2.6 Demographic history analysis
To reconstruct historical relationships among North Atlantic Harbour
porpoises, we inferred a maximum likelihood bifurcating population tree
using Treemix (v1.13) (Pickrell & Pritchard, 2012). The
genotypes (vcf ) were filtered to retain only sites with no
missing data. We performed the Treemix analysis 1,000
times at the population level with a window size of 1,000 SNPs,
specifying the Black Sea subspecies as outgroup and with the option-noss to turn off sample size correction, as suggested by the
authors. We obtained a consensus tree and bootstrap values with the R
package BITE (Milanesi et al., 2017).
We also inferred changes in effective population sizes
(Ne ) through time with the software SMC++(Terhorst et al., 2017). We randomly chose three individuals per
population, except for the Iberian porpoises, where only one individual
was selected for the analysis as the other IBE porpoise was identified
as a migrant. This analysis was run only using scaffolds larger than
1Mba (160 scaffolds) and no MAF filtering was applied on the vcf .
As repetitive and excessive coverage regions were removed from thebam files, these uncalled regions were marked as missing data, as
suggested by the authors (Terhorst et al., 2017). These regions could be
misidentified as very long runs of homozygosity, erroneously decreasing
the N e estimate, and hence compromising the power
to infer true population contractions. In addition, we formed composite
likelihoods by varying the distinct individual (-d ) among the
three individuals, also as suggested by the authors. Then, the
population size histories were computed by using the optionestimate with the default settings, a generation time of 11.9
years (Taylor et al., 2007) and a mutation rate of
2.56x10-8 (Yim et al., 2014).