Demographic histories and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history

Ancient DNA indicates a century of overhunting did not reduce genetic diversity in Pacific Walruses (Odobenus rosmarus divergens)

Pacific Walruses (Odobenus rosmarus divergens [Illiger 1815]) are gregarious marine mammals considered to be sentinels of the Arctic because of their dependence on sea ice for feeding, molting, and parturition. Like many other marine mammal species, their population sizes were decimated by historical overhunting in the nineteenth and twentieth centuries. Although they have since been protected from nearly all commercial hunting pressure, they now face rapidly accelerating habitat loss as global warming reduces the extent of summer sea ice in the Arctic. To investigate how genetic variation was impacted by overhunting, we obtained mitochondrial DNA sequences from historic Pacific Walrus samples in Alaska that predate the period of overhunting, as well as from extant populations. We found that genetic variation was unchanged over this period, suggesting Pacific Walruses are resilient to genetic attrition in response to reduced population size, and that this may be related to their high vagility and lack of population structure. Although Pacific Walruses will almost certainly continue to decline in number as the planet warms and summer sea ice is further reduced, they may be less susceptible to the ratcheting effects of inbreeding that typically accompany shrinking populations.

No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.

Dietary Shifts in the Adaptation to Changing Marine Resources: Insights from a Decadal Study on Greater Lizardfish (Saurida tumbil) in the Beibu Gulf, South China Sea

Understanding dietary behavior during the individual development of marine predators and its temporal variations elucidates how species adapt to changes in marine resources. This is crucial for predicting marine predators' habitat selection and the natural population's responses to environmental changes. The authors conducted a comparative analysis of dietary shift strategies and trophic level variations in Greater lizardfish (Saurida tumbil) in the Beibu Gulf during two distinct periods (2010 and 2020) using stomach content and stable isotope analysis methods. Possible driving factors for these changes were also explored. Changes in the fishery community structure and the decline in the abundance of primary prey resources have led the S. tumbil population to diversify their prey species, utilize alternative resources, and expand their foraging space. However, the species' foraging strategy, characterized by chasing and preying on schooling and pelagic prey, promoted stability in their feeding behavior across spatial and temporal scales. The main prey items remained demersal and pelagic fish species, followed by cephalopods and crustaceans. Similar to other generalist fish species, ontogenetic dietary shifts (ODSs) indicated a partial transition towards larger prey items. However, the timing and magnitude of the ODSs varied between the two periods, reflecting life-history variations and adaptive adjustments to environmental changes. In comparison to 2010, the population's mean body length (BL) increased in 2020, and the proportion of the population feeding on pelagic-neritic prey significantly increased. However, the δ15N values were lower, indicating that the shift in the ecological niche of preferred prey from demersal to pelagic-neritic was the primary cause of the decrease in trophic levels. In the future, we will conduct further quantitative research integrating the spatiotemporal data of both predators and prey to clarify the relationships between marine predators' feeding behavior, trophic levels, and changes in prey community structure.

Conservation macrogenetics: harnessing genetic data to meet conservation commitments

Genetic biodiversity is rapidly gaining attention in global conservation policy. However, for almost all species, conservation relevant, population-level genetic data are lacking, limiting the extent to which genetic diversity can be used for conservation policy and decision-making. Macrogenetics is an emerging discipline that explores the patterns and processes underlying population genetic composition at broad taxonomic and spatial scales by aggregating and reanalyzing thousands of published genetic datasets. Here we argue that focusing macrogenetic tools on conservation needs, or conservation macrogenetics, will enhance decision-making for conservation practice and fill key data gaps for global policy. Conservation macrogenetics provides an empirical basis for better understanding the complexity and resilience of biological systems and, thus, how anthropogenic drivers and policy decisions affect biodiversity.

Genetic diversity and demographic history of the leopard seal: A Southern Ocean top predator

Leopard seals (Hydrurga leptonyx) are top predators that can exert substantial top-down control of their Antarctic prey species. However, population trends and genetic diversity of leopard seals remain understudied, limiting our understanding of their ecological role. We investigated the genetic diversity, effective population size and demographic history of leopard seals to provide fundamental data that contextualizes their predatory influence on Antarctic ecosystems. Ninety leopard seals were sampled from the northern Antarctic Peninsula during the austral summers of 2008-2019 and a 405bp segment of the mitochondrial control region was sequenced for each individual. We uncovered moderate levels of nucleotide (π = 0.013) and haplotype (Hd = 0.96) diversity, and the effective population size was estimated at around 24,000 individuals (NE = 24,376; 95% CI: 16,876-33,126). Consistent with findings from other ice-breeding pinnipeds, Bayesian skyline analysis also revealed evidence for population expansion during the last glacial maximum, suggesting that historical population growth may have been boosted by an increase in the abundance of sea ice. Although leopard seals can be found in warmer, sub-Antarctic locations, the species' core habitat is centered on the Antarctic, making it inherently vulnerable to the loss of sea ice habitat due to climate change. Therefore, detailed assessments of past and present leopard seal population trends are needed to inform policies for Antarctic ecosystems.

Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

Genomic evidence uncovers inbreeding and supports translocations in rescuing the genetic diversity of a landlocked seal population

Fragmentation of isolated populations increases the risk of inbreeding and loss of genetic diversity. The endemic Saimaa ringed seal (Pusa hispida saimensis) is one of the most endangered pinnipeds in the world with a population of only ~ 400 individuals. The current genetic diversity of this subspecies, isolated in Lake Saimaa in Finland for ca. 1000 generations, is alarmingly low. We performed whole-genome sequencing on Saimaa ringed seals (N = 30) and analyzed the level of homozygosity and genetic composition across the individual genomes. Our results show that the Saimaa ringed seal population has a high number of runs of homozygosity (RoH) compared with the neighboring Baltic ringed seal (Pusa hispida botnica) reference population (p < 0.001). There is also a tendency for stillborn seal pups to have more pronounced RoH. Since the population is divided into semi-isolated subpopulations within the Lake Saimaa exposing the population to deleterious genomic effects, our results support augmented gene flow as a genetic conservation action. Based on our results suggesting inbreeding depression in the population, we recommend Pihlajavesi as a potential source and Southern Saimaa as a potential recipient subpopulation for translocating individuals. The Saimaa ringed seal is a recognized subspecies and therefore translocations should be considered only within the lake to avoid an unpredictable risk of disease, the introduction of deleterious alleles, and severe ecological issues for the population.

Demographic history and conservation genomics of caribou (Rangifer tarandus) in Québec

The loss of genetic diversity is a challenge many species are facing, with genomics being a potential tool to inform and prioritize decision-making. Most caribou (Rangifer tarandus) populations have experienced significant recent declines throughout Québec, Canada, and are considered of concern, threatened or endangered. Here, we calculated the ancestral and contemporary patterns of genomic diversity of five representative caribou populations and applied a comparative population genomics framework to assess the interplay between demographic events and genomic diversity. We first calculated a caribou specific mutation rate, μ, by extracting orthologous genes from related ungulates and estimating the rate of synonymous mutations. Whole genome re-sequencing was then completed on 67 caribou: from these data we calculated nucleotide diversity, θ π and estimated the coalescent or ancestral effective population size (N e), which ranged from 12,030 to 15,513. When compared to the census size, N C, the endangered Gaspésie Mountain caribou population had the highest ancestral N e:N C ratio which is consistent with recent work suggesting high ancestral N e:N C is of conservation concern. In contrast, values of contemporary N e, estimated from linkage-disequilibrium, ranged from 11 to 162, with Gaspésie having among the highest contemporary N e:N C ratio. Importantly, classic conservation genetics theory would predict this population to be of less concern based on this ratio. Interestingly, F varied only slightly between populations, and despite evidence of bottlenecks across the province, runs of homozygosity were not abundant in the genome. Tajima's D estimates mirrored the demographic models and current conservation status. Our study highlights how genomic patterns are nuanced and potentially misleading if viewed only through a contemporary lens; we argue a holistic conservation genomics view should integrate ancestral N e and Tajima's D into management decisions.

A novel SNP assay reveals increased genetic variability and abundance following translocations to a remnant Allegheny woodrat population

BACKGROUND

Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species' range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population.

RESULTS

We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population.

CONCLUSIONS

Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.

The antique genetic plight of the Mediterranean monk seal (Monachus monachus)

Disentangling the impact of Late Quaternary climate change from human activities can have crucial implications on the conservation of endangered species. We investigated the population genetics and demography of the Mediterranean monk seal (Monachus monachus), one of the world's most endangered marine mammals, through an unprecedented dataset encompassing historical (extinct) and extant populations from the eastern North Atlantic to the entire Mediterranean Basin. We show that Cabo Blanco (Western Sahara/Mauritania), Madeira, Western Mediterranean (historical range) and Eastern Mediterranean regions segregate into four populations. This structure is probably the consequence of recent drift, combined with long-term isolation by distance (R2 = 0.7), resulting from prevailing short-distance (less than 500 km) and infrequent long-distance dispersal (less than 1500 km). All populations (Madeira especially), show high levels of inbreeding and low levels of genetic diversity, seemingly declining since historical time, but surprisingly not being impacted by the 1997 massive die-off in Cabo Blanco. Approximate Bayesian Computation analyses support scenarios combining local extinctions and a major effective population size decline in all populations during Antiquity. Our results suggest that the early densification of human populations around the Mediterranean Basin coupled with the development of seafaring techniques were the main drivers of the decline of Mediterranean monk seals.

Palaeoclimatic changes resulted in range expansion and subsequent divergence in brown fur seals, Arctocephalus pusillus

Past climatic change as a driving force of marine diversification is still largely unclear, particularly for Southern Hemisphere species. Here, we present a case using the brown fur seal, Arctocephalus pusillus, assessing the geographical structure and demographic history using mitochondrial and nuclear data. Results show the two previously defined subspecies (one from Australia and the other from southern Africa) are phylogeographically distinct. Migration analyses based on nuclear data suggest the absence of migrants among the two genetically close assemblages. The demographic history of A. pusillus is characterized by a glacial population expansion (approx. 18 kya) in the southern African lineage, which coincides with time estimates of population expansion of prey species of seals. Approximate Bayesian calculations support an eastward dispersal event during the Last Glacial Maximum when sea levels were lower, followed by a postglacial divergence event, approximately 13 kya. The demographic history of the brown fur seal in the Southern Oceans provides support that recent palaeoclimatic changes could have facilitated expansions in some marine species and that postglacial sea-level rise may have acted as a dispersal barrier for species mostly confined to continental shelves.

High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal

Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.

Population Genetics and Phylogeography of Galapagos Fur Seals

Pinnipeds found across islands provide an ideal opportunity to examine the evolutionary process of population subdivision affected by several mechanisms. Here, we report the genetic consequences of the geographic distribution of rookeries in Galapagos fur seals (GFS: Arctocephalus galapagoensis) in creating population structure. We show that rookeries across four islands (nine rookeries) are genetically structured into the following major groups: 1) a western cluster of individuals from Fernandina; 2) a central group from north and east Isabela, Santiago, and Pinta; and possibly, 3) a third cluster in the northeast from Pinta. Furthermore, asymmetric levels of gene flow obtained from eight microsatellites found migration from west Isabela to Fernandina islands (number of migrants Nm = 1), with imperceptible Nm in any other direction. Our findings suggest that the marked structuring of populations recovered in GFS is likely related to an interplay between long-term site fidelity and long-distance migration in both male and female individuals, probably influenced by varying degrees of marine productivity.

Effects of insularity on genetic diversity within and among natural populations

We conducted a quantitative literature review of genetic diversity (GD) within and among populations in relation to categorical population size and isolation (together referred to as “insularity”). Using populations from within the same studies, we were able to control for between‐study variation in methodology, as well as demographic and life histories of focal species. Contrary to typical expectations, insularity had relatively minor effects on GD within and among populations, which points to the more important role of other factors in shaping evolutionary processes. Such effects of insularity were sometimes seen—particularly in study systems where GD was already high overall. That is, insularity influenced GD in a study system when GD was high even in non‐insular populations of the same study system—suggesting an important role for the “scope” of influences on GD. These conclusions were more robust for within population GD versus among population GD, although several biases might underlie this difference. Overall, our findings indicate that population‐level genetic assumptions need to be tested rather than assumed in nature, particularly for topics underlying current conservation management practices.

Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the ‘krill surplus hypothesis’. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology.

Can DNA help trace the local trade of pangolins? Conservation genetics of white-bellied pangolins from the Dahomey Gap (West Africa)

Background

African pangolins are currently experiencing unprecedented levels of harvesting, feeding both local demands and the illegal international trade. So far, the lack of knowledge on the population genetics of African pangolins has hampered any attempts at assessing their demographic status and tracing their trade at the local scale. We conducted a pioneer study on the genetic tracing of the African pangolin trade in the Dahomey Gap (DG). We sequenced and genotyped 189 white-bellied pangolins from 18 forests and 12 wildlife markets using one mitochondrial fragment and 20 microsatellite loci.

Results

Tree-based assignment procedure showed that the pangolin trade is endemic to the DG region, as it was strictly fed by the the Dahomey Gap lineage (DGL). DGL populations were characterized by low levels of genetic diversity, an overall absence of equilibrium, important inbreeding levels, and lack of geographic structure. We identified a 92–98% decline in DGL effective population size 200–500 ya—concomitant with major political transformations along the ‘Slave Coast’—leading to contemporaneous estimates being inferior to minimum viable population size (< 500). Genetic tracing suggested that wildlife markets from the DG sourced pangolins through the entire DGL range. Our loci provided the necessary power to distinguish among all the genotyped pangolins, tracing the dispatch of a same individual on the markets and within local communities. We developed an approach combining rarefaction analysis of private allele frequencies with cross-validation of observed data that traced five traded pangolins to their forest origin, c. 200–300 km away from the markets.

Conclusions

Although the genetic toolkit that we designed from traditional markers can prove helpful to trace the illegal trade in pangolins, our tracing ability was limited by the lack of population structure within the DGL. Given the deleterious combination of genetic, demographic, and trade-related factors affecting DGL populations, the conservation status of white-bellied pangolins in the DG should be urgently re-evaluated.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-01971-5.

Evolutionary history of two rare endemic conifer species from the eastern Qinghai-Tibet Plateau

BACKGROUND AND AIMS

Understanding the population genetics and evolutionary history of endangered species is urgently needed in an era of accelerated biodiversity loss. This knowledge is most important for regions with high endemism that are ecologically vulnerable, such as the Qinghai-Tibet Plateau (QTP).

METHODS

The genetic variation of 84 juniper trees from six populations of Juniperus microsperma and one population of Juniperus erectopatens, two narrow-endemic junipers from the QTP that are sister to each other, was surveyed using RNA-sequencing data. Coalescent-based analyses were used to test speciation, migration and demographic scenarios. Furthermore, positively selected and climate-associated genes were identified, and the genetic load was assessed for both species.

KEY RESULTS

Analyses of 149 052 single nucleotide polymorphisms showed that the two species are well differentiated and monophyletic. They diverged around the late Pliocene, but interspecific gene flow continued until the Last Glacial Maximum. Demographic reconstruction by Stairway Plot detected two severe bottlenecks for J. microsperma but only one for J. erectopatens. The identified positively selected genes and climate-associated genes revealed habitat adaptation of the two species. Furthermore, although J. microsperma had a much wider geographical distribution than J. erectopatens, the former possesses lower genetic diversity and a higher genetic load than the latter.

CONCLUSIONS

This study sheds light on the evolution of two endemic juniper species from the QTP and their responses to Quaternary climate fluctuations. Our findings emphasize the importance of speciation and demographic history reconstructions in understanding the current distribution pattern and genetic diversity of threatened species in mountainous regions.

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

Opportunities and challenges of macrogenetic studies

The rapidly emerging field of macrogenetics focuses on analysing publicly accessible genetic datasets from thousands of species to explore large-scale patterns and predictors of intraspecific genetic variation. Facilitated by advances in evolutionary biology, technology, data infrastructure, statistics and open science, macrogenetics addresses core evolutionary hypotheses (such as disentangling environmental and life-history effects on genetic variation) with a global focus. Yet, there are important, often overlooked, limitations to this approach and best practices need to be considered and adopted if macrogenetics is to continue its exciting trajectory and reach its full potential in fields such as biodiversity monitoring and conservation. Here, we review the history of this rapidly growing field, highlight knowledge gaps and future directions, and provide guidelines for further research.

Charting a course for genetic diversity in the UN Decade of Ocean Science

The health of the world's oceans is intrinsically linked to the biodiversity of the ecosystems they sustain. The importance of protecting and maintaining ocean biodiversity has been affirmed through the setting of the UN Sustainable Development Goal 14 to conserve and sustainably use the ocean for society's continuing needs. The decade beginning 2021-2030 has additionally been declared as the UN Decade of Ocean Science for Sustainable Development. This program aims to maximize the benefits of ocean science to the management, conservation, and sustainable development of the marine environment by facilitating communication and cooperation at the science-policy interface. A central principle of the program is the conservation of species and ecosystem components of biodiversity. However, a significant omission from the draft version of the Decade of Ocean Science Implementation Plan is the acknowledgment of the importance of monitoring and maintaining genetic biodiversity within species. In this paper, we emphasize the importance of genetic diversity to adaptive capacity, evolutionary potential, community function, and resilience within populations, as well as highlighting some of the major threats to genetic diversity in the marine environment from direct human impacts and the effects of global climate change. We then highlight the significance of ocean genetic diversity to a diverse range of socioeconomic factors in the marine environment, including marine industries, welfare and leisure pursuits, coastal communities, and wider society. Genetic biodiversity in the ocean, and its monitoring and maintenance, is then discussed with respect to its integral role in the successful realization of the 2030 vision for the Decade of Ocean Science. Finally, we suggest how ocean genetic diversity might be better integrated into biodiversity management practices through the continued interaction between environmental managers and scientists, as well as through key leverage points in industry requirements for Blue Capital financing and social responsibility.

Genetic and demographic history define a conservation strategy for earth's most endangered pinniped, the Mediterranean monk seal Monachus monachus

The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species' unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.

Resistance and resilience of genetic and phenotypic diversity to "black swan" flood events: A retrospective analysis with historical samples of guppies

Rare extreme "black swan" disturbances can impact ecosystems in many ways, such as destroying habitats, depleting resources, and causing high mortality. In rivers, for instance, exceptional floods that occur infrequently (e.g., so-called "50-year floods") can strongly impact the abundance of fishes and other aquatic organisms. Beyond such ecological effects, these floods could also impact intraspecific diversity by elevating genetic drift or dispersal and by imposing strong selection, which could then influence the population's ability to recover from disturbance. And yet, natural systems might be resistant (show little change) or resilient (show rapid recovery) even to rare extreme events - perhaps as a result of selection due to past events. We considered these possibilities in two rivers where native guppies experienced two extreme floods - one in 2005 and another in 2016. For each river, we selected four sites and used archived "historical" samples to compare levels of genetic and phenotypic diversity before vs. after floods. Genetic diversity was represented by 33 neutral microsatellite markers, and phenotypic diversity was represented by body length and male melanic (black) colour. We found that genetic diversity and population structure was mostly "resistant" to even these extreme floods; whereas the larger impacts on phenotypic diversity were short-lived, suggesting additional "resilience". We discuss the determinants of these two outcomes for guppies facing floods, and then consider the general implications for the resistance and resilience of intraspecific variation to black swan disturbances.

Population demographic history and adaptability of the vulnerable Lolokou Sucker Frog

Amphibians are experiencing worldwide declines due to increasing anthropogenetic disturbances. However, the genetic variability and hence adaptability are still unknown for most frogs. We integrated the mitochondrial (ND2 gene), nuclear (TYR gene) and major histocompatibility complex (MHC) loci, to clarify the demographic patterns and immune-gene diversity of the Lolokou Sucker Frog (Amolops loloensis). Demographic analysis of the ND2 and TYR genes suggested that the Lolokou Sucker Frog experienced a population expansion within the last 10,000 years. High MHC diversity was detected, which has likely resulted from positive selection, indicating the current diversity bodes well for the species' adaptive potential to pathogenic challenges. These findings broaden our knowledge on the population history and evolution adaptation of the reclusive torrent frog, and conservation implications are provided.

Mitogenomics of the endangered Mediterranean monk seal (Monachus monachus) reveals dramatic loss of diversity and supports historical gene-flow between Atlantic and eastern Mediterranean populations

The Mediterranean monk seal Monachus monachus is one of the most threatened marine mammals, with only 600–700 individuals restricted to three populations off the coast of Western Sahara and Madeira (North Atlantic) and between Greece and Turkey (eastern Mediterranean). Its original range was from the Black Sea (eastern Mediterranean) to Gambia (western African coast), but was drastically reduced by commercial hunting and human persecution since the early stages of marine exploitation.

We here analyse 42 mitogenomes of Mediterranean monk seals, from across their present and historical geographic ranges to assess the species population dynamics over time. Our data show a decrease in genetic diversity in the last 200 years. Extant individuals presented an almost four-fold reduction in genetic diversity when compared to historical specimens. We also detect, for the first time, a clear segregation between the two North Atlantic populations, Madeira and Cabo Blanco, regardless of their geographical proximity. Moreover, we show the presence of historical gene-flow between the two water basins, the Atlantic Ocean and the Mediterranean Sea, and the presence of at least one extinct maternal lineage in the Mediterranean. Our work demonstrates the advantages of using full mitogenomes in phylogeographic and conservation genomic studies of threatened species.

Determinants of genetic variation across eco-evolutionary scales in pinnipeds

The effective size of a population (N_e), which determines its level of neutral variability, is a key evolutionary parameter. N_e can substantially depart from census sizes of present-day breeding populations (N_C) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent N_e for 17 pinniped species represented by 36 population samples (total n = 458 individuals). N_e estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with N_C ([Formula: see text] = 0.59; P = 0.0002). N_e/N_C ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in N_e/N_C, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary N_C than would be expected from their long-term N_e. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.

Chromosomal-level genome assembly of the scimitar-horned oryx: Insights into diversity and demography of a species extinct in the wild

Captive populations provide a valuable insurance against extinctions in the wild. However, they are also vulnerable to the negative impacts of inbreeding, selection and drift. Genetic information is therefore considered a critical aspect of conservation management. Recent developments in sequencing technologies have the potential to improve the outcomes of management programmes; however, the transfer of these approaches to applied conservation has been slow. The scimitar-horned oryx (Oryx dammah) is a North African antelope that has been extinct in the wild since the early 1980s and is the focus of a large-scale and long-term reintroduction project. To enable the selection of suitable founder individuals, facilitate post-release monitoring and improve captive breeding management, comprehensive genomic resources are required. Here, we used 10X Chromium sequencing together with Hi-C contact mapping to develop a chromosomal-level genome assembly for the species. The resulting assembly contained 29 chromosomes with a scaffold N50 of 100.4 Mb, and displayed strong chromosomal synteny with the cattle genome. Using resequencing data from six additional individuals, we demonstrated relatively high genetic diversity in the scimitar-horned oryx compared to other mammals, despite it having experienced a strong founding event in captivity. Additionally, the level of diversity across populations varied according to management strategy. Finally, we uncovered a dynamic demographic history that coincided with periods of climate variation during the Pleistocene. Overall, our study provides a clear example of how genomic data can uncover valuable insights into captive populations and contributes important resources to guide future management decisions of an endangered species.

Harnessing paleo-environmental modeling and genetic data to predict intraspecific genetic structure

Spatially explicit simulations of gene flow within complex landscapes could help forecast the responses of populations to global and anthropological changes. Simulating how past climate change shaped intraspecific genetic variation can provide a validation of models in anticipation of their use to predict future changes. We review simulation models that provide inferences on population genetic structure. Existing simulation models generally integrate complex demographic and genetic processes but are less focused on the landscape dynamics. In contrast to previous approaches integrating detailed demographic and genetic processes and only secondarily landscape dynamics, we present a model based on parsimonious biological mechanisms combining habitat suitability and cellular processes, applicable to complex landscapes. The simulation model takes as input (a) the species dispersal capacities as the main biological parameter, (b) the species habitat suitability, and (c) the landscape structure, modulating dispersal. Our model emphasizes the role of landscape features and their temporal dynamics in generating genetic differentiation among populations within species. We illustrate our model on caribou/reindeer populations sampled across the entire species distribution range in the Northern Hemisphere. We show that simulations over the past 21 kyr predict a population genetic structure that matches empirical data. This approach looking at the impact of historical landscape dynamics on intraspecific structure can be used to forecast population structure under climate change scenarios and evaluate how species range shifts might induce erosion of genetic variation within species.

The genetic legacy of extreme exploitation in a polar vertebrate

Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species' circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. Coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150-200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history.

What do we know about the fossil record of pinnipeds? A historiographical investigation

The fossil record of pinnipeds (seals, fur seals and walruses) is globally distributed, spanning from the late Oligocene to the Holocene. This record shows a complex evolutionary history that could not otherwise be inferred from their extant relatives, including multiple radiations and iterative ecomorphological specializations among different lineages, many of which are extinct. The fossil record of pinnipeds is not uniformly represented in space and time, however, leaving some gaps in our knowledge. We performed a historiographical investigation of the published fossil record of pinnipeds based on the information available in the Paleobiology Database, with the aim to broadly characterize and evaluate it from a taxonomic, geographical and temporal perspective. We identified major trends, strengths and weaknesses of the pinniped fossil record, including potential biases that may affect our interpretations. We found that 39% of the record corresponds to extant taxa, which are essentially from the Pleistocene and Holocene. There is a larger record from the Northern Hemisphere, suggesting biases in sampling and collection effort. The record is not strongly biased by sedimentary outcrop bias. Specifically, for extinct species, nearly half of them are represented by a single occurrence and a large proportion have type specimens consisting of single isolated postcranial elements. While the pinniped fossil record may have adequate temporal and taxonomic coverage, it has a strong geographical bias and its comparability is hindered by the incompleteness of type specimens. These results should be taken into account when addressing patterns of their past diversity, evolutionary history and paleoecology.

Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals

Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity-fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome-wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.