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).