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.Heterozygosity for 100 kb windowsThe proportion of all genotyped sites that are heterozygous sites per 100 kb window for each individual. Only sites with an individual depth of coverage of 5X were considered.lark78.ST.DP5AN2.het.w100m100s100.csv.gzDepth of coverageFor each individual (columns), the number of sites in the genome with a given depth of coverage (rows) is given.lark78.coverage_counts.tsvSite frequency spectra (SFS) (14 files)Site requency spectra (SFS) estimated using ANGSD from RAD-seq data mapped to the reference genome. Four types of files are provided: (1) SFS for the whole genome (with 20 bootstrap replicates), (2) for males only (with 20 bootstrap replicates), (3) for 'normal-recombination' scaffolds only (with 20 bootstrap replicates), (4) for 'normal-recombination' scaffolds with drop-one-out replicates.frequency_spectra.tar.gzScaffold order and orientation for pseudo-chromosomal assemblyChromosome, start and end position and orientation for each scaffold, based on mummer alignment of the Eurasian skylark scaffolds against the zebra finch genome, with additional manual edits.Tgut_skylark_scaf1M.len5k.order_manual.transfers.tsvInput files and relatedness estimates from NgsRelate (6 files)Input VCF files and output files from NgsRelate. Files of sample names for each individual are also provided.NgsRelate.tar.gzInput files and relatedness estimates from KGDInput files produced using ANGSD and relatedness matrices estimated using KGD.KGD.tar.gzStairwayplot best modelOutput from Stairwayplot for the best fitting model of population size over time for Raso lark.raso_two-epoch_fold.final.summaryWhole genome alignment between Eurasian skylark and zebra finchWhole genome alignment .delta file from the nucmer tool of MUMmer. Only scaffolds larger than 1 Mb and alignments longer than 5 kb are included.Tgut_skylark_scaf1M.len5k.delta.gzGenotypes from RAD-seq dataGenotype calls from RAD-seq data for 78 individuals against the Skylark reference genome. Only genotypes with in individual depth of coverage of at least 5X are included. This file was used to compute individual heterozygosity in sliding windows across the genome.lark78.ST.DP5AN2.geno.g