1. Introduction
The wellbeing of populations depends on an array of intrinsic and
extrinsic factors, but effective population size and genetic diversity
are among the most crucial. Reduction of genetic diversity in a
population can lead to detrimental outcomes such as loss of adaptive
potential and inbreeding depression, produced by the accumulation of
slightly deleterious mutations due to reduced efficiency of purifying
selection (Tanaka, 2000). Understanding the processes that influence
current genetic variation is essential for the management and
conservation of the diversity of a species (Kardos et al., 2021).
Variation in genetic diversity is the result of historical and present
demographic, geographic, ecological and behavioral mechanisms that
influence gene flow, genetic drift and/or selection levels (Stange,
Barret & Hendry, 2021). Overarching processes such as glacial
contractions and post-glacial expansions have influenced current
patterns of genetic structure and diversity in many European species,
creating population subdivisions and hybrid zones by secondary contact
(Hewitt, 1999; 2000; 2001). However, neutral evolutionary processes are
not the only factor contributing to population subdivisions, as
selective processes such as local adaptation could also produce
different evolutionary trajectories (Barret & Schluter, 2008).
Therefore, both neutral and adaptive processes must be considered when
studying genetic diversity and population structure. Dispersal ability
over vast geographical distances may facilitate gene flow among distant
locations and hence hinder population differentiation (Slatkin, 1987).
The marine habitat is a perfect example of an environment where a lack
of physical barriers offers a continuous environment such that highly
mobile species could present large homogenous populations and an absence
of genetic structure. Yet, several cetacean species show fine-scale
population structure, as for instance Northern bottlenose whale (de
Greef et al., 2022), Finless porpoise (Zhou et al., 2018), Killer whale
(Foote et al., 2016), and bottlenose dolphins (Louis et al., 2021).
The Harbour porpoise (Phocoena phocoena ) is a great example of
complex genetic differentiation in a highly mobile cetacean species. It
belongs to the Phocoenidae family, a group of seven species (Ben
Chehida et al., 2020) containing some of the most threatened cetaceans
(Carlén, Nunny & Simmonds, 2021): the Vaquita (Phocoena sinus ),
one of the most endangered mammals on planet earth, with a population
size of ~10 individuals (Jaramillo-Legorreta et al.,
2019), and the Yangtze finless porpoise (Neophocaena
asiaeorientalis asiaeorientalis), with only
~1,000 individuals extant (Zhao et al., 2008). Porpoises
are mainly affected by incidental bycatch (Brownell et al., 2019),
pollutants such as PCBs (Berggren et al., 1999; Karlson et al., 2000),
parasites (Dzido et al., 2021; Reckendorf et al., 2021; Ryeng et al.,
2022), and noise pollution issued from offshore infrastructure
developments, shipping routes and underwater explosions (Siebert et al.,
2022). Harbour porpoises inhabit coastal and shelf waters across the
Northern hemisphere and at least three subspecies have been described:P.p. vomeria in the North Pacific, P.p. phocoena in the
North Atlantic, and P.p. relicta in the Black Sea. A fourth
subspecies near the Iberian Peninsula and in Mauritanian waters
(P.p. meridionalis ) has been proposed (Fontaine et al., 2007;
2014), although a formal description has not yet been made.
The North Atlantic subspecies (P.p. phocoena ) has a continuous
distribution in the North Atlantic extending from the French Biscayan
waters to the Baltic and Barents Sea and from the Norwegian Sea to the
western North Atlantic coast of Canada and the United States, crossing
Faroese, Icelandic and Greenlandic waters (Gaskin, 1992; Read 1999). The
genetic structure of North Atlantic harbour porpoises has been widely
studied (Alfonsi et al., 2012; Luna et al., 2012; Quintela et al., 2020
among others) and microsatellite data suggests that both sides of the
Atlantic belong to the same lineage (Chehida et al., 2021). However,
genetic and distribution densities suggest the presence of different
ecotypes or populations on the peripheral waters of the Baltic Sea
(Tiedemann et al., 1996; Wiemann et al., 2010; Lah et al., 2016) and
West Greenland (Olsen et al., 2022). The Baltic Sea is a remarkable
sub-basin of the Atlantic Ocean formed less than 10,000 years before
present (BP) as a postglacial marine environment. Baltic populations of
several marine organisms are genetically distinct from conspecifics from
the North Sea and the Atlantic, possibly due to isolation, bottlenecks,
and local adaptation (Wennerstrom et al., 2013). A series of small
basins are separated by shallow underwater ridges ranging from the North
Sea through Skagerrak, Kattegat, Belt Seas to the entrance of the proper
Baltic Sea, making dispersal and gene flow limited (Johannesson &
André, 2006). Moreover, the Baltic Sea is an extreme marine environment
with low winter temperatures and one of the strongest salinity gradients
in the world, ranging from ~34 practical salinity units
(psu) in the Skagerrak to ~2 psu in the innermost parts
of the Baltic (Feistel et al., 2010). These conditions make Baltic
species a prime system to study local adaptation (DeFaveri et al., 2014;
Wrange et al., 2014;
Sjöqvist
et al., 2015) and speciation in the marine environment (Riginos &
Cunningham, 2005, Stuckas et al., 2009; Pereyra et al., 2009). Passive
acoustic (Carlén et al., 2018), telemetry (Svegaard et al., 2015),
morphological (Huggenberger et al., 2002; Galatius et al., 2012), and
genetic data (Tiedemann et al., 1996; Wiemann et al., 2010; Lah et al.,
2016) suggest the presence of three harbour porpoise populations in the
Baltic region: one in the North Sea, Skagerrak and northern parts of
Kattegat (North Sea population, NOS), another in southern parts of
Kattegat and Belt Seas (Belt Sea population, BES) and a third one in the
Baltic Proper (Proper Baltic Sea population,
PBS). Although overlap between
the three populations has been reported based on both genetic (Wiemann
et al., 2010; Lah et al., 2016) and satellite tracking data (Svegaard et
al., 2015), borders among them have been postulated based on
geographical separation during the reproductive season (Svegaard et al.,
2015; Carlén et al., 2018, Amundin et al., 2022).
Harbour porpoise abundance estimates vary greatly among regions: Black
Sea porpoise population size is unknown, but declined by
~90% between the 1930s and the 1980s (Birkun, 2002);
the European Atlantic Shelf is estimated to be inhabited by
~375,000 individuals (Hammond et al., 2013),
~20,000 animals are estimated in the Belt Sea and only
~500 in the Proper Baltic Sea (Amundin et al., 2022).
The Black Sea subspecies and the Proper Baltic Sea population are
considered endangered and critically endangered, respectively. To date,
no assessment of genetic diversity, Ne or
population structure has been conducted on North Atlantic porpoises at
the whole-genome level. Historically, conservation and evolutionary
geneticists have leaned on a handful of molecular markers, such as
mitochondrial DNA and microsatellites, for the study of genetic
variation among populations (Schweizer et al., 2021). However, with the
development of high-throughput sequencing there has been a transition
from genetics to genomics (Formenti et al., 2022). The ever-decreasing
cost of reduced-representation and whole genome sequencing methods has
positioned conservation genomics as a prominent tool for the
characterization of biodiversity and preservation of species
(Fuentes-Pardo & Ruzzante,
2017). Nowadays, the democratization of sequencing costs allows to
resequence the genome of a set of individuals to assess genetic
variation across thousands or millions of markers and address
long-standing questions in evolutionary biology not fully resolved with
traditional markers or reduced-representation methods (Foote et al.,
2021; Robinson et al., 2022; Wolf et al., 2022). This increase of
statistical power to unravel subtle patterns not fully captured by less
dense datasets has had and will continue to have a remarkable impact in
the field of conservation genomics (Lou et al., 2021; Szarmach et al.,
2021).
Here, we used genomics approaches to study the population structure,
genetic diversity, evolutionary history and local adaptation of the
Harbour porpoise (Phocoena phocoena ). We generated the most
comprehensive data set of North Atlantic harbour porpoises so far, by
resequencing the whole-genome of 74 harbour porpoises from eight regions
across the North Atlantic and adjacent waters. Our results shed light on
the expansion of harbour porpoise populations across the North Atlantic,
demonstrate that genome-wide data can unravel subtle population
structure and contribute to understand how marine species adapt to their
local environment. The results have great conservation implications as
we found major levels of inbreeding and low genetic diversity in the
endangered Black Sea subspecies and identified the critically endangered
Proper Baltic Sea porpoises as a separate population.
2. Material and Methods