3.2 Evolutionary and demographic history
We explored the post-glacial expansion of North Atlantic harbour porpoises by inferring the evolutionary relationships among populations, quantifying their genetic diversity, and estimating historical variation in effective population size (Ne ). Treemix results (Figure 3A) show how the harbour porpoise colonized and dispersed across the North Atlantic from a southern refugium. The first to split were IBE porpoises, followed by NOS. Thereafter, the ancestral porpoise Atlantic subspecies diverged in Baltic populations and the rest of the Atlantic. All internal nodes had a high bootstrap support (90-100%), except the branch with NOS porpoises (71%) which presented a lower support, and the ancestral node of CA and BAS localities (49%) which was statistically not supported, such that the ancestry among the northern North Atlantic porpoises of BAS, CA, and ICE was not resolved in our analysis.
The SMC++ results (Figure 3B) indicate that overall North Atlantic Harbour porpoises experienced a population expansion and that the Ne of both BLS and IBE subspecies was lower. BLS porpoises’ inferred Ne was stable until ~100,000 years before present (yBP), followed by a steady population contraction up to ~25,000yBP, when theNe started to increase. IBE porpoises had a very similar trajectory, except that inferred population sizes were slightly higher. The Atlantic and Baltic populations had a related inferred demographic history, with an expansion from ~250,000yBP until ~75,000yBP, when populations trajectories started to diverge. Around 25,000yBP, the Atlantic population (CA, ICE, BAS, NOS) experienced a population contraction, while BES and PBS populations expanded.
Individual genome-wide heterozygosity estimates (Figure 4A) were lower in BLS porpoises compared to the other porpoises. The Iberian individual potentially belonging to a different subspecies also presented a low level of heterozygosity. Among P.p.phocoena porpoises, heterozygosity estimates were slightly lower in both populations of the Baltic Sea, compared to the Atlantic sampling locations. Individual inbreeding coefficients (F ) were high in BLS porpoises (0.32-0.34) and in the porpoise potentially belonging toP.p.meridionalis subspecies (~0.2) (Figure 4A). Atlantic and Baltic populations had inbreeding coefficients close to zero, apart from one individual from PBS that presented a higherF (0.06). Regarding Watterson’s theta estimates (Figure S5), the BLS and IBE subspecies as well as the PBS population exhibit low diversity, compared to the BES population and Atlantic locations. Consequently, Tajima’s D estimates (Figure 4B) were negative in all regions, except for the PBS population and the BLS subspecies, where they were positive. No Tajima’s D was calculated for the Iberian individual, because of too low sample size (n=1).