Research projects

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Evolution of ecological and species diversity in freshwater fishes 

Supervisors: Kathryn Elmer, Arne Jacobs, Colin Adams

Project description: Ecological, morphological and evolutionary diversification among sympatric individuals often reflects divergent selective pressures along environmental gradients. In many lineages, these have repeatedly produced a range of specialist phenotypes within populations, despite non-existent or incomplete reproductive isolation.

A renowned example for such adaptive divergence in nature are the radiations and replicate evolution of postglacial fishes. Across many species, populations expanded into new ecological and geographic areas, which opened with warming climate and retreating glaciers. Within-lake divergences in freshwater fishes typically specialise along a lake depth gradient and a concordant suite of environmental selection pressures.

In some lineages these divergences have promoted high rates of sympatric and allopatric speciation and consequently elevated regional organismal biodiversity, such as in trout, whitefish, and charr. Our recent work has shown that the demographic and evolutionary histories of these populations can be highly variable and yet the functional expression and ultimate ecomorphological outcomes significantly parallel.

As a next step, it is vital to dig more deeply into the molecular mechanisms driving these patterns. This project will examine replicate divergences into specialist ecotypes and seek to identify their associated and underlying genetics. Specifically, it will examine parallel evolution of genomic divergence, gene expression levels, and alternative splice variants to query and evaluate topical questions in the parallel/convergent basis of complex phenotypes.

This project will build on existing datasets and with opportunity for new experiments. The ideal candidate will have some familiarity with bioinformatics and a degree in evolutionary biology or related discipline.

References

1. Elmer KR (2016) Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr. Hydrobiologia, 783, 191–208.
2. Jacobs A, Elmer KR (2021) Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish. Molecular Ecology, 30 (20), 4955–4969, https://doi.org/10.1111/mec.15817.
3. Jacobs A, Carruthers M, Yurchenko A, Gordeeva NV, Alekseyev SS, Hooker O, Leong JS, Minkley DR, Rondeau EB, Koop BF, Adams CE, Elmer KR (2020) Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish. PLOS

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Overview

Within evolutionary analysis, our specific areas of interest include the basis of adaptation to changing biotic and abiotic environments, the process and underlying mechanisms of speciation, the role of mating systems, host-parasite interactions, and the linkage among ecological and evolutionary processes. Frequently, this work requires the integration of genetic information with other types of data (e.g. phenotypic, geographic, demographic); developing novel bioinformatic tools and approaches to achieve this integration therefore represents another research focus.
 
Due to evolutionary principles being fundamental to all aspects of biology, our research activities are naturally linked with those of other research themes within the institute and throughout the College of Medical, Veterinary & Life Sciences, with particular ties to the Glasgow Polyomics Facility, the Scottish Centre for Ecology and the Natural Environment (SCENE), and the Centre for Virus Research.

Individual research projects are tailored around the expertise of principal investigators within the institutes. A variety of approaches are used, including ecology, epidemiology, mathematical, computational and statistical modelling, bioinformatics, parasitology, immunology and polyomics (genomics, transcriptomics, proteomics, metabolomics). Basic and applied science projects are available for study, as are field-based projects with research programs underway in both the UK and overseas.

Specific areas of interest include:

• host/parasite interactions and coevolution
• evolutionary arms races between parasitic trypanosomes and their hosts
• molecular ecology and evolution in infectious diseases of wild and domestic animals
• behavioural ecology of fish
• influence of genomic, ecological and environmental factors on emergence of new species
• viral and bacterial population genomics
• antimicrobial and anthelminthic resistance
• evolution of viviparity in animals
• physiology and behavioural ecology of marine and freshwater fishes
• physiology and behavioural ecology of birds in urban and rural environments
• evolutionary implications of daily rhythms, life-cycle timing and seasonal movements
• phylodynamics of multi-host pathogens
• life-history evolution, resource allocation, sexual selection and community ecology
• evolution of resistance
• evolutionary and conservation genetics
• evolutionary developmental biology
• gene family evolution, polyploidy, and mating systems
• interaction between parasites, African trypanosomes and their hosts
• organism response to their environment, both natural and captivity
• attack and Escape Strategies in Aquatic Predator-Prey Interactions
• phyloinformatics, biodiversity informatics, biological data visualisation
• genetic and developmental basis of craniofacial shape in fish
• role of divergent natural selection for determining phenotypes
• phenotypic plasticity
• mathematical, computational and statistical analysis of biological datasets, particularly those of pathogens and vaccines
• ecological genomics and adaptive divergence in animals and plants

Study options

PhD

• Duration: 3/4 years full-time; 5 years part-time

Individual research projects are tailored around the expertise of principal investigators.

MSc (Research)

• Duration: 1 year full-time; 2 years part-time