1 INTRODUCTION
Many wildlife populations are currently under threat from climate
change, pollution, loss of habitat and in some cases exploitation.
Genomic approaches in non-model organisms are becoming an important tool
to study population structure and history that can help protect
endangered species (Hohenlohe et al., 2020). The analysis of whole
genomes can help provide detailed information on demographic changes,
genetic diversity, detection of introgression in organisms (Miller et
al., 2012) and the population structure in species with wide ranges
(Foote et al., 2019; Sinding et al., 2018). These genomic tools are also
ideal to develop an understanding of global population histories in
whales with limited barriers to movement across the oceans (Foote et
al., 2019). Temporal sampling of genomic data from historical specimens
held in museum collections can provide valuable baselines to accurately
quantify genetic threats and can help decipher genomic changes in
endangered species (Díez-del-Molino et al., 2018; Ewart et al., 2019;
Mikheyev, Tin, Arora, & Seeley., 2015). Advances in genomic approaches
can moreover help identify genes that affect the fitness of a species in
relation to anthropogenic threats (Meyer et al., 2018).
The blue whale (Balaenoptera musculus musculus ) is the largest
animal that has ever lived, with individuals reaching 30 m in length and
weighing up to 150 tonnes (Sears & Perrin, 2018). Blue whales are found
in oceans across the globe, but were historically most abundant in the
Southern Ocean (Sears & Perrin, 2018). Commercial hunting of these
whales started in the North Atlantic (NA) in 1860 and spread to all
other oceans (Thomas et al., 2016). The large size of blue whales made
them a prime target for the commercial whaling industry during the 20th
century and they were hunted to the brink of extinction with an
estimated 379,185 whales taken globally (Rocha et al., 2014). Whether
blue whales in the NA represent a single population or two distinct
populations, separated between the west and east is unresolved (Lesage
et al., 2016; McDonald et al., 2006). The Northwest Atlantic (NWA) has a
lower number of blue whales, with some 250 adults (COSEWIC,
2012.), whereas in the Northeast Atlantic (NEA) there
are ~3000 individuals (Pike et al., 2019). The movement
patterns of blue whales in the NA and the location(s) of their wintering
sites and breeding areas are still elusive (Lesage et al., 2017). The
blue whales’ distribution in the NWA, based on sightings and
photo-identification studies, ranges from the mid Atlantic westward to
the Davis Strait and west coast of Greenland in the north and southward
along the eastern coasts of Canada and USA (COSEWIC, 2012; Lesage et
al., 2017). In the NEA, blue whale sightings occur from Svalbard, Norway
(Storrie et al. 2018) in the north to the Azores in the south, with rare
sightings off Mauritania (Pike et al. 2019). Vocalization records
indicate the presence of blue whales near the Mid-Atlantic Ridge in
winter (Nieukirket al., 2004), but it is not known whether these animals
are from the NEA or NWA. The small number of NA blue whales that have
been followed using satellite tracking show no evidence of east-west
movements across the North Atlantic (Lesage et al., 2017; Silva et al.,
2013). Comparison of blue whale photo-identifications taken near Iceland
and the Azores (NEA) to NWA blue whales also suggests two distinct
populations in the Northwest and Northeast (Lesage et al., 2017; Ramp &
Sears, 2013). However, blue whale songs recorded from the NEA and NWA
are similar to each other and distinct from blue whales in other oceans,
suggesting that the NA may represent a single population (McDonald et
al., 2006).
Blue whale bones exposed to the elements have been used to extract
mitochondrial DNA (Tebbutt et al., 2000) and the potential for
historical blue whale bone samples t can help decipher population
structure (Rosenbaum et al., 1997), as well as to study changes in the
genome, from changes in levels of heterozygosity to interspecific
hybridization among other things. Purported blue whale/fin whale hybrids
were reported by early whalers from the coast of Norway, Gulf of Alaska,
Icelandic waters and the coast of Spain (Pampoulie et al., 2020). In the
last few decades, the identification of hybrids has been conclusively
demonstrated using molecular evidence (Pampoulie et al., 2020). But it
is not clear if this hybridization has led to significant gene flow
between the two species (Westbury et al., 2019). Significant levels of
gene flow from fin whales (population size >80,000,
Pampoulie et al., 2020) to blue whales could represent a threat to the
maintenance of a genetically distinct NA population(s) of blue whales.
In the NA, blue whales are classified as being Endangered in Europe
(IUCN Red List, Pampoulie et al., 2020) and in North America they are
listed under the Canadian Species at Risk Act and the US Endangered
Species Act (Lesage et al., 2017). Blue whales are threatened by ship
strikes, fishing gear entanglement, marine pollutants and the impacts of
climate change (COSEWIC, 2012). Knowledge of the genetic structure and
distribution of blue whales in the NA is essential for the protection of
this vulnerable species. Challenges to the study of movement of large
marine mammals includes attaching instruments to these fast swimming
animals and retaining the tracking devices on the animals long enough to
document seasonal patterns (Lesage et al., 2017). This has left a gap in
our understanding of NA blue whale population structuring. Therefore,
the principal goals of this study were to construct a highly accuratede novo assembly of a NWA blue whale genome and to use it to
study our unique collection of present-day and historical specimens to
gain insights into population structure, introgression, historic
population size and dynamics of the world’s largest animal.