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My primary motivation is to understand the role of natural selection and the environment in the diversification of species. By focusing on replicate geographical contexts and benefiting from our burgeoning ability to "genomicize" ecological model systems, I endeavour to address long-standing questions about evolution in new ways. My research program is built upon two major hierarchies of questions:
- How does natural selection act on the genomic and phenotypic variability of populations to promote speciation? How and when can we discern selective from non-selective factors in evolution?
- What is the role of intrinsic properties of taxa (e.g. genetic variation, genome architecture) in the potential for adaptation and speciation?
To answer these questions I pursue an integrated genetic, genomic, and ecological approach in a comparative framework. In particular, I focus on parallel adaptive radiations, especially of "ichs and herps". Such closely related taxa in a radiation represent phylogenetically-controlled "speciation in action", from the initial stages of population divergence through to behavioural and genetic isolation. We apply a range of genomic tools, especially population genomics using next-generation sequence data, ecological transcriptomics, and whole genome structural comparisons.
This represents a selection of my research interests and projects, many conducted in collaboration with undergraduate, Masters and PhD students. Please contact me if you wish further information or, for students, wish to discuss ideas for tailoring your own project within our team.
Ecological genomics of adaptive polymorphisms
A great challenge of evolutionary biology is that many processes occur on long timescales and are difficult to study or replicate. Therefore, I am especially fascinated by parallel evolution, or the repeated evolution of phenotypically similar species in spatially isolated but similar environments. In those cases we can use these ‘natural experiments’ to dissect the ecological, phenotypic, and genetic mechanisms and responses in diversification (see e.g. Elmer & Meyer (2011) Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends in Ecology & Evolution, 26, 298–306). Of particular interest are ecologically relevant trophic phenotypes and colour variants. We are pursuing this research with two models: primarily adaptive radiations of northern freshwater salmonids such as Arctic charr and European whitefish (e.g. Elmer, K. R., 2016. Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr. Hydrobiologia) and also evolutionary radiations of salamanders. Work in collaboration with researchers at the University of Konstanz focuses on trophic and colour variants in parallel radiations of crater lake cichlid fishes (e.g. Kusche et al. 2015 Sympatric ecological divergence associated with a colour polymorphism, BMC Biology; Elmer et al. 2014 Parallel evolution of Nicaraguan crater lake cichlid fishes by non-parallel routes. Nature Communications).
Funding (partial list): Marie Curie Career Integration Grant (FP7) including studentship (prev H. Recknagel, currently A. Jacobs); Catalyst Fund, Wellcome Trust Institutional Strategic Support (Univ. Glasgow); Pilot Funding, Wellcome Trust Institutional Strategic Support (Univ. Glasgow); BBSRC-DTP studentship to M. Carruthers (with C. Adams); NERC Studentship to J. Burgon (with B. Mable).
The genetics of major evolutionary transitions
Life history variations provide key insights to species ecology and evolution across changing landscapes. We are studying the evolutionary history, comparative genomics, and ecological genomics of live-bearing vs egg-laying in squamate lizards. We are combining field research, experimental approaches on captive populations, and genomics of landscape patterns and deep evolutionary variations.
Funding (partial list): Lord Kelvin Adam Smith studentship to H. Recknagel (Univ. Glasgow, with N. Kamenos in Geography); NERC Standard Grant (RCUK).
Speciation in megadiverse groups
Species rich groups provide a good system to test demography and environment in speciation because there are numerous lineages to assess as replicates. For example, the forests on the slopes of the Andes mountains are a famous but poorly understood ‘biodiversity hotspot’. I have inferred evolutionary histories of morphological stasis despite deep genetic divergence (cryptic species) in species complexes of frogs and salamanders. We found that species branching was much older than expected and may have been promoted by ancient landscape changes (e.g. Elmer KR, Dávila JA, Lougheed SC (2007) Cryptic diversity and deep divergence in an upper Amazonian frog, Eleutherodactylus ockendeni.
BMC Evolutionary Biology; Elmer, K. R., R. M. Bonett, D. B. Wake, and S. C. Lougheed. 2013. Early Miocene origin and cryptic diversification of South American salamanders.
BMC Evolutionary Biology).