Here - University of Bristol`s Palaeobiology Research Group

University of Bristol MSc Palaeobiology: Thesis Projects 2015-2016
1) The palaeoenvironment and biostratigraphical significance of the conchostracans from
the Late Triassic fissure deposits of Bristol and South Wales.
2
2) Body size evolution in Parareptilia and the influence of (re-)scaling on
macroevolutionary studies
3
3) Evolution of ecospace occupancy by marine reptiles during the Mesozoic
4
4) Conulariid affinity, cnidarian phylogeny and the origin of Eumetazoa
5
5) Establishing an evolutionary timescale for the plant kingdom using fossils and
molecules
6
6) Evolution of disparity in human language and culture
7
7) Ungulate Community Dynamics in North America – A Study of the Radiation of
North American Camelids
8
8) Was the testudine radiation driven by climatic changes?
9
9) To what extent do 2D FEA models capture 3D mechanical behaviour
10
10) Reconstructing the function of early mammals
12
11) Anatomy and function of the rhizodont skull
14
12) Carnivore Community Dynamics in Africa – Changes in Hyaenidae ecological
diversity and the influence of Canidae
16
13) Links between rates of change and ecosystem reaction in the fossil record
17
14) Mechanisms of evolution – assessing heterochrony
18
15) Environmental impacts on foraminiferal calcification
19
16) Anomalocaridid frontal appendage functional diversity
20
17) Constraining the origin of bivalves: morphology, fossils and molecules
21
18) Bacteria or melanosomes?
22
19) Re-evaluating the root of the tree of life
23
20) The evolution of branching forms in plants
25
1) The palaeoenvironment and biostratigraphical significance of the conchostracans from the
Late Triassic fissure deposits of Bristol and South Wales.
Supervisors: Mike Benton, Manja Hethke (Free University of Berlin) and David Whiteside
There has been much debate about the dating and palaeoenvironment of Triassic terrestrial vertebrate
faunas of the fissure fillings in the Carboniferous limestone outcrops in and around Bristol. The
presence of numerous ‘clam shrimps’, fossils of the conchostracan Euestheria, are a key feature of the
deposits that can provide critical evidence but have never been investigated.
The study will investigate the population structure and environmental evidence deduced from
the conchostracans that are associated with tetrapod-bearing rocks from Cromhall, Tytherington and
Pant-y-ffynnon. Those quarries can be visited to study the fissures in the field. The student will
compile descriptions of hand specimens containing hundreds of individual clam shrimps collected
previously and the option of searching for others in the field. It will then be necessary to establish how
the fissure conchostracans relate biostratigraphically and palaeoenvironmentally to Euestheria from
other Late Triassic beds in the U.K. and elsewhere.
The project involves detailed descriptions of previously unstudied fossils, including in
national museum collections, and the analysis of the sedimentology of the containing rock. In addition
there is the possibility of using the electron microscope, CT scanning techniques and fieldwork. There
are extant conchostracans that can provide evidence of their fossil relatives’ lifestyle. The
palaeoecology and morphometrics of the specimens will be analysed using standard numerical
techniques to determine differences in population structures, growth patterns, and sexual dimorphism,
using protocols developed by supervisor Hethke in her studies of the Jurassic and Cretaceous
conchostracans of China.
Training will be acquired in palaeoecology, sedimentology, biostratigraphy, fieldwork,
sedimentary logging, fossil description, and population statistics.
Greaves, P.M., 2012. An introduction to the
branchiopod crustaceans. Quekett Journal of
Microscopy, 41, 679-694.
Hethke, M. 2014: A multiproxy approach to
studying lake ecosystems in the Mesozoic. –
Dissertation thesis, Universität ErlangenNürnberg:
https://opus4.kobv.de/opus4fau/frontdoor/index/index/docId/6147
Whiteside, D. I. & Marshall, J. E. A. 2008.
The age, fauna and palaeoenvironment of the
Late Triassic fissure deposits of Tytherington,
South Gloucestershire, UK. Geological
Magazine 145, 105-147.
Figure: Fourier shape analysis of an Early
Cretaceous Eosestheria-middendorfii cohort and separation of female and male carapace shapes,
illustrated by synthetic outlines (Hethke et al., submitted).
2 2) Body size evolution in Parareptilia and the influence of (re-)scaling on macroevolutionary
studies
Supervisors: Mike Benton, Armin Elsler, Max Stockdale
Parareptilia is an enigmatic clade of early tetrapods, known from the latest Carboniferous to the latest
Triassic (Modesto et al., 2015; Sues et al., 2000), that once was considered to contain modern turtles
(Tsuji and Müller, 2009). Unlike other tetrapod clades such as Diapsida and Synapsida, this clade has
so far not been analysed in a macroevolutionary context.
The project aims to determine patterns of body size evolution and associated rate shifts
among parareptiles. The ratio between identical skeletal elements present in both larger and more
complete specimens can be used to rescale the smaller (but more complete) specimens to address the
distorting effect of ontogeny on macroevolutionary analyses. Such an approach, however, does not
take into account allometry. In the course of this project it shall also be determined, whether rescaling
of skeletal elements has a significant effect on the results of evolutionary rate and rate shift analyses.
A compilation of all currently valid parareptile taxa including different body size proxies will be
refined to address the rescaling problem. An informal supertree of parareptiles is provided for the
macroevolutionary analyses. These analyses will be carried out using standard phylogenetic
comparative methods.
Possible expansion: Study can possibly be extended to include disparity analyses (using the
functional measurements proposed in Anderson et al., 2011 and Anderson et al., 2013). Other clades
can be added as well to determine whether the influence of rescaling in macroevolutionary analyses is
tied to certain groups.
The student will receive training in vertebrate palaeontology, database management, statistics,
and numerical phylogenetic comparative methods. These are all useful techniques for a broad range of
future research careers.
Anderson, P.S.L., Friedman, M.,
Brazeau, M.D., Rayfield, E.J., 2011.
Initial radiation of jaws demonstrated
stability despite faunal and environmental
change. Nature 476, 206–209.
Anderson, P.S.L., Friedman, M., Ruta,
M., 2013. Late to the table: diversification
of tetrapod mandibular biomechanics
lagged
behind
the
evolution
of
terrestriality. Integr. Comp. Biol. 53, 197–
208. doi:10.1093/icb/ict006
Modesto, S.P., Scott, D.M., MacDougall,
M.J., Sues, H.-D., Evans, D.C., Reisz,
R.R., 2015. The oldest parareptile and the
Lond. B Biol. Sci. 282, 20141912.
early diversification of reptiles. Proc. R. Soc.
doi:10.1098/rspb.2014.1912
Sues, H.-D., Olsen, P.E., Scott, D.M., Spencer, P.S., 2000. Cranial osteology of Hypsognathus
fenneri, a latest Triassic procolophonid reptile from the Newark Supergroup of eastern North
America.
J.
Vertebr.
Paleontol.
20,
275–284.
doi:10.1671/02724634(2000)020[0275:COOHFA]2.0.CO;2
Tsuji, L.A., Müller, J., 2009. Assembling the history of the Parareptilia: phylogeny, diversification,
and a new definition of the clade. Foss. Rec. 12, 71–81. doi:10.1002/mmng.200800011
3 3) Evolution of ecospace occupancy by marine reptiles during the Mesozoic
Supervisors: Mike Benton, Tom Stubbs, and Benjamin Moon
Several major clades of reptiles – such as ichthyosaurs, sauropterygians, crocodilians, turtles, and
mosasaurs – occupied different ecological roles in marine ecosystems through the Mesozoic. The
initial wave of marine invasion began in the Early Triassic, and marine reptiles appear to have rapidly
spread into many niches. The Triassic–Jurassic mass extinction may have stimulated a phase of
ecological turnover, but other turnovers were perhaps related to different evolutionary stimuli.
Up to now, these ecological diversifications and changeovers have been described largely in a
qualitative manner. A recent paper (Dick & Maxwell 2015) attempted to quantify ecospace
occupation for the clade Ichthyosauromorpha. However, issues with the formulation of their
characters – repeated states and erroneous coding – means that the true ecospace occupation of
ichthyosaurs may not have been adequately recorded. This project will revisit these results and extend
the method to other marine reptile clades.
The aim of this project is to document the ecospace occupancy of marine reptiles as an
adaptive assemblage and also explore trends in each marine reptile clade. The student will use
quantitative ecospace modelling, by coding ecological categories for over 350 marine reptile species
according to key components such as body size, mode of swimming, and feeding mode (based on
tooth morphology, mandible shape, and inferred bite forces). Using multivariate techniques, the
student will create ecospaces to visualise contractions and expansions during times of extinction and
diversification.
The student will receive training in vertebrate palaeontology and palaeoecology, multivariate
statistical techniques, and numerical phylogenetic comparative methods in macroevolution and
macroecology. These are all useful techniques for a broad range of future research careers.
Completion of this project will allow for publication in a peer-reviewed journal.
Bush, A. M. & Novack-Gottshall, P. M. (2012). Modelling the ecological-functional diversification
of marine Metazoa on geological time scales. Biology Letters, 8, 151–155.
Dick, D. G. & Maxwell, E. E. (2015). The evolution and extinction of the ichthyosaurs from the
perspective of quantitative ecospace modelling. Biology Letters, 11, 20150339.
Motani, R., Chen, X. H., Jiang, D. Y., Cheng, L., Tintori, A. & Rieppel, O. (2015). Lunge feeding
in early marine reptiles and fast evolution of marine tetrapod feeding guilds. Scientific reports, 5.
Thorne, P. M., Ruta, M., & Benton, M. J. (2011). Resetting the evolution of marine reptiles at the
Triassic-Jurassic boundary. Proceedings of the National Academy of Sciences, 108, 8339–8344.
4 4) Conulariid affinity, cnidarian phylogeny and the origin of Eumetazoa
Supervisors: Philip Donoghue, Luke Parry, Davide Pisani
Conulariids are an enigmatic group of cnidarians represented in the fossil record largely by the
mineralised external skeleton that would have armoured the polyp stage within a life cycle that would
also have encompassed a jellyfish stage [1]. However, the anatomy of conulariids is not well
constrained and neither, consequently, is their phylogenetic affinity among cnidarians – with existing
hypotheses based on dubious homologies like the present of ‘corners’ in their polyp skeletons. This is
a pity since conulariids and their kin are among the older fossil remains of animals, including
Corumbella which is known from deep within the Ediacaran [2] and so they have the potential to
inform on the timing of origin of animals, including the establishment of the Eumetazoan bodyplan
shared by cnidarians and bilaterians.
The aim of this project is to establish a time-calibrated phylogeny for cnidarians among their
metazoan relatives, based largely on comparative morphological data. This will be achieved through a
review and reanalysis of the anatomy of conulariids and their immediate kin, based on analysis of
macroscopic remains conulariids, hexanguloconulariids and Corumbella, supplemented by
microanatomical analysis of skeletal structure using synchrotron-based computed tomography. You
will use these data to revise and develop existing comparative morphological datasets for living and
fossil cnidarians [3] which will be supplemented with molecular data [4] to undertake a Total
Evidence Dating analysis [5] from which a timescale for cnidarian and eumetazoan phylogeny will be
derived. This will provide the basis for evaluating the tempo, sequence and mode of bodyplan
assembly among these two fundamental clades of animals.
You will be provided with training in the comparative anatomy of cnidarians, computed
tomography, morphological and molecular phylogenetic analysis (not as scary as it sounds), as well as
divergence time estimation. Previous experience is not required.
1.
Van Iten H., Marques A.C., Leme J.d.M., Pacheco M.L.A.F., Simões M.G., Smith A.
2014 Origin and early diversification of the phylum Cnidaria Verrill: major developments in the
analysis
of
the
taxon's
Proterozoic-Cambrian
history.
Palaeontology,
n/a-n/a.
(doi:10.1111/pala.12116).
2.
Pacheco M.L.A.F., Galante D., Rodrigues F., de M. Leme J., Bidola P., Hagadorn J.W.,
Stockmar M., Herzen J., Rudnitzki I.D., Pfeiffer F., et al. 2015 Insights into the skeletonization,
lifestyle, and affinity of the unusual Ediacaran fossil Corumbella. PLoS One 10, e0114219.
(doi:10.1371/journal.pone.011421910.1371/journal.pone.0114219.g001).
3.
van Iten H., Leme J.d.M., Simòes M.G., Marques A.C., Collins A.G. 2006 Reassessment
of the phylogenetic position of conulariids (?Ediacaran-Triassic) within the subphylum Medusozoa
(Phylum Cnidaria). Journal of Systematic Palaeontology 4(2), 109-118.
4.
Zapata F., Goetz F.E., Smith S.A., Howison M., Siebert S., Church S.H., Sanders S.M.,
Ames C.L., McFadden C.S., France S.C., et al. 2015 Phylogenomic Analyses Support Traditional
Relationships within Cnidaria. PLoS One 10(10), e0139068. (doi:10.1371/journal.pone.0139068).
5.
Ronquist F., Klopfstein S., Vilhelmsen L., Schulmeister S., Murray D.L., Rasnitsyn A.P.
2012 A total-evidence approach to dating with fossils, applied to the early radiation of the
Hymenoptera. Systematic Biology 61(6), 973-999. (doi:10.1093/sysbio/sys058).
5 5) Establishing an evolutionary timescale for the plant kingdom using fossils and molecules
Supervisors: Philip Donoghue, James Clark, Joe O’Reilly
The origin and diversification of the plant kingdom transformed our planet, terraforming the
continents and forever changing Earth Systems. However, the timing and, therefore, the evolutionary
tempo of this formative episode are poorly constrained, with current scenarios based principally on
the stratigraphic appearance of fossil remains of the earliest land plants in the rock record [1]. The aim
of this project is to establish a new timescale for plant evolution using the latest methods in
divergence time estimation that allow the inclusion of morphological data and, therefore, allow fossil
species of known age to be included among their living relatives [2]. This Total Evidence Dating
(TED) approach yields evolutionary timescales that are supposedly more precise and less subject to
assumptions about the overall age of the clade [3], be a key objective of this project.
The molecular sequence data and much of the morphological data required are already
available, though there remains a need to modify certain morphological characters and extend their
coding for certain fossil and living species. The bulk of the research would entail performing the
TED analyses, using the dataset to explore the effect of potential artefacts, such as the amount of
missing data and taxonomic rank, on the resulting timescale. Thus, not only will this study be the first
attempt to perform total evidence dating at the scale of the plant kingdom, it will establish a timescale
that can be used to measure and test hypotheses on the role that plants have played in the evolution of
the biosphere, as well as inform our understanding of the TED method and its development.
The student need not have any prior knowledge of plant science or phylogenetic methods, but
they must have ambition to match the scale and significance of the project.
[1] Kenrick, P., Wellman, C.H., Schneider, H. & Edgecombe, G.D. 2012 A timeline for
terrestrialization: consequences for the carbon cycle in the Palaeozoic. Philosophical Transactions of
the Royal Society, Series B: Biological Sciences 367, 519-536.
[2] O'Reilly, J., dos Reis, M. & Donoghue, P.C.J. 2015 Dating tips for divergence time estimation.
Trends in Genetics.
[3] Ronquist, F., Klopfstein, S., Vilhelmsen, L., Schulmeister, S., Murray, D.L. & Rasnitsyn,
A.P. 2012 A total-evidence approach to dating with fossils, applied to the early radiation of the
Hymenoptera. Systematic Biology 61, 973-999.
6 6) Evolution of disparity in human language and culture
Supervisors: Fiona Jordan (School of Archaeology and Anthropology), Bradley Deline (University of
West Georgia), Thomas Stubbs and Philip Donoghue
It has been recognised since the time of the Ancients that the diversity of life is not continuous but,
rather, it is clumped into discrete types of organisms among regions of what can be considered design
space (without a designer). The question of why this might be so, remains a topic of vigorous debate:
do these clusters in design space reflect fitness peaks? Are the intervening regions of design space
impossible to realise? Are regions of design space unoccupied because insufficient time has elapsed
for them to have been explored by life? Are these regions unoccupied today because of extinction in
the past? Similarly, there is debate over whether this range of designs is realised progressively
through time, or whether there is an early burst and subsequent stasis – reflecting debates among
opponents who view macroevolutionary change as the consequence of uniformitarian versus nonuniformitarian mechanisms, respectively. Ultimately, almost all of this debate exists because of a
general failure to quantify the phenomena under investigation.
Recent years have witnessed attempts to remedy this shortcoming, and the evolution of animal and
plant bodyplans has been a particular focus, yielding what appears to be a general trend in the
evolution of morphological variance. Instead of the traditional expectation that evolution would lead
to a gradual increase in variance, most disparity studies have discovered a phenomenon of maximal
initial disparity, that is, the range of form increases explosively early in the history of lineages, after
which variation is confined to initial bounds [1]. The aim of this project is to explore whether this
trend is general to other evolutionary phenomena and, in particular, to the evolution of language and
culture in humans, considered among the most significant of all evolutionary transitions in the history
of life [2, 3]. Like anatomy, which has been the focus of previous studies of evolutionary disparity,
both language and culture have been the subject of phylogenetics studies [4], the datasets underlying
which provide the basis for phenetic analyses of evolutionary disparity. The project will entail the
adaptation of existing datasets reflecting the shared characteristics among languages and, time
allowing, cultures and religions. These will be analysed using established statistical ordination
methods and the results compared with patterns of morphological disparity obtained from these and
other clades.
The project would suit someone with an interest in anthropology or the analysis of evolutionary
trends. Training in statistical methods will be provided and prior knowledge or experience are not
needed.
1.
Hughes M., Gerber S., Wills M.A. 2012 Clades reach highest morphological disparity early
in their evolution. Proceedings of the National Academy of Sciences, USA 110, 13875-13879.
2.
Szathmary E., Maynard Smith J. 1995 The major evolutionary transitions. Nature 374,
227-232.
3.
Maynard Smith J., Szathmáry E. 1997 The major transitions in evolution. New York,
Oxford University Press.
4.
Gray R.D., Jordan F.M. 2000 Language trees support the express-train sequence of
Austronesian expansion. Nature 405, 1052-1055.
7 7) Ungulate Community Dynamics in North America – A Study of the Radiation of North
American Camelids
Supervisors: Christine Janis (Bristol), Laura K. Säilä (University of Helsinki), Chris Venditti
(University of Reading)
Present day camelids are found in Eurasia and Africa (camels) and in South America (llamas): this
disjunct modern distribution reflects their origination in North America around 45 Ma and their
migration from this continent in the late Miocene/early Pliocene. Camelids were a diverse and
successful radiation in North America, despite their end-Pleistocene demise (along with many other
larger herbivores, such as horses). Although there have been some studies on their paleoecology (see
Janis et al., 2002; Semprebon & Rivals, 2010) little attention has been paid to their role in ungulate
(hoofed mammal) community evolution. In the later Cenozoic of the Old World there was a massive
radiation of ruminant artiodactyls (even-toed ungulates: bovids in the south and cervids in the north),
and their success has been attributed to the key innovation of the omasum in the digestive tract
(Clauss and Rossner, 2014). Yet the North American camelid radiation took place in the presence of
several kinds of endemic ruminants (the only survivor today being the pronghorn), and they were the
only artiodactyls to evolve into large body sizes (see Janis et al. 1994). Present-day camelids have a
relatively low metabolism and rate of food intake (Dittmann et al., 2014): this might be a reason why
they eclipsed the radiation of the North American ruminants, especially as the North American
habitats were more arid than those in the Old World (Eronen et al., 2012), and camelids today are
mainly restricted to arid habitats. This project aims to study the community evolution of the North
American Miocene and Pliocene ungulate faunas and to document the role played by camelids
(including body size and diet), including changes over time with the spread of the grassland habitats
on this continent, with the intent of uncovering the dynamics that led to camelid success.
As a part of this literature-based project, the student will improve and expand the North
American ungulate records of NOW (New and Old Worlds) database of fossil mammals
(http://www.helsinki.fi/science/now/), focusing on the Camelidae occurrences, as well as their
taxonomy and ecomorphology (some data on the other ungulates, especially the ruminants, will also
be updated). The NOW database contains extensive information on land mammal taxa and localities,
but a key strength of the database is that the taxa are recorded with their ecomorphological properties,
such as body size, diet and habitat type. Historically, NOW has had a focus on Neogene mammals of
Eurasia but this project is a part of the process of improving and expanding the temporal and
geographic coverage of NOW. The student will receive training in using suitable analytic methods
and software for estimates of morphological and functional diversity and extinction rates. The student
will gain experience in inputting and using data stored in a large-scale fossil database, and needs to
have an interest in taxonomy and functional morphology, as well as macroevolution and ecology.
Clauss, M & Rossner, G. 2014. Old world ruminant morphophysiology, life history, and fossil
record: exploring key innovations of a diversification sequence. Ann. Zool. Fennici 51:80-94.
Dittman, MT et al. (2015). Characterizing an artiodactyl family inhabiting arid habitats by its
metabolism and maintenance requirements in camelids. J. Arid Environ. 107: 41-48.
Eronen, JT et al. 2012. Neogene aridification of the Northern Hemisphere. Geology 40: 823-826.
Janis, CM et al. 1994. Modelling equid/ruminant competition in the fossil record. Hist. Biol. 8:15-29.
Janis, CM et al. 2002. Locomotor evolution in camels revisited: a quantitative analysis of pedal
anatomy and the acquisition of the pacing gait. J. Vertebr. Paleontol. 22:110-121.
Semprebon, GM & Rivals, F. 2010. Trends in the paleodietary habitats of fossil camels from the
Tertiary and Quarternary of North America. Paleogeol., Palaeoclimatol., Palaeoecol. 295:131-145.
8 8) Was the testudine radiation driven by climatic changes?
Supervisors: Davide Pisani, Amy Waterson, Lucy Holloway, Nick Longrich (Bath), Jakob Vinther.
Introduction: Testudines are divided into two lineages: Cryptodira and Pleurodira (Guillon et
al. 2013). Cryptodira is much more species rich, has a wider geographic distribution, and seemingly
an older origin (Early Jurassic). Conversely, Pleurodira are limited to the southern hemisphere, it
includes less species and its fossil record only dates to the lower Cretaceous. Here we propose to
integrate fossil, biogeographical, climatic, and body size data with an already available, species-level,
testudine molecular dataset including almost 300 taxa (the largest majority of the extant turtle
biodiversity) that was assembled in house. The aim of the project is to use these data to test
hypotheses of turtle evolution. In particular, we shall implement phyloclimatic approaches (Yesson
and Culham 2006) to test whether the differential success of the two lineages was linked to their
different adaptability to climate change.
Methods: This project will take advantage of the data generated in 2015 by Lucy Holloway as
part of her MSc project. Available fossil information will be obtained through palaeoDB and
integrated with the available molecular data using the framework provided by the recently developed
Fossilized Birth Death Model (Heath et al. 2014), in the context of Bayesian tip dating analyses
(Ronquist et al. 2012). The time–calibrated phylogeny will include extant and extinct taxa and will be
used to estimate optimal environmental temperatures and biogeographic distributions for ancestral
testudines (the internal nodes in our phylogeny) using cutting edge Bayesian methods (Lartillot 2014).
The results will be plotted against palaeoclimatic data obtained from a fully-coupled global climate
model (HadCM3L) to test whether biogeographic and climatic tolerance of ancient turtles could have
allowed for a greater distribution of Cryptodira with respect to Pleurodira. Alternatively, it is possible
that the Cryptodira radiated before the Pleurodira and occupied the ecospace effectively blocking the
pleurodiran radiation.
Training & required skills: This project would suit a numerically minded student and requires
a high degree of organisational skills. The student working on this project will gain a strong
knowledge of the analytical tools used in modern phylogenetics and evolutionary biology, including
the use of tools implemented in “R”, Bayesian phylogenetics, tip dating methods, and the integration
of fossils climatological, and molecular data to test evolutionary hypotheses. All the skills the student
will learn are highly transferrable and will be useful irrespective of what career path they will choose
after completing their MSc course.
Guillon et al. 2012 A large phylogeny of turtles (Testudines) using molecular data Contributions to
Zoology, 81 (3) 147-158
Heath T., Huelsenback J.P., and Stadler, T. 2014 The fossilized birth–death process for coherent
calibration of divergence-time estimates. PNAS E2957–E2966.
Lartillot N., 2014. A phylogenetic Kalman filter for ancestral trait reconstruction using molecular
data. Bioinformatics 30:488-496
F. Ronquist et al., A total-evidence approach to dating with fossils, applied to the early radiation of
the Hymenoptera. Systematic Biology 61, 973-999 (2012)
Yesson and Culham, 2006. Phyloclimatic Modeling: Combining Phylogenetics and Bioclimatic
modeling. Systematic Biology. 55;5. 785 - 802.
9 9) To what extent do 2D FEA models capture 3D mechanical behaviour
Supervisors: Emily Rayfield and JJ Hill (Bristol)
Finite element analysis (FEA) is an engineering method that calculates stress, strain and deformation
within a structure in response to user defined loads and material properties that mimic a functional
simulation. In the past 15 or so years it has been increasingly applied to studies of organismal function
in extant and extinct taxa (Rayfield 2007) to simulate the mechanical response of structures to
particular behaviours such as feeding or, less commonly, locomotion or environmental stressors.
Usually three-dimensional (3D) models of the structure of interest are created (e.g. Button et al. 2014;
Lautenschlager et al. 2013; Walmsley et al. 2013; Wroe et al. 2013). These models have the
advantage of capturing the actual geometry of the structure, but are time-consuming to create, require
3D scanning technologies such a computed tomography, laser scanning or photogrammetry and can
be computationally expensive. In contrast, very early studies of biological function employed 2D FE
models of sections through structures, such as teeth (Spears & Macho 1998) to generate hypotheses of
tooth function, particularly in extinct hominids. More recently, 2D models that approximate a ‘slice’
through the structure of interest have been used to study function in dinosaur skulls (Rayfield 2004,
2005, 2011a), ungulate (Fletcher et al. 2010) and early tetrapod jaws (Neenan et al. 2013) and
conodont elements (Murdock et al. 2014; Martinez-Perez et al. 2014). 2D models can be created
relatively quickly and this offers the potential to study evolutionary trends in function by modelling
comparative mechanics (e.g. Fletcher et al. 2010; Neenan et al. 2013).
A major criticism of the 2D approach is that is does not and indeed cannot capture the
accurate mechanical behaviour of a complex 3D structure. This is of course the case – accurate
magnitudes of bone stress and strain will never be recovered via a 2D approach. However, a key
question still remains: what, if anything, can 2D models tell us about the mechanics of a 3D structure?
The aim of this project is therefore to compare the mechanical performance of 2D and 3D FE models
of the same structure – the tetrapod jaw – to test if there is any similarity in the mechanical behavior
of the 2D cross-section and the 3D structure. The tetrapod jaw is a good model because a single
mandible often approximates a 2D planar structure, albeit with varying degrees of curvature towards
the symphysis, and mandibles have been the focus of previous 2D FEA papers. The hypothesis to be
tested is that 2D models do not approximate absolute magnitudes of stress and strain calculated in 3D
models, but that 2D models do capture (i) the overall, gross deformation and (ii) the same patterns of
stress and strain distribution observed in the 3D jaw models.
The study will focus on the jaws of an alligator, ostrich and mouse. These models provide
adequate taxonomic coverage, variable morphologies and for two of the taxa, validation studies have
been performed to assess how accurately the FE models represent experimentally recorded strain
(Rayfield 2011b; Porro et al. 2013). The student will create 2D models of each taxon and under
common loading conditions, compare the stress, strain and deformation of models to their 3D
counterparts. The student will then also create a series of 3D models of varying geometric complexity
– from extrusion of 2D shapes, through to solid 3D, hollow 3D and hollow 3D models with varying
bone properties and compare performance metrics (stress, strain, deformation) across models. Full
training will be provide in processing of CT-data and digital reconstruction in Avizo, and finite
element modelling in Hypermesh and Abaqus. If executed well, the project is publishable in a good
subject specific journal such as The Anatomical Record or Journal of Anatomy.
*Key Reference
Button DJ, Rayfield EJ & Barrett PM 2014 Cranial biomechanics underpins high sauropod
diversity in resource-poor environments. Proceedings of the Royal Society of London, B. 281: DOI:
10.1098/rspb.2014.2114
Fletcher TM, Janis CM & Rayfield EJ. 2010. Finite element analysis of ungulate jaws: can mode of
digestive physiology be determined? Palaeontologica Electronica 13(3) 21A, 15p
Lautenschlager S, Altangerel P, Witmer LM. & Rayfield EJ 2013 Edentulism, beaks and
biomechanical innovations in the early evolution of theropod dinosaurs. Proceedings of the National
Academy of Sciences 110: 20657-20662 DOI: 10.1073/pnas.1310711110
10 Martinez-Perez C, Rayfield EJ, Purnell MA & Donoghue PCJ 2014 Finite element, occlusal,
microwear and microstructural analyses indicate that conodont microstructure is adapted to dental
function. Palaeontology 57: 1059-1066.
Murdock DJE, Rayfield EJ & Donoghue PCJ 2014 Functional adaptation underpinned the
evolutionary assembly of the earliest vertebrate skeleton. Evolution and Development 16: 354-361.
DOI: 10.1111/ede.12096
Neenan JM, Ruta M, Clack JA & Rayfield EJ 2014 Feeding biomechanics in Acanthostega and
across the fish-tetrapod transition. Proceedings of the Royal Society B 281 1781
*Porro LB, Metzger KA, Iriarte-Diaz J & Ross CF. 2013. In vivo bone strain and finite element
modeling of the mandible of Alligator mississippiensis. Journal of Anatomy 223: 195-227.
Rayfield EJ. 2004. Cranial mechanics and feeding in Tyrannosaurus rex. Proceedings of the Royal
Society of London, B. 271: 1451-1459
Rayfield EJ. 2005. Aspects of comparative cranial mechanics in the theropod dinosaurs Coelophysis,
Allosaurus and Tyrannosaurus. Zoological Journal of the Linnean Society 144, 309-316.
*Rayfield EJ. 2007. Finite element analysis and understanding the biomechanics and evolution of
living and fossil organisms. Annual Review of Earth and Planetary Sciences 35: 541-576.
*Rayfield EJ. 2011a. Structural performance of tetanuran theropod skulls, with emphasis on the
Megalosauridae, Spinosauridae and Carcharodontosauridae. Special Papers in Palaeontology 86: 241253. DOI: 10.1111/j.1475-4983.2011.01081.x
Rayfield EJ. 2011b. Strain in the ostrich mandible during simulated pecking and validation of
specimen-specific finite element models. Journal of Anatomy 218: 47-58. DOI: 10.1111/j.14697580.2010.01296.x
Spears IR, Macho GA. 1998. Biomechanical behavior of modern human molars: implications for
interpreting the fossil record. Am. J. Phys. Anthropol. 106:467–482.
Walmsley, C. W., Smits, P. D., Quayle, M. R., McCurry, M. R., Richards, H. S., Oldfield, C. C.,
Wroe, S., Clausen, P. D., and McHenry, C. R. 2013. Why the Long Face? The Mechanics of
Mandibular Symphysis Proportions in Crocodiles: PLoS ONE, 8, e53873.
Wroe S., Chamoli U., Parr W., Clausen P., Ridgely R., Witmer L. 2013. Comparative
Biomechanical Modeling of Metatherian and Placental Saber-Tooths: A Different Kind of Bite for an
Extreme Pouched Predator. PLoS ONE 8, e66888.
11 10) Reconstructing the function of early mammals
Supervisors: Emily Rayfield & Stephan Lautenschlager (Bristol), Michael Fagan (Hull)
The origin and radiation of mammals are key events in the history of life, with fossils placing the
origin at 220 million years ago, in the Late Triassic period. Recently, much progress has been made in
understanding the pattern and timing of the radiation of mammals, revealing successive waves of
taxonomic and ecomorphological diversification in the Middle–Late Jurassic including gliding,
scansorial and fossorial forms (Luo 2007). Recently, we have provided multiple lines of evidence to
show that this ecomorphological diversity extends further down the tree, and that the earliest
mammaliaformes were already specialised for feeding on different types of insectivorous prey (Gill et
al. 2014). The small shrew-like taxon Morganucodon has a more robust jaw, capable of feeding on
harder foodstuffs than its contemporary Kuehneotherium. Moreover, quantitative tooth microwear
demonstrates how Morganucodon fed on hard prey similar to beetles, whereas Kuehneotherium
ingested softer prey such as scorpion flies (Gill et al. 2014).
These conclusions were, in part, based upon finite element modelling of fossil mammal jaws.
FEA is an engineering technique that reconstructs stress, strain and deformation within a structure
after the application of simulated functional loads (Rayfield 2007). We assume that our FE models of
early mammal jaws represent the actual mechanical behaviour of the jaws, but our model results
remain to be validated against experimental data. Furthermore, we have no way of knowing the exact
material properties of early mammal jaw bone and the subsequent impact that variation in material
properties will have on the outcome of our FE models.
The aim of this project is to construct and conduct a validation test of a rapid prototype (RP)
model of the skull of Morganucodon oehleri, in order to test how accurately FEA can reproduce
experimental strains in the RP model during loading, and the impact on model validity of introducing
variability in material properties. The approach will follow that outlined in recent validation studies
(e.g. Cuff et al. 2015; Toro-Ibacache et al. 2015; Bright & Rayfield 2011) where the specimen of
interest will be secured within a loading rig and subjected to an applied load. Prior to this, the student
will be required to create rapid prototype models of scaled mammalian skulls for analysis. Resulting
strains will be recorded via strain gauges and full-field strain analysis via DSPI and DIC (see ToroIbacache et al. 2015; Groning et al. 2012). DSPI will be performed at the University of Hull and DIC
and strain gauge analysis in Bristol. The student (with help from the supervisors) will be required to
consult with the Earth Sciences workshop in order to construct a suitable loading rig to perform
experimental analysis. Experimental results will be compared to an FE model of the same specimen
with the material properties of RP resin, then material properties will be varied, to ascertain to what
degree variation in material properties influences mechanical behaviour. Results of different model
simulations will be compared using geometric morphometrics (e.g. see Fitton et al. 2015). If time,
there is the possibility to prepare samples and conduct nanoindentation tests to determine the actual
material properties of extant insectivorous taxa such as hedgehogs.
Full training will be provided in all methodologies and the project would suit a student
interested in mammals and/or functional analysis. The project is part of a larger research effort to
understand the functional evolution of the mammalian jaw and the student will become part of that
team effort, with the potential for the project work to be published in a high impact journal.
Bright JA & Rayfield EJ. 2011. Sensitivity and ex vivo validation of finite element models of the
domestic pig cranium. Journal of Anatomy 219: 456-471.
Cuff AR, Bright JA & Rayfield EJ. 2015. Validation experiments on finite element models of an
ostrich (Struthio camelus) cranium. PeerJ e1294; DOI 10.7717/peerj.1294
Fitton LC, Próa M, Rowland C, et al. 2015. The impact of simplifications on the performance of a
finite element model of a Macaca fascicularis cranium. Anat Rec 298, 107–121.
Gill PG, Purnell MA, Crumpton N, Robson Brown K, Gostling NJ, Stampanoni M & Rayfield
EJ. 2014. Dietary specializations and diversity in feeding ecology of the earliest stem mammals.
Nature 512: 303-305.
Gröning F, Bright JA, Fagan MJ, O’Higgins P. 2012. Improving the validation of finite element
models with quantitative full-field strain comparisons. Journal of Biomechanics 45: 1498-1506.
12 Luo Z-X. 2007. Transformation and diversification in early mammal evolution. Nature 450: 10111019.
Rayfield EJ. 2007. Finite element analysis and understanding the biomechanics and evolution of
living and fossil organisms. Annual Review of Earth and Planetary Sciences 35: 541-576.
Toro-Ibacache V, Fitton LC, Fagan MJ, O’Higgins P. 2015. Validity and sensitivity of a human
cranial finite element model: implications for comparative studies of biting performance. Journal of
Anatomy doi: 10.1111/joa.12384
13 11) Anatomy and function of the rhizodont skull
Supervisors: Emily Rayfield (Bristol), Laura Porro (RVC, , Jennifer Clack
Rhizodonts are an extinct group of predatory, sarcopterygian fishes and one of the most basal clades
within Tetrapodomorpha (Swartz, 2012), the lineage leading to all terrestrial vertebrates, including
humans. Rhizodonts lived from the middle Devonian to the late Carboniferous (380 – 310 Mya) and
inhabited tropical freshwater rivers and lakes across a wide geographic range. Some species attained
enormous sizes, with body lengths of up to 7 metres, making them amongst the largest freshwater fish
that ever lived.
Rhizodont skulls – particularly those of derived taxa – feature a number of unique
morphological adaptations thought to be related to feeding. These include small marginal dentition
coupled with large fangs on the palate and coronoid and enormous fangs near the symphysis
(Johanson and Ahlberg, 2001; Brazeau, 2005). Most early tetrapodomorphs – including
porolepiforms, ‘osteolepiforms’ and elpistostegids – had an ossified Meckelian element, a rod of
endochondral bone surrounded by the dermal bones of the lower jaw. In contrast, nearly all rhizodonts
feature a completely unossified Meckelian element (Jeffery, 2003; Brazeau, 2005), a trend that
occurred convergently in much later, increasingly terrestrial tetrapods, such as Acanthostega (Porro et
al., 2015). There are additional peculiarities involving the arrangement of the adsymphysial and
coronoid bones, closure of the precoronoid and intercoronoid fossae, and exposure of the Meckelian
element at the symphysis in rhizodonts (Vorobyeva and Obrucheva, 1977; Ahlberg, 1992; Johanson
and Ahlberg, 2001; Jeffery, 2003; Brazeau, 2005).
The unique anatomy of rhizodont skulls – particularly their lower jaws – has led researchers
to suggest a novel feeding mechanism for these animals: Jeffery (2003) proposed that a longitudinal,
intramandibular hinge was present in the lower jaw of rhizodonts. This permitted movement between
the tooth-bearing bones of the lower jaws and bones forming the jaw joint and to which muscles
attached. Furthermore, this kinetic mechanism permitted the two halves of lower jaw to rotate inwards
(towards each other during biting). Jeffery (2003) suggested that this mechanism would have resulted
in the teeth penetrating deeply into prey during biting, improving grip. However, the potential for
such a mechanism has not been rigorously tested and the functional morphology of the rhizodont skull
is poorly understood compared to other tetrapodomorph groups.
The aim of the proposed project is to fully document the anatomy, test the kinetic potential
and explore the mechanical response of rhizodont skulls more broadly, and then focus on a study of
the feeding mechanics of a well-preserved rhizodont skull from the collections of the University
Museum of Zoology in Cambridge (CAMZM). Pilot scans of a portion of the skull have demonstrated
excellent contrast between matrix and bone. The student will be trained to use this dataset and
visualization software to create a digital, 3D model of the cranium and lower jaws, learning various
techniques for repairing damage and correcting for deformation. This dataset will be used to produce
a detailed anatomical description of this specimen; furthermore, various lines of evidence will be used
to assess the likelihood of the proposed ‘longitudinal intramandibular hinge’ of Jeffery (2003) and its
functional consequences. This includes: sutural morphology and the potential for movement between
individual bones; permissive kinematic linkages throughout the lower and upper jaws; and
osteological correlates of jaw closing muscles that may have powered (or resisted) such movements.
Finally, the 3D digital reconstruction will serves as the basis for a detailed, 3D finite element model
that will be used to explore the mechanical response of a rhizodont skull under feeding loads for the
first time.
The prospective student will receive full training on rhizodont (and, more generally,
tetrapodomorph) skull anatomy, the anatomical requirements/drivers and phylogenetic distribution of
cranial kinesis, processing of CT-data and digital reconstruction in Avizo, and finite element
modelling in the software Strand7.
*Key reference
Ahlberg, P. E. 1992. A new holoptychiid porolepiform fish from the Upper Frasnian of Elgin,
Scotland. Palaeontology, 35, 813–828.
14 *Brazeau, M. D. 2005. A new genus of rhizodontid (Sarcopterygii, Tetrapodomorpha) from the
Lower Carboniferous Horton Bluff Formation of Nova Scotia, and the evolution of the lower jaws in
this group. Canadian Journal of Earth Sciences, 42, 1481–1499.
*Jeffery, J. E. 2003. Mandibles of rhizodontids: anatomy, function and evolution within the tetrapod
stem-group. Transactions of the Royal Society of Edinburgh: Earth Sciences, 93, 255–276.
*Johanson, Z. and Ahlberg , P. E. 2001. Devonian rhizodontids and tristichopterids (Sarcopterygii;
Tetrapodomorpha) from East Gondwana. Transactions of the Royal Society of Edinburgh: Earth
Sciences, 92, 43–74.
Porro, L. B., Rayfield, E. J. & Clack J. A. 2015. Descriptive anatomy and three-dimensional
reconstruction of the skull of Acanthostega gunnari Jarvik, 1952. PLoS One, 10 (3), e0118882.
doi:10.1371/journal.pone.0118882
*Rayfield EJ. 2007. Finite element analysis and understanding the biomechanics and evolution of
living and fossil organisms. Annual Review of Earth and Planetary Sciences 35: 541-576.
Swartz, B. 2012. A marine stem-tetrapod from the Devonian of Western North America. PLoS ONE
7 (3): e33683. doi:10.1371/journal.pone.0033683
Vorobyeva, E. I. & Obrucheva, H. D. 1977. Rhizodont crossopterygian fishes (Fam. Rhizodontidae)
from the Middle Palaeozoic deposits of the Asian part of the USSR. 89–97. In Essays on phylogeny
and systematics of fossil agnathans and fishes. Nauka, Moscow. [In Russian]
15 12) Carnivore Community Dynamics in Africa – Changes in Hyaenidae ecological diversity and
the influence of Canidae
Supervisors: Laura K. Säilä (University of Helsinki), Christine Janis (Bristol), Chris Venditti
(University of Reading)
The three of the extant species of hyenas (Hyaenidae, Carnivora) form a morphologically and
ecologically homogeneous group of meat and bone-eating predators (the exception is the ant-eating
aardwolf) but during the Miocene and Pliocene Hyaenidae was a diverse group that also included
various omnivores and insectivores. Originating in Europe, hyaeanids first arrive in Africa around 14
Ma and achieve peak species diversity at around 11-7 Ma. Near the end of the Miocene, a wave of
extinctions occurred among the Hyaenidae and the hardest-hit here were the smaller civet- and doglike hyenas. However, we also see the appearance of both modern large bone-crushing forms and now
extinct cheetah-like forms at this time (Werdelin & Solounias 1991). Recent studies have shown that
the radiation of the arriving carnivore lineages from North America to Eurasia coincides with the
decline of established Eurasian carnivore lineages (Pires et al. 2015). Canidae (dogs and relatives)
reach Africa during late Miocene, having originated in North America and migrated through Eurasia
(Bonis 2007; Säilä & Matzke 2015). This project aims to test whether the diversity and extinction
rates of African Hyaenidae were affected by the arrival of Canidae in a similar manner to that
observed in Eurasian carnivore faunas by Pires et al. (2015).
As a part of this project, the student will update the African carnivore records of NOW (New
and Old Worlds; http://www.helsinki.fi/science/now/) database of fossil mammals, focusing on the
Hyaenidae occurrences, as well as their taxonomy and ecomorphology (some Canidae data will also
be updated). Historically, NOW has had a focus on Neogene mammals of Eurasia but this project is a
part of the process of improving and expanding the temporal and geographic coverage of NOW. The
database updates will be literature based, but will be complemented with morphological data (project
will include museum visits and/or obtaining photographs and measurements from museums by other
means). These data will be used for estimating the ecomorphological properties of the African
Hyaenidae (and Canidae) taxa. The student will receive training in using suitable analytic methods
and software for estimates of morphological and functional diversity and extinction rates. The student
will gain experience in inputting and using data stored in a large-scale fossil database, and needs to
have an interest in taxonomy and functional morphology, as well as macroevolution and ecology.
Bonis, L.de et al. (2007). The oldest African fox (Vulpes riffautae n. sp., Canidae, Carnivora)
recovered in late Miocene deposits of the Djurab desert, Chad. Naturwissenschaften 94: 575-580.
Pires et al. (2015). Continental faunal exchange and the asymmetrical radiation of carnivores. Proc.
R. Soc. B 282: 20151952
Säilä & Matzke (2015). Around the world in 146 dogs: A new global fossil canid phylogeny and the
historical phylobiogeography of Caninae. SVPCA 2015 / Systematic Association Biennial 2015
abstracts; paper in prep.
Werdelin & Solounias (1991). The Hyaenidae: taxonomy, systematics and evolution. Fossils and
Strata 30:1-104.
16 13) Links between rates of change and ecosystem reaction in the fossil record
Supervisors: Prof Daniela Schmidt and Dr Kirsty Edgar
There is a growing concern about the impact of global change on ecosystems. What is not clear
though is, if there are “tipping points” in the system, thresholds beyond which an abrupt shift of
ecological states occurs, which is long-lasting and hard to reverse. We also do not know if there is a
strict relationship between the size of the environmental change and the ecological impact. What is
more important the rate or the amplitude of environmental change?
We will use body size of planktic foraminifers as a measure of the ecological reaction to
climate change over the Cenozoic. Body size in foraminifers is the product of a number of biological
processes including growth rate, metabolism, nutrition and environment (Schmidt et al., 2004a) and is
an easy-to-measure tracer for macroevolutionary studies (Schmidt et al., 2004b). Organisms typically
obtain their maximum body size under optimum environmental conditions; in contrast when
organisms become stressed they are relatively smaller (Schmidt et al., 2003).
The student will use an automated light microscope in the Schmidt Lab which enables rapid
measurements of thousands of specimens. You will collect high temporal resolution datasets of
foraminiferal body size across several climate perturbations such as the Pliocene warmth, the
Paleogene hyperthermals or the K/Pg boundary (e.g., Davis et al., 2013; Jennions et al., 2015). These
data will be used to constrain 1) the direction, magnitude and rate of any changes in the distribution of
foraminiferal assemblage size, 2) the response of high vs low latitude assemblages to identify the
most sensitive areas/groups and 3) the links between rate and amplitude of environmental change and
biological reaction.
The student will also learn how to prepare sediment samples, pick and identify fossil
foraminifera, conduct biometric analyses, develop preservation metrics to test for taphonomic biases
and be trained to use the scanning electron microscope. This project will provide the student with a
diverse skill-set suited to future research in palaeontology, ecology, biometrics or palaeoceanography.
All these skills are highly prized in the hydrocarbon industry.
Davis, C.V., Badger, M.P.S., Bown, P.R., Schmidt, D.N., 2013. The response of calcifying plankton
to climate change in the Pliocene. Biogeosciences 10, 6131-6139.
Jennions, S.M., Thomas, E., Schmidt, D.N., Lunt, D., Ridgwell, A., 2015. Changes in benthic
ecosystems and ocean circulation in the Southeast Atlantic across Eocene Thermal Maximum 2.
Paleoceanography 30, 1059-1077.
Schmidt, D.N., Renaud, S., Bollmann, J., 2003. Response of planktic foraminiferal size to late
Quaternary climate change. Paleoceanography 18, 10.1029/2002PA000831.
Schmidt, D.N., Renaud, S., Bollmann, J., Schiebel, R., Thierstein, H.R., 2004a. Size distribution
of Holocene planktic foraminifer assemblages: biogeography, ecology and adaptation. Marine
Micropaleontology 50, 319-338.
Schmidt, D.N., Thierstein, H.R., Bollmann, J., Schiebel, R., 2004b. Abiotic Forcing of Plankton
Evolution in the Cenozoic. Science 303, 207-210.
17 14) Mechanisms of evolution – assessing heterochrony
Supervisors: Prof Daniela Schmidt and Dr Tom Davies
Changes in timing of development, heterochrony, have been suggested to be a mechanisms for
evolution. Heterochrony can be expressed by an earlier or later onset of a development, an
increase/decrease in growth between developmental stages, or a delay in the development. These
changes are often expressed in changes in size and shape which are preserved in the fossil record.
Most organisms though do not preserve their evolutionary history and hence the relevance of
heterochrony in an event leading from one species to the next cannot be assessed.
Planktic foraminifers are a major part of the marine fossilised plankton. Uniquely, these single-celled
microfossils grow by sequentially adding chambers that adhere to and envelop, but do not obliterate,
previous developmental stages. Microfossils are traditionally studied using light and scanning electron
microscopy. The late Neogene Globorotalia tumida lineage is a well-studied example for
morphological changes (Malmgren et al., 1983) used to define the idea of punctuated equilibrium in
evolutionary transitions (Malmgren et al., 1984). While the overall shape changes in the lineage are
well documented, it is not clear how these relate to changes in the timing and sequence of
development.
Synchrotron-based X-ray tomographic microscopy allows us to unpick previous
developmental stages in three dimensions, and thus generate 3D reconstructions of all life history
stages of these tiny organisms (Schmidt et al., 2013). We have collected SRXTM scan data from a
number
of
species
of
foraminifers
at
the
Swiss
Light
Source
(http://sls.web.psi.ch/view.php/about/index.html), Paul Scherrer Institut, Switzerland. The aim of this
project is to use this data to generate 3D reconstructions of foraminiferal morphology throughout its
developmental history – i.e. picking apart each growth stage digitally at intervals in the evolutionary
history of the lineage. This will provide information on the ontogenetic history of these organisms in
unprecedented detail. The potential changes in the developmental history will be linked to the
evolutionary history of the lineage.
Full training will be provided in all computational techniques. The student will be introduced
into the use of the 3D reconstruction software AVIZO and learn to generate 3D models. The
reconstructions will be morphologically analysed using simple landmark and volumetric
measurements, i.e. size of chambers, thickness, shape etc. You will generate morphological data,
statistically compare and contrast the data. The project will provide the student with a diverse range of
skills that they will be able to apply to future research in palaeontology, oceanography and
biomechanics.
Malmgren, B.A., Berggren, W.A., Lohman, G.P., 1983. Evidence for punctuated gradualism in the
Late Neogene Globorotalia tumida lineage of planktonic foraminifera. Paleobiology 9, 377-389.
Malmgren, B.A., Berggren, W.A., Lohmann, G.P., 1984. Species Formation through Punctuated
Gradualism in Planktonic Foraminifera. Science 225, 317-319.
Schmidt, D.N., Rayfield, E.J., Cocking, A., Marone, F., 2013. Linking evolution and development:
Synchrotron Radiation X-ray tomographic microscopy of planktic foraminifers. Palaeontology 56,
741-749.
18 15) Environmental impacts on foraminiferal calcification
Supervisors: Prof Daniela Schmidt
Increasing CO2 in the atmosphere and its uptake by the ocean is causing directly ocean acidification
and indirectly warming and increases in stratification (Pörtner et al., 2014). These changing
environmental conditions are predicted to be problematic for marine organisms, particularly due to the
rapid rate of change today, compared with episodes of warming and acidification in the geological
past (Ridgwell and Schmidt, 2010). Marine calcifying organisms may be particularly under threat as
they rely on components of the carbonate system, altered during ocean acidification, to produce their
shells and skeletons (Kroeker et al., 2010).
Planktic foraminifers and coccolithophores each generate 50% of the open ocean carbonate
and thereby impact global biogeochemical cycles. As their hard parts are preserved in the fossil record
they can be used as indicators of calcification response to climate change. Studies of the last glacial to
interglacial transition have suggested that foraminifers may have responded to this change by
decreasing their calcification by 40-50% (Barker and Elderfield, 2002). This is not a clear cut story
though, as the limited number of studies show geographically diverse and species specific responses.
Additionally, there remain many unanswered questions about what exactly controls calcification (e.g.
temperature, saturation state, optimal growth conditions, and nutrients).
This project aims to understand the changes in calcification observed in different foraminifers and
coccolithophores in response to climate change. Ultimately we aim to build a more coherent picture of
how marine calcifiers might be affected by future warming and ocean acidification, the ‘other CO2
problem’. The project will have two parts: 1) assembly of a geographic dataset of foraminiferal
calcification with clearly defined morphotypes 2) analysis of a very high resolution core which allows
to quantify the impact of climate change over the last two centuries on marine calcifiers (foraminifers
and coccolithophores).
The student will be introduced to the taxonomy of both fossil groups and perform
morphometric analysis including shape, size of chambers, thickness, shape etc. You will generate
morphological data, statistically compare and contrast the data. The project will provide the student
with a diverse range of skills that they will be able to apply to future research in palaeontology,
oceanography and global change.
Barker, S., Elderfield, H., 2002. Foraminiferal calcification response to glacial-interglacial changes
in atmospheric CO2. Science 297, 833-836.
Beaufort, L., Probert, I., de Garidel-Thoron, T., Bendif, E.M., Ruiz-Pino, D., Metzl, N., Goyet,
C., Buchet, N., Coupel, P., Grelaud, M., et al. 2011 Sensitivity of coccolithophores to carbonate
chemistry and ocean acidification. Nature 476, 80-83.
Kroeker, K.J., Kordas, R.L., Crim, R.N., Singh, G.G., 2010. Meta-analysis reveals negative yet
variable effects of ocean acidification on marine organisms. Ecology Letters, 13, 1419–1434.
Pörtner, H.O., Karl, D., Boyd, P.W., Cheung, W., Lluch-Cota, S.E., Nojiri, Y., Schmidt, D.N.,
Zavialov, P., 2014. Ocean systems, in: Field, C.B. et al. (Eds.), Climate Change 2014: Impacts,
Adaptation, and Vulnerability. Part A: Global and Sectoral Aspects. Contribution of Working Group
II to the 5th Assessment Report of the IPCC. Cambridge University Press, Cambridge, UK and New
York, NY, USA, pp. 411-484.
Ridgwell, A., Schmidt, D.N., 2010. Past constraints on the vulnerability of marine calcifiers to
massive carbon dioxide release. Nature Geoscience 3, 196-200.
19 16) Anomalocaridid frontal appendage functional diversity
Supervisors: Jakob Vinther, Emily Rayfield and Stephan Lautenschlager
Anomalocaridids were the first apex predator in the Early Cambrian oceans and grew to significant
size. Recent research has found that the anomalocaridid body plan was significantly modified in
different lineages in terms of their trunk morphology and their frontal appendages (1-3).
Since the frontal appendages are the entire feeding apparatus, their functional morphology allow for
hypothesising on styles of modes of feeding and thus the ecology of the organism. Recent studies
have shown that some anomalocaridids evolved to become filter feeders (4), which is of interest for
understanding trajectories in predator evolution, adaptive radiations and niche partitioning (4). In fact,
separate lineages of anomalocaridids evolved to become filter feeders and survived into the
Ordovician and grew to whopping 2 meters (5, 6).
In spite of the great diversity of appendage morphologies in anomalocaridids and their
bearing for understanding the nature of the group.
This project seeks to investigate anomalocaridid anatomy and functional morphology and investigate
the functional limitations of the frontal appendages in order to capture the ecological breadth of the
first major predators on Earth.
Simple models of appendages can be produced graphically, either by drawing or by digital
modelling and the range of movements can be reconstructed. By investigating a range of scenarios of
movements of the appendages, the most parsimonious range of movements in order to capture a prey
and move it to the mouth can be postulated.
The student will get training in computational 3D modelling, functional morphology and
adaptive evolution.
1.
2.
3.
4.
5.
6.
A. C. Daley, J. Bergström, The oral cone of Anomalocaris is not a classic "Peytoia".
Naturwissenschaften 99, 501-504 (2012).
A. C. Daley, G. E. Budd, New anomalocaridid appendages from the Burgess Shale, Canada.
Palaeontology 53, 721-738 (2010).
A. C. Daley, G. E. Budd, J. B. Caron, G. D. Edgecombe, D. Collins, The Burgess Shale
Anomalocaridid Hurdia and Its Significance for Early Euarthropod Evolution. Science 323,
1597-1600 (2009).
J. Vinther, M. Stein, N. R. Longrich, D. A. Harper, A suspension-feeding anomalocarid
from the Early Cambrian. Nature 507, 496-499 (2014).
P. Van Roy, D. E. Briggs, A giant Ordovician anomalocaridid. Nature 473, 510-513 (2011).
P. Van Roy, A. C. Daley, D. E. Briggs, Anomalocaridid trunk limb homology revealed by a
giant filter-feeder with paired flaps. Nature, (2015).
20 17) Constraining the origin of bivalves: morphology, fossils and molecules
Supervisors: Jakob Vinther, Luke Parry
Bivalves are the most diverse class of molluscs after gastropods, their likely sister group, and have a
rich fossil that is vital to unravelling their evolutionary history. There is currently a wealth of
sequence data (1-3) and morphological data (4) for extant taxa, but a comprehensive morphological
matrix for fossil bivalves is lacking. This project seeks to combine the data available for extant taxa
with data from the fossil record in order to construct a total evidence tip dating analysis, as outlined in
(5). Key outcomes will include constraining the origin of the group, elucidating the timings of key
radiations and understanding the character transitions that define major clades. The student will gain
skills in the handling of molecular sequence data, the formulation of morphological matrices and
performing a range of phylogenetic analyses, all of which are key components in a palaeontologist’s
skillset. If time allows, there will be the opportunity to expand this project outside of bivalves to
encompass the whole of Conchifera or the entire phylum Mollusca.
1.
2.
3.
4.
5.
S. A. Smith et al., Resolving the evolutionary relationships of molluscs with phylogenomic
tools. Nature 480, 364-367 (2011).
K. M. Kocot et al., Phylogenomics reveals deep molluscan relationships. Nature 477, 452456 (2011).
V. L. González et al., A phylogenetic backbone for Bivalvia: an RNA-seq approach.
Proceedings of the Royal Society of London B: Biological Sciences 282, 20142332 (2015).
R. Bieler et al., Investigating the Bivalve Tree of Life–an exemplar-based approach
combining molecular and novel morphological characters. Invertebrate Systematics 28, 32115 (2014).
F. Ronquist et al., A total-evidence approach to dating with fossils, applied to the early
radiation of the Hymenoptera. Systematic Biology 61, 973-999 (2012).
21 18) Bacteria or melanosomes?
Supervisors: Jakob Vinther, Chris Rogers and Fiann Smithwick
The discovery of fossil melanosomes has lead to the great possibility of reconstructing original
aspects of colouration from ancient organisms, such as dinosaurs (1-4). However, melanosomes also
resemble bacteria, which they originally had been interpreted as (5, 6).
Recent studies have highlighted a potential drawback with interpreting melanosomes from fossils
because of bacteria (7, 8). They have made the following statements:
1. Bacteria are everywhere
2. Bacteria fossilise easily
3. Bacteria resemble melanosomes
These statements are testable. This project will seek to investigate bacterial colonisation of
sediments, carcasses and melanin bearing tissues. Measure their morphology and compare to
melanosomes. Furthermore, we will test 1 and 2 by investigating fossil bedding planes associated with
melanosome bearing fossils and carcasses to see if any microbodies similar to bacteria or
melanosomes are found outside of the melanin bearing tissue and if they fit any of the predictions
made from studies of modern bacterial communities.
The student will get training in experimental protocolling, SEM, microbiology, melanosome
diversity and function and scientific epistemology.
1.
2.
3.
4.
5.
6.
7.
8.
Q. Li et al., Reconstruction of Microraptor and the evolution of iridescent plumage. Science
335, 1215-1219 (2012).
Q. Li et al., Plumage color patterns of an extinct dinosaur. Science 327, 1369-1372 (2010).
J. Vinther, D. E. G. Briggs, J. Clarke, G. Mayr, R. O. Prum, Structural coloration in a
fossil feather. Biol Letters 6, 128-131 (2010).
J. Vinther, D. E. G. Briggs, R. O. Prum, V. Saranathan, The colour of fossil feathers. Biol
Letters 4, 522-525 (2008).
M. Wuttke, Weichteil-Erhaltung durch lithifizierte Mikroorganismen bei mittel-Eozänen
Vertebraten aus den Ölschiefern der Grube Messel bei Darmstadt. Senckenbergiana lethaea
64, 509-527 (1983).
P. G. Davis, D. E. G. Briggs, Fossilization of feathers. Geology 23, 783-786 (1995).
M. H. Schweitzer, J. Lindgren, A. E. Moyer, Melanosomes and ancient coloration re‐
examined: A response to Vinther 2015 (DOI 10.1002/bies. 201500018). BioEssays, (2015).
J. Lindgren et al., Interpreting melanin-based coloration through deep time: a critical review.
Proceedings. Biological sciences / The Royal Society 282, (2015).
22 19) Re-evaluating the root of the tree of life
Supervisors: Tom Williams, Davide Pisani, and Philip Donoghue
Life on Earth is thought to have existed since ~ 3.4 billion years ago [1]⁠, and a crucial problem in
palaeobiology is to understand the organismal lineages and metabolisms that already existed deep in
the history of life. This is crucial to understand Archaean geobiology, and the early evolution of the
Earth system.
Cellular life as we know it is classified into three major lineages, or domains: the Bacteria,
Archaea, and eukaryotes --- these last being the compartmentalised, nucleated cells that form the basis
of complex multicellular life [2–4]⁠. The deep structure of the universal tree, and the relationships
between these three domains, remain mired in controversy and debate, and are among the most
fundamental unanswered questions in palaeobiology. This project seeks to tackle one specific, critical
aspect of the problem: where is the root of the universal tree – the starting point for the radiation of
cellular life? Answering this question is fundamental to establishing the first organismal lineages and
metabolic pathways to evolve, and to evaluate how the earliest lifeforms shaped the evolution of the
archaean Earth. This problem was initially tackled in the late 1980s but – surprisingly - has not been
reassessed since. The earliest studies were based on gene and protein sequences, and placed the root
of life between Bacteria and the other cellular domains [5,6]⁠, suggesting that the deepest split in the
tree of life lay within the prokaryotes, and that eukaryotes and Archaea are more closely related to
each other than they are to Bacteria. Although the controversy has never been definitely resolved [7]⁠,
that original result remains widely accepted – even though we now possess far more genomic data
from all three domains, and can also benefit from three decades of improvements in evolutionary
algorithms. It is high time to bring the full power of modern phylogenomic approaches to bear on the
root of the universal tree.
This project is ideally suited to a student with interests in the deepest history of life on Earth.
You will build phylogenetic trees for ancient genes already present at the time of the last universal
common ancestor (LUCA) in order to trace the history of cellular life back to its roots on the early
Earth. Your analyses will take full advantage of the broad genomic sampling that is now available for
each of the cellular domains in order to provide a definitive test of the bacterial root. The results will
either provide much-needed support for a venerable, influential but surprisingly fragile hypothesis, or
will suggest provocative new hypotheses for the universal root which will move the debate forward in
this exciting and controversial field: a new root for the tree of life would not only transform our
understanding of the evolution of the three cellular domains, but would also have profound
consequences for inferences of the conditions under which the earliest lifeforms first evolved – on
Earth or elsewhere.
1.
2.
3.
4.
5.
6.
Shih, P. M. 2015 Photosynthesis and early Earth. Curr. Biol. 25, R855–R859.
Woese, C. R., Kandler, O. & Wheelis, M. L. 1990 Towards a natural system of organisms:
proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. U. S. A. 87,
4576–9.
Williams, T. a., Foster, P. G., Cox, C. J. & Embley, T. M. 2013 An archaeal origin of
eukaryotes supports only two primary domains of life. Nature 504, 231–236.
(doi:10.1038/nature12779)
McInerney, J. O., O’Connell, M. J. & Pisani, D. 2014 The hybrid nature of the Eukaryota
and a consilient view of life on Earth. Nat. Rev. Microbiol. 12, 449–55.
(doi:10.1038/nrmicro3271)
Iwabe, N., Kuma, K., Hasegawa, M., Osawa, S. & Miyata, T. 1989 Evolutionary
relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of
duplicated
genes.
Proc.
Natl.
Acad.
Sci.
U.
S.
A.
86,
9355–9359.
(doi:10.1073/pnas.86.23.9355)
Gogarten, J. P. et al. 1989 Evolution of the vacuolar H+-ATPase: implications for the origin
of eukaryotes. Proc. Natl. Acad. Sci. U. S. A. 86, 6661–5.
23 7.
Gouy, R., Baurain, D. & Philippe, H. 2015 Rooting the Tree of Life: the phylogenetic jury is
still out. Philos Trans R Soc L. B Biol Sci in press. (doi:10.1098/rstb.2014.0329)
24 20) The evolution of branching forms in plants.
Supervisor: Jill Harrison (School of Biological Sciences)
Evo-devo research aims to determine the genetic basis of morphological transitions that occurred
during evolution. One of the most fundamental architectural changes occurring in plant evolution was
the innovation of a branching body plan. Branching permitted plants to get much larger, live much
longer, reproduce over longer timescales and colonise space in response to the environment. The
innovation of branching underpinned a tenfold increase in species numbers between the earliest
bryophyte-like land plants and later vascular plants.
Mechanistic understanding of branching is almost exclusive to flowering plants. Transport of the plant
hormone auxin is a primary determinant of branching patterns and is mediated by PINFORMED1
(PIN) auxin efflux carriers. PIN-mediated transport generates auxin minima in leaf axils which are
required for branch initiation. PINs provide long-range polar transport in stems to co-ordinate branch
outgrowth. If long-range transport is disrupted by removal of shoot apices, branches elsewhere on the
plant can grow out.
The patterns of auxin transport are similar amongst vascular plants. Disruption of auxin
transport with inhibitors can disrupt the pattern of branching in a lycophyte, but role of PINs is not yet
known. In mosses, the auxin transport mechanisms are divergent between sporophyte and
gametophyte generations. Whereas sporophytic auxin transport patterns are similar to those in
vascular plants, gametophytic auxin transport patterns are similar to those in other bryophytes,
showing less polarity (Figure 1).
Our recent work showed that auxin transport by PIN auxin efflux carriers drives sporophyte
development in a moss, and that disruption in PIN function can induce branching. The resultant forms
are intermediate between bryophytes and vascular plants and resemble the earliest branching fossils.
We also showed that, although auxin transport drives gametophyte branching, PINs do not
generate the requisite transport. We proposed an alternative transport mechanism involving
intercellular connectivity via plasmodesmata.
This project aims to determine the role of plasmodesmata in moss gametophyte branching.
The project will involve techniques such as 1/ Plant tissue culture 2/ Aniline blue staining of
plasmodesmata in WT and mutant plants 3/ Confocal microscopy and image analysis 4/ Generation
and molecular screening of mutants with defective plasmodesmata 5/ Analysis of branching patterns
in WT plants and mutants with defective plasmodesmata.
The student will work alongside Dr Yoan Coudert (lab 324) in Dr Jill Harrison’s (Office 314) group.
[1] Harrison CJ. 2015. Shooting through time: new insights from transcriptomic data. Trends in
Plant Science. DOI:10.1016/j.tplants.2015.06.003.
[2] Coudert YN, Palubicki W, Ljung K, Leyser O, and Harrison CJ. Three ancient hormone
pathways regulate shoot branching in a moss. eLife 4 e06808.
[3] Bennett et al. (2014a). Plasma membrane targeted PIN proteins regulate shoot development in a
moss. Current Biology 24: 1-10.
[4] Bennett et al. (2014b). Paralogous radiations of PIN proteins with multiple origins of noncanonical PIN structure. Molecular Biology and Evolution (doi:molbev.msu147).
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