Airports for the genetic rescue of a former agricultural pest

The intensification of agricultural practices and urbanisation are widespread causes of biodiversity loss. However, the role of artificial habitats in genetic rescue is an aspect that is not well understood. Implementing genetic rescue measures to improve gene flow and maintain a viable population of keystone species is a crucial prerequisite for promoting diverse and resilient ecosystems. Landscape fragmentation and modern agricultural methods have caused the decline and the isolation of the remnant colonies of the endangered European ground squirrel (Spermophilus citellus) throughout its range. However, the artificial habitat, such as airport fields with regular grass mowing, provides suitable conditions for this grassland specialist. We measured home range size and genetic variation of seven souslik colonies in western Slovakia. Based on the 6904 ddRAD SNPs, we found significantly higher individual heterozygosity in colonies on airports compared to colonies on pastures. This indicates a potential for higher fitness of individuals from airport colonies, which can serve as a source for evidence-based translocations. Such an intervention can preserve the genetic diversity of small and isolated populations in the region. We emphasize that conservation management strategies would be strengthened including a specific focus on human-made grassland habitats.

Patterns of Genetic Diversity and Gene Flow Associated With an Aridity Gradient in Populations of Common Mole-rats, Cryptomys hottentotus hottentotus

Genetic adaptation is the change of a population toward a phenotype that best fits the present ecological conditions of the environment it inhabits. As environmental conditions change, allele frequencies shift, resulting in different populations of the same species possessing genetic variation and divergent phenotypes. Cooperatively breeding common mole-rats (Cryptomys hottentotus hottentotus) inhabit environments along an aridity gradient in South Africa, which provides an opportunity for local genetic adaptations to occur. Using one mitochondrial gene (cytochrome b) and 3,540 SNP loci across the whole genome, we determined the phylogenetic relationship, population structure and genetic diversity of five populations of C. h. hottentotus located along an aridity gradient. Mitochondrial data identified population-specific clades that were less distinct in the two mesic populations, potentially indicating historical or recent gene flow, or the retention of ancestral haplotypes. Arid and semi-arid populations formed a distinct cluster from the non-arid populations. Genetic diversity and gene flow were higher in arid-dwelling individuals, suggesting greater connectivity and interactions between colonies in arid regions in comparison to mesic ones. Using an Aridity Index, we determined that isolation by environment, rather than isolation by geographical distance, best explains the genetic distance between the populations. Further analyses using target loci may determine if there are differing underlying genetic adaptations among populations of C. h. hottentotus. These analyses could help unravel population differences in response to environmental factors within a subspecies of bathyergid mole-rat and determine the adaptive capacity of this small nonmigratory subterranean rodent species in response to aridification in the face of climate change.

Outbreeding reduces survival during metamorphosis in a headwater stream salamander

Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.

Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and often wrong

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.

Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)

Identifying and analysing isolated populations is critical for conservation. Isolation can make populations vulnerable to local extinction due to increased genetic drift and inbreeding, both of which should leave imprints of decreased genome-wide heterozygosity. While decreases in heterozygosity among populations are frequently investigated, fewer studies have analysed how heterozygosity varies among individuals, including whether heterozygosity varies geographically along lines of discrete population structure or with continuous patterns analogous to isolation by distance. Here we explore geographical patterns of differentiation and individual heterozygosity in the threatened eastern barred bandicoot (Perameles gunnii) in Tasmania, Australia, using genomic data from 85 samples collected between 2008 and 2011. Our analyses identified two isolated demes undergoing significant genetic drift, and several areas of fine-scale differentiation across Tasmania. We observed discrete genetic structures across geographical barriers and continuous patterns of isolation by distance, with little evidence of recent or historical migration. Using a recently developed analytical pipeline for estimating autosomal heterozygosity, we found individual heterozygosities varied within demes by up to a factor of two, and demes with low-heterozygosity individuals also still contained those with high heterozygosity. Spatial interpolation of heterozygosity scores clarified these patterns and identified the isolated Tasman Peninsula as a location where low-heterozygosity individuals were more common than elsewhere. Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualised metric for identifying source animals for translocation.

Increased homozygosity due to endogamy results in fitness consequences in a human population

Recessive alleles have been shown to directly affect both human Mendelian disease phenotypes and complex traits. Pedigree studies also suggest that consanguinity results in increased childhood mortality and adverse health phenotypes, presumably through penetrance of recessive mutations. Here, we test whether the accumulation of homozygous, recessive alleles decreases reproductive success in a human population. We address this question among the Namibian Himba, an endogamous agro-pastoralist population, who until very recently practiced natural fertility. Using a sample of 681 individuals, we show that Himba exhibit elevated levels of "inbreeding," calculated as the fraction of the genome in runs of homozygosity (FROH). Many individuals contain multiple long segments of ROH in their genomes, indicating that their parents had high kinship coefficients. However, we do not find evidence that this is explained by first-cousin consanguinity, despite a reported social preference for cross-cousin marriages. Rather, we show that elevated haplotype sharing in the Himba is due to a bottleneck, likely in the past 60 generations. We test whether increased recessive mutation load results in observed fitness consequences by assessing the effect of FROH on completed fertility in a cohort of postreproductive women (n = 69). We find that higher FROH is significantly associated with lower fertility. Our data suggest a multilocus genetic effect on fitness driven by the expression of deleterious recessive alleles, especially those in long ROH. However, these effects are not the result of consanguinity but rather elevated background identity by descent.

Genomic population structure and inbreeding history of Lake Superior caribou

Caribou (Rangifer tarandus) have experienced dramatic declines in both range and population size across Canada over the past century. Boreal caribou (R. t. caribou), 1 of the 12 Designatable Units, has lost approximately half of its historic range in the last 150 years, particularly along the southern edge of its distribution. Despite this overall northward contraction, some populations have persisted at the trailing range edge, over 150 km south of the continuous boreal caribou range in Ontario, along the coast and nearshore islands of Lake Superior. The population history of caribou along Lake Superior remains unclear. It appears that these caribou likely represent a remnant distribution at the trailing edge of the receding population of boreal caribou, but they may also exhibit local adaptation to the coastal environment. A better understanding of the population structure and history of caribou along Lake Superior is important for their conservation and management. Here, we use high-coverage whole genomes (N = 20) from boreal, eastern migratory, and barren-ground caribou sampled in Manitoba, Ontario, and Quebec to investigate population structure and inbreeding histories. We discovered that caribou from the Lake Superior range form a distinct group but also found some evidence of gene flow with the continuous boreal caribou range. Notably, caribou along Lake Superior demonstrated relatively high levels of inbreeding (measured as runs of homozygosity; ROH) and genetic drift, which may contribute to the differentiation observed between ranges. Despite inbreeding, caribou along Lake Superior retained high heterozygosity, particularly in genomic regions without ROH. These results suggest that they present distinct genomic characteristics but also some level of gene flow with the continuous range. Our study provides key insights into the genomics of the southernmost range of caribou in Ontario, beginning to unravel the evolutionary history of these small, isolated caribou populations.

Tropical forest loss and geographic location drive the functional genomic diversity of an endangered palm tree

Human activity has diminished forests in different terrestrial ecosystems. This is well illustrated in the Brazilian Atlantic Forest, which still hosts high levels of species richness and endemism, even with only 28% of its original extent remaining. The consequences of such forest loss in remaining populations can be investigated with several approaches, including the genomic perspective, which allows a broader understanding of how human disturbance influences the genetic variability in natural populations. In this context, our study investigated the genomic responses of Euterpe edulis Martius, an endangered palm tree, in forest remnants located in landscapes presenting different forest cover amount and composed by distinct bird assemblage that disperse its seeds. We sampled 22 areas of the Brazilian Atlantic Forest in four regions using SNP markers inserted into transcribed regions of the genome of E. edulis, distinguishing neutral loci from those putatively under natural selection (outlier). We demonstrate that populations show patterns of structure and genetic variability that differ between regions, as a possible reflection of deforestation and biogeographic histories. Deforested landscapes still maintain high neutral genetic diversity due to gene flow over short distances. Overall, we not only support previous evidence with microsatellite markers, but also show that deforestation can influence the genetic variability outlier, in the scenario of selective pressures imposed by these stressful environments. Based on our findings, we suggest that, to protect genetic diversity in the long term, it is necessary to reforest and enrich deforested areas, using seeds from populations in the same management target region.

Impacts of large herbivores on terrestrial ecosystems

Large herbivores play unique ecological roles and are disproportionately imperiled by human activity. As many wild populations dwindle towards extinction, and as interest grows in restoring lost biodiversity, research on large herbivores and their ecological impacts has intensified. Yet, results are often conflicting or contingent on local conditions, and new findings have challenged conventional wisdom, making it hard to discern general principles. Here, we review what is known about the ecosystem impacts of large herbivores globally, identify key uncertainties, and suggest priorities to guide research. Many findings are generalizable across ecosystems: large herbivores consistently exert top-down control of plant demography, species composition, and biomass, thereby suppressing fires and the abundance of smaller animals. Other general patterns do not have clearly defined impacts: large herbivores respond to predation risk but the strength of trophic cascades is variable; large herbivores move vast quantities of seeds and nutrients but with poorly understood effects on vegetation and biogeochemistry. Questions of the greatest relevance for conservation and management are among the least certain, including effects on carbon storage and other ecosystem functions and the ability to predict outcomes of extinctions and reintroductions. A unifying theme is the role of body size in regulating ecological impact. Small herbivores cannot fully substitute for large ones, and large-herbivore species are not functionally redundant - losing any, especially the largest, will alter net impact, helping to explain why livestock are poor surrogates for wild species. We advocate leveraging a broad spectrum of techniques to mechanistically explain how large-herbivore traits and environmental context interactively govern the ecological impacts of these animals.

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.

Polyandry and non-random fertilisation maintain long-term genetic diversity in an isolated island population of adders (Vipera berus)

Conservation genetic theory suggests that small and isolated populations should be subject to reduced genetic diversity i.e., heterozygosity and allelic diversity. Our 34 years study of an isolated island population of adders (Vipera berus) in southern Sweden challenges this notion. Despite a lack of gene flow and a yearly mean estimated reproductive adult population size of only 65 adult adders (range 12-171), the population maintains high levels of heterozygosity and allelic diversity similar to that observed in two mainland populations. Even a 14-year major "bottleneck" i.e., a reduction in adult adder numbers, encompassing at least four adder generations, did not result in any reduction in the island adders' heterozygosity and allelic diversity. Female adders are polyandrous, and fertilisation is non-random, which our empirical data and modelling suggest are underpinning the maintenance of the population's high level of heterozygosity. Our empirical results and subsequent modelling suggest that the positive genetic effects of polyandry in combination with non-random fertilisation, often overlooked in conservation genetic analyses, deserve greater consideration when predicting long-term survival of small and isolated populations.

Understanding Local Adaptation to Prepare Populations for Climate Change

Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.

Landscape Genomics to Enable Conservation Actions: The California Conservation Genomics Project

The California Conservation Genomics Project (CCGP) is a unique, critically important step forward in the use of comprehensive landscape genetic data to modernize natural resource management at a regional scale. We describe the CCGP, including all aspects of project administration, data collection, current progress, and future challenges. The CCGP will generate, analyze, and curate a single high-quality reference genome and 100-150 resequenced genomes for each of 153 species projects (representing 235 individual species) that span the ecological and phylogenetic breadth of California's marine, freshwater, and terrestrial ecosystems. The resulting portfolio of roughly 20 000 resequenced genomes will be analyzed with identical informatic and landscape genomic pipelines, providing a comprehensive overview of hotspots of within-species genomic diversity, potential and realized corridors connecting these hotspots, regions of reduced diversity requiring genetic rescue, and the distribution of variation critical for rapid climate adaptation. After 2 years of concerted effort, full funding ($12M USD) has been secured, species identified, and funds distributed to 68 laboratories and 114 investigators drawn from all 10 University of California campuses. The remaining phases of the CCGP include completion of data collection and analyses, and delivery of the resulting genomic data and inferences to state and federal regulatory agencies to help stabilize species declines. The aspirational goals of the CCGP are to identify geographic regions that are critical to long-term preservation of California biodiversity, prioritize those regions based on defensible genomic criteria, and provide foundational knowledge that informs management strategies at both the individual species and ecosystem levels.

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.

Challenges in quantifying genome erosion for conservation

Massive defaunation and high extinction rates have become characteristic of the Anthropocene. Genetic effects of population decline can lead populations into an extinction vortex, where declining populations show lower genetic fitness, in turn leading to lower populations still. The lower genetic fitness in a declining population due to a shrinking gene pool is known as genetic erosion. Three different types of genetic erosion are highlighted in this review: overall homozygosity, genetic load and runs of homozygosity (ROH), which are indicative of inbreeding. The ability to quantify genetic erosion could be a very helpful tool for conservationists, as it can provide them with an objective, quantifiable measure to use in the assessment of species at risk of extinction. The link between conservation status and genetic erosion should become more apparent. Currently, no clear correlation can be observed between the current conservation status and genetic erosion. However, the high quantities of genetic erosion in wild populations, especially in those species dealing with habitat fragmentation and habitat decline, may be early signs of deteriorating populations. Whole genome sequencing data is the way forward to quantify genetic erosion. Extra screening steps for genetic load and hybridization can be included, since they could potentially have great impact on population fitness. This way, the information yielded from genetic sequence data can provide conservationists with an objective genetic method in the assessment of species at risk of extinction. However, the great complexity of genome erosion quantification asks for consensus and bridging science and its applications, which remains challenging.

Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout

The current extinction crisis requires effective assessment and monitoring tools. Genetic approaches are appealing given the relative ease of field sampling required to estimate genetic diversity characteristics assumed related to population size, evolutionary potential, and extinction risk, and to evaluate hybridization with non‐native species simultaneously. However, linkages between population genetic metrics of diversity from survey‐style field collections and demographic estimates of population size and extinction risk are still in need of empirical examples, especially for remotely distributed species of conservation concern where the approach might be most beneficial. We capitalized on an exceptional opportunity to evaluate congruence between genetic diversity metrics and demographic‐based estimates of abundance and extinction risk from a comprehensive Multiple Population Viability Analysis (MPVA) in a threatened fish, the Lahontan cutthroat trout (LCT). We sequenced non‐native trout reference samples and recently collected and archived tissue samples of most remaining populations of LCT (N = 60) and estimated common genetic assessment metrics, predicting minimal hybridization with non‐native trout, low diversity, and declining diversity over time. We further hypothesized genetic metrics would correlate positively with MPVA‐estimated abundance and negatively with extinction probability. We uncovered several instances of hybridization that pointed to immediate management needs. After removing hybridized individuals, cautious interpretation of low effective population sizes (2–63) suggested reduced evolutionary potential for many LCT populations. Other genetic metrics did not decline over time nor correlate with MPVA‐based estimates of harmonic mean abundance or 30‐year extinction probability. Our results demonstrate benefits of genetic monitoring for efficiently detecting hybridization and, though genetic results were disconnected from demographic assessment of conservation status, they suggest reduced evolutionary potential and likely a higher conservation risk than currently recognized for this threatened fish. We emphasize that genetic information provides essential complementary insight, in addition to demographic information, for evaluating species status.

Chromosomal-level reference genome assembly of the North American wolverine (Gulo gulo luscus): a resource for conservation genomics

We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.

Genomic status of yellow-breasted bunting following recent rapid population decline

Global biodiversity is facing serious threats. However, knowledge of the genomic consequences of recent rapid population declines of wild organisms is limited. Do populations experiencing recent rapid population decline have the same genomic status as wild populations that experience long-term declines? Yellow-breasted Bunting (Emberiza aureola) is a critically endangered species that has been experiencing a recent rapid population decline. To answer the question, we assembled and annotated the whole genome of Yellow-breasted Bunting. Furthermore, we found high genetic diversity, low linkage disequilibrium, and low proportion of long runs of homozygosity in Yellow-breasted Bunting, suggesting that the populations following recent rapid declines have different genomic statuses from the population that experienced long-term population decline.

Phylogenomics of the world's otters

Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,^1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.

Non-invasive monitoring and reintroduction biology of the brush-tailed rock-wallaby (

Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.

Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations

The deleterious effects of inbreeding have been of extreme importance to evolutionary biology, but it has been difficult to characterize the complex interactions between genetic constraints and selection that lead to fitness loss and recovery after inbreeding. Haploid organisms and selfing organisms like the nematode Caenorhabditis elegans are capable of rapid recovery from the fixation of novel deleterious mutation; however, the potential for recovery and genomic consequences of inbreeding in diploid, outcrossing organisms are not well understood. We sought to answer two questions: 1) Can a diploid, outcrossing population recover from inbreeding via standing genetic variation and new mutation? and 2) How does allelic diversity change during recovery? We inbred C. remanei, an outcrossing relative of C. elegans, through brother-sister mating for 30 generations followed by recovery at large population size. Inbreeding reduced fitness but, surprisingly, recovery from inbreeding at large populations sizes generated only very moderate fitness recovery after 300 generations. We found that 65% of ancestral single nucleotide polymorphisms (SNPs) were fixed in the inbred population, far fewer than the theoretical expectation of ∼99%. Under recovery, 36 SNPs across 30 genes involved in alimentary, muscular, nervous, and reproductive systems changed reproducibly across replicates, indicating that strong selection for fitness recovery does exist. Our results indicate that recovery from inbreeding depression via standing genetic variation and mutation is likely to be constrained by the large number of segregating deleterious variants present in natural populations, limiting the capacity for recovery of small populations.

Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies

The rate of global climate change is projected to outpace the ability of many natural populations and species to adapt. Assisted migration (AM), which is defined as the managed movement of climate-adapted individuals within or outside the species ranges, is a conservation option to improve species' adaptive capacity and facilitate persistence. Although conservation biologists have long been using genetic tools to increase or maintain diversity of natural populations, genomic techniques could add extra benefit in AM that include selectively neutral and adaptive regions of the genome. In this review, we first propose a framework along with detailed procedures to aid collaboration among scientists, agencies, and local and regional managers during the decision-making process of genomics-guided AM. We then summarize the genomic approaches for applying AM, followed by a literature search of existing incorporation of genomics in AM across taxa. Our literature search initially identified 729 publications, but after filtering returned only 50 empirical studies that were either directly applied or considered genomics in AM related to climate change across taxa of plants, terrestrial animals, and aquatic animals; 42 studies were in plants. This demonstrated limited application of genomic methods in AM in organisms other than plants, so we provide further case studies as two examples to demonstrate the negative impact of climate change on non-model species and how genomics could be applied in AM. With the rapidly developing sequencing technology and accumulating genomic data, we expect to see more successful applications of genomics in AM, and more broadly, in the conservation of biodiversity.

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.

Life-history traits and habitat availability shape genomic diversity in birds: implications for conservation

More than 25% of species assessed by the International Union for Conservation of Nature (IUCN) are threatened with extinction. Understanding how environmental and biological processes have shaped genomic diversity may inform management practices. Using 68 extant avian species, we parsed the effects of habitat availability and life-history traits on genomic diversity over time to provide a baseline for conservation efforts. We used published whole-genome sequence data to estimate overall genomic diversity as indicated by historical long-term effective population sizes (Ne) and current genomic variability (H), then used environmental niche modelling to estimate Pleistocene habitat dynamics for each species. We found that Ne and H were positively correlated with habitat availability and related to key life-history traits (body mass and diet), suggesting the latter contribute to the overall genomic variation. We found that H decreased with increasing species extinction risk, suggesting that H may serve as a leading indicator of demographic trends related to formal IUCN conservation status in birds. Our analyses illustrate that genome-wide summary statistics estimated from sequence data reflect meaningful ecological attributes relevant to species conservation.

Genomic methods reveal independent demographic histories despite strong morphological conservatism in fish species

Human overexploitation of natural resources has placed conservation and management as one of the most pressing challenges in modern societies, especially in regards to highly vulnerable marine ecosystems. In this context, cryptic species are particularly challenging to conserve because they are hard to distinguish based on morphology alone, and thus it is often unclear how many species coexist in sympatry, what are their phylogenetic relationships and their demographic history. We answer these questions using morphologically similar species of the genus Mugil that are sympatric in the largest coastal Marine Protected Area in the Tropical Southwestern Atlantic marine province. Using a sub-representation of the genome, we show that individuals are assigned to five highly differentiated genetic clusters that are coincident with five mitochondrial lineages, but discordant with morphological information, supporting the existence of five species with conserved morphology in this region. A lack of admixed individuals is consistent with strong genetic isolation between sympatric species, but the most likely species tree suggests that in one case speciation has occurred in the presence of interspecific gene flow. Patterns of genetic diversity within species suggest that effective population sizes differ up to two-fold, probably reflecting differences in the magnitude of population expansions since species formation. Together, our results show that strong morphologic conservatism in marine environments can lead to species that are difficult to distinguish morphologically but that are characterized by an independent evolutionary history, and thus that deserve species-specific management strategies.

Genomic time-series data show that gene flow maintains high genetic diversity despite substantial genetic drift in a butterfly species

Effective population size affects the efficacy of selection, rate of evolution by drift, and neutral diversity levels. When species are subdivided into multiple populations connected by gene flow, evolutionary processes can depend on global or local effective population sizes. Theory predicts that high levels of diversity might be maintained by gene flow, even very low levels of gene flow, consistent with species long-term effective population size, but tests of this idea are mostly lacking. Here, we show that Lycaeides buttery populations maintain low contemporary (variance) effective population sizes (e.g., ~200 individuals) and thus evolve rapidly by genetic drift. In contrast, populations harbored high levels of genetic diversity consistent with an effective population size several orders of magnitude larger. We hypothesized that the differences in the magnitude and variability of contemporary versus long-term effective population sizes were caused by gene flow of sufficient magnitude to maintain diversity but only subtly affect evolution on generational time scales. Consistent with this hypothesis, we detected low but non-trivial gene flow among populations. Furthermore, using short-term population-genomic time-series data, we documented patterns consistent with predictions from this hypothesis, including a weak but detectable excess of evolutionary change in the direction of the mean (migrant gene pool) allele frequencies across populations, and consistency in the direction of allele frequency change over time. The documented decoupling of diversity levels and short-term change by drift in Lycaeides has implications for our understanding of contemporary evolution and the maintenance of genetic variation in the wild.

ASSESSMENT OF DISEASE RISK ASSOCIATED WITH POTENTIAL REMOVAL OF ANTHROPOGENIC BARRIERS TO MOJAVE DESERT TORTOISE (GOPHERUS AGASSIZII) POPULATION CONNECTIVITY

The Mojave Desert tortoise (Gopherus agassizii), federally listed as threatened, has suffered habitat loss and fragmentation due to human activities. Upper respiratory tract disease (URTD), a documented health threat to desert tortoises, has been detected at the Large-Scale Translocation Study Site (LSTS) in southwestern Nevada, US, a fenced recipient site for translocated animals. Our study aimed to 1) estimate prevalence of URTD and Mycoplasma infection at LSTS and three nearby unfenced sites; 2) assess whether Mycoplasma infection status was associated with developing clinical signs of URTD; and 3) determine whether such an association differed between LSTS and unfenced areas. We sampled 421 tortoises in 2016 to describe the current status of these populations. We evaluated three clinical signs of URTD (nasal discharge, ocular discharge, nasal erosions) and determined individual infection status for Mycoplasma agassizii and Mycoplasma testudineum by quantitative PCR and enzyme-linked immunosorbent assay. In 2016, LSTS had the highest prevalence of M. agassizii (25.0%; 33/132), M. testudineum (3.0%; 4/132), and URTD clinical signs (18.9%; 25/132). Controlling for other factors, clinical sign(s) were positively associated with M. agassizii infection (odds ratio [OR]=7.7, P=0.001), and this effect was similar among study sites (P>0.99). There was no association with M. testudineum status (P=0.360). Of the 196 tortoises in a longitudinal comparison of 2011-14 with 2016, an estimated 3.2% converted from M. agassizii-negative to positive during the study period, and incidence was greater at LSTS (P=0.002). Conversion to positive M. agassizii status was associated with increased incidence of clinical signs in subsequent years (OR=11.1, P=0.018). While M. agassizii and URTD are present outside the LSTS, there is a possibility that incidence of Mycoplasma infection and URTD would increase outside LSTS if these populations were to reconnect. Population-level significance of this risk appears low, and any risk must be evaluated against the potential long-term benefits to population viability through increased connectivity.

The long-standing significance of genetic diversity in conservation

Since allozymes were first used to assess genetic diversity in the 1960s and 1970s, biologists have attempted to characterize gene pools and conserve the diversity observed in domestic crops, livestock, zoos and (more recently) natural populations. Recently, some authors have claimed that the importance of genetic diversity in conservation biology has been greatly overstated. Here, we argue that a voluminous literature indicates otherwise. We address four main points made by detractors of genetic diversity's role in conservation by using published literature to firmly establish that genetic diversity is intimately tied to evolutionary fitness, and that the associated demographic consequences are of paramount importance to many conservation efforts. We think that responsible management in the Anthropocene should, whenever possible, include the conservation of ecosystems, communities, populations and individuals, and their underlying genetic diversity.

Response to Comment on "Individual heterozygosity predicts translocation success in threatened desert tortoises"

Hansson et al argue that our main finding could provide an overly simplistic metric for maximizing genetic rescue. They agree that translocating the most genetically diverse individuals led to a large increase in translocated tortoise survival, but recommend instead moving individuals that have low genetic load and the greatest representation of metapopulation diversity. Their recommendation is based on specific model assumptions and fitness effects that are often unknown and are not generalizable to many endangered species applications.

Response to Comment on "Individual heterozygosity predicts translocation success in threatened desert tortoises"

Hedrick brings up several potential concerns that he feels challenge or limit our main finding. Hedrick does not comment on our empirical results, but rather argues that several factors may confound or invalidate our conclusion. Many of these concerns focus on unknown ecological aspects of the translocated tortoises, but we believe there is no reason to conclude that they bias the results or interpretation as presented in our original paper.

Comment on "Individual heterozygosity predicts translocation success in threatened desert tortoises"

Scott et al (Reports, 27 November 2020, p. 1086) suggest, on the basis of conclusions obtained from a desert tortoise reintroduction program, that higher genomic heterozygosity should be used to identify individuals for successful translocation. I contend that this recommendation is questionable given these relocated tortoises' unknown origin, their high mortality, insufficient data on resident tortoises and other components of fitness, and potential allelic dropout.