
impacts of plastic pollution is the endangerment of marine wildlife through entanglement or
ingestion (Mattlin and Cawthorn 1986, Gregory 2009).
Ingestion of plastic by adult seabirds and offloading to chicks has been widely
documented from the high Arctic and northern Pacific Ocean (Provencher et al. 2010, Van
Franeker et al. 2011) to the sub- and continental Antarctic (Furness 1985, Van Franeker and Bell
1988) and most places in-between (Laist 1997). The potential effects of plastic consumption on
seabirds include: internal and external wounds, blockage of the digestive tract, impairment of
feeding capacity, reduction in reproductive capacity, and poisoning from the absorption of toxic
compounds (Gregory 2009). Due to the regurgitation of plastic to chicks, the death of chicks or
fledglings with large loads of plastic in their stomach, and the regurgitation of large indigestible
materials (i.e. plastic) by chicks, seabirds can act as vectors, introducing plastic fragments to
their breeding grounds (Huin and Croxall 1996).
The New Zealand archipelago has the highest diversity of seabird species’ in the world,
dominated by burrow-nesting procellariiforms (Taylor 2000). They are however, threatened by
human disturbance, habitat alteration, and introduced predators, which have resulted in the
extirpation of most species from the mainland (Taylor 2000, Holdaway et al. 2001). The impact
of plastic pollution on the conservation status of New Zealand’s seabirds and the amount of
plastic deposited at their breeding grounds are currently unknown. Plastic debris and pellets
wash up frequently onto beaches around New Zealand (Gregory 1977, 1999); furthermore,
plastic pellets have been documented in the stomachs of prions (Pachyptila spp.) found wrecked
around New Zealand as early as 1960 (Harper and Fowler 1987). Given the large populations of
procellariiform seabirds found in New Zealand, as well as the tendency for birds of this order to
ingest more plastic than others (Azzarelo and Van Vleet 1987), the potential for plastic affecting
seabirds in New Zealand is likely to be high.
While surveying burrow-nesting seabird colonies on islands with ‘nature reserve’ status
in northern New Zealand, we noted the presence of non-research related plastic fragments. We
therefore recorded the presence/absence and number of fragments in all surveyed colonies. We
then compared the distribution of plastic fragments with the presence, local density, and
occupancy of breeding burrows in order to test whether plastic was associated with seabird
colonies.
F.3 Methods
Study area and search method
We surveyed burrow-nesting seabird colonies on six islands located in the Hauraki Gulf,
off the northeastern coast of the North Island of New Zealand: Taranga, Mauitaha,
Ruamaahuanui, Ohinau, Korapuki, and Kawhitu (Fig. 1). All study islands had long histories of
human occupation and modification through burning and terracing, and/or the introduction of
Pacific rats (Rattus exulans) by Māori (Skegg 1963, 1964, Atkinson 2004), but have been
protected as nature reserves and have remained undisturbed since the mid-19th Century. We
visited the islands between September and December in 2011 and 2012. This period represented
the pre-breeding to egg hatching stages of the breeding cycles of burrow-nesting seabirds present
on our study islands. Those species included grey-faced petrel (Pterodroma macroptera gouldi),
flesh-footed shearwaters (Puffinus carneipes), common diving petrels (Pelecanoides urinatrix),
fluttering shearwaters (Puffinus gavia), little shearwater (Puffinus assimilis), Pycroft’s petrel
(Pterodroma pycrofti), sooty shearwater (Puffinus griseus), and little blue penguin (Eudyptula
minor).
In order to survey the seabird colonies and the distributions of colony-associated plastic
fragments, we spread colony survey plots along evenly-spaced transects which ran from coast to
coast, parallel to the short edge of each island. Approximately 35 transects per island resulted in
distances of 10-40 m between transects, depending on island size (Table 1). The transect method
was not employed on two islands: Ruamaahuanui, due to high burrow density and thus high risk
of burrow collapse; and Taranga, due to hazardous terrain. Instead, previously selected,
randomly generated GPS (Global Positioning System) points were used on Ruamaahuanui; and
modified transects constrained by proximity to existing tracks, were employed on Taranga.
Depending on the transect length, one to six random distances (chosen from a random
numbers table) were measured from the transect start. This distance was measured using a
handheld GPS (Garmin 60CSx). At each random distance, the centre of a 3 m radius circular
plot was marked with a metal stake. Within the 28.27 m2 we counted all seabird burrows whose
entrances fell more than halfway inside the plot limits. The contents of each burrow were
assessed using an infrared burrow camera (Taupe professional ‘burrowscope’, Sextant
Technology Ltd.).
Figure 1: Location of study islands which were surveyed between September to
December in 2011 and 2012. The main map is of the North Island of New Zealand.
Table 1: Details of transects and plots surveyed on islands in the Hauraki Gulf, New Zealand.
Taranga1 Mauitaha Ohinau
Kawhitu Korapuki Ruamaahuanui2
Number of transects
61
31
33
33
38
n/a
Number of plots
120
68
100
132
101
76
Area searched (m )
3392.4
1922.4
2827
3731.6
2855.3
2148.5
% Island searched
0.072
0.961
0.883
0.373
1.586
1.023
2
1
A modified transect method, constrained by proximity to existing tracks, was employed on Taranga.
2
Randomly positioned points were used to survey burrow density and occupancy and plastic occurrence on Ruamaahuanui.
Generally, different petrel species do not use the same burrow during the same breeding
season, thus we assumed that burrow occupancy by a species was indicative of seasonal
occupancy. While surveying a plot, RTB performed a visual search for the presence of plastic
fragments (no leaf litter or other natural debris were displaced). Equal search effort (< 5 mins)
was made within each plot on each island. Any fragments found were counted and collected.
Statistical analysis
To determine if more plastic fragments were observed in plots with seabird burrows
present we used a general linear model (GLM) with a binomial error structure and logit link. To
determine if areas with plastic had a higher burrow density than areas with no plastic we used a
GLM with a Poisson error structure and log link. Finally, to examine the relationship between
burrow density and plastic density we used a GLM with a Gaussian error structure and an
identity link. Analyses were performed in R version 2.11.1 (R Development Core Team 2010),
statistical significance is assumed at α < 0.5, and unless specified, all data are presented as mean
± SE.
F.4 Results
The most common species, found nesting on all islands, were grey-faced petrel and little
shearwater. Also common were little blue penguin and Pycroft’s petrel (Table 2).
The majority of plastic fragments that we detected were found were on Ohinau (Table 2;
Fig 2). We observed three plastic fragments on Kawhitu (0.0008 pieces/m2) and ten on Korapuki
(0.0035 pieces/ m2), all of which appeared to have been associated with previous research-related
activities (e.g. small pieces of flagging tape or plot markers). No plastic fragments were found
on Taranga, Mauitaha, and Ruamaahuanui.
On Ohinau, we found 89 plastic fragments (0.031 pieces/m2), all but two of which were
found in plots with burrows (Z = 2.154, P = 0.0312). There was a significantly higher density of
burrows in plots with plastic observed than in plots without plastic (Z = 7.346, P < 0.001), and a
positive relationship between burrow density and plastic density (T = 2.795, P < 0.006; Fig. 3).
Although burrow occupancy was low on Ohinau (7.4%), flesh-footed shearwaters were the most
commonly detected species found within burrows (67% of birds detected; Table 3).
Table 2: Burrow density, plastic density, and burrow-nesting seabird species found within plots in the Hauraki Gulf, New Zealand. Y
= species was present (GFPE-grey-faced petrel, LISH-little shearwater, PYPE-Pycroft's petrel, LBPE-little blue penguin, FLSHfluttering shearwater, CDPE-common diving petrel, FFSH-flesh-footed shearwater, SOSH-sooty shearwater)
Species present
Island
Mean burrow
Mean Plastic
density (m-2)
density (m-2)
GFPE
LISH
PYPE
LBPE
FLSH
Taranga
0.053±0.005
0
Y
Y
Y
Y
Y
Mauitaha
0.034±0.006
0
Y
Y
Y
Ohinau
0.058±0.006
0.031±0.001
Y
Y
Kawhitu
0.075±0.008
0.001±0.001
Y
Y
Y
Y
Y
Korapuki
0.088±0.010
0.004±0.002
Y
Y
Y
Y
Y
0
Y
Y
Y
Y
Ruamaahuanui 0.229±0.031
CDPE
Y
FFSH
SOSH
Y
Y
Y
Y
Y
Figure 2: Plastic fragments found on the island of Ohinau. The two plastic fragments on the left
were observed in survey plots with no burrows; plastic fragments on the right were observed in
plots containing flesh-footed shearwater (Puffinus carneipes) burrows.
Figure 3: The linear regression line shows a positive relationship between the density of burrow
entrances (of all species) and the density of plastic fragments within 3 m circular plots on Ohinau
in northern New Zealand.
Table 3: The total number of burrows occupied (N occ.) and percent occupancy (% occ.) by species on each study islands in the
Hauraki Gulf, New Zealand in 2011 and 2012. (GFPE-grey-faced petrel, LISH-little shearwater, PYPE-Pycroft's petrel, LBPE-little
blue penguin, FLSH-fluttering shearwater, CDPE-common diving petrel, FFSH-flesh-footed shearwater, SOSH-sooty shearwater)
Mauitaha
Taranga
Ohinau
Kawhitu
Korapuki
Ruamaahuanui
N occ.
% occ
N occ.
% occ
N occ.
% occ
N occ.
% occ
N occ.
% occ N occ. % occ
GFPE
10
18.18
64
36.78
5
3.09
69
30.40
40
15.81
68
16.83
LISH
3
5.45
2
1.15
1
0.62
1
0.44
9
3.56
8
1.98
LBPE
0
0
2
1.15
0
0
2
0.88
3
1.19
1
0.25
PYPE
1
1.82
1
0.57
0
0
8
3.52
3
1.19
1
0.25
FLSH
1
1.82
2
1.15
0
0
0
0
0
0
36
8.91
CDPE
0
0
1
0.57
0
0
0
0
4
1.58
19
4.70
FFSH
2
3.64
0
0
12
7.41
0
0
0
0
0
0
SOSH
0
0
0
0
0
0
0
0
2
0.79
0
0
Unknown
1
1.82
1
0.57
0
0
5
2.20
2
0.79
7
1.73
Most plastic fragments were too damaged to be identifiable. Of the pieces whose source
was recognizable however, two appeared to be fragmented rope, several were fragments of bottle
caps, and two were fragments of coffee lids (Fig. 2).
F.5 Discussion
We found little evidence of plastic fragments on most of the islands we surveyed in
northeastern New Zealand. Plastic was common on one island only: in a relatively large fleshfooted shearwater colony on Ohinau.
Flesh-footed shearwaters are known to ingest large amounts of plastic (Reid et al. 2013).
For example, on Lord Howe Island, 96% of breeding flesh-footed shearwaters were found to
have ingested plastic (J. Lavers unpub. data). In a study by Hutton et al. (2008), plastic
fragments made up at least 31% of the volume of proventricular cavities of all failed flesh-footed
shearwater fledglings on Lord Howe Island. Furthermore, plastics were found in 79% of the
proventricular cavities of near-fledged chicks, in volumes of up to 15%.
We found large numbers of plastic fragments in flesh-footed shearwater colonies on
Ohinau, but not on Mauitaha, despite the presence of flesh-footed shearwaters on both islands.
One possible explanation for the difference between islands is the higher burrow density and
occupancy of flesh-footed shearwaters on Ohinau (Table 3). Our occupancy estimates on
Ohinau were likely lower because we surveyed burrows during the pre-breeding season
(October), rather than during incubation (Baker et al. 2010). However, previous surveys during
incubation and chick rearing (January) confirm very few flesh-footed shearwaters on Mauitaha
and much larger and denser colonies of this species on Ohinau (Baker et al. 2010).
Possible explanations for the lack of plastics found in other procellariiform species’
colonies could be: 1) inter-specific differences in plastic ingestion due to different concentrations
of plastic at respective foraging grounds, 2) differences in each species ability to regurgitate
plastic to chicks, and thus for plastic to accumulate at nesting sites; and 3) different detectability
of plastics by visual survey because of, e.g. different patterns in plastic deposition from inside a
burrow to the areas surrounding a burrow.
Evidence suggests that plastic loads often differ between species of seabird breeding at
the same colony. On Lord Howe Island, plastic levels were significantly lower in wedge-tailed
shearwater stomachs than flesh-footed shearwater stomachs, possibly due to different densities of
plastic within foraging locations (Hutton et al. 2008) and differences in foraging behavior
(Young et al. 2009). Foraging ranges differ between the species’ present on our study islands.
Common diving petrels, fluttering shearwaters, little shearwaters, and little blue penguins feed
mostly within the inshore region, while, grey-faced petrels, flesh-footed shearwaters, and sooty
shearwaters forage far offshore over a much wider area (Marchant and Higgins 1990). A large
aggregation of plastic has been located in the southern pacific gyre, with the centre
approximately 450 km southeast of Easter Island spreading west to Pitcairn Island (Eriksen et al.
2013). The fact that plastic was only found in flesh-footed shearwater colonies may reflect a
wider foraging strategy, where birds are feeding closer to this south-eastern gyre.
In seabirds, the regurgitation of plastic is restricted by the size of the constriction between
the proventriculus and gizzard. There is a tendency for procellariiforms to retain hard
indigestible objects, due to the size limitation of this constriction (Azzarelo and Van Vleet 1987).
Thus, the lack of plastic fragments found at other species colonies could reflect different sizes of
constriction, rather than a true lack of plastic.
The large amount of plastic found strewn about a forested, rarely visited nature reserve in
this study suggests the need for more research into plastic ingestion by New Zealand’s seabirds.
Seabirds throughout the New Zealand archipelago are benefitting from large-scale predator
removal projects (Towns et al. 2006), but the impact of other factors, such as plastic ingestion,
may put hitherto unaccounted for constraints on the recovery of seabird populations.
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Appendices Appendix A1 - Otago University Research Archive

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