Data from: Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Small effective population sizes could expose island species to inbreeding
and loss of genetic variation. Here, we investigate factors shaping
genetic diversity in the Raso lark, which has been restricted to a single
islet for approximately 500 years, with a population size of a few
hundred. We assembled a reference genome for the related Eurasian skylark
and then assessed diversity and demographic history using RAD-seq data (75
samples from Raso larks and two related mainland species). We first
identify broad tracts of suppressed recombination in females, indicating
enlarged neo-sex chromosomes. We then show that genetic diversity across
autosomes in the Raso lark is lower than in its mainland relatives, but
inconsistent with long-term persistence at its current population size.
Finally, we find that genetic signatures of the recent population
contraction are overshadowed by an ancient expansion and persistence of a
very large population until the human settlement of Cape Verde. Our
findings show how genome-wide approaches to study endangered species can
help avoid confounding effects of genome architecture on diversity
estimates, and how present-day diversity can be shaped by ancient
demographic events.