Exploring adaptation and divergence in Berthelot’s pipit (Anthus berthelotii) through contemporary and historical population genomics

Sheppard, Eleanor Claire (2024) Exploring adaptation and divergence in Berthelot’s pipit (Anthus berthelotii) through contemporary and historical population genomics. Doctoral thesis, University of East Anglia.

Preview

PDF Download (4MB) | Preview

Abstract

Understanding the interplay between demographic and environmental factors, including anthropogenic influences, in driving evolutionary changes within small, isolated natural populations is fundamental to conservation and evolution. This thesis aims to deepen our understanding of these dynamics through genome-wide analyses of variation, adaptation, and divergence across populations of Berthelot’s pipit (Anthus berthelotii), an endemic island bird species. Host genetic variation was examined in relation to pathogen infection prevalence within and across populations. While a candidate gene approach targeting known immune genes yielded no association with avian pox infection, a genotype-environment association approach, combined with RAD-seq data, strongly linked avian pox prevalence to variation at specific genes involved in cellular stress signalling and immune responses. Also, avian malaria and pox prevalence were strongly correlated across island populations, underlining the need to study multiple pathogens simultaneously for a comprehensive understanding of host-pathogen evolution. Subsequently, a second genotype-environment association analysis focusing on avian malaria prevalence identified multiple novel candidate genes involved in various physiological processes, some of which were also identified in the pox analysis. These findings indicate that pathogen-mediated selection plays an important role in shaping genetic variation across populations, and they identify a range of new candidate genes with which to explore natural immunogenetic evolution. Next, whole-genome analyses, incorporating temporal comparisons using museum DNA, indicated range-wide reductions in genetic variation in the pipit over the 20th century, exacerbating population divergence across archipelagos, with pronounced effects in the smallest, most recently colonised, population. These results highlight the lasting impacts of historical founder events on genetic diversity, while also raising the possibility that recent environmental changes, including anthropogenic pressures, may have influenced genetic decline. Overall, these findings advance our understanding of how neutral and adaptive processes contribute to genomic evolution and divergence across natural populations.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	08 Apr 2025 07:33
Last Modified:	08 Apr 2025 07:33
URI:	https://ueaeprints.uea.ac.uk/id/eprint/98982
DOI:

Downloads

Actions (login required)

View Item