DOI: 10.5061/dryad.rg576jq
title: Data from: Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

description: 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.
description: Whole genome alignment
 between Eurasian skylark and zebra finch 
 [Tgut_skylark_scaf1M.len5k.delta.gz] Whole genome alignment
 .delta file from the nucmer tool of MUMmer. Only scaffolds larger than 1
 Mb and alignments longer than 5 kb are included.   Scaffold order and
 orientation for pseudo-chromosomal assembly
 [Tgut_skylark_scaf1M.len5k.order_manual.transfers.tsv]
 Chromosome,
 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.   Depth of
 coverage [lark78.coverage_counts.tsv]
 For each
 individual (columns), the number of sites in the genome with a given depth
 of coverage (rows) is given.  
 VCF
 files (genotypes) based on RAD-seq reads mapped to the skylark genome (7
 files) [VCF.tar.gz] Genotype calls from
 RAD-seq data 7 populations (75 individuals) individuals against the
 Eurasian skylark reference genome. These were used to compute individual
 heterozygosity in sliding windows across the genome.
   
 Heterozygosity for 250
 kb windows (14 Files) [Heterozygosity for 250kb
 windows.tar.gz] The proportion of all genotyped sites
 that are heterozygous sites per 250 kb window for each individual. Only
 sites with an individual depth of coverage of 5X were considered. Each
 population was analysed separately. Two versions of each file are given -
 one based on the original genome coordinates and one with coordinates
 lifted over to pseudo-chromosomes, as plotted in figure 2 of the
 paper.   Scaffold Assignments (2
 files) [Scaffold_assignments.tar.gz]   Lists of confidently-inferred normal recombination (NR) and suppressed -recombination (SR) scaffolds (see figure S3 in the paper).   Input files and relatedness estimates from NgsRelate (6 files) [NgsRelate.tar.gz] Input VCF files and output files from NgsRelate. Files of sample names for each individual are also provided.   Input files and relatedness estimates from KGD [KGD.tar.gz] Input files produced using ANGSD and relatedness matrices estimated using KGD.     Site frequency spectra (SFS) (14 files) [Frequency_spectra.tar.gz] 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.   <b>dadi models</b> [dadi_models.tar.gz] Model data for four models fitted with dadi. For each model, fitted parameters are listed in pairs of (i) the length of a period in units of 2N generations, and (ii) the population size (relative to ancestral size) for that period. A table of parameters converted to number of individuals and time in years is also provided.   Stairwayplot best model [raso_two-epoch_fold.final.summary] Output from Stairwayplot for the best fitting model of population size over time for Raso lark.