Data from: Neo-sex chromosomes and demography shape genetic diversity in the critically endangered Raso lark

Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. This is partly explained by an unusual and dramatic effect of enlarged neo-sex chromosomes, which preserve high heterozygosity across 13% of the genome in females, and account for half of the overall genetic diversity in the population. In addition, by reconstructing past demography 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. Nevertheless, relatedness analyses suggest that the population is at risk of inbreeding depression. Our findings are particularly important in that they reveal the hidden effects of genome architecture in shaping diversity estimates, and hence demonstrate the value of a reference genome and population genomic analyses over conventional metrics to study diversity in non-model and endangered species