Inbreeding reduces long-term growth of Alpine ibex populations

Meeting Report on the Symposium "Evolutionary Applications" at the 3rd Joint Congress on Evolutionary Biology

The symposium "Evolutionary Applications" took place on June 28, 2024 in the virtual part of the 3rd Joint Congress on Evolutionary Biology. It was contributed to the conference by the European Society for Evolutionary Biology (ESEB). The symposium highlighted research on evolutionary biology applied to address questions and contemporary problems in medicine and public health, conservation biology, and food production and agriculture. Each of the six talks covered a different application and a different organism: domestication of cheese-making fungi, restoration of long-lived bird populations, evolution of herbicide resistance, coral reef conservation, gene drive systems targeting Malaria vectors, and antibiotic resistance evolution in bacteria. By including speakers who are active in a consortium or work in an NGO, the symposium also showed how to make the step from scientific findings to practical application. The symposium furthermore featured a range of scientific methods, ranging from genomic analyses and mathematical modeling to laboratory evolution and field experiments. Speakers from across 15 time zones highlighted the potential of virtual symposia to foster global collaboration in evolutionary biology.

Genomic Insights Into Inbreeding and Adaptive Divergence of Trout Populations to Inform Genetic Rescue

Genetic rescue, specifically translocation to facilitate gene flow among populations and reduce the effects of inbreeding, is an increasingly used approach in conservation. However, this approach comes with trade-offs, wherein gene flow may reduce fitness when populations have adaptive differentiation (i.e., outbreeding depression). A better understanding of the interaction between isolation, inbreeding, and adaptive divergence in key traits, such as life history traits, will help to inform genetic rescue efforts. Stream-dwelling salmonids, such as the westslope cutthroat trout (Oncorhynchus lewisi; WCT), are well-suited for examining these trade-offs because they are increasingly isolated by habitat degradation, exhibit substantial variation in life history traits among populations, and include many species of conservation concern. However, few genomic studies have examined the potential trade-offs in inbreeding versus outbreeding depression in salmonids. We used > 150,000 SNPs to examine genomic variation and inbreeding coefficients in 565 individuals across 25 WCT populations that differed in their isolation status and demographic histories. Analyses of runs of homozygosity revealed that several isolated WCT populations had "flatlined" having extremely low genetic variation and high inbreeding coefficients. Additionally, we conducted genome scans to identify potential outlier loci that could explain life history differences among 10 isolated populations. Genome scans identified one candidate genomic region that influenced maximum length and age-1 to age-2 growth. However, the limited number of candidate loci suggests that the life history traits examined may be driven by many genes of small effect or phenotypic plasticity. Although adaptive differentiation should be considered, the high inbreeding coefficients in several populations suggest that genetic rescue may benefit the most genetically depauperate WCT populations.

Geography and Environment Shape Spatial Genetic Variation and Predict Climate Maladaptation Across Isolated and Disjunct Populations of Pinus muricata

Assessing the evolutionary potential of rare species with limited migration amidst ongoing climate change requires an understanding of patterns of genetic variation and local adaptation. In contrast to the large distributions and population sizes of most pines, Pinus muricata (bishop pine) occurs in a few isolated populations along coastal western North America and is listed as threatened by the IUCN. To quantify how current genetic variation is influenced by distribution and environment, we generated reduced representation DNA sequencing data for most extant populations of P. muricata (12 locations, 7828 loci). We assessed geographic variation in differentiation and diversity and used genetic-environment association (GEA) analyses to characterise the contribution of environmental variables to local adaptation and genetic structure. Based on these inferences, we quantified genomic offset as a relative estimate of potential maladaptation under mild (SSP1-2.6) and severe (SSP5-8.5) climate change scenarios across 2041-2060 and 2081-2100. Despite occurring in small, isolated populations, genetic diversity was not low in P. muricata. Population differentiation was, however, defined across a hierarchy of spatial scales, with stands generally forming genetically identifiable groups across latitude and environments. GEA analyses implicated temperature- and soil-related variables as most strongly contributing to local adaptation. Estimates of maladaptation to future climate varied non-linearly with latitude, increased with severity of projections and over time, and were predicted by increases in annual temperature. Our results suggest that isolation and local adaptation have shaped genetic variation among disjunct populations and that these factors may shape maladaptation risk under projected climate change.

Increasing Aridity May Threaten the Maintenance of a Plant Defence Polymorphism

It is unclear how environmental change influences standing genetic variation in wild populations. Here, we characterised environmental conditions that protect versus erode polymorphic chemical defences in Boechera stricta (Brassicaceae), a short-lived perennial wildflower. By manipulating drought and herbivory in a 4-year field experiment, we measured the effects of driver variation on vital rates of genotypes varying in defence chemistry and then assessed interacting driver effects on total fitness (estimated as each genotype's lineage growth rate, λ) using demographic models. Drought and herbivory interacted to shape vital rates, but contrasting defence genotypes had equivalent total fitness in many environments. Defence polymorphism thus may persist under a range of conditions; however, ambient field conditions fall close to the boundary of putatively polymorphic environment space, and increasing aridity may drive populations to monomorphism. Consequently, elevated intensity and/or frequency of drought under climate change may erode genetic variation for defence chemistry in B. stricta.

What Can Genome Sequence Data Reveal About Population Viability?

Biologists have long sought to understand the impacts of deleterious genetic variation on fitness and population viability. However, our understanding of these effects in the wild is incomplete, in part due to the rarity of sufficient genetic and demographic data needed to measure their impact. The genomics revolution is promising a potential solution by predicting the effects of deleterious genetic variants (genetic load) bioinformatically from genome sequences alone bypassing the need for costly demographic data. After a historical perspective on the theoretical and empirical basis of our understanding of the dynamics and fitness effects of deleterious genetic variation, we evaluate the potential for these new genomic measures of genetic load to predict population viability. We argue that current genomic analyses alone cannot reliably predict the effects of deleterious genetic variation on population growth, because these depend on demographic, ecological and genetic parameters that need more than just genome sequence data to be measured. Thus, while purely genomic analyses of genetic load promise to improve our understanding of the composition of the genetic load, they are currently of little use for evaluating population viability. Demographic data and ecological context remain crucial to our understanding of the consequences of deleterious genetic variation for population fitness. However, when combined with such demographic and ecological data, genomic information can offer important insights into genetic variation and inbreeding that are crucial for conservation decision making.

Density dependence maintains long-term stability despite increased isolation and inbreeding in the Florida Scrub-Jay

Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.

Inbreeding avoidance and cost in a small, isolated trout population

The persistence of small populations is influenced by the degree and cost of inbreeding, with the degree of inbreeding depending on whether close-kin mating is passively or actively avoided. Few studies have simultaneously studied these factors. We examined inbreeding in a small, isolated population of westslope cutthroat trout using extensive genetic and demographic data. Passive inbreeding avoidance was low, with predicted lifetime dispersal of approximately 36 and 74 m for females and males, respectively. Additionally, we found limited evidence for active inbreeding avoidance during reproduction. Relatives remained spatially clustered into adulthood, and observed relatedness among mate pairs was greater than expected under random mating by 0.09, suggesting that inbreeding is a concern in this population. Further, we examined sex-specific inbreeding depression throughout the life cycle and provide evidence for inbreeding depression in some fitness components, including family size, juvenile survival and reproductive success. Our results suggest that, in an at-risk trout population, limited passive and active inbreeding avoidance lead to a higher degree of inbreeding than expected under random mating. Observed inbreeding, along with evidence for fitness reduction due to inbreeding depression, could put the population at a heightened risk of decline or extirpation.

Genetic evidence of a hybrid swarm between Alpine ibex (Capra ibex) and domestic goat (C. hircus)

Improving the understanding of the causes and effects of anthropogenic hybridization is fundamental to ensure species conservation, particularly in the case of hybridization between wild species and their domestic relatives. Knowledge is missing for many species also because of a lack of appropriate tools for hybrid identification. Here, coupling genotype and phenotype analysis, we carried out an extensive investigation of ongoing hybridization in Alpine ibex Capra ibex, a mountain ungulate of conservation concern from a genetic perspective. By genotyping 63 diagnostic and 465 neutral SNPs, 20 suspected hybrids and 126 Alpine ibex without suspicious phenotype, representing 8 populations across a major part of the species distribution, we found evidence for ongoing hybridization between Alpine ibex and domestic goat. We identified different levels of hybridization including backcrosses into both Alpine ibex and domestic goat. Our results suggest a lack of reproductive barriers between the two species and good survival and reproductive success of the hybrids. Hybridization was locally intense, like a hybrid swarm, but not spread across the rest of the species distribution. Most of the hybrids were discovered in two locations in the north-west of Italy, while random sampling of individuals from different areas did not provide evidence of recent hybridization. Our method, based on amplicon sequencing of 63 diagnostic SNPs specifically developed for this purpose, allowed us to identify hybrids and backcrosses up to the fourth to fifth generations and was suitable for genetic samples of different quality, although with varying levels of certainty regarding the exact number of generations passed since hybridization. Based on the paired analysis of genotype and phenotype, we provide guidelines for the first identification of hybrids in the field and suggest a procedure for the reliable identification of hybrids.

Impacts of increasing isolation and environmental variation on Florida Scrub-Jay demography

Isolation caused by anthropogenic habitat fragmentation can destabilize populations. Populations relying on the inflow of immigrants can face reduced fitness due to inbreeding depression as fewer new individuals arrive. Empirical studies of the demographic consequences of isolation are critical to understand how populations persist through changing conditions. We used a 34-year demographic and environmental dataset from a population of cooperatively-breeding Florida Scrub-Jays ( Aphelocoma coerulescens ) to create mechanistic models linking environmental and demographic factors to population growth rates. We found that the population has not declined despite both declining immigration and increasing inbreeding, owing to a coinciding response in breeder survival. We find evidence of density-dependent immigration, breeder survival, and fecundity, indicating that interactions between vital rates and local density play a role in buffering the population against change. Our study elucidates the impacts of isolation on demography and how long-term stability is maintained via demographic responses.

Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction

High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.

How density dependence, genetic erosion and the extinction vortex impact evolutionary rescue

Following severe environmental change that reduces mean population fitness below replacement, populations must adapt to avoid eventual extinction, a process called evolutionary rescue. Models of evolutionary rescue demonstrate that initial size, genetic variation and degree of maladaptation influence population fates. However, many models feature populations that grow without negative density dependence or with constant genetic diversity despite precipitous population decline, assumptions likely to be violated in conservation settings. We examined the simultaneous influences of density-dependent growth and erosion of genetic diversity on populations adapting to novel environmental change using stochastic, individual-based simulations. Density dependence decreased the probability of rescue and increased the probability of extinction, especially in large and initially well-adapted populations that previously have been predicted to be at low risk. Increased extinction occurred shortly following environmental change, as populations under density dependence experienced more rapid decline and reached smaller sizes. Populations that experienced evolutionary rescue lost genetic diversity through drift and adaptation, particularly under density dependence. Populations that declined to extinction entered an extinction vortex, where small size increased drift, loss of genetic diversity and the fixation of maladaptive alleles, hindered adaptation and kept populations at small densities where they were vulnerable to extinction via demographic stochasticity.

Functional genomic diversity is correlated with neutral genomic diversity in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation, yet this widely used approach has recently been questioned in the genomics era. Here, we leverage a chromosome-level genome assembly of an endangered rattlesnake (Sistrurus catenatus) combined with whole genome resequencing data (N = 110 individuals) to evaluate the relationship between levels of genome-wide neutral and functional diversity over historical and future timescales. As predicted, we found positive correlations between genome-wide estimates of neutral genetic diversity (π) and inferred levels of adaptive variation and an estimate of inbreeding mutation load, and a negative relationship between neutral diversity and an estimate of drift mutation load. However, these correlations were half as strong for projected future levels of neutral diversity based on contemporary effective population sizes. Broadly, our results confirm that estimates of neutral genetic diversity provide an accurate measure of genetic erosion in populations of a threatened vertebrate. They also provide nuance to the neutral-functional diversity controversy by suggesting that while these correlations exist, anthropogenetic impacts may have weakened these associations in the recent past and into the future.

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer

Anthropogenic reintroduction can supplement natural recolonization in reestablishing a species' distribution and abundance. However, both reintroductions and recolonizations can give rise to founder effects that reduce genetic diversity and increase inbreeding, potentially causing the accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonizations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonized populations without admixture possessed much lower heterozygosity, higher inbreeding and longer runs of homozygosity, possibly caused by serial population founder effects and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonized populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonization in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.

Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States

Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.

Inbreeding depression explains killer whale population dynamics

Understanding the factors that cause endangered populations to either grow or decline is crucial for preserving biodiversity. Conservation efforts often address extrinsic threats, such as environmental degradation and overexploitation, that can limit the recovery of endangered populations. Genetic factors such as inbreeding depression can also affect population dynamics but these effects are rarely measured in the wild and thus often neglected in conservation efforts. Here we show that inbreeding depression strongly influences the population dynamics of an endangered killer whale population, despite genomic signatures of purging of deleterious alleles via natural selection. We find that the 'Southern Residents', which are currently endangered despite nearly 50 years of conservation efforts, exhibit strong inbreeding depression for survival. Our population models suggest that this inbreeding depression limits population growth and predict further decline if the population remains genetically isolated and typical environmental conditions continue. The Southern Residents also had more inferred homozygous deleterious alleles than three other, growing, populations, further suggesting that inbreeding depression affects population fitness. These results demonstrate that inbreeding depression can substantially limit the recovery of endangered populations. Conservation actions focused only on extrinsic threats may therefore fail to account for key intrinsic genetic factors that also limit population growth.

Are genetic variation and demographic performance linked?

Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ S) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re-census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.

Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors

Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.

How methodological changes have influenced our understanding of population structure in threatened species: insights from tiger populations across India

Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60-70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue 'Celebrating 50 years since Lewontin's apportionment of human diversity'.

Ancient mitochondrial and modern whole genomes unravel massive genetic diversity loss during near extinction of Alpine ibex

Population bottlenecks can have dramatic consequences for the health and long-term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10-20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1-2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations from the emergence of a species through its near extinction up to the recent past.

Inbreeding is associated with shorter early-life telomere length in a wild passerine

Inbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows (Passer domesticus) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows (n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres (n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.

Hybridization between Alpine Ibex and Domestic Goat in the Alps: A Sporadic and Localized Phenomenon?

Simple Summary

The Alpine ibex (Capra ibex) is a protected wild ungulate. The species is known to have a low genetic variability and to occasionally suffer from local population decline as a consequence of epidemic diseases. Another, less investigated, threat for the species’ long-term conservation is represented by the hybridization with feral domestic goats that may breed with ibex if abandoned in the mountain at the end of the summer pasture. Further reproduction and the spread of hybrids may jeopardize the genetic integrity of wild Alpine ibex. By means of an online survey and using a network of experts, we mapped unpublished evidence on observed hybridization events between Alpine ibex and feral domestic goats. The results of this study suggested that hybrids are currently distributed in several countries, and their presence is not a rare event, with some clusters including 4–20 probable hybrids. This calls for more studies clearly quantifying hybrids in Alpine ibex colonies, but also highlights the need for conservation actions aimed at controlling this phenomenon, such as the effective management of domestic herds grazing in Alpine ibex core areas and clear guidelines on hybrid management.

Abstract

The Alpine ibex (Capra ibex) is a mountain ungulate living in the European Alps. Although being currently classified as a species of Least Concern (LC) by the IUCN, a potential threat for its long-term conservation is introgression following hybridization with domestic goats (Capra hircus). Hybridization has been documented in Switzerland in captive and free ranging animals, although accurate data to assess the extent of this phenomenon in natural conditions in the Alps are lacking. Using an online survey and a network of experts, we collected and mapped unpublished evidence of hybridization events that occurred between Alpine ibex and feral domestic goats from 2000 to 2021. The results of this study showed that hybrids are distributed in most of the Alpine countries, and their presence is not a sporadic event, with some clusters including 4–20 probable hybrids. Our results illustrated the need for establishing a standardized and effective protocol to identify hybrids in the field (such as a formal description of the morphological traits characterizing hybrids), as well as clear guidelines for hybrid management. Even more importantly, this study also highlighted the need for actions aimed at avoiding hybridization, such as the effective management of domestic herds grazing in Alpine ibex core areas.

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.

Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization

In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad-scale geographic origin assignment using nuclear markers to support law enforcement.

The crucial role of genome-wide genetic variation in conservation

The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.

Integrating advances in population and evolutionary ecology with conservation strategy through long-term studies of red-billed choughs

Conceptual and methodological advances in population and evolutionary ecology are often pursued with the ambition that they will help identify demographic, ecological and genetic constraints on population growth rate (λ), and ultimately facilitate evidence-based conservation. However, such advances are often decoupled from conservation practice, impeding translation of scientific understanding into effective conservation and of conservation-motivated research into wider conceptual understanding. We summarise key outcomes from long-term studies of a red-billed chough Pyrrhocorax pyrrhocorax population of conservation concern, where we proactively aimed to achieve the dual and interacting objectives of advancing population and evolutionary ecology and advancing effective conservation. Estimation of means, variances and covariances in key vital rates from individual-based demographic data identified temporal and spatial variation in subadult survival as key constraints on λ, and simultaneously provided new insights into how vital rates can vary as functions of demographic structure, natal conditions and parental life history. Targeted analyses showed that first-year survival increased with prey abundance, implying that food limitation may constrain λ. First-year survival then decreased dramatically, threatening population viability and prompting emergency supplementary feeding interventions. Detailed evaluations suggested that the interventions successfully increased first-year survival in some years and additionally increased adult survival and successful reproduction, thereby feeding back to inform intervention refinements and understanding of complex ecological constraints on λ. Genetic analyses revealed novel evidence of expression of a lethal recessive allele, and demonstrated how critically small effective population size can arise, thereby increasing inbreeding and loss of genetic variation. Population viability analyses parameterised with all available demographic and genetic data showed how ecological and genetic constraints can interact to limit population viability, and identified ecological management as of primacy over genetic management to ensure short-term persistence of the focal population. This case study demonstrates a full iteration through the sequence of primary science, evidence-based intervention, quantitative evaluation and feedback that is advocated in conservation science but still infrequently achieved. It thereby illustrates how pure science advances informed conservation actions to ensure the (short-term) stability of the target population, and how conservation-motivated analyses fed back to advance fundamental understanding of population processes.

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.

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125-234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.

Using long-term data for a reintroduced population to empirically estimate future consequences of inbreeding

Inbreeding depression is an important long-term threat to reintroduced populations. However, the strength of inbreeding depression is difficult to estimate in wild populations because pedigree data are inevitably incomplete and because good data are needed on survival and reproduction. Predicting future population consequences is especially difficult because this also requires projecting future inbreeding levels and their impacts on long-term population dynamics, which are subject to many uncertainties. We illustrate how such projections can be derived through Bayesian state-space modeling methods based on a 26-year data set for North Island Robins (Petroica longipes) reintroduced to Tiritiri Matangi Island in 1992. We used pedigree data to model increases in the average inbreeding level (F) over time based on kinship of possible breeding pairs and to estimate empirically N_e /N (effective/census population size). We used multiple imputation to model the unknown components of inbreeding coefficients, which allowed us to estimate effects of inbreeding on survival for all 1458 birds in the data set while modeling density dependence and environmental stochasticity. This modeling indicated that inbreeding reduced juvenile survival (1.83 lethal equivalents [SE 0.81]) and may have reduced subsequent adult survival (0.44 lethal equivalents [0.81]) but had no apparent effect on numbers of fledglings produced. Average inbreeding level increased to 0.10 (SE 0.001) as the population grew from 33 (0.3) to 160 (6) individuals over the 25 years, giving a Ne/N ratio of 0.56 (0.01). Based on a model that also incorporated habitat regeneration, the population was projected to reach a maximum of 331-1144 birds (median 726) in 2130, then to begin a slow decline. Without inbreeding, the population would be expected stabilize at 887-1465 birds (median 1131). Such analysis, therefore, makes it possible to empirically derive the information needed for rational decisions about inbreeding management while accounting for multiple sources of uncertainty.

Scaling the extinction vortex: Body size as a predictor of population dynamics close to extinction events

Mutual reinforcement between abiotic and biotic factors can drive small populations into a catastrophic downward spiral to extinction-a process known as the "extinction vortex." However, empirical studies investigating extinction dynamics in relation to species' traits have been lacking.We assembled a database of 35 vertebrate populations monitored to extirpation over a period of at least ten years, represented by 32 different species, including 25 birds, five mammals, and two reptiles. We supplemented these population time series with species-specific mean adult body size to investigate whether this key intrinsic trait affects the dynamics of populations declining toward extinction.We performed three analyses to quantify the effects of adult body size on three characteristics of population dynamics: time to extinction, population growth rate, and residual variability in population growth rate.Our results provide support for the existence of extinction vortex dynamics in extirpated populations. We show that populations typically decline nonlinearly to extinction, while both the rate of population decline and variability in population growth rate increase as extinction is approached. Our results also suggest that smaller-bodied species are particularly prone to the extinction vortex, with larger increases in rates of population decline and population growth rate variability when compared to larger-bodied species.Our results reaffirm and extend our understanding of extinction dynamics in real-life extirpated populations. In particular, we suggest that smaller-bodied species may be at greater risk of rapid collapse to extinction than larger-bodied species, and thus, management of smaller-bodied species should focus on maintaining higher population abundances as a priority.

Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

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.

Bronchopulmonary Nematodes in Alpine Ibex: Shedding of First Stage Larvae Analyzed at the Individual Host Level

Pneumonia is the most frequent cause of death for Alpine ibex (Capra ibex) in Gran Paradiso National Park, (Italy). The etiology of this form of pneumonia is currently unknown and the identification of the primary etiological agent remains difficult due to biological and logistic constraints. Uncovering individual differences in Protostrongylid prevalence and intensity is important to further investigate the epidemiology of respiratory diseases and their relationship to heterozygosity and inbreeding in a once almost extinct population like C. ibex. In a group of 21 individually recognizable adult male we monitored monthly prevalence and intensity of Protostrongylid first-stage larvae using Baerman's technique from June to September 2019. First-stage larvae of 5 genera were detected. Muellerius (P = 100%, CI_95% = 84–100) and Protostrongylus (P = 86%, CI_95%:71–100) were two dominant genera according to Bush's importance index. Neostrongylus (P = 38%,CI_95%: 17–59), Cystocaulus (P = 33%,CI_95% = 13–53) were classified as co-dominant genera while Dictyocaulus filaria (P = 0.05%, CI_95% = 0.04–0.13) was detected, for the first time in Alpine ibex, in one subject. Protostrongylidae larval excretion varied significantly over time, with minimum L1 excretion in July. Individual median larval intensity ranged from 4.4 lpg to 82.2 lpg with Poulin's discrepancy index showing highly aggregated distribution patterns for Muellerius spp. (D = 0.283, CI_95% = 0.760–0.895) and Protostrongylus spp. (D = 0.635, CI_95% = 0.580–0.705). Presented data provide the necessary base point to further investigate how lungworm infection account for the different rates of progression of pneumonia in C. ibex. Individual aggregation of larval intensity must be further evaluated to determine whether these differences mirror different levels of parasitic infection related to individual differences in immune response, hormonal-states or genetic fitness.

Reproductive Strategies That May Facilitate Invasion Success: Evidence From a Spider Mite

With significant surge of international trade in recent decades, increasingly more arthropod species have become established outside their natural range of distribution, causing enormous damage in their novel habitats. However, whether a species can colonize its new environment depends on its ability to overcome various barriers which may result in establishment failure, such as inbreeding depression and difficulty to find mates. Here, we used a haplodiploid pest, Tetranychus ludeni Zacher (Acari: Tetranychidae), which is native to Europe but now cosmopolitan, to investigate whether its reproductive strategies have facilitated its invasion success, providing knowledge to develop programs for prediction and management of biological invasions. We show that inbreeding had no negative influence on female reproductive outputs and longevity over 11 successive generations, allowing mother-son and brother-sister mating to occur at the invasion front without adverse consequences in fitness. Virgin females produced maximum number of sons in their early life to ensure subsequent mother-son mating but later saved resources to prolong longevity for potential future mating. Females maximized their resource allocation to egg production immediately after mating to secure production of maximum number of both daughters and sons as early as possible. Furthermore, mated females with mating delay increased proportion of daughters in offspring produced to compensate the loss of production of daughters during their virgin life. We suggest that the lack of inbreeding depression in successive generations and the ability to adjust resource allocations depending whether and when mating occurs may be the key features that have facilitated its invasion success.

Conservation biology of threatened Mediterranean chasmophytes: The case of Asperula naufraga endemic to Zakynthos island (Ionian islands, Greece)

Asperula naufraga is a rare and threatened obligate chasmophyte, endemic to Zakynthos island (Ionian islands, Greece). In this study, we provide a combined approach (including monitoring of demographic and reproductive parameters and study of genetic diversity) to assess the current conservation status of the species and to estimate its future extinction risk. The five subpopulations of A. naufraga were monitored for five years (2014-2018). Population size markedly fluctuated between 68-130 mature individuals during the monitoring period. The extent of occurrence (EOO) was estimated at 28.7 km2 and the area of occupancy (AOO) was 8 km2. Stage-structure recordings were similar for all subpopulations, characterized by high proportions of adult and senescent individuals, following a common pattern, which has been observed in other cliff-dwelling plants. Preliminary genetic analysis with SSRs markers revealed low heterozygosity within subpopulations and significant departure from H-W equilibrium, which combined with small population size suggest increased threat of genetic diversity loss. Our results indicate that the species should be placed in the Critically Endangered (CR) IUCN threat category, while according to Population Viability Analysis results its extinction risk increases to 47.8% in the next 50 years. The small population size combined with large fluctuations in its size, low recruitment and low genetic diversity, indicate the need of undertaking effective in situ and ex situ conservation measures.

Multiple life-stage inbreeding depression impacts demography and extinction risk in an extinct-in-the-wild species

Inbreeding can depress individuals’ fitness traits and reduce population viability. However, studies that directly translate inbreeding depression on fitness traits into consequences for population viability, and further, into consequences for management choices, are lacking. Here, we estimated impacts of inbreeding depression (B, lethal equivalents) across life-history stages for an extinct-in-the-wild species, the sihek (Guam kingfisher, Todiramphus cinnamominus). We then projected population growth under different management alternatives with our B estimates incorporated, as well as without inbreeding depression (B = 0) or with a conventional default B. We found that inbreeding depression severely impacted multiple life-history stages, and directly translated into an effect on population viability under management alternatives. Simulations including our B estimates indicated rapid population decline, whereas projections without inbreeding depression or with default B suggested very gradual population decline. Further, our results demonstrate that incorporation of B across life-history stages can influence management decisions, as projections with our B estimates suggested a need to switch to increased breeding management to avoid species extinction and support wild releases. Our results demonstrate that magnitude of B across life-history stages can translate into demographic consequences, such that incorporation of multiple life-stage B into population models can be important for informed conservation management decision-making.

IUCN Red List and the value of integrating genetics

Many species on endangered species lists such as the IUCN Red List (RL) are categorized using demographic factors such as numbers of mature individuals. Genetic factors are not currently used in the RL even though their explicit consideration, including effective population size (Ne) and expected heterozygosity-loss (H-loss), could improve the assessment of extinction risk. Here, we consider the estimation of Ne and H-loss in the context of RL species. First, we investigate the reporting of number of mature individuals for RL Endangered species, which is needed to estimate Ne and H-loss. We found 77% of species assessments studied here did not report methods used to estimate the number of mature adults, and that these assessments rarely report other important determinants of Ne (e.g., sex ratio, variance in family size). We therefore applied common rules of thumb to estimate Ne, and found that Ne was likely < 50 for at least 25% of the 170 RL Endangered species studied here. We also estimated mean expected H-loss for these species over the next 100 years, and found it to be 9–29%. These estimates of high H-loss and low Ne suggest that some species listed as Endangered likely warrant listing as Critically Endangered if genetic considerations were included. We recommend that RL and other assessment frameworks (i) report methods used for estimating the number of mature adults, (ii) include standardized information on species traits that influence Ne to facilitate Ne estimation, and (iii) consider using concepts like Ne and heterozygosity-loss in risk assessments.

Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex

Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species.

Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.