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The sub-Antarctic waters of South Georgia Island (Islas Georgias del Sur, SG/IG) are a regularly visited feeding ground for southern right whales (Eubalaena australis, SRW) in the southwest Atlantic. Satellite telemetry and photo-identification records were compared to better understand the role of SG/IG in the SRW migratory network. We present the first insights from SRW satellite-tracked from the SG/IG feeding ground, habitat use patterns in the Scotia Arc, and movements to Antarctic habitats. Photo-identification comparisons to calving and feeding areas across the South Atlantic and a review of sightings of cetaceans reported from Bird Island (west of SG/IG) since 1979 illuminate long-term habitat use patterns in SG/IG. We present the first recorded migratory movement between SG/IG and multiple countries: Argentina, Uruguay, and Brazil. Photo-identification (1) linked SG/IG to a female SRW with a long-term sighting history in Brazil, and (2) provided the first match between SG/IG and the western Antarctic Peninsula, suggesting the latter could extend the feeding area for southwest Atlantic SRW. Satellite tracking and opportunistic sightings suggest that shelf and coastal waters west of SG/IG represent an important multi-season SRW feeding habitat and add to our overall understanding of habitats and ranges occupied by recovering southwest Atlantic SRW.

South Georgia island in the sub-Antarctic waters of the South Atlantic is where modern whaling began in Southern Ocean waters in the early twentieth century (Tønnessen & Johnsen, 1982). By 1900, historical and modern whaling had drastically reduced or effectively wiped out some populations of baleen whales across much of the North Atlantic and North Pacific (Clapham & Baker, 2002) and whalers were keen to exploit new seas. Norwegian whaler Captain C. A. Larsen first visited South Georgia island in 1892 while prospecting for new whaling sites. Larsen identified that the abundance of whales made South Georgia a promising site, particularly for whaling of blue (Balaenoptera musculus) and fin (B. physalus) whales (Hart, 2021), and identified the more protected north side of the island, and in particular the wide natural harbor of Cumberland Bay, as the best site for operations (Figure 1). After securing expedition funding, including one whale catcher vessel (the 33.5 m Fortuna), Larsen and his team arrived in South Georgia on November 16, 1904, to set up the Grytviken whaling station in Cumberland Bay.

The major histocompatibility complex (MHC) is a highly polymorphic gene family that is crucial in immunity, and its diversity can be effectively used as a fitness marker for populations. Despite this, MHC remains poorly characterised in non‐model species (e.g., cetaceans: whales, dolphins and porpoises) as high gene copy number variation, especially in the fast‐evolving class I region, makes analyses of genomic sequences difficult. To date, only small sections of class I and IIa genes have been used to assess functional diversity in cetacean populations. Here, we undertook a systematic characterisation of the MHC class I and IIa regions in available cetacean genomes. We extracted full‐length gene sequences to design pan‐cetacean primers that amplified the complete exon 2 from MHC class I and IIa genes in one combined sequencing panel. We validated this panel in 19 cetacean species and described 354 alleles for both classes. Furthermore, we identified likely assembly artefacts for many MHC class I assemblies based on the presence of class I genes in the amplicon data compared to missing genes from genomes. Finally, we investigated MHC diversity using the panel in 25 humpback and 30 southern right whales, including four paternity trios for humpback whales. This revealed copy‐number variable class I haplotypes in humpback whales, which is likely a common phenomenon across cetaceans. These MHC alleles will form the basis for a cetacean branch of the Immuno‐Polymorphism Database (IPD‐MHC), a curated resource intended to aid in the systematic compilation of MHC alleles across several species, to support conservation initiatives.

Significance Assessing change in Southern Ocean ecosystems is challenging due to its remoteness. Large-scale datasets that allow comparison between present-day conditions and those prior to large-scale ecosystem disturbances caused by humans (e.g., fishing/whaling) are rare. We infer the contemporary offshore foraging distribution of a marine predator, southern right whales (n = 1,002), using a customized stable isotope-based assignment approach based on biogeochemical models of the Southern Ocean. We then compare the contemporary distributions during the late austral summer and autumn to whaling catch data representing historical distributions during the same seasons. We show remarkable consistency of mid-latitude distribution across four centuries but shifts in foraging grounds in the past 30 y, particularly in the high latitudes that are likely driven by climate-associated alterations in prey availability. Abstract Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW

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 harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species’ range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal’s remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.

The deep sea is the largest ecosystem on Earth, yet little is known about the processes driving patterns of genetic diversity in its inhabitants. Here, we investigated the macro- and microevolutionary processes shaping genomic population structure and diversity in two poorly understood, globally distributed, deep-sea predators: Cuvier's beaked whale (Ziphius cavirostris) and Blainville's beaked whale (Mesoplodon densirostris). We used double-digest restriction associated DNA (ddRAD) and whole mitochondrial genome (mitogenome) sequencing to characterise genetic patterns using phylogenetic trees, cluster analysis, isolation-by-distance, genetic diversity and differentiation statistics. Single nucleotide polymorphisms (SNPs; Blainville's n = 43 samples, SNPs=13988; Cuvier's n = 123, SNPs= 30479) and mitogenomes (Blainville's n = 27; Cuvier's n = 35) revealed substantial hierarchical structure at a global scale. Both species display significant genetic structure between the Atlantic, Indo-Pacific and in Cuvier's, the Mediterranean Sea. Within major ocean basins, clear differentiation is found between genetic clusters on the east and west sides of the North Atlantic, and some distinct patterns of structure in the Indo-Pacific and Southern Hemisphere. We infer that macroevolutionary processes shaping patterns of genetic diversity include biogeographical barriers, highlighting the importance of such barriers even to highly mobile, deep-diving taxa. The barriers likely differ between the species due to their thermal tolerances and evolutionary histories. On a microevolutionary scale, it seems likely that the balance between resident populations displaying site fidelity, and transient individuals facilitating gene flow, shapes patterns of connectivity and genetic drift in beaked whales. Based on these results, we propose management units to facilitate improved conservation measures for these elusive species.

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonized its current range. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic single nucleotide polymorphisms from 286 individuals sampled from 22 localities across the species’ range. Our results point to a Northeast Pacific origin of the harbour seal, colonization of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonize and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.

Following their near extirpation by industrial whaling of the 20th century, the population status of Southern Hemisphere fin whales (SHFW) remains unknown. Systematic surveys estimating fin whale abundance in the Southern Ocean are not yet available. Records of fin whale sightings have been collected by a variety of organisations over the past few decades, incorporating both opportunistic data and dedicated survey data. Together, these isolated data sets represent a potentially valuable source of information on the seasonality, distribution and abundance of SHFW. We compiled records across 40 years from the Antarctic Peninsula and Scotia Sea from multiple sources and used a novel approach combining ensemble learning and a maximum entropy model to estimate abundance and distribution of SHFW in this region. Our results show a seasonal distribution pattern with pronounced centres of distribution from January - March along the West Antarctic Peninsula. Our new approach allowed us to estimate abundance of SHFW for discrete areas from a mixed data set of mainly opportunistic presence only data.

Southern right whale vocalizations were recorded concurrently with visual observations off the sub-Antarctic Island of South Georgia, and the characteristics of these calls were described. Calls were also compared to those of humpback whales at South Georgia, to determine how the two species might reliably be distinguished acoustically. The southern right whale calls measured (which were all upcalls) had lower frequency with peak energy and were mostly shorter in duration than the calls measured from humpback whales. The frequency upsweep and the lack of harmonics of southern right whale calls were also diagnostic characteristics.

The massive impact that open-boat historical whaling (18th to 20th centuries) had on whale populations has been traditionally estimated from records of oil and baleen plate production. However, an unknown proportion of hunted whales were struck, wounded, eventually killed, but lost, and not included in these records, suggesting that whaling impact may be critically underestimated. Whaling logbooks provide a key source for assessing past catches and losses. Here, we extract detailed records of 19875 days of activity in the southwestern Atlantic Ocean from 255 logbooks of offshore whaling voyages. During the period considered (1776–1923), whalers first targeted southern right whales (Eubalaena australis, 2497 sightings and 658 catches), gradually substituted by sperm whales (Physeter macrocephalus, 1157 sightings and 843 catches) after 1840. Loss rate factors, calculated to account for the number of “struck and lost” whales, decreased across time for both species, and were particularly high (ranging 1.09–1.6) for the southern right whale, whose population was drastically reduced by whaling, as compared to previous estimates based on rough catch records. Accurate accounting for these “lost” individuals is essential for reconstructing the impact of whaling on cetacean populations and for a proper assessment of their initial population size and demographic trends.

The dramatic increase in the application of genomic techniques to non-model organisms (NMOs) over the past decade has yielded numerous valuable contributions to evolutionary biology and ecology, many of which would not have been possible with traditional genetic markers. We review this recent progression with a particular focus on genomic studies of marine mammals, a group of taxa that represent key macroevolutionary transitions from terrestrial to marine environments and for which available genomic resources have recently undergone notable rapid growth. Genomic studies of NMOs utilize an expanding range of approaches, including whole genome sequencing, restriction site-associated DNA sequencing, array-based sequencing of single nucleotide polymorphisms and target sequence probes (e.g., exomes), and transcriptome sequencing. These approaches generate different types and quantities of data, and many can be applied with limited or no prior genomic resources, thus overcoming one traditional limitation of research on NMOs. Within marine mammals, such studies have thus far yielded significant contributions to the fields of phylogenomics and comparative genomics, as well as enabled investigations of fitness, demography, and population structure. Here we review the primary options for generating genomic data, introduce several emerging techniques, and discuss the suitability of each approach for different applications in the study of NMOs.