Genomic insights into population history, drift and adaptation in the island endemic Berthelot’s pipit

This thesis aims to use genomic techniques to elucidate how drift and selection shape genetic diversity across spatial and temporal scales, and thus develop our understanding of their role in incipient speciation. To accomplish this, I focus on Berthelot’s pipit (Anthus berthelotii), an island endemic species, to gain insight into population history, drift and adaptation across this species’ fragmented range. First, using RAD-seq I show that genome-wide divergence across the species range is largely shaped by initial colonisation and resulting bottlenecks, with limited evidence of subsequent gene flow between populations. Then, using a genome scan approach with this RAD-seq dataset, I identify loci putatively under differential selection within archipelagos, including a locus potentially involved in craniofacial development. I then use whole genome sequences to understand how colonisation events, associated bottlenecks, gene flow and genetic drift shape contemporary patterns of genetic diversity across populations. I show that there was a substantial loss of genetic diversity across the genome as a result of the initial island colonisation event by the ancestor of the Berthelot’s pipit and its sister species the tawny pipit (Anthus campestris) ca 2.1 million years ago. These results show that population history, especially founder effects, can have a long-term influence on genome-wide genetic diversity, and that small contemporary Ne can result in signatures of severe inbreeding. Lastly, I investigate genomic landscapes of divergence through speciation from the tawny pipit to Berthelot’s pipit, and across the three archipelago populations of Berthelot’s pipit. Genome-wide divergence correlated with estimated colonisation timescales, with a few strongly divergent ‘genomic islands’ identified in each comparison. I investigate putative drivers of divergence across archipelagos, and find that selection interacts with founder effects and inbreeding to shape adaptation across these populations. Taken together, these findings suggest that evolution at genes involved with bill/body size, immune response, eye development and metabolism acts repeatedly to drive local adaptation across spatial and temporal scales. Collectively, this thesis furthers understanding of how different evolutionary mechanisms shape patterns of genetic diversity and divergence following the establishment of new populations, and how this may lead to eventual speciation