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.