Island populations diverge from the mainland and from each other by both natural selection and neutral forces such as founder effects and genetic drift. In this work we aim to determine the relative roles of selection and drift in the diversification of chaffinches (Fringilla spp.) in Macaronesia. We tested the hypothesis that taxa inhabiting Macaronesian archipelagos, which exhibit significant differences in habitat and climate compared to the mainland, should experience distinct ecological pressures, leading to divergence at loci under selection related to environmental variables. To determine the role of local adaptation in the differentiation of these taxa, we performed genotype-environment association (GEA) analyses using ten environmental variables and 52,306 single-nucleotide polymorphism markers obtained from genotyping-by-sequencing (GBS) in 79 chaffinches. Redundancy analysis (RDA) revealed that genomic variation is associated with environmental variables, and identified candidate genes related to phenotypic traits and environmental variables. Variables associated with habitat type and precipitation, together with drift, played an important role in the genomic differentiation between chaffinches from Macaronesia and the mainland, as well as within the Canarian archipelago. Genetic drift was identified as the main factor in the differentiation of North African chaffinches from Macaronesia and mainland Europe, as well as Madeira chaffinches from those in the Canary Islands. Finally, chaffinches from the Canary Islands show an incipient diversification process at the genetic and phenotypic level driven by both selection and neutral processes. Our results suggest that both habitat-driven local adaptation and drift have played a role in the radiation of chaffinch taxa in Macaronesia.

Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) - a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.