Sherlock, Miranda Beatrice; (2024) The application of reduced-representation genomic data to amphibian phylogeography and phylogenetics. Doctoral thesis (Ph.D), UCL (University College London).

Text Miranda_Sherlock_Thesis_2024_corrected_redacted.pdf - Accepted Version Access restricted to UCL open access staff until 1 August 2025. Download (30MB)

Abstract

This thesis investigates the use of reduced-representation genomic data in amphibian phylogeography and phylogenetics. Chapter one relays central concepts for phylogeography, glacial refugia, island biogeography and amphibian biology. For chapter two, a reduced-representation genomic dataset (ddRADseq) generated for 468 individuals encompassing the entire range of the Iberian frog Rana iberica was utilised. Population genetic and demographic simulation analyses were applied to identify the spatial distribution of genetic structure and diversity and to model dispersal routes and timings. The phylogeographic patterns identified fit the isolation- by-distance model, indicating long-distance stepwise dispersal of R. iberica during climatically suitable periods. Sistema Central populations were identified as highly distinct, likely due to post-glacial fragmentation of their range and isolation in small refugia. For chapter three, ddRADseq data was generated for an island radiation of caecilian amphibians whose relationships have proven difficult to resolve. Phylogenetic analyses were applied to 30 individuals from all eight Seychellean species to evaluate any discordance and its causes. This dataset was also used to investigate the impacts of missing data on branch support and tree resolution. Using 129,154 SNPs, a resolved and well-supported tree confirms the paraphyly of Hypogeophis and Grandisonia and identifies a single origin of the diminutive, pointy- snouted Hypogeophis species. Expanding on the Seychelles system, for chapter four, ddRADseq data was generated for 90 individuals of Hypogeophis rostratus. Population genetic and demographic simulation approaches were implemented to infer the dispersal route of extant populations and to evaluate how larger palaeo- islands that were exposed at lower sea levels influenced population genetic structure. The presence of multiple lineages within single islands and instances of higher affinity between than within islands suggests that high historic long-term connectivity has been more significant than recent marine vicariance. The final chapter integrates the major findings of this work, and discusses future directions for these systems.

Download activity - last month

Export as CSVXMLJSON

Download activity - last 12 months

Export as XMLJSONCSV

Downloads by country - last 12 months

Export as CSVXMLJSON

Archive Staff Only

View Item