The biological productivity in the Southern Ocean is mainly driven by the abundance of phytoplankton, which changes with seasons, fluctuations in sea ice and iron as well as light availability. The distribution of biological productivity is further modulated by ocean currents. Diatoms are a key element in the Southern Ocean's food web; thus, the effects of environmental changes on diatom population sizes have important implications for the overall ecosystem's productivity. In this study, we employed genomic data to assess the effects of glacial cycles on the population sizes and connectivity of the diatom Fragilariopsis kerguelensis in the Atlantic sector of the Southern Ocean. We detected three distinct variants among the 47 strains sampled along a latitudinal transect, all found in sympatry along the Polar Front. Demographic inferences identified major events during the last 100,000 years for two variants, characterized by a large decrease in effective population sizes followed by a rapid increase. These events overlapped with the change in environmental conditions during Pleistocene glacial cycles. Further research on mutation rates, generation time estimates and how changing environmental conditions influence these parameters in diatoms will improve the accuracy of the inferences drawn from these kinds of data. Although the use of genomic approaches in diatom species is in its infancy, this study highlights their potential to provide new insights into diatom past population sizes, responses and resilience to climate change and its effects on other trophic levels in the Southern Ocean.

Fin whales (Balaenoptera physalus), humpback whales (Megaptera novaeangliae) and minke whales (Balaenoptera acutorostrata) seasonally coexist in sympatry in the Gulf of St. Lawrence (Canada) where they feed to replenish their energy reserves. Over the past decades, these three species have experienced significant shifts in resource availability as the St. Lawrence ecosystem encountered major trophodynamic changes due to climatic and anthropogenic perturbations. This study aimed to understand how the realized trophic niche of these rorqual species has changed over time. To achieve this objective, stable nitrogen and carbon isotope ratios from 1110 whale skin biopsies sampled between 1992 and 2019 were used to define the isotopic niche of each species, quantify their diet using Bayesian isotopic mixing models, and assess the degree of individual diet specialization. Resource partitioning among these three sympatric species increased during the 2011–2019 period, as highlighted by the limited overlap observed among their isotopic niches. A recent dietary shift toward an increased reliance on pelagic fish (capelin, herring and/or mackerel) in fin whale and minke whale and a reduced contribution of krill suggests a possible reduction in krill abundance in the Gulf of St. Lawrence in recent years. These findings provide a unique insight into the ability of three generalist species to coexist through partitioning food resources, and adapt to ecosystem changes. Given the climatic context, knowledge of preferred prey is crucial for the conservation of these species.

Evaluating the health of baleen whale populations is crucial for understanding how environmental changes impact these top predators. Methodological advances, particularly in endocrine profiling, have enabled us to measure reproductive rates of populations as a proxy for population health. The Gulf of St. Lawrence (GSL), Canada, is an important summer feeding ground for various North Atlantic baleen whale species and has undergone major ecosystem changes in recent decades. To explore the potential impacts on population health of minke whales Balaenoptera acutorostrata, we combined genetic analyses, endocrine profiling, and environmental data on prey availability to investigate population demographics and possible drivers of pregnancy rates between 2007 and 2015. Biopsy samples collected between May and October were sexed (n = 187) using PCR, revealing a strong female bias (88.2%). Pregnancy status was determined through blubber progesterone quantification, with progesterone concentrations of 0.061-8.04 ng g-1 for non-pregnant individuals and 10.02-359.73 ng g-1 for pregnant individuals. High annual pregnancy rates were observed, ranging from 60 to 89% (mean: 74 +/- 10%), with no consistent trend detected over the study period. Generalised linear model results suggested species-specific prey availability in the year prior to pregnancy did not explain annual variation in pregnancy rates. We posit that this is due to the generalist feeding behaviour of minke whales. The results presented here indicate minke whales in the GSL exhibit sex-specific and reproductive spatial segregation. These pregnant females are likely using the area as a feeding ground prior to giving birth, with sufficient behavioural plasticity to withstand fluctuating food availability.

The authors declare no conflicts of interest. Data sharing is not applicable to this article as no new data were created or analyzed in this study.

Genetic diversity is declining globally, a trend that may particularly affect exploited populations that must adapt to rapid environmental change and other threats. Estimated genomic changes in effective population size mirrored known whaling history and shifts in technology. In the Southern Ocean, a comparison of genomes from historical and contemporary populations indicated that the contemporary genomes have less diversity and an elevated realized mutation load for moderately deleterious mutations, likely due to the effects of whaling. Our results demonstrate that the relatively recent, brief, and marked depletion of humpback whale populations by whaling likely had subtle but discernible, negative, and lasting effects on the whales' genomes. Thus, even as some humpback whale populations are now recovering to pre-exploitation numbers, they likely do so with a diminished adaptive capacity in the face of future conditions and threats.

The narwhal (Monodon monoceros) is an Arctic endemic odontocete that is particularly sensitive to climate change. Narwhals are also a key species in subsistence hunts in both Canada and Greenland. Understanding the genetic population structure is crucial to help management authorities set sustainable harvest quotas to avoid overexploitation of vulnerable narwhal groups. Additionally, estimates of population divergence times and their correlation with potential environmental drivers may be informative regarding the effects of environmental change. Herein, 2236 genome-wide single-nucleotide polymorphisms from 40 narwhals were used to infer population structure and divergence times. Samples were collected in six localities, one in East Greenland, four in West Greenland and one in the Eastern Canadian Arctic. The highest degree of genetic differentiation was observed between narwhals from Kangertittivaq (East Greenland) and Tasiujaq (Eastern Canadian Arctic), with a θ of 0.021 (95

Hundreds of large whales have been tracked using consolidated (Type‐C) satellite tags, yet there have been few studies on their impacts on whale health. In 2011, we initiated the first study designed to evaluate the effects of these tags on a baleen whale. Between 2011 and 2018, we tagged 79 North Atlantic humpback whales (Megaptera novaeangliae) in the Gulf of Maine. We initially deployed commonly‐used tags with an articulation between the anchor and transmitter (n = 35, 2011–12), before evidence of breakage prompted the development and use of more robust, integrated tags (n = 45). Tagged individuals were photographed immediately before, during and up to 11 years after tagging. They were re‐encountered on an average of 41.3 days (SD = 44.3), yielding 2,971 photographed sightings through 2022. An objective scoring system was developed to characterise tag‐site tissue responses based on photographs and to identify risk factors for prolonged healing. The initial tissue response to tagging was minimal, followed by skin loss around the tag, sometimes a degree of subcutaneous swelling, occasional extrusion of blubber, changes in skin colour, local depression formation around the implant site, tag loss and skin healing over the tag site, sometimes with a depression remaining. At last sighting, most non‐integrated and integrated tag sites exhibited small, shallow skin depressions (58.8% and 66.7%, respectively). Some exhibited deeper depressions with differing adjacent skin coloration (26.5% and 15.6%, respectively) or barely detectable marks (11.8% and 15.6%, respectively). Mild subcutaneous swellings occasionally persisted at the tag site, but this was uncommon for both tag designs (2.9% and 2.2%, respectively). More severe tissue responses were associated with non‐integrated tags and placements lower on the body. This study highlights the importance of using robust tag designs to minimise negative effects from Type‐C tags. Furthermore, because tag placement was shown to affect outcome, precision equipment, experienced taggers and vessel operators are critical for optimal deployment.

Abstract Background The life cycle of most baleen whales involves annual migrations from low-latitude breeding grounds to high latitude feeding grounds. In most species, these migrations are traditionally considered to be carried out according to information acquired through vertical social learning during the first months of life and made individually. However, some recent studies have suggested a more complex scenario, particularly for the species of the Balaenoptera genus. Methods Here, we studied the variation of δ15N and δ13C values along the growth axis of the baleen plate from 24 fin whales feeding off western Iceland to delve into their pattern of movements and to identify potential associations between individuals. The segment of baleen plate analyzed informed about at least two complete migratory cycles. We performed cluster analyses through two different methodologies and, whenever possible, we genotyped 20 microsatellite loci to determine potential existence of kinship. Results Results of the of δ15N and δ13C values agree with a dispersion strategy in the winter breeding grounds. However, and despite the overall large variability, several pairs or groups of individuals with no kinship showed highly similar isotopic patterns for two consecutive years for both δ15N and δ13C values. Conclusions Our results suggest that, notably, some whales without kinship share the same migratory regime and destinations. We hypothesize that this could reflect either: (i) the sharing of particularly beneficial migratory regimes, and/or (ii) long-term association between individuals.

Whales are long-lived, slow-reproducing species that were decimated by commercial whaling. Although some populations seem close to recovery, others are challenging to assess. We studied humpback whales ( Megaptera novaeangliae ) in the Gulf of Maine, an area of the North Atlantic (NA) with well-documented threats. Long-term studies and mark-recapture data were used to estimate humpback whale apparent survival, abundance and population growth from 2000 through 2019. Estimates were derived from a hierarchical, Bayesian state-space model with sex, age, and random time effects on survival while accounting for individual capture probability. Abundance increased from 744 (95% CI: 726-762) in 2000 to 1,706 (95% CI: 1,639-1,771) in 2019, with 4.6% mean annual growth. However, adult males exhibited higher survival and outnumbered adult females by the end of the study. Over time, fewer calves were observed, calf survival varied and the juvenile class declined. These are rare insights into the dynamics underlying whale abundance trends and they revealed similarities to an endangered species that is declining due to environmental and human impacts. The results inform a listing change under the U.S. Endangered Species Act, a mortality event of unprecedented magnitude off the U.S and humpback whale recovery from historical whaling in the NA.### Competing Interest StatementThe authors have declared no competing interest.

Phylogenomics has the power to uncover complex phylogenetic scenarios across the genome. In most cases, no single topology is reflected across the entire genome as the phylogenetic signal differs among genomic regions due to processes, such as introgression and incomplete lineage sorting. Baleen whales are among the largest vertebrates on Earth with a high dispersal potential in a relatively unrestricted habitat, the oceans. The fin whale (Balaenoptera physalus) is one of the most enigmatic baleen whale species, currently divided into four subspecies. It has been a matter of debate whether phylogeographic patterns explain taxonomic variation in fin whales. Here we present a chromosome-level whole genome analysis of the phylogenetic relationships among fin whales from multiple ocean basins. First, we estimated concatenated and consensus phylogenies for both the mitochondrial and nuclear genomes. The consensus phylogenies based upon the autosomal genome uncovered monophyletic clades associated with each ocean basin, aligning with the current understanding of subspecies division. Nevertheless, discordances were detected in the phylogenies based on the Y chromosome, mitochondrial genome, autosomal genome and X chromosome. Furthermore, we detected signs of introgression and pervasive phylogenetic discordance across the autosomal genome. This complex phylogenetic scenario could be explained by a puzzle of introgressive events, not yet documented in fin whales. Similarly, incomplete lineage sorting and low phylogenetic signal could lead to such phylogenetic discordances. Our study reinforces the pitfalls of relying on concatenated or single locus phylogenies to determine taxonomic relationships below the species level by illustrating the underlying nuances that some phylogenetic approaches may fail to capture. We emphasize the significance of accurate taxonomic delineation in fin whales by exploring crucial information revealed through genome-wide assessments.

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of genetic markers in genetic studies in ecology, behavior and conservation. Here we characterize a new, universal set of ten STR loci in seven species of baleen whales, optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides a convenient starting point for new genetic studies in baleen whales aimed at identifying individuals and populations. Data from the new STR loci were combined with genotypes from previously published STR loci to assess the power to assign parentage using paternity exclusion in four species: fin whale (Balaenoptera physalus), humpback whale (Megaptera novaeangliae), blue whale (B. musculus) and bowhead whale (Balaena mysticetus). Our results suggest that parentage studies should always be accompanied by a power analysis in order to ascertain that each individual specific study is based upon data with sufficient power to assign parentage with statistical rigor.

Phylogeny-based estimates suggesting a low germline mutation rate (μ) in baleen whales have influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. We estimated μ directly from pedigrees in four baleen whale species for both the mitochondrial control region and nuclear genome. The results suggest values higher than those obtained through phylogeny-based estimates and similar to pedigree-based values for primates and toothed whales. Applying our estimate of μ reduces previous genetic-based estimates of preexploitation whale abundance by 86% and suggests that μ cannot explain low cancer rates in gigantic mammals. Our study shows that it is feasible to estimate μ directly from pedigrees in natural populations, with wide-ranging implications for ecological and evolutionary research.

Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Here, we present PHFinder, a Python-based, open-source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. The program was tested with Sanger sequencing data from 100 humpback whales (Megaptera novaeangliae) tissue samples with known heteroplasmies. PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. PHFinder is flexible and enables explicit specification of key parameters to infer double peaks (i.e., heteroplasmies).

Thirteen sperm whales were sampled, using sloughed skin, in the Mediterranean Sea during six distinct encounters. Individuals were discriminated using the results of molecular sexing, mitochondrial control region sequencing and microsatellite genotyping (3 loci). Samples from 57 specimens were available from sperm whale strandings on northern European coasts. The first ~ 200bp of the mitochondrial DNA (mtDNA) control region of each sample were sequenced and three different haplotypes were identified. The frequency of each haplotype was significantly different between the Mediterranean Sea and the eastern North Atlantic, suggesting that sperm whales in the two areas comprise different maternal entities.

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) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

Based on 25 microsatellites, first order relatedness was established for three dyads of individuals contained in the Norwegian minke whale DNA-register. One large female minke whale was a member of all three dyads. Two competing genealogies were considered and under both of these the quartet contained siblings that with high probability must be half-siblings, as opposed to being full siblings.

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of markers for genetic analyses in ecology, behavior and conservation. We characterize a new universal set of ten STR loci (from 28 potential candidate loci) in seven baleen whale species, which are optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides an ideal starting point for new studies in baleen whales aimed at individual-based and population genetic studies, and facilitates data sharing among research groups. Data from the new STR loci were combined with genotypes from other published STR loci to assess the power to assign parentage (paternity) using exclusion in four species: fin whales, humpback whales, blue whales and bowhead whales. We argue that parentage studies should present a power analysis to demonstrate that the specific data are sufficiently informative to assign parentage with statistical rigor.

Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.

Current low germline mutation rate ( μ ) estimates in baleen whales have greatly influenced research ranging from assessments of whaling impacts to evolutionary cancer biology. However, the reported rates were subject to methodological errors and uncertainty. We estimated μ directly from pedigrees in natural populations of four baleen whale species and the results were similar to primates. The implications of revised μ values include pre-exploitation population sizes at 14% of previous genetic diversity-based estimates and the conclusion that μ in itself is insufficient to explain low cancer rates in gigantic mammals (i.e., Peto’s Paradox). We demonstrate the feasibility of estimating μ from whole genome pedigree data in natural populations, which has wide-ranging implications for the many ecological and evolutionary inferences that rely on μ.

Historical abundance estimates are important for establishing baselines from which trends can be determined using more recent data. Long-term studies based on photo-identification were merged and used to estimate population size, survival rate and sex ratio (biopsy sampling) of fin whales in the North-western Mediterranean. Merging four existing photo-id catalogues yielded a Mediterranean catalogue with 507 individually identified fin whales. Ninety-five (18.7%) individuals were resighted at least once during the study period (1990-2007): 71 whales were resighted in different years, 24 within the same season and 13 both in the same season and in different years. The number of resightings within-season ranged from one to four, over periods from 1 to 90 days. Capture histories from these individuals were used in the capture-recapture analyses. Estimates of the animals present in the area each year between 1991 and 1995 through different modelling approaches were consistent: 900-1,000 from a POPAN open population model; 1,200 from a multi-sample closed population model; and 900-1,100 from simple two-sample closed population models for pairs of consecutive years, all with heavily overlapping 95% confidence intervals. The estimated apparent survival rate of 0.916 (95% CI = 0.773-0.972) was lower than expected, which may be linked to temporary or permanent emigration, or mortality possibly owing to ship strikes. Conservation and mitigation measures such as Important Marine Mammal Areas and Particularly Sensitive Sea Areas are presented and discussed.