Demographic History
We used MSMC2 (Schiffels & Wang, 2020) to infer the historical demography of the Balearic shearwater. MSMC2 implements a MSMC model, which allows the estimation of the effective population size (N e) over time. To generate input files for MSMC2, we mapped Illumina short reads to scaffolds larger than 1 Mbp (343 scaffolds spanning 71.8% of the assembled genome) using BWA-MEM 0.7.17 (H. Li & Durbin, 2009), as recommended in Gower et al., 2018). First, we called the SNPs using samtools mpileup (Samtools mpileup 1.9 -q 20 -Q 20 -C 50) and then bcftools 1.9 -c -V indels. The input files were then generated by converting the SNPs obtained to MSMC input format using the bamCaller.py script accounting for the mean coverage of each scaffold. Multiple sequentially Markovian coalescent (MSMC) for two haplotypes, known as PSMC’, was run with MSMC2 with time patterning specified as -p 1*4+30*2+1*4+1*6+1*10.
We ran 100 bootstraps of 29 pseudo-chromosomes (Yamashina & Udagawa, 1954) sampling 20 chunks of 1.508.752 bp with replacement using multihetsep_bootstrap.py. We scaled time and population size using a generation time for the Balearic shearwater of 12.8 years (Genovart et al., 2016) and the Northern fulmar (Fulmarus glacialis ) mutation rate (2.89x10-9 substitutions per nucleotide per generation, Nadachowska-Brzyska et al., 2015).