Survival and divergence in a small group: The extraordinary genomic history of the endangered Apennine brown bear stragglers

Fitness consequences of population bottlenecks in an invasive blowfly

Invasive species often undergo demographic bottlenecks that cause a decrease in genetic diversity and associated reductions in population fitness. Despite this, they manage to thrive in novel environments. Investigating the effects of inbreeding and genetic bottlenecks on population fitness for invasive species is, therefore, key to understanding how they may survive in new environments. We used the blowfly Calliphora vicina (Sciences, Mathématiques et Physique, 1830, 2, 1), which is native to Europe and was introduced to Australia and New Zealand, to examine the effects of genetic diversity on population fitness. We first collected 59 samples from 15 populations across New Zealand and one in Australia, and used 20,501 biallelic SNPs to investigate population genomic diversity, structure and admixture. We then explored the impacts of repeated experimental bottlenecks on population fitness by creating inbred and outbred lines of C. vicina and measuring a variety of fitness traits. In wild-caught samples, we found low overall genetic diversity, signals of genetic admixture and limited (<3%) genetic differentiation between North and South Island populations, with genetic links between the South Island and Australia. Following experimental bottlenecks, we found significant reductions in fitness for inbred lines. However, fitness effects were not felt equally across all phenotypic traits. Moreover, they were not enough to cause population collapse in any experimental line, suggesting that C. vicina (when under relaxed selection, as in laboratory settings) may be able to compensate for population bottlenecks even when highly inbred. Our results demonstrate the value of a tractable experimental system for investigating processes that may facilitate or hamper biological invasion.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques

Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counterintuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here, we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify seven deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild nonhuman primates.

The influence of gene flow on population viability in an isolated urban caracal population

Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.

Conservation genomics provides insights into genetic resilience and adaptation of the endangered Chinese hazelnut, Corylus chinensis

Global climate change has increased concerns regarding biodiversity loss. However, many key conservation issues still required further research, including demographic history, deleterious mutation load, adaptive evolution, and putative introgression. Here we generated the first chromosome-level genome of the endangered Chinese hazelnut, Corylus chinensis, and compared the genomic signatures with its sympatric widespread C. kwechowensis-C. yunnanensis complex. We found large genome rearrangements across all Corylus species and identified species-specific expanded gene families that may be involved in adaptation. Population genomics revealed that both C. chinensis and the C. kwechowensis-C. yunnanensis complex had diverged into two genetic lineages, forming a consistent pattern of southwestern-northern differentiation. Population size of the narrow southwestern lineages of both species have decreased continuously since the late Miocene, whereas the widespread northern lineages have remained stable (C. chinensis) or have even recovered from population bottlenecks (C. kwechowensis-C. yunnanensis complex) during the Quaternary. Compared with C. kwechowensis-C. yunnanensis complex, C. chinensis showed significantly lower genomic diversity and higher inbreeding level. However, C. chinensis carried significantly fewer deleterious mutations than C. kwechowensis-C. yunnanensis complex, as more effective purging selection reduced the accumulation of homozygous variants. We also detected signals of positive selection and adaptive introgression in different lineages, which facilitated the accumulation of favorable variants and formation of local adaptation. Hence, both types of selection and exogenous introgression could have mitigated inbreeding and facilitated survival and persistence of C. chinensis. Overall, our study provides critical insights into lineage differentiation, local adaptation, and the potential for future recovery of endangered trees.

The Maintenance of Deleterious Variation in Wild Chinese Rhesus Macaques

Understanding how deleterious variation is shaped and maintained in natural populations is important in conservation and evolutionary biology, as decreased fitness caused by these deleterious mutations can potentially lead to an increase in extinction risk. It is known that demographic processes can influence these patterns. For example, population bottlenecks and inbreeding increase the probability of inheriting identical-by-descent haplotypes from a recent common ancestor, creating long tracts of homozygous genotypes called runs of homozygosity (ROH), which have been associated with an accumulation of mildly deleterious homozygotes. Counter intuitively, positive selection can also maintain deleterious variants in a population through genetic hitchhiking. Here we analyze the whole genomes of 79 wild Chinese rhesus macaques across five subspecies and characterize patterns of deleterious variation with respect to ROH and signals of recent positive selection. We show that the fraction of homozygotes occurring in long ROH is significantly higher for deleterious homozygotes than tolerated ones, whereas this trend is not observed for short and medium ROH. This confirms that inbreeding, by generating these long tracts of homozygosity, is the main driver of the high burden of homozygous deleterious alleles in wild macaque populations. Furthermore, we show evidence that homozygous LOF variants are being purged. Next, we identify 7 deleterious variants at high frequency in regions putatively under selection near genes involved with olfaction and other processes. Our results shed light on how evolutionary processes can shape the distribution of deleterious variation in wild non-human primates.

Fine scale diversity in the lava: genetic and phenotypic diversity in small populations of Arctic charr Salvelinus alpinus

BACKGROUND

A major goal in evolutionary biology is to understand the processes underlying phenotypic variation in nature. Commonly, studies have focused on large interconnected populations or populations found along strong environmental gradients. However, studies on small fragmented populations can give strong insight into evolutionary processes in relation to discrete ecological factors. Evolution in small populations is believed to be dominated by stochastic processes, but recent work shows that small populations can also display adaptive phenotypic variation, through for example plasticity and rapid adaptive evolution. Such evolution takes place even though there are strong signs of historical bottlenecks and genetic drift. Here we studied 24 small populations of the freshwater fish Arctic charr (Salvelinus alpinus) found in groundwater filled lava caves. Those populations were found within a few km2-area with no apparent water connections between them. We studied the relative contribution of neutral versus non-neutral evolutionary processes in shaping phenotypic divergence, by contrasting patterns of phenotypic and neutral genetic divergence across populations in relation to environmental measurements. This allowed us to model the proportion of phenotypic variance explained by the environment, taking in to account the observed neutral genetic structure.

RESULTS

These populations originated from the nearby Lake Mývatn, and showed small population sizes with low genetic diversity. Phenotypic variation was mostly correlated with neutral genetic diversity with only a small environmental effect.

CONCLUSIONS

Phenotypic diversity in these cave populations appears to be largely the product of neutral processes, fitting the classical evolutionary expectations. However, the fact that neutral processes did not explain fully the phenotypic patterns suggests that further studies can increase our understanding on how neutral evolutionary processes can interact with other forces of selection at early stages of divergence. The accessibility of these populations has provided the opportunity for long-term monitoring of individual fish, allowing tracking how the environment can influence phenotypic and genetic divergence for shaping and maintaining diversity in small populations. Such studies are important, especially in freshwater, as habitat alteration is commonly breaking populations into smaller units, which may or may not be viable.

Genomic consequences of isolation and inbreeding in an island dingo population

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

The origins and diversification of Holarctic brown bear populations inferred from genomes of past and present populations

The brown bear (Ursus arctos) is one of the survivors of the Late Quaternary megafauna extinctions. However, despite being widely distributed across the Holarctic, brown bears have experienced extensive range reductions, and even extirpations in some geographical regions. Previous research efforts using genetic data have provided valuable insights into their evolutionary history. However, most studies have been limited to contemporary individuals or mitochondrial DNA, limiting insights into population processes that preceded the present. Here, we present genomic data from two Late Pleistocene brown bears from Honshu, Japan and eastern Siberia, and combine them with published contemporary and ancient genomes from across the Holarctic range of brown bears to investigate the evolutionary relationships among brown bear populations through time and space. By including genomic data from Late Pleistocene and Holocene individuals sampled outside the current distribution range, we uncover diversity not present in contemporary populations. Notably, although contemporary individuals display geographically structured populations most likely driven by isolation-by-distance, this pattern varies among the ancient samples across different regions. The inclusion of ancient brown bears in our analysis provides novel insights into the evolutionary history of brown bears and contributes to understanding the populations and diversity lost during the Late Quaternary.

Conservation genomics analysis reveals recent population decline and possible causes in bumblebee Bombus opulentus

Bumblebees are a genus of pollinators (Bombus) that play important roles in natural ecosystem and agricultural production. Several bumblebee species have been recorded as under population decline, and the proportion of species experiencing population decline within subgenus Thoracobombus is higher than average. Bombus opulentus is 1 species in Thoracobombus, but little is known about its recent population dynamics. Here, we employed conservation genomics methods to investigate the population dynamics of B. opulentus during the recent past and identify the likely environmental factors that may cause population decline. Firstly, we placed the scaffold-level of B. opulentus reference genome sequence onto chromosome-level using Hi-C technique. Then, based on this reference genome and whole-genome resequencing data for 51 B. opulentus samples, we reconstructed the population structure and effective population size (Ne ) trajectories of B. opulentus and identified genes that were under positive selection. Our results revealed that the collected B. opulentus samples could be divided into 2 populations, and 1 of them experienced a recent population decline; the declining population also exhibited lower genetic diversity and higher inbreeding levels. Genes related to high-temperature tolerance, immune response, and detoxication showed signals of positive selection in the declining population, suggesting that climate warming and pathogen/pesticide exposures may contribute to the decline of this B. opulentus population. Taken together, our study provided insights into the demography of B. opulentus populations and highlighted that populations of the same bumblebee species could have contrasting Ne trajectories and population decline could be caused by a combination of various stressors.

Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia

'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.

Evolution of the Mutation Spectrum Across a Mammalian Phylogeny

Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clock-like mutational signatures previously inferred from human cancers cannot explain the phylogenetic signal exhibited by the mammalian mutation spectrum, despite the ability of these signatures to fit each species' 3-mer spectrum with high cosine similarity. In contrast, parental aging signatures inferred from human de novo mutation data appear to explain much of the 1-mer spectrum's phylogenetic signal in combination with a novel mutational signature. We posit that future models purporting to explain the etiology of mammalian mutagenesis need to capture the fact that more closely related species have more similar mutation spectra; a model that fits each marginal spectrum with high cosine similarity is not guaranteed to capture this hierarchy of mutation spectrum variation among species.

Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations

Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.

Detection of Mycobacterium tuberculosis Complex Genetic Material in a Free-Living Brown Bear (Ursus arctos)

Mycobacterium tuberculosis complex (MTBC) has rarely been detected in bears (Ursidae). We describe detection of MTBC genetic material using a single-tube, high-multiplex PCR and fluorescence-based detection system in a throat swab collected from a free-living, problem individual during immobilization and telemetry collar deployment. Mycobacterial culture was negative in all samples.

Demographic history and genomic consequences of 10,000 generations of isolation in a wild mammal

Increased human activities caused the isolation of populations in many species-often associated with genetic depletion and negative fitness effects. The effects of isolation are predicted by theory, but long-term data from natural populations are scarce. We show, with full genome sequences, that common voles (Microtus arvalis) in the Orkney archipelago have remained genetically isolated from conspecifics in continental Europe since their introduction by humans over 5,000 years ago. Modern Orkney vole populations are genetically highly differentiated from continental conspecifics as a result of genetic drift processes. Colonization likely started on the biggest Orkney island and vole populations on smaller islands were gradually split off, without signs of secondary admixture. Despite having large modern population sizes, Orkney voles are genetically depauperate and successive introductions to smaller islands resulted in further reduction of genetic diversity. We detected high levels of fixation of predicted deleterious variation compared with continental populations, particularly on smaller islands, yet the fitness effects realized in nature are unknown. Simulations showed that predominantly mildly deleterious mutations were fixed in populations, while highly deleterious mutations were purged early in the history of the Orkney population. Relaxation of selection overall due to benign environmental conditions on the islands and the effects of soft selection may have contributed to the repeated, successful establishment of Orkney voles despite potential fitness loss. Furthermore, the specific life history of these small mammals, resulting in relatively large population sizes, has probably been important for their long-term persistence in full isolation.

Deleterious Variation in Natural Populations and Implications for Conservation Genetics

Deleterious mutations decrease reproductive fitness and are ubiquitous in genomes. Given that many organisms face ongoing threats of extinction, there is interest in elucidating the impact of deleterious variation on extinction risk and optimizing management strategies accounting for such mutations. Quantifying deleterious variation and understanding the effects of population history on deleterious variation are complex endeavors because we do not know the strength of selection acting on each mutation. Further, the effect of demographic history on deleterious mutations depends on the strength of selection against the mutation and the degree of dominance. Here we clarify how deleterious variation can be quantified and studied in natural populations. We then discuss how different demographic factors, such as small population size, nonequilibrium population size changes, inbreeding, and gene flow, affect deleterious variation. Lastly, we provide guidance on studying deleterious variation in nonmodel populations of conservation concern.

Range-wide whole-genome resequencing of the brown bear reveals drivers of intraspecies divergence

Population-genomic studies can shed new light on the effect of past demographic processes on contemporary population structure. We reassessed phylogeographical patterns of a classic model species of postglacial recolonisation, the brown bear (Ursus arctos), using a range-wide resequencing dataset of 128 nuclear genomes. In sharp contrast to the erratic geographical distribution of mtDNA and Y-chromosomal haplotypes, autosomal and X-chromosomal multi-locus datasets indicate that brown bear population structure is largely explained by recent population connectivity. Multispecies coalescent based analyses reveal cases where mtDNA haplotype sharing between distant populations, such as between Iberian and southern Scandinavian bears, likely results from incomplete lineage sorting, not from ancestral population structure (i.e., postglacial recolonisation). However, we also argue, using forward-in-time simulations, that gene flow and recombination can rapidly erase genomic evidence of former population structure (such as an ancestral population in Beringia), while this signal is retained by Y-chromosomal and mtDNA, albeit likely distorted. We further suggest that if gene flow is male-mediated, the information loss proceeds faster in autosomes than in X chromosomes. Our findings emphasise that contemporary autosomal genetic structure may reflect recent population dynamics rather than postglacial recolonisation routes, which could contribute to mtDNA and Y-chromosomal discordances.

Genetic architecture and evolution of color variation in American black bears

Color variation is a frequent evolutionary substrate for camouflage in small mammals, but the underlying genetics and evolutionary forces that drive color variation in natural populations of large mammals are mostly unexplained. The American black bear, Ursus americanus (U. americanus), exhibits a range of colors including the cinnamon morph, which has a similar color to the brown bear, U. arctos, and is found at high frequency in the American southwest. Reflectance and chemical melanin measurements showed little distinction between U. arctos and cinnamon U. americanus individuals. We used a genome-wide association for hair color as a quantitative trait in 151 U. americanus individuals and identified a single major locus (p < 10-13). Additional genomic and functional studies identified a missense alteration (R153C) in Tyrosinase-related protein 1 (TYRP1) that likely affects binding of the zinc cofactor, impairs protein localization, and results in decreased pigment production. Population genetic analyses and demographic modeling indicated that the R153C variant arose 9.36 kya in a southwestern population where it likely provided a selective advantage, spreading both northwards and eastwards by gene flow. A different TYRP1 allele, R114C, contributes to the characteristic brown color of U. arctos but is not fixed across the range.

Like a rolling stone: Colonization and migration dynamics of the gray reef shark (Carcharhinus amblyrhynchos)

Designing appropriate management plans requires knowledge of both the dispersal ability and what has shaped the current distribution of the species under consideration. Here, we investigated the evolutionary history of the endangered gray reef shark (Carcharhinus amblyrhynchos) across its range by sequencing thousands of RADseq loci in 173 individuals in the Indo-Pacific (IP). We first bring evidence of the occurrence of a range expansion (RE) originating close to the Indo-Australian Archipelago (IAA) where two stepping-stone waves (east and westward) colonized almost the entire IP. Coalescent modeling additionally highlighted a homogenous connectivity (Nm ~ 10 per generation) throughout the range, and isolation by distance model suggested the absence of barriers to dispersal despite the affinity of C. amblyrhynchos to coral reefs. This coincides with long-distance swims previously recorded, suggesting that the strong genetic structure at the IP scale (F ST ~ 0.56 between its ends) is the consequence of its broad current distribution and organization in a large number of demes. Our results strongly suggest that management plans for the gray reef shark should be designed on a range-wide rather than a local scale due to its continuous genetic structure. We further contrasted these results with those obtained previously for the sympatric but strictly lagoon-associated Carcharhinus melanopterus, known for its restricted dispersal ability. Carcharhinus melanopterus exhibits a similar RE dynamic but is characterized by a stronger genetic structure and a nonhomogeneous connectivity largely dependent on local coral reefs availability. This sheds new light on shark evolution, emphasizing the roles of IAA as source of biodiversity and of life-history traits in shaping the extent of genetic structure and diversity.

Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity

Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.

From high masked to high realized genetic load in inbred Scandinavian wolves

When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.

An isolated population reveals greater genetic structuring of the Australian dingo

The Australian dingo is a recent anthropogenic addition to the Australian fauna, which spread rapidly across the continent and has since widely interbred with modern dogs. Genetic studies of dingoes have given rise to speculation about their entry to the continent and subsequent biogeographic effects, but few studies of their contemporary population structure have been conducted. Here we investigated the dingo ancestry and population structure of free-living dogs in western Victoria and contrasted it with a wider southern Australian sample. We wished to determine whether their geographic isolation was mirrored in genetic isolation. To address this question, we analysed 34 microsatellite markers using Bayesian clustering and discriminant analysis of principal components, and summarised genetic diversity at the population and individual level. The broader southern Australia sample (n = 1138) comprised mostly hybrid animals, with 30% considered pure dingoes. All western Victorian individuals (n = 59) appeared to be hybrids with high dingo ancestry. The population showed no evidence of admixture with other populations and low genetic diversity on all measures tested. Based upon our characterisation of this unusual mainland population, we advise against assuming homogeneity of dingoes across the continent.

Circadian activity of small brown bear populations living in human-dominated landscapes

Whereas numerous studies on large carnivores have focused on analyzing spatial patterns and habitat use, the temporal dimension of their activity has been relatively little investigated, making this a topic of growing interest, especially in human-dominated landscapes. Relict and isolated Apennine brown bears (Ursus arctos marsicanus) have been living in a human-modified landscape since millennia, but no information is available on their activity patterns. By means of GPS telemetry (26,880 GPS locations collected from 18 adult Apennine brown bears) we investigated their circadian rhythms, using hourly movement rates as an index of bear activity. Based on a Bayesian modeling approach, circadian activity of Apennine brown bears was described by a bimodal curve, with peaks of activity around sunrise and sunset. We revealed seasonal effects, with bears exhibiting higher movement rates throughout the mating season, but no relevant influence of sex. In addition, bears increased their movement rate at distances < 100–500 m to roads and settlements exclusively during spring and late summer, suggesting a trade-off between foraging opportunities and risk avoidance. The absence of a marked nocturnality in Apennine brown bears suggests a relatively low degree of habitat encroachment and disturbance by humans. Yet, the occurrence of crepuscular activity patterns and the responses in proximity of anthropogenic landscape features likely indicate a coadaptation by bears to human presence through a shift in their temporal niche. Further studies should aim to unveil fitness implications of such modifications in activity patterns.

Invasive Bullfrogs Maintain MHC Polymorphism Including Alleles Associated with Chytrid Fungal Infection

Maintenance of genetic diversity at adaptive loci may facilitate invasions by non-native species by allowing populations to adapt to novel environments, despite the loss of diversity at neutral loci that typically occurs during founder events. To evaluate this prediction, we compared genetic diversity at major histocompatibility complex (MHC) and cytochrome b (cytb) loci from 20 populations of the American bullfrog (Rana catesbeiana) across theinvasive and native ranges in North America and quantified the presence of the pathogen Batrachochytrium dendrobatidis (Bd). Compared to native populations, invasive populations had significantly higher Bd prevalence and intensity, significantly higher pairwise MHC and cytb FST, and significantly lower cytb diversity, but maintained similar levels of MHC diversity. The two most common MHC alleles (LiCA_B and Rapi_33) were associated with a significant decreased risk of Bd infection, and we detected positive selection acting on four peptide binding residues. Phylogenetic analysis suggested invasive populations likely arose from a single founding population in the American Midwest with a possible subsequent invasion in the northwest. Overall, our study suggests that the maintenance of diversity at adaptive loci may contribute to invasion success and highlights the importance of quantifying diversity at functional loci to assess the evolutionary potential of invasive populations.

Give and Take: Effects of Genetic Admixture on Mutation Load in Endangered Florida Panthers

Genetic admixture is a biological event inherent to genetic rescue programs aimed at the long-term conservation of endangered wildlife. Although the success of such programs can be measured by the increase in genetic diversity and fitness of subsequent admixed individuals, predictions supporting admixture costs to fitness due to the introduction of novel deleterious alleles are necessary. Here, we analyzed nonsynonymous variation from conserved genes to quantify and compare levels of mutation load (i.e., proportion of deleterious alleles and genotypes carrying these alleles) among endangered Florida panthers and non-endangered Texas pumas. Specifically, we used canonical (i.e., non-admixed) Florida panthers, Texas pumas, and F1 (canonical Florida x Texas) panthers dating from a genetic rescue program and Everglades National Park panthers with Central American ancestry resulting from an earlier admixture event. We found neither genetic drift nor selection significantly reduced overall proportions of deleterious alleles in the severely bottlenecked canonical Florida panthers. Nevertheless, the deleterious alleles identified were distributed into a disproportionately high number of homozygous genotypes due to close inbreeding in this group. Conversely, admixed Florida panthers (either with Texas or Central American ancestry) presented reduced levels of homozygous genotypes carrying deleterious alleles but increased levels of heterozygous genotypes carrying these variants relative to canonical Florida panthers. Although admixture is likely to alleviate the load of standing deleterious variation present in homozygous genotypes, our results suggest introduced novel deleterious alleles (temporarily present in heterozygous state) in genetically rescued populations could potentially be expressed in subsequent generations if their effective sizes remain small.

Genetic load: genomic estimates and applications in non-model animals

Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.

Genomic evidence for inbreeding depression and purging of deleterious genetic variation in Indian tigers

Increasing habitat fragmentation leads to wild populations becoming small, isolated, and threatened by inbreeding depression. However, small populations may be able to purge recessive deleterious alleles as they become expressed in homozygotes, thus reducing inbreeding depression and increasing population viability. We used whole-genome sequences from 57 tigers to estimate individual inbreeding and mutation load in a small-isolated and two large-connected populations in India. As expected, the small-isolated population had substantially higher average genomic inbreeding (FROH = 0.57) than the large-connected (FROH = 0.35 and FROH = 0.46) populations. The small-isolated population had the lowest loss-of-function mutation load, likely due to purging of highly deleterious recessive mutations. The large populations had lower missense mutation loads than the small-isolated population, but were not identical, possibly due to different demographic histories. While the number of the loss-of-function alleles in the small-isolated population was lower, these alleles were at higher frequencies and homozygosity than in the large populations. Together, our data and analyses provide evidence of 1) high mutation load, 2) purging, and 3) the highest predicted inbreeding depression, despite purging, in the small-isolated population. Frequency distributions of damaging and neutral alleles uncover genomic evidence that purifying selection has removed part of the mutation load across Indian tiger populations. These results provide genomic evidence for purifying selection in both small and large populations, but also suggest that the remaining deleterious alleles may have inbreeding-associated fitness costs. We suggest that genetic rescue from sources selected based on genome-wide differentiation could offset any possible impacts of inbreeding depression.

Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole-genome sequencing

Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable N_e during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid N_e decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Genomic signatures of inbreeding in a critically endangered parrot, the kākāpō

Events of inbreeding are inevitable in critically endangered species. Reduced population sizes and unique life-history traits can increase the severity of inbreeding, leading to declines in fitness and increased risk of extinction. Here, we investigate levels of inbreeding in a critically endangered flightless parrot, the kākāpō (Strigops habroptilus), wherein a highly inbred island population and one individual from the mainland of New Zealand founded the entire extant population. Genotyping-by-sequencing (GBS), and a genotype calling approach using a chromosome-level genome assembly, identified a filtered set of 12,241 single-nucleotide polymorphisms (SNPs) among 161 kākāpō, which together encompass the total genetic potential of the extant population. Multiple molecular-based estimates of inbreeding were compared, including genome-wide estimates of heterozygosity (FH), the diagonal elements of a genomic-relatedness matrix (FGRM), and runs of homozygosity (RoH, FRoH). In addition, we compared levels of inbreeding in chicks from a recent breeding season to examine if inbreeding is associated with offspring survival. The density of SNPs generated with GBS was sufficient to identify chromosomes that were largely homozygous with RoH distributed in similar patterns to other inbred species. Measures of inbreeding were largely correlated and differed significantly between descendants of the two founding populations. However, neither inbreeding nor ancestry was found to be associated with reduced survivorship in chicks, owing to unexpected mortality in chicks exhibiting low levels of inbreeding. Our study highlights important considerations for estimating inbreeding in critically endangered species, such as the impacts of small population sizes and admixture between diverse lineages.

Demographic History of the Brown Bear (Ursus arctos) on Hokkaido Island, Japan, Based on Whole-Genomic Sequence Analysis

Previous studies of the brown bear (Ursus arctos) on Hokkaido Island, Japan, have detected three geographically distinct subpopulations representing different mitochondrial lineages and shown that gene flow between subpopulations has occurred due to male-biased dispersal. In this study, we determined whole-genomic sequences for six Hokkaido brown bears and analyzed these data along with previously published genomic sequences of 17 brown bears from other parts of the world. We found that the Hokkaido population is genetically distinct from the other populations, keeping genetic diversity higher than the endangered populations in western Europe but lower than most populations on the continents. A reconstruction of historical demography showed no increase in population size for the Hokkaido population during the Eemian interglacial period (130,000–114,000 years ago). In a phylogenetic analysis of the autosomal data, the Hokkaido population formed a clade distinct from North American and European populations, showing that it has maintained genetic diversity independently from continental populations following geographical isolation on the island. This autosomal genetic similarity contrasts with the geographically separate mitochondrial lineages on Hokkaido and indicates the occurrence of male-driven gene flow between subpopulations.

Genomic signatures of inbreeding and mutation load in a threatened rattlesnake

Theory predicts that threatened species living in small populations will experience high levels of inbreeding that will increase their genetic load, but recent work suggests that the impact of load may be minimized by purging resulting from long-term population bottlenecks. Empirical studies that examine this idea using genome-wide estimates of inbreeding and genetic load in threatened species are limited. Here we use individual genome resequencing data to compare levels of inbreeding, levels of genetic load (estimated as mutation load) and population history in threatened Eastern massasauga rattlesnakes (Sistrurus catenatus), which exist in small isolated populations, and closely related yet outbred Western massasauga rattlesnakes (Sistrurus tergeminus). In terms of inbreeding, S. catenatus genomes had a greater number of runs of homozygosity of varying sizes, indicating sustained inbreeding through repeated bottlenecks when compared to S. tergeminus. At the species level, outbred S. tergeminus had higher genome-wide levels of mutation load in the form of greater numbers of derived deleterious mutations compared to S. catenatus, presumably due to long-term purging of deleterious mutations in S. catenatus. In contrast, mutations that escaped species-level drift effects within S. catenatus populations were in general more frequent and more often found in homozygous genotypes than in S. tergeminus, suggesting a reduced efficiency of purifying selection in smaller S. catenatus populations for most mutations. Our results support an emerging idea that the historical demography of a threatened species has a significant impact on the type of genetic load present, which impacts implementation of conservation actions such as genetic rescue.

First core microsatellite panel identification in Apennine brown bears (Ursus arctos marsicanus): a collaborative approach

BACKGROUND

The low cost and rapidity of microsatellite analysis have led to the development of several markers for many species. Because in non-invasive genetics it is recommended to genotype individuals using few loci, generally a subset of markers is selected. The choice of different marker panels by different research groups studying the same population can cause problems and bias in data analysis. A priority issue in conservation genetics is the comparability of data produced by different labs with different methods. Here, we compared data from previous and ongoing studies to identify a panel of microsatellite loci efficient for the long-term monitoring of Apennine brown bears (Ursus arctos marsicanus), aiming at reducing genotyping uncertainty and allowing reliable individual identifications overtimes.

RESULTS

We examined all microsatellite markers used up to now and identified 19 candidate loci. We evaluated the efficacy of 13 of the most commonly used loci analyzing 194 DNA samples belonging to 113 distinct bears selected from the Italian national biobank. We compared data from 4 different marker subsets on the basis of genotyping errors, allelic patterns, observed and expected heterozygosity, discriminatory powers, number of mismatching pairs, and probability of identity. The optimal marker set was selected evaluating the low molecular weight, the high discriminatory power, and the low occurrence of genotyping errors of each primer. We calibrated allele calls and verified matches among genotypes obtained in previous studies using the complete set of 13 STRs (Short Tandem Repeats), analyzing six invasive DNA samples from distinct individuals. Differences in allele-sizing between labs were consistent, showing a substantial overlap of the individual genotyping.

CONCLUSIONS

The proposed marker set comprises 11 Ursus specific markers with the addition of cxx20, the canid-locus less prone to genotyping errors, in order to prevent underestimation (maximizing the discriminatory power) and overestimation (minimizing the genotyping errors) of the number of Apennine brown bears. The selected markers allow saving time and costs with the amplification in multiplex of all loci thanks to the same annealing temperature. Our work optimizes the available resources by identifying a shared panel and a uniform methodology capable of improving comparisons between past and future studies.

Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change

We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.

Gaining insight into the assimilated diet of small bear populations by stable isotope analysis

Apennine brown bears (Ursus arctos marsicanus) survive in an isolated and critically endangered population, and their food habits have been studied using traditional scat analysis. To complement current dietary knowledge, we applied Stable Isotope Analysis (SIA) to non-invasively collected bear hairs that had been individually recognized through multilocus genotyping. We analysed carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotopes of hair sections and bear key foods in a Bayesian mixing models framework to reconstruct the assimilated diet on a seasonal basis and to assess gender and management status effects. In total, we analysed 34 different seasonal bear key foods and 35 hair samples belonging to 27 different bears (16 females and 11 males) collected during a population survey in 2014. Most bears showed wide δ¹⁵N and δ¹³C ranges and individual differences in seasonal isotopic patterns. Vegetable matter (herbs, fleshy fruits and hard mast) represented the major component of the assimilated diet across the dietary seasons, whereas vegetable crops were rarely and C4 plants (i.e., corn) never consumed. We confirmed an overall low consumption of large mammals by Apennine bears consistently between sexes, with highest values in spring followed by early summer but null in the other seasons. We also confirmed that consumption of fleshy fruits peaked in late summer, when wild predominated over cultivated fleshy fruits, even though the latter tended to be consumed in higher proportion in autumn. Male bears had higher δ ¹⁵N values than females in spring and autumn. Our findings also hint at additional differences in the assimilated diet between sexes, with females likely consuming more herbs during spring, ants during early summer, and hard mast during fall compared to males. In addition, although effect sizes were small and credibility intervals overlapped considerably, management bears on average were 0.9‰ lower in δ ¹³C and 2.9‰ higher in δ ¹⁵N compared to non-management bears, with differences in isotopic values between the two bear categories peaking in autumn. While non-management bears consumed more herbs, wild fleshy fruits, and hard mast, management bears tended to consume higher proportions of cultivated fruits, ants, and large mammals, possibly including livestock. Although multi-year sampling and larger sample sizes are needed to support our findings, our application confirms that SIA can effectively integrate previous knowledge and be efficiently conducted using samples non-invasively collected during population surveys.

The genome of the Pyrenean desman and the effects of bottlenecks and inbreeding on the genomic landscape of an endangered species

The Pyrenean desman (Galemys pyrenaicus) is a small semiaquatic mammal endemic to the Iberian Peninsula. Despite its limited range, this species presents a strong genetic structure due to past isolation in glacial refugia and subsequent bottlenecks. Additionally, some populations are highly fragmented today as a consequence of river barriers, causing substantial levels of inbreeding. These features make the Pyrenean desman a unique model in which to study the genomic footprints of differentiation, bottlenecks and extreme isolation in an endangered species. To understand these processes, the complete genome of the Pyrenean desman was sequenced and assembled using a Bloom filter-based approach. An analysis of the 1.83 Gb reference genome and the sequencing of five additional individuals from different evolutionary units allowed us to detect its main genomic characteristics. The population differentiation of the species was reflected in highly distinctive demographic trajectories. In addition, a severe population bottleneck during the postglacial recolonization of the eastern Pyrenees created one of the lowest genomic heterozygosity values recorded in a mammal. Moreover, isolation and inbreeding gave rise to a high proportion of runs of homozygosity (ROH). Despite these extremely low levels of genetic diversity, two key multigene families from an eco-evolutionary perspective, the major histocompatibility complex and olfactory receptor genes, showed heterozygosity excess in the majority of individuals, revealing that functional diversity can be maintained up to a certain extent. Furthermore, these two classes of genes were significantly less abundant than expected within ROH. In conclusion, the genomic landscape of each analysed Pyrenean desman turned out to be strikingly distinctive and was a clear reflection of its recent ancestry and current conservation conditions. These results may help characterize the genomic health of each individual, and can be crucial for the conservation and management of the species.

Cost of Coexisting with a Relict Large Carnivore Population: Impact of Apennine Brown Bears, 2005-2015

Human-carnivore conflicts are a major conservation issue. As bears are expanding their range in Europe's human-modified landscapes, it is increasingly important to understand, prevent, and address human-bear conflicts and evaluate mitigation strategies in areas of historical coexistence. Based on verified claims, we assessed costs, patterns, and drivers of bear damages in the relict Apennine brown bear population in the Abruzzo Lazio and Molise National Park (PNALM), central Italy. During 2005-2015, 203 ± 71 (SD) damage events were verified annually, equivalent to 75,987 ± 30,038 €/year paid for compensation. Most damages occurred in summer and fall, with livestock depredation, especially sheep and cattle calves, prevailing over other types of damages, with apiaries ranking second in costs of compensation. Transhumant livestock owners were less impacted than residential ones, and farms that adopted prevention measures loaned from the PNALM were less susceptible to bear damages. Livestock farms chronically damaged by bears represented 8 ± 3% of those annually impacted, corresponding to 24 ± 6% of compensation costs. Further improvements in the conflict mitigation policy adopted by the PNALM include integrated prevention, conditional compensation, and participatory processes. We discuss the implications of our study for Human-bear coexistence in broader contexts.

The ecological causes and consequences of hard and soft selection

Interactions between natural selection and population dynamics are central to both evolutionary-ecology and biological responses to anthropogenic change. Natural selection is often thought to incur a demographic cost that, at least temporarily, reduces population growth. However, hard and soft selection clarify that the influence of natural selection on population dynamics depends on ecological context. Under hard selection, an individual's fitness is independent of the population's phenotypic composition, and substantial population declines can occur when phenotypes are mismatched with the environment. In contrast, under soft selection, an individual's fitness is influenced by its phenotype relative to other interacting conspecifics. Soft selection generally influences which, but not how many, individuals survive and reproduce, resulting in little effect on population growth. Despite these important differences, the distinction between hard and soft selection is rarely considered in ecology. Here, we review and synthesize literature on hard and soft selection, explore their ecological causes and implications and highlight their conservation relevance to climate change, inbreeding depression, outbreeding depression and harvest. Overall, these concepts emphasise that natural selection and evolution may often have negligible or counterintuitive effects on population growth-underappreciated outcomes that have major implications in a rapidly changing world.

Developmental instability and phenotypic evolution in a small and isolated bear population

We explored fluctuating asymmetry (FA) and morphological integration (MI) in the skull of the small, highly inbred and divergent Apennine bear (Ursus arctos marsicanus), to explore its uniqueness and investigate any potential effects of inbreeding depression. We used 3D geometric morphometrics contrasting Apennine bears with other two large outbred bear populations from Scandinavia and Kamchatka as controls. Shape divergence and variability were explored by a principal component analysis on aligned coordinates of 39 landmarks. Procrustes ANOVA, morphological disparity and the global integration index were used to explore FA, shape variance and MI. By remarking Apennine bears as a highly divergent phenotype, we recorded the highest FA and deviation from self-similarity compared with the other two control populations. We conclude that Apennine bears are likely facing developmental instability as a consequence of inbreeding depression, whereas the divergent trait covariance pattern may represent a potential source of evolutionary novelties. We discuss the implications for the conservation and management of this imperiled taxon.

Does genetic variation on the shy–bold continuum influence carnivore attacks on people? Evidence from the brown bear

Little is known about the heritable behavioural traits of attacks by large carnivores on people. During the last 30 years attacks by brown bears Ursus arctos on people in the Cantabrian Mountains of Spain have been disproportionately concentrated in the eastern subpopulation. Excluding factors such as the existence of a single unusually bold bear, a higher human population density, particular human activities promoting encounters, or clear habitat differences in the area of this subpopulation, we propose that a plausible explanation for the unbalanced geographical attack pattern is that this subpopulation, separated a century earlier from the western subpopulation, may harbour a higher proportion of bolder bears. In the absence of genetic analyses this explanation remains speculative, but supports the hypothesis that genetic variation on the shy–bold continuum may influence attacks of large carnivores on people.

Vital rates of two small populations of brown bears in Canada and range-wide relationship between population size and trend

Identifying mechanisms of population change is fundamental for conserving small and declining populations and determining effective management strategies. Few studies, however, have measured the demographic components of population change for small populations of mammals (<50 individuals). We estimated vital rates and trends in two adjacent but genetically distinct, threatened brown bear (Ursus arctos) populations in British Columbia, Canada, following the cessation of hunting. One population had approximately 45 resident bears but had some genetic and geographic connectivity to neighboring populations, while the other population had <25 individuals and was isolated. We estimated population-specific vital rates by monitoring survival and reproduction of telemetered female bears and their dependent offspring from 2005 to 2018. In the larger, connected population, independent female survival was 1.00 (95% CI: 0.96-1.00) and the survival of cubs in their first year was 0.85 (95% CI: 0.62-0.95). In the smaller, isolated population, independent female survival was 0.81 (95% CI: 0.64-0.93) and first-year cub survival was 0.33 (95% CI: 0.11-0.67). Reproductive rates did not differ between populations. The large differences in age-specific survival estimates resulted in a projected population increase in the larger population (λ = 1.09; 95% CI: 1.04-1.13) and population decrease in the smaller population (λ = 0.84; 95% CI: 0.72-0.95). Low female survival in the smaller population was the result of both continued human-caused mortality and an unusually high rate of natural mortality. Low cub survival may have been due to inbreeding and the loss of genetic diversity common in small populations, or to limited resources. In a systematic literature review, we compared our population trend estimates with those reported for other small populations (<300 individuals) of brown bears. Results suggest that once brown bear populations become small and isolated, populations rarely increase and, even with intensive management, recovery remains challenging.

Population genomics for wildlife conservation and management

Biodiversity is under threat worldwide. Over the past decade, the field of population genomics has developed across nonmodel organisms, and the results of this research have begun to be applied in conservation and management of wildlife species. Genomics tools can provide precise estimates of basic features of wildlife populations, such as effective population size, inbreeding, demographic history and population structure, that are critical for conservation efforts. Moreover, population genomics studies can identify particular genetic loci and variants responsible for inbreeding depression or adaptation to changing environments, allowing for conservation efforts to estimate the capacity of populations to evolve and adapt in response to environmental change and to manage for adaptive variation. While connections from basic research to applied wildlife conservation have been slow to develop, these connections are increasingly strengthening. Here we review the primary areas in which population genomics approaches can be applied to wildlife conservation and management, highlight examples of how they have been used, and provide recommendations for building on the progress that has been made in this field.

A comparative genomics multitool for scientific discovery and conservation

The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe a whole-genome alignment of 240 species of considerable phylogenetic diversity, comprising representatives from more than 80% of mammalian families. We find that regions of reduced genetic diversity are more abundant in species at a high risk of extinction, discern signals of evolutionary selection at high resolution and provide insights from individual reference genomes. By prioritizing phylogenetic diversity and making data available quickly and without restriction, the Zoonomia Project aims to support biological discovery, medical research and the conservation of biodiversity.

A whole-genome alignment of 240 phylogenetically diverse species of eutherian mammal—including 131 previously uncharacterized species—from the Zoonomia Project provides data that support biological discovery, medical research and conservation.

Large scale genome reconstructions illuminate Wolbachia evolution

Wolbachia is an iconic example of a successful intracellular bacterium. Despite its importance as a manipulator of invertebrate biology, its evolutionary dynamics have been poorly studied from a genomic viewpoint. To expand the number of Wolbachia genomes, we screen over 30,000 publicly available shotgun DNA sequencing samples from 500 hosts. By assembling over 1000 Wolbachia genomes, we provide a substantial increase in host representation. Our phylogenies based on both core-genome and gene content provide a robust reference for future studies, support new strains in model organisms, and reveal recent horizontal transfers amongst distantly related hosts. We find various instances of gene function gains and losses in different super-groups and in cytoplasmic incompatibility inducing strains. Our Wolbachia-host co-phylogenies indicate that horizontal transmission is widespread at the host intraspecific level and that there is no support for a general Wolbachia-mitochondrial synchronous divergence.

By greatly expanding the number of assembled genomes for Wolbachia (a group of intracellular bacteria) and constructing robust phylogenies, this study finds strong rate heterogeneity among Wolbachiapopulations and no support for synchronous divergence between Wolbachia and host mitochondria.