CLIMIGRATE: Integrating ancient DNA and ecological modelling to quantify the impact of climate change on biodiversity (Funded by the European Union's FP7 ERA-NET program, BiodivERsA.)
The main goal of this project is to enhance conservation efforts for European wild mammals by establishing the tempo and mode of population response to climate change. We are using ancient DNA from nine mammal species to try to understand whether certain species are more likely than others to move with their habitat as the geographical range of that habitat changes.
This information will then be used to build on, and improve existing mathematical models, which can then be used to forecast how climate change may alter species distributions. The ability to predict the effects of climate change could help in the development of conservation and management strategies for those species that are most at risk.
Population history of the Hispaniolan hutia (funded by the Centre for Ecology and Evolution and NERC)
Hispaniola (divided politically into the Dominican Republic and Haiti) is a large West Indian island, containing several distinct biogeographic regions. The Hispaniolan hutia (Plagiodontia aedium) is one of only two remaining endemic land mammals to the region and has consistently been considered rare, threatened and declining.
Conventional modern sampling through field trapping of this rare and cryptic mammal has provided insufficient material. I am therefore examining a diverse range of low-quality samples for DNA recovery in order to conduct molecular systematic, phylogeographic and diversity analyses of hutia populations across Haiti and the Dominican Republic.
I have a widespread interest in phylogenetics and molecular evolution. Understanding the processes of molecular evolution (for example, how substitution rates evolve) is essential for accurately reconstructing the evolutionary history of species using molecular data. My previous research has included both the study of molecular evolution as well as phylogenetic reconstruction, the latter of these primarily focussing on aquatic insects.
Life History Correlates of Rates of Molecular Evolution
My PhD thesis focussed on how species substitution rates can be affected by different life history traits. Using comparative methods, I investigated correlates of molecular rate across the Metazoa, including body size, metabolic rate, generation time, longevity & species richness. Unlike in vertebrates, where there is a strong correlation between species size and substitution rate (smaller taxa, such as mice, have much faster rates of molecular evolution than artiodactyls or primates), I found no evidence of an invertebrate ‘body size’ effect. Nor is there is any observed correlation between rates of molecular evolution and metabolic rate. Instead, substitution rates across invertebrate taxa are found to co-vary with species generation time and longevity. This provides interesting clues as to the causal factors behind the ‘body size’ effect in vertebrates.
Assoc. Prof. Lindell Bromham (Australian National University, Australia)
Dr John Welch (University of Cambridge)
Dr Robert Lanfear (Australian National University, Australia)
The Palaeoptera Problem
The winged insects, or Pterygota, have traditionally been divided into two major groups: the Palaeoptera (the mayflies, dragonflies and extinct Palaeodictyoptera) and the Neoptera (comprising everything else). However, while the monophyly of the Neoptera has been almost universally accepted, the monophyly of the Palaeoptera is still the subject of much debate, and different researchers have argued for all three possible branching patterns between the three groups. Resolving the relationships between the three basal pterygotan lineages has significant implications for determining the ancestral winged insect characteristics, important for understanding the origins of insect flight.
Dr John Welch (University of Cambridge)
Dr John Trueman (Australian National University, Australia)
Dr. Andrew Rambaut (University of Edinburgh)
The Evolution of Dragonfly Flight
In collaboration with researchers at Rutgers University and the Australian National University, I am also examining the evolution of flight in dragonflies. Wing venation is commonly used in odonate taxonomy and phylogenetics. However, differences in wing morphology are likely to arise from ecological adaptations for flight, for example, different flight behaviours such as long distance flying or aerial agility. Investigating the patterns and timing of flight evolution in dragonflies may shed light on how, in association with the changing environment, flight has evolved across the Odonata.
Dr Jessica Ware (Rutgers University, NJ, USA)
Dr Karl Kjer (Rutgers University, NJ, USA)
Dr John Trueman (ANU, Australia)
Prof. Mike May (Rutgers University, NJ, USA)
Phylogenetics of the Trichoptera (caddisflies)
The Trichoptera is the insect order most closely related to the Lepidoptera (butterflies and moths). Unlike the Lepidoptera, however, trichopteran larvae are solely aquatic, and the order is commonly divided into three lineages characterised by the behaviour and habitat of their larval forms. These three groups are the Annulipalpia (whose larvae live in fast flowing water, such as streams or rivers, and spin nets from silk), the Integrepalpia (which live in still water, e.g., ponds, and make cases from the surrounding substrate; see images) and the Spicipalpia (a potentially paraphyletic group, with a mix of different habitats and behaviours, including free living predatory juvenile stages). I am interested in understanding the ancestral traits of this taxa, by using phylogenetics to investigate how these three groups relate to each other.
Dr Karl Kjer (Rutgers University, NJ, USA)
Dr Xin Zhou (University of Guelph, Canada)
June 2010 onwards.........Post-Doc, Royal Holloway, University of London (NERC)
Mar. 2010 - May 2010....Visiting Researcher, Australian National Uni., Australia
Feb. 2009 - Feb. 2010....Post-Doc, Rutgers University, New Jersey, USA
Aug. 2008 - Jan. 2009....Research Assistant, Sequencing Service, U. of Edinburgh
Oct. 2004 - July 2008.....PhD in Molecular Evolution (JMS Scholarship), U. of Sussex
July 2004 - Sept. 2004....Research Assistant, Blaxter Nematode Genomics Lab., U. of Edinburgh
Oct. 2000 - June 2004....B.Sc. (Hons) Genetics (First Class), U. of Edinburgh
Thomas, J.A., Trueman, J.W.H., Rambaut A. and Welch, J.J., Relaxed Phylogenetics and the Palaeoptera Problem: Resolving Deep Ancestral Splits in the Insect Phylogeny. (submitted)
Teacher, A.G.F., Thomas, J.A., & Barnes, I. (2011) Phylogeography of modern and ancient red fox in Europe shows an unusual lack of structuring, and differing responses within the carnivores to historical climatic change. BMC Evolutionary Biology, 11:214
Thomas, J.A., and Ware, J. Molecular and Fossil Dating: a compatible match? (2011) Entomology Americana, 117(1&2):1-8.
Ho, S.Y.W., Lanfear, R., Phillips, M.J., Barnes, I., Thomas, J.A., Kolokotronis, S.-O., and Shapiro, B. (2011) Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology, 60(3): 366-375.
Thomas, J.A., Welch, J.J., Lanfear, R., and Bromham, L. (2010). A generation time effect in invertebrate molecular evolution. Molecular Biology and Evolution, 27:1173–1180.
Lanfear, R., Thomas, J.A., Welch, J.J., Brey, T. and Bromham, L. (2007) Metabolic rate does not calibrate the molecular clock. Proceedings of the National Academy of Science, USA, 104:15388-15393.
Fontanillas, E., Welch, J.J., Thomas, J.A., and Bromham, L. (2007) The influence of body size and net diversification rate on molecular evolution during the radiation of animal phyla. BMC Evolutionary Biology, 7: 95-107.
Thomas, J.A., Welch, J.J., Woolfit, M., and Bromham, L. (2006) There is no universal molecular clock for invertebrates, but rate variation does not scale with body size. Proceedings of the National Academy of Science, USA, 103:7366-7371.
Publications in prep
Thomas, J.A., Ware, J., May, M. and Kjer, K. Time to fly: Dating the evolution of flight in Odonata. (in prep.)
Thomas, J.A., Scott, E., Zhou, X., Hozenthal, R. and Kjer, K. The origins of larval case making behaviour in caddisflies. (in prep.)