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New plant species from old genes?

  • Full or part time
    Prof A Hudson
    Dr Catherine Kidner
    Dr A Twyford
  • Application Deadline
    Sunday, January 05, 2020
  • Competition Funded PhD Project (Students Worldwide)
    Competition Funded PhD Project (Students Worldwide)

Project Description

Hybridisation opposes speciation, because recombination in hybrids breaks down the combinations of adaptive genes (haplotypes) assembled in their parents. However, recent genomics evidence suggests that hybridisations can seed rapid radiations of new species—e.g., in Lake Victoria Cichlids (doi: 10.1038/ncomms14363). This project aims to examine whether hybridisation can account for rapid evolution of a group of plant species--the genus Antirrhinum (snapdragons).
Antirrhinum species are either small alpines or large lowland plants. Using genome resequencing, we have show that their evolutionary history began with divergence of lowland and alpine forms. However, alpines later re-evolved from within the lowland group in southeast Spain and lowland forms within the alpine group. We propose that this involved hybridisation and survival of old alpine-adapted gene combinations within in a lowland genome, or vice versa.

The two forms are typified by two sympatic species in SE Spain, which hybridize and share almost all of their genomes but remain morphologically distinct. Using a mapping population, we have shown that their differences are determined by many, unlinked genomic regions (identified as quantitative trait loci, QTL) that can recombine in hybrids and are inherited normally—i.e., we cannot find a simple genetic explanation for why the species remain different. Therefore we propose i) that their differences are maintained by ecological adaptations, which both limit formation of hybrids and make hybrids unfit, ii) that the two species resulted from hybridisation between older alpine and lowland species and iii) that older mutations underlying the original alpine-lowland divergence were recycled in formation of the two new species.
This project aims to test these ideas and to identify underlying, adaptive genes, in the following ways:

1) Genome resequencing of populations of the two species will identify regions that are not shared through hybridisation. These private regions are expected to contain adaptive genes. Their contribution to species differences can be examined by comparing their genome locations to those of known QTL or candidate genes (see 2).
2) Were genes distinguishing the focal species were recycled from genes involved in the early alpine-lowland divergence? Were some old genes not reused? This can be tested with specific genes that we know underlie variation in flower colour, organ size and trichome density, or with SNPs marking larger genome regions.
3) Estimate the level of hybridisation between the focal species (using population genetic metrics and by genotyping offspring of field-collected seeds) and what might limit this (e.g., phenology, pollinator specialisation, pollen preference, ecological adaptation).
4) Understanding the adaptive significance of the two forms. It is possible that adaptation to spatially separated habitats limits gene flow (ecological isolation). Correlation between the occurrence of the species and environmental variables that vary in space (soil pH, chemistry depth & moisture, aspect, cover etc) would support this idea. It could be tested further by comparing the fitness of hybrids with novel character combinations in different environments.

The project will involve training in genomics and bioinformatics, population genetics and phylogenetics and field work in southern Spain.

http://hudson.bio.ed.ac.uk/
https://www.rbge.org.uk/about-us/organisational-structure/staff/tropical-diversity/dr-catherine-kidner/
http://twyford.bio.ed.ac.uk/home

Funding Notes

The “Visit Website” button on this page will take you to our Online Application checklist. Please complete each step and download the checklist which will provide a list of funding options and guide you through the application process.

If you would like us to consider you for one of our scholarships you must apply by 5 January 2020 at the latest.

References

Marques DA, Meier JI, Seehausen O (2019). A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol. 34:531-44. DOI: 10.1016/j.tree.2019.02.008
Wilson Y, Hudson A (2011). The evolutionary history of Antirrhinum suggests that ancestral phenotype combinations survived repeated hybridisations. Plant J. 66:1032-43. doi: 10.1111/j.1365-313X.2011.04563.x
Tan Y, Barnbrook M, Wilson Y, Molnár A, Hudson A. Loss of a glutaredoxin gene underlies parallel evolution of multicellular trichome patterns in the genus Antirrhinum. http://biorxiv.org/cgi/content/short/518183v2.

How good is research at University of Edinburgh in Biological Sciences?

FTE Category A staff submitted: 109.70

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