Monopisthocotylan parasites have been proposed as tags for studying host population structure due to their direct life cycles and short generation times. However, their effectiveness in reflecting host population connectivity remains under scrutiny. The poorly-understood connectivity of fisheries stocks in Lake Tanganyika, the second deepest lake in the world with a permanently stratified, relatively species-poor and well-delimited pelagic zone, serves as a case-study to test utility of parasites for fish stock identification. This study investigates the population structure of two Kapentagyrus species parasitizing dorosomatid fish in Lake Tanganyika, by analyzing variation in mitochondrial protein-coding genes across a geographic gradient. The study comprised 12 population genomic datasets from the central and southern subbasins of the lake sampled within the same week to account for host migration. We observed differences in geographic population structure of the two parasite species, with restricted gene flow in Kapentagyrus limnotrissae infecting a single dorosomatid species and smaller hosts preferring the littoral zone. Conversely, K. tanganicanus exhibited no geographical structure, reflecting its broader host range and preference for larger hosts preferring the pelagic zone. The results also highlight that other mitochondrial genes such as those from the dehydrogenase family or atp6 provide higher resolution for population genetic studies in these parasites than the frequently used cox1. The study also compared two sequencing strategies—individual versus pooled sequencing (PoolSeq)—for assessing population structure of monopisthocotylan parasites, and found that PoolSeq yielded similar results with lower demands on individual DNA quantity and sequencing costs. This work supports the use of host-specific, directly transmitted parasites as ecosystem tags and provides valuable insights into the role of host ecology and parasite life-history traits in shaping population dynamics.

This study investigated the variability within populations of the copepod Eurytemora velox. Integrative taxonomy confirmed significant genetic heterogeneity among the studied populations supported the hypothesis of E. velox being a species complex. To assess morphological variability, morphometric traits and ordination analyses were utilized. For molecular assessment, the mitochondrial cytochrome c oxidase subunit 1 (COI) and cytochrome b (cyt b) and the nuclear 18S ribosomal DNA (18S) and the internal transcribed spacer 2 (ITS2) were employed. Both morphological and molecular data facilitated the identification of at least two species: E. velox s. str. and a new cryptic species, E. nilsseni sp. nov. The former one, E. velox s. str. is an expansive, widely distributed species that inhabits diverse water bodies, including transformed river systems, particularly those with altered water parameters such as high salinity. Within this species, no population-specific morphological differences were observed; however, COI data revealed clear genetic structuring in E. velox s. str., with distinct mitochondrial haplotype clades associated with different drainage basins, whereas nuclear markers showed only limited differentiation among populations. In contrast, E. nilsseni sp. nov. is an endemic and likely relict species recorded exclusively in ponds on the Skagerrak coast islands.

Bowhead whales were heavily exploited during commercial whaling between the 16th and 20th centuries. Current and near-future climate warming poses a new threat. Assessing bowhead vulnerability to climatic change remains challenging due to insufficient knowledge regarding responses to past climates and pre-whaling population dynamics. We integrate paleogenomics and stable isotopes (δ13C and δ15N) from 206 bowhead fossils from the Atlantic Arctic with paleoclimate and ecological modeling based on 823 radiocarbon-dated fossils, including 140 from this study. We find long-term resilience of bowheads to Holocene environmental perturbations, with no detectable changes in genetic diversity or population structure. Simulated commercial-whaling-driven genetic and fitness changes indicate that population subdivision and loss of genetic diversity are unlikely to be fully realized, despite nearly a century since whaling ceased. Furthermore, even in simulated complete population recovery scenarios, overall fitness did not return to pre-whaling levels, potentially compromising the future resilience of bowhead whales.

In a rapidly warming Arctic, genetic variation might serve to buffer organisms against the effects of environmental change, such as sea ice loss and ocean warming. Yet, this concept remains largely unexplored because comprehensive genome-wide studies across the full ranges of Arctic marine taxa are rare. Bowhead whales (Balaena mysticetus) have a strong association with sea ice and polar water masses, a long history of human exploitation, and a circumpolar distribution, making them a valuable model for evaluating how past environmental and anthropogenic factors have shaped contemporary population variation. We analysed both nuclear and mitochondrial genomes from bowhead whales sampled across the species' range, encompassing all four recognised stocks. Firstly, our results indicate the existence of three genetic groupings instead of four: (1) Okhotsk Sea; (2) East Greenland-Svalbard-Barents Sea; and (3) a population containing two recognised stocks-the Bering-Chukchi-Beaufort and East Canada-West Greenland. We utilised high-resolution ecological niche modelling and bowhead whale movement data to reconstruct inter-stock habitat connectivity over the last 11,700 years, finding that this explains our identified genetic groupings. Bowhead whale populations exhibit little-to-no evidence of recent inbreeding and retain high genetic diversity relative to other mammalian species despite centuries of intensive commercial whaling. The most vulnerable population is that in the Okhotsk Sea, which has the lowest genetic diversity, most inbreeding, and the highest realised genetic load. Collectively, our findings elucidate the recent history and dynamics of bowhead whales, offering valuable baseline data and context on present-day genetic structure and diversity to support effective conservation and management strategies.

BackgroundStress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness. We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses.ResultsWe assembled the sequences of 48 stress-related genes and report the first foraging (For) gene orthologs in flatworms. We found duplications of heat shock (Hsp) and oxidative stress genes in Cichlidogyrus compared to Kapentagyrus. We also observed positive selection patterns in genes related to mitochondrial protein import (Hsp) and behaviour (For) in species of Cichlidogyrus infecting East African cichlids-a host lineage under adaptive radiation. These patterns are consistent with a potential adaptation linked to a co-radiation of these parasites and their hosts. Additionally, the absence of cytochrome P450 and kappa and sigma-class glutathione S-transferases in monogenean flatworms is reported, genes considered essential for metazoan life.ConclusionsThis study potentially identifies the first molecular function linked to a flatworm radiation. Furthermore, the observed gene duplications and positive selection indicate the potentially important role of stress responses for the ecological adaptation of parasite species.

Understanding how past environmental and anthropogenic factors shaped contemporary genetic patterns is essential for assessing the vulnerability of species in the face of ongoing climate change. The bowhead whale ( Balaena mysticetus ) – the only baleen whale found in the Arctic year-round – has a strong association with sea ice, long history of human exploitation, and a circumpolar distribution, making it a valuable model for investigating how these factors have shaped population structure in the marine Arctic. We analysed both nuclear and mitochondrial genomes from bowhead whale individuals sampled across the species’ circumpolar range, encompassing all four recognized management stocks. Our results reveal three not four genetically differentiated populations: the Sea of Okhotsk stock; the East Greenland-Svalbard-Barents Sea stock; and a combined population containing the Bering-Chukchi-Beaufort Seas and East Canada-West Greenland stocks. We utilised ecological niche modeling and bowhead whale telemetry data to model stock connectivity over the past 11,700 years, and identify past habitat connectivity as a key driver of current population structure. Despite centuries of intensive commercial whaling, the three bowhead whale populations exhibit little-to-no evidence of recent inbreeding and retain high genetic diversity relative to other mammalian species. The lowest genetic diversity, most inbreeding, and highest realised genetic load being in the Sea of Okhotsk population. Collectively, our findings shed light on the recent population history and dynamics of bowhead whales, and offer valuable baseline data on present-day genetic structure and diversity to support effective conservation and management strategies. ### Competing Interest Statement The authors have declared no competing interest. Villum Fonden, 37352 DFF, 9064-00025B

Within the last 800 million years, animals evolved a vast range of diversity of species exhibiting an enormous disparity of forms and lifestyles. The process involved an increase in complexity from life forms with few cell types to organisms with many hundreds of cell types. However, neither genome size nor number of protein-coding genes can explain these differences, and their biological basis remains elusive. Yet, recent studies suggest that the evolution of complexity is closely linked to the acquisition of a class of noncoding gene regulators called microRNAs. To test this hypothesis, we investigated the association between loss of organismal complexity and microRNAs in Syndermata, an invertebrate group including free-living wheel animals (Monogononta, Bdelloidea), epibiotic Seisonidea, and endoparasitic thorny-headed worms (Acanthocephala). Analyses of genomic, transcriptomic, and morphological data of altogether 25 syndermatan species revealed strong correlations of microRNA losses with reductions of protein-coding genes and morphological traits. The hierarchical pattern sums up to ∼85% loss of microRNAs and a ∼50% loss of conserved metazoan core genes (Benchmarking Universal Single-Copy Orthologs) on the lineage to thorny-headed worms. Extraordinarily reduced microRNA complements were confirmed by small RNA sequencing data. Endoparasitic Acanthocephala was additionally distinguished by the most morphological reductions of ancestral features, such as the digestive tract. Together, we observed that reductions of ∼400 protein-coding genes and 10 metazoan core genes tended to accompany the loss of single microRNA families. Furthermore, 4 microRNA families and 34 metazoan core genes appeared to be associated, on average, with the reduction of a single morphological trait.

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.

During the last 800 million years of evolution animals radiated into a vast range of diversity of species and disparity of forms and lifestyles. The process involved a near hierarchical increase in complexity from life forms with few cell types to organisms with many hundreds of cell-types. However, neither genome size nor number of protein-coding genes can explain these differences and their biological basis remains elusive. Yet, recent studies have suggested that the evolution of complexity is closely linked to the acquisition of a class of protein coding gene-regulators called microRNAs. In a regressive approach, to investigate the association between loss of organismal complexity and microRNAs, we here studied Syndermata, an invertebrate group including free-living rotifers (Monogononta, Bdelloidea), the epibiotic Seisonidea and the endoparasitic Acanthocephala. Genomic, transcriptomic and morphological characterization and comparisons across 25 syndermatan species revealed a strong correlation between loss of microRNAs, loss of protein-coding genes and decreasing morphological complexity. The near hierarchical loss extends to ~85% loss of microRNAs and a ~50% loss of BUSCO genes in the endoparasitic Acanthocephala, the most reduced group we studied. Together, the loss of ~400 protein-coding genes and ~10 metazoan core gene losses went along with one microRNA family loss. Furthermore, the loss of ~4 microRNA families or ~34 metazoan core genes associated with one lost morphological feature. These are the first quantitative insights into the regulatory impact of microRNAs on organismic complexity as a predictable consequence in regressive evolution of parasites. ### Competing Interest Statement The authors have declared no competing interest.

The endangered Galápagos sea lion ( Zalophus wollebaeki ) inhabits the Galápagos Islands off the coast of Ecuador. We present a complete mitochondrial genome (16 465 bp) of a female paratype from the collections of the Natural History Museum Oslo, Norway, assembled from next-generation sequencing reads. It contains all canonical protein-coding, rRNA, tRNA genes, and the D-loop region. Sequence similarity is 99.93% to a previously published conspecific mitogenome sequence and 99.37% to the mitogenome sequence of the sister species Z. californianus . Sequence similarity of the D-loop region of the Z. wollebaeki paratype mitogenome is >99%, while the sequence difference to the Z. californianus sequences exceeds 2.5%. The paratype mitogenome sequence supports the taxonomic status of Z. wollebaeki as a separate species.

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.

The East Greenland-Svalbard-Barents Sea (EGSB) bowhead whale stock (Balaena mysticetus) was hunted to near extinction and remains Endangered on the International Union of Conservation of Nature Red List. The intense, temporally extensive hunting pressure may have left the population vulnerable to other perturbations, such as environmental change. However, the lack of genomic baseline data renders it difficult to evaluate the impacts of various potential stressors on this stock. Twelve EGSB bowhead whales sampled in 2017/2018 were re-sequenced and mapped to a previously published draft genome. All individuals were unrelated and void of significant signs of inbreeding, with similar observed and expected homo- and heterozygosity levels. Despite the small population size, mean autosome-wide heterozygosity was 0.00102, which is higher than that of most mammals for which comparable estimates are calculated using the same parameters, and three times higher than a conspecific individual from the Eastern-Canada-West-Greenland bowhead whale stock. Demographic history analyses indicated a continual decrease of N-e from ca. 1.5 million to ca. 250,000 years ago, followed by a slight increase until ca. 100,000 years ago, followed by a rapid decrease in N-e between 50,000 and 10,000 years ago. These estimates are lower than previously suggested based on mitochondrial DNA, but suggested demographic patterns over time are similar.

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.

The polar bear (Ursus maritimus) has become a symbol of the threat to biodiversity from climate change. Understanding polar bear evolutionary history may provide insights into apex carnivore responses and prospects during periods of extreme environmental perturbations. In recent years, genomic studies have examined bear speciation and population history, including evidence for ancient admixture between polar bears and brown bears (Ursus arctos). Here, we extend our earlier studies of a 130,000- to 115,000-y-old polar bear from the Svalbard Archipelago using a 10× coverage genome sequence and 10 new genomes of polar and brown bears from contemporary zones of overlap in northern Alaska. We demonstrate a dramatic decline in effective population size for this ancient polar bear’s lineage, followed by a modest increase just before its demise. A slightly higher genetic diversity in the ancient polar bear suggests a severe genetic erosion over a prolonged bottleneck in modern polar bears. Statistical fitting of data to alternative admixture graph scenarios favors at least one ancient introgression event from brown bears into the ancestor of polar bears, possibly dating back over 150,000 y. Gene flow was likely bidirectional, but allelic transfer from brown into polar bear is the strongest detected signal, which contrasts with other published work. These findings may have implications for our understanding of climate change impacts: Polar bears, a specialist Arctic lineage, may not only have undergone severe genetic bottlenecks but also been the recipient of generalist, boreal genetic variants from brown bears during critical phases of Northern Hemisphere glacial oscillations.

Biologiske arter beskrives på bakgrunn av morfologiske, fysiologiske, utviklings-, atferds- og/eller genetiske trekk. Individer som tilhører samme art skal være «like», i den mening at vi kan identifisere dem som samme art, og individer som tilhører forskjellige arter bør være såpass ulike at de kan skilles fra hverandre. Helt siden Carl von Linné (1707–1778) utarbeidet den binomiale nomenklaturen, har artene fått navn som består av to ledd; hvorav det første leddet er navnet til slekten arten tilhører, og det andre er selve artsnavnet: For eksempel Cervus elaphus (hjort), en art med artsnavnet elaphus, som tilhører slekten Cervus (ekte hjorter)).

Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom-bust scenario, combining a slight Pleistocene population growth 25 000-35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 x 10(-8) substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353-83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy.

Loss of Arctic sea ice owing to climate change is predicted to reduce both genetic diversity and gene flow in ice-dependent species, with potentially negative consequences for their long-term viability. Here, we tested for the population-genetic impacts of reduced sea ice cover on the polar bear ( Ursus maritimus ) sampled across two decades (1995–2016) from the Svalbard Archipelago, Norway, an area that is affected by rapid sea ice loss in the Arctic Barents Sea. We analysed genetic variation at 22 microsatellite loci for 626 polar bears from four sampling areas within the archipelago. Our results revealed a 3–10% loss of genetic diversity across the study period, accompanied by a near 200% increase in genetic differentiation across regions. These effects may best be explained by a decrease in gene flow caused by habitat fragmentation owing to the loss of sea ice coverage, resulting in increased inbreeding of local polar bears within the focal sampling areas in the Svalbard Archipelago. This study illustrates the importance of genetic monitoring for developing adaptive management strategies for polar bears and other ice-dependent species.