Historical Mitogenomic Diversity and Population Structuring of Southern Hemisphere Fin Whales

Abstract

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.

The Evolutionary History of Baleen Whales in The Genome Era

“…The topology of the phylogeny inferred from the mitochondrial genome sequences in this study largely agrees with earlier studies based on mitochondrial genome sequences, some of which were complemented with a few nuclear loci (Archer et al, 2013;Bérubé et al, , 2002Buss et al, 2023;Cabrera et al, 2019;Pérez-Alvarez et al, 2021). In agreement with the work by Cabrera and co-workers (2019), the new mitochondrial genome haplotypes detected in this study revealed all ocean basins to be polyphyletic or paraphyletic, likely a result of the increased sample sizes.…”

“…We were unable to detect any well-supported subclades among samples from the Southern Ocean in the phylogeny estimated from the whole autosomal genomes in agreement with (Buss et al, 2023;Pérez-Alvarez et al, 2021). However, the samples from the Southern Ocean in our study were restricted to the western Antarctic Peninsula and may not adequately capture the overall intra-oceanic genetic variance.…”

“…We detected 23 novel haplotypes among the 200 mitochondrial genomes. The most likely phylogeny inferred from the mitochondrial genomes did not align fully with ocean basins, as shown earlier (Archer et al, 2013;Buss et al, 2023;Cabrera et al, 2019).…”

“…Among baleen whales, ancient genomics is still a growing field. Most aDNA investigations have focused on species identifications of osseous remains from a few or a single, loci, providing insights into past distributions of different baleen whale species (Biard et al, 2017;Rodrigues et al, 2018;Speller et al, 2016) or temporal diversity loss of the mitochondrial lineages (Buss et al, 2023;Lindqvist et al, 2009;Sremba et al, 2023). Most effort has been directed towards the bowhead and grey whales (e.g., Foote et al, 2013;Grond et al, 2019;McLeod et al, 2010McLeod et al, , 2012Rastogi et al, 2004).…”

“…The fin whale (Balaenoptera physalus) is the second largest mysticete and was subjected to intense whaling during the 20th Century in all ocean basins (Rocha, Jr. et al, 2015). Based on morphological differences, Lönnberg (1906) proposed that fin whales in the Southern Hemisphere be assigned to their own subspecies, Globally distributed and potentially highly migratory, these intraspecific taxonomic divisions have been a subject of debate, centring on whether subspecies should be recognized based on their phylogeographical pattern (Archer et al, 2019;Buss et al, 2023;Cabrera et al, 2019;Pérez-Alvarez et al, 2021). Cabrera and colleagues (2019) pointed to the well-known issues in defining subspecies based solely on the phylogeographic pattern in the uni-parentally inherited mitochondrial genome in fin whales and demonstrated how uneven sampling efforts resulted in different mitochondrial phylogenies.…”