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).