Metapopulation effective size and conservation genetic goals for the Fennoscandian wolf (Canis lupus) population

Demographic history shapes North American gray wolf genomic diversity and informs species' conservation

Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, grey wolves in the northern Rocky Mountains have lower genomic diversity than wolves of the western Great Lakes and have declined over time. Effective population size estimates revealed the historical signatures of continental efforts of predator extermination, despite a quarter century of recovery efforts. We are the first to provide molecular estimates of effective population size across distinct grey wolf populations in North America, which ranged between Ne  ~ 275 and 3050 since early 1980s. We provide data that inform managers regarding the status and importance of effective population size estimates for grey wolf conservation, which are on average 5.2-9.3% of census estimates for this species. We show that while grey wolves fall above minimum effective population sizes needed to avoid extinction due to inbreeding depression in the short term, they are below sizes predicted to be necessary to avoid long-term risk of extinction.

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data

International policy recently adopted commitments to maintain genetic diversity in wild populations to secure their adaptive potential, including metrics to monitor temporal trends in genetic diversity - so-called indicators. A national programme for assessing trends in genetic diversity was recently initiated in Sweden. Relating to this effort, we systematically assess contemporary genome-wide temporal trends (40 years) in wild populations using the newly adopted indicators and whole genome sequencing (WGS). We use pooled and individual WGS data from brown trout (Salmo trutta) in eight alpine lakes in protected areas. Observed temporal trends in diversity metrics (nucleotide diversity, Watterson's ϴ and heterozygosity) lie within proposed acceptable threshold values for six of the lakes, but with consistently low values in lakes above the tree line and declines observed in these northern-most lakes. Local effective population size is low in all lakes, highlighting the importance of continued protection of interconnected systems to allow genetic connectivity for long-term viability of these populations. Inbreeding (FROH ) spans 10%-30% and is mostly represented by ancient (<1 Mb) runs of homozygosity, with observations of little change in mutational load. We also investigate adaptive dynamics over evolutionarily short time frames (a few generations); identifying putative parallel selection across all lakes within a gene pertaining to skin pigmentation as well as candidates of selection unique to specific lakes and lake systems involved in reproduction and immunity. We demonstrate the utility of WGS for systematic monitoring of natural populations, a priority concern if genetic diversity is to be protected.

Assessment of the Global Variance Effective Size of Subdivided Populations, and Its Relation to Other Effective Sizes

The variance effective population size ([Formula: see text]) is frequently used to quantify the expected rate at which a population's allele frequencies change over time. The purpose of this paper is to find expressions for the global [Formula: see text] of a spatially structured population that are of interest for conservation of species. Since [Formula: see text] depends on allele frequency change, we start by dividing the cause of allele frequency change into genetic drift within subpopulations (I) and a second component mainly due to migration between subpopulations (II). We investigate in detail how these two components depend on the way in which subpopulations are weighted as well as their dependence on parameters of the model such a migration rates, and local effective and census sizes. It is shown that under certain conditions the impact of II is eliminated, and [Formula: see text] of the metapopulation is maximized, when subpopulations are weighted proportionally to their long term reproductive contributions. This maximal [Formula: see text] is the sought for global effective size, since it approximates the gene diversity effective size [Formula: see text], a quantifier of the rate of loss of genetic diversity that is relevant for conservation of species and populations. We also propose two novel versions of [Formula: see text], one of which (the backward version of [Formula: see text]) is most stable, exists for most populations, and is closer to [Formula: see text] than the classical notion of [Formula: see text]. Expressions for the optimal length of the time interval for measuring genetic change are developed, that make it possible to estimate any version of [Formula: see text] with maximal accuracy.

Variance effective population size is affected by census size in sub-structured populations

Measurement of allele frequency shifts between temporally spaced samples has long been used for assessment of effective population size (N_e ), and this 'temporal method' provides estimates of N_e referred to as variance effective size (N_eV ). We show that N_eV of a local population that belongs to a sub-structured population (a metapopulation) is determined not only by genetic drift and migration rate (m), but also by the census size (N_c ). The realized N_eV of a local population can either increase or decrease with increasing m, depending on the relationship between N_e and N_c in isolation. This is shown by explicit mathematical expressions for the factors affecting N_eV derived for an island model of migration. We verify analytical results using high-resolution computer simulations, and show that the phenomenon is not restricted to the island model migration pattern. The effect of N_c on the realized N_eV of a local subpopulation is most pronounced at high migration rates. We show that N_c only affects local N_eV , whereas N_eV for the metapopulation as a whole, inbreeding (N_eI ), and linkage disequilibrium (N_eLD ) effective size are all independent of N_c . Our results provide a possible explanation to the large variation of N_e /N_c ratios reported in the literature, where N_e is frequently estimated by N_eV . They are also important for the interpretation of empirical N_e estimates in genetic management where local N_eV is often used as a substitute for inbreeding effective size, and we suggest an increased focus on metapopulation N_eV as a proxy for N_eI .

Effects of subpopulation extinction on effective size (Ne) of metapopulations

Population extinction is ubiquitous in all taxa. Such extirpations can reduce intraspecific diversity, but the extent to which genetic diversity of surviving populations are affected remains largely unclear. A key concept in this context is the effective population size (Ne), which quantifies the rate at which genetic diversity within populations is lost. Ne was developed for single, isolated populations while many natural populations are instead connected to other populations via gene flow. Recent analytical approaches and software permit modelling of Ne of interconnected populations (metapopulations). Here, we apply such tools to investigate how extinction of subpopulations affects Ne of the metapopulation (NeMeta) and of separate surviving subpopulations (NeRx) under different rates and patterns of genetic exchange between subpopulations. We assess extinction effects before and at migration-drift equilibrium. We find that the effect of extinction on NeMeta increases with reduced connectivity, suggesting that stepping stone models of migration are more impacted than island-migration models when the same number of subpopulations are lost. Furthermore, in stepping stone models, after extinction and before a new equilibrium has been reached, NeRx can vary drastically among surviving subpopulations and depends on their initial spatial position relative to extinct ones. Our results demonstrate that extinctions can have far more complex effects on the retention of intraspecific diversity than typically recognized. Metapopulation dynamics need heightened consideration in sustainable management and conservation, e.g., in monitoring genetic diversity, and are relevant to a wide range of species in the ongoing extinction crisis.

Genetic variation of endangered Jankowski’s Bunting (Emberiza jankowskii): High connectivity and a moderate history of demographic decline

Introduction

Continued discovery of “mismatch” patterns between population size and genetic diversity, involving wild species such as insects, amphibians, birds, mammals, and others, has raised issues about how population history, especially recent dynamics under human disturbance, affects currently standing genetic variation. Previous studies have revealed high genetic diversity in endangered Jankowski’s Bunting. However, it is unclear how the demographic history and recent habitat changes shape the genetic variation of Jankowski’s Bunting.

Methods

To explore the formation and maintenance of high genetic diversity in endangered Jankowski’s Bunting, we used a mitochondrial control region (partial mtDNA CR) and 15 nuclear microsatellite markers to explore the recent demographic history of Jankowski’s Bunting, and we compared the historical and contemporary gene flows between populations to reveal the impact of habitat change on population connectivity. Specifically, we aimed to test the following hypotheses: (1) Jankowski’s Bunting has a large historical Ne and a moderate demographic history; and (2) recent habitat change might have no significant impact on the species’ population connectivity.

Results

The results suggested that large historical effective population size, as well as severe but slow population decline, may partially explain the high observable genetic diversity. Comparison of historical (over the past 4Ne generations) and contemporary (1–3 generations) gene flow indicated that the connectivity between five local populations was only marginally affected by landscape changes.

Discussion

Our results suggest that high population connectivity and a moderate history of demographic decline are powerful explanations for the rich genetic variation in Jankowski’s Bunting. Although there is no evidence that the genetic health of Jankowski’s Bunting is threatened, the time-lag effects on the genetic response to recent environmental changes is a reminder to be cautious about the current genetic characteristics of this species. Where possible, factors influencing genetic variation should be integrated into a systematic framework for conducting robust population health assessments. Given the small contemporary population size, inbreeding, and ecological specialization, we recommend that habitat protection be maintained to maximize the genetic diversity and population connectivity of Jankowski’s Bunting.

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

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

Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator

Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔF_ST , respectively) and assess the effective population size (N_e -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The N_e indicator showed values below the threshold (N_e  ≤ 500) in 20 populations with five showing N_e  < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.

Potential Futures for Coastal Wolves and Their Ecosystem Services in Alaska, With Implications for Management of a Social-Ecological System

Carnivores across much of the world are declining, leading to loss of biodiversity as well as the ecosystem services carnivores provide. In 2020, the Alexander Archipelago (AA) wolf was petitioned for protection under the U.S. Endangered Species Act (ESA) for the third time in 30 years. Concerns included habitat alteration from industrial timber harvest and subsequent declines in prey (deer), human-caused mortality, climate change, and genetic inbreeding. However, the underlying biogeography and ecology of these wolves continues to suggest resiliency across the subspecies’ range, even though local populations may go extinct. If local wolf populations go extinct, it will result in loss of their ecosystem services (e.g., interactions of wolves with their prey, which prevents over-browsing and protects carbon sequestration in soils and trees), which will likely have major consequences for the local social-ecological system. Here, we updated a model we constructed for the last ESA listing process (2015) to examine the dynamics of wolf and deer populations on Prince of Wales Island (the primary geographic focus of all three petitions) in response to future environmental and management scenarios developed with stakeholders. Further, we considered how changes in deer abundance impact predation services (prevention of over-browsing by deer). We found that wolf populations generally persisted over 30 years, but dropped below an effective population size of 50 wolves in 10–98% of years simulated. Low wolf abundance resulted in higher deer abundance, which increased hunting opportunity, but also browsing damages (e.g., 19% of areas would be over-browsed if wolf harvest caps are removed, and &gt;30% of areas would be over-browsed if wolves go extinct). Human harvest of wildlife was a key regulator of abundance and ecosystem services within the coastal rainforest social-ecological system; wolf abundance was most affected by wolf harvest regulations; and deer harvest restrictions increased wolf and deer abundances, but also greatly increased browsing impacts (&gt;70% of areas heavily browsed if hunting ceased). Our findings support an integrated approach to management of this social-ecological system, such that social and ecological sciences are both used to monitor important components of the system (e.g., measuring public sentiment and likelihood of poaching, alongside wolf and deer numbers). Integration and adaptive approaches are needed to ensure that the many ecosystem services humans depend on are valued, conserved, and restored, including the cryptic predation services wolves have historically provided to the timber industry via reduced browsing pressure by deer.

Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population

Transboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.

Appeasing Pheromones for the Management of Stress and Aggression during Conservation of Wild Canids: Could the Solution Be Right under Our Nose?

Simple Summary

Many canid species are declining globally. It is important to conserve these species that often serve as important predators within ecosystems. Continued human expansion and the resulting habitat fragmentation necessitate conservation interventions, such as translocation, artificial pack formation, and captive breeding programs. However, chronic stress often occurs during these actions, and can result in aggression, and the physiological suppression of immunity and reproduction. Limited options are currently available for stress and aggression management in wild canids. Pheromones provide a promising natural alternative for stress management; an appeasing pheromone has been identified for multiple domestic species and may reduce stress and aggression behaviours. Many pheromones are species-specific, and the appeasing pheromone has been found to have slight compositional changes across species. In this review, the benefits of a dog appeasing pheromone and the need to investigate species-specific derivatives to produce more pronounced and beneficial behavioural and physiological modulation in target species as a conservation tool are examined.

Abstract

Thirty-six species of canid exist globally, two are classified as critically endangered, three as endangered, and five as near threatened. Human expansion and the coinciding habitat fragmentation necessitate conservation interventions to mitigate concurrent population deterioration. The current conservation management of wild canids includes animal translocation and artificial pack formation. These actions often cause chronic stress, leading to increased aggression and the suppression of the immune and reproductive systems. Castration and pharmaceutical treatments are currently used to reduce stress and aggression in domestic and captive canids. The undesirable side effects make such treatments inadvisable during conservation management of wild canids. Pheromones are naturally occurring chemical messages that modulate behaviour between conspecifics; as such, they offer a natural alternative for behaviour modification. Animals are able to distinguish between pheromones of closely related species through small compositional differences but are more likely to have greater responses to pheromones from individuals of the same species. Appeasing pheromones have been found to reduce stress- and aggression-related behaviours in domestic species, including dogs. Preliminary evidence suggests that dog appeasing pheromones (DAP) may be effective in wild canids. However, the identification and testing of species-specific derivatives could produce more pronounced and beneficial behavioural and physiological changes in target species. In turn, this could provide a valuable tool to improve the conservation management of many endangered wild canids.

Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management

Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively adaptive loci in order to evaluate the relative effects of genetic drift and local adaptation on population divergence. We sampled individuals across the Utah prairie dog species range and generated 2955 single nucleotide polymorphisms using double digest restriction site-associated DNA sequencing. Genetic diversity was lower in low-elevation sites compared to high-elevation sites. Population divergence was high among sites and followed an isolation-by-distance model. Our results indicate that genetic drift plays a substantial role in the population divergence of the Utah prairie dog, and colonies would likely benefit from translocation of individuals between recovery units, which are characterized by distinct elevations, despite the detection of environmental associations with outlier loci. By understanding the processes that shape genetic structure, better informed decisions can be made with respect to the management of threatened species to ensure that adaptation is not stymied.

Wolf Delisting Challenges Demonstrate Need for an Improved Framework for Conserving Intraspecific Variation under the Endangered Species Act

Recent advances in genomics have increased our understanding of geographic patterns of intraspecific variation and the importance of this variation in enhancing species’ potential to adapt to novel threats. However, as part of an effort to limit the scope of the Endangered Species Act (ESA), the US government has proposed the removal of the gray wolf from the list of protected species on the basis of a claim that the statute permits a species to be declared recovered given the existence of a single presently secure population. We rebut this interpretation and propose a framework for the conservation of adaptive potential that builds on current agency practice in delineating subspecific recovery units and reconciles the definition of significance in the statute's “distinct population segment” and “significant portion of range” clauses. Such a coordinated policy would enhance the ESA's effectiveness in stemming loss of biodiversity in the face of climate change and other factors altering Earth's ecosystems.

Biological and Sociopolitical Sources of Uncertainty in Population Viability Analysis for Endangered Species Recovery Planning

Although population viability analysis (PVA) can be an important tool for strengthening endangered species recovery efforts, the extent to which such analyses remain embedded in the social process of recovery planning is often unrecognized. We analyzed two recovery plans for the Mexican wolf that were developed using similar data and methods but arrived at contrasting conclusions as to appropriate recovery goals or criteria. We found that approximately half of the contrast arose from uncertainty regarding biological data, with the remainder divided between policy-related decisions and mixed biological-policy factors. Contrasts arose from both differences in input parameter values and how parameter uncertainty informed the level of precaution embodied in resulting criteria. Policy-related uncertainty originated from contrasts in thresholds for acceptable risk and disagreement as to how to define endangered species recovery. Rather than turning to PVA to produce politically acceptable definitions of recovery that appear science-based, agencies should clarify the nexus between science and policy elements in their decision processes. The limitations we identify in endangered-species policy and how PVAs are conducted as part of recovery planning must be addressed if PVAs are to fulfill their potential to increase the odds of successful conservation outcomes.

Genomic analyses suggest adaptive differentiation of northern European native cattle breeds

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within-breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum-likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long-term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

Do estimates of contemporary effective population size tell us what we want to know?

Estimation of effective population size (N_e) from genetic marker data is a major focus for biodiversity conservation because it is essential to know at what rates inbreeding is increasing and additive genetic variation is lost. But are these the rates assessed when applying commonly used N_e estimation techniques? Here we use recently developed analytical tools and demonstrate that in the case of substructured populations the answer is no. This is because the following: Genetic change can be quantified in several ways reflecting different types of N_e such as inbreeding (N_eI), variance (N_eV), additive genetic variance (N_eAV), linkage disequilibrium equilibrium (N_eLD), eigenvalue (N_eE) and coalescence (N_eCo) effective size. They are all the same for an isolated population of constant size, but the realized values of these effective sizes can differ dramatically in populations under migration. Commonly applied N_e‐estimators target N_eV or N_eLD of individual subpopulations. While such estimates are safe proxies for the rates of inbreeding and loss of additive genetic variation under isolation, we show that they are poor indicators of these rates in populations affected by migration. In fact, both the local and global inbreeding (N_eI) and additive genetic variance (N_eAV) effective sizes are consistently underestimated in a subdivided population. This is serious because these are the effective sizes that are relevant to the widely accepted 50/500 rule for short and long term genetic conservation.  The bias can be infinitely large and is due to inappropriate parameters being estimated when applying theory for isolated populations to subdivided ones.

Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations

The number of effective breeders (Nb ) and effective population size (Ne ) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium-based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993-2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on Nb and Ne , by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for Ne were larger than Nb and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of Nb and Ne . Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on Nb and Ne .

Genomic consequences of intensive inbreeding in an isolated wolf population

Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F _ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors ≤10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F _P) was strongly correlated with realized inbreeding measured with the entire genome (r ² = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F _ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F _P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.

Estimating demographic contributions to effective population size in an age-structured wild population experiencing environmental and demographic stochasticity

A population's effective size (N_e ) is a key parameter that shapes rates of inbreeding and loss of genetic diversity, thereby influencing evolutionary processes and population viability. However, estimating N_e , and identifying key demographic mechanisms that underlie the N_e to census population size (N) ratio, remains challenging, especially for small populations with overlapping generations and substantial environmental and demographic stochasticity and hence dynamic age-structure. A sophisticated demographic method of estimating N_e /N, which uses Fisher's reproductive value to account for dynamic age-structure, has been formulated. However, this method requires detailed individual- and population-level data on sex- and age-specific reproduction and survival, and has rarely been implemented. Here, we use the reproductive value method and detailed demographic data to estimate N_e /N for a small and apparently isolated red-billed chough (Pyrrhocorax pyrrhocorax) population of high conservation concern. We additionally calculated two single-sample molecular genetic estimates of N_e to corroborate the demographic estimate and examine evidence for unobserved immigration and gene flow. The demographic estimate of N_e /N was 0.21, reflecting a high total demographic variance (σ2dg) of 0.71. Females and males made similar overall contributions to σ2dg. However, contributions varied among sex-age classes, with greater contributions from 3 year-old females than males, but greater contributions from ≥5 year-old males than females. The demographic estimate of N_e was ~30, suggesting that rates of increase of inbreeding and loss of genetic variation per generation will be relatively high. Molecular genetic estimates of N_e computed from linkage disequilibrium and approximate Bayesian computation were approximately 50 and 30, respectively, providing no evidence of substantial unobserved immigration which could bias demographic estimates of N_e . Our analyses identify key sex-age classes contributing to demographic variance and thus decreasing N_e /N in a small age-structured population inhabiting a variable environment. They thereby demonstrate how assessments of N_e can incorporate stochastic sex- and age-specific demography and elucidate key demographic processes affecting a population's evolutionary trajectory and viability. Furthermore, our analyses show that N_e for the focal chough population is critically small, implying that management to re-establish genetic connectivity may be required to ensure population viability.

gesp: A computer program for modelling genetic effective population size, inbreeding and divergence in substructured populations

The genetically effective population size (N_e) is of key importance for quantifying rates of inbreeding and genetic drift and is often used in conservation management to set targets for genetic viability. The concept was developed for single, isolated populations and the mathematical means for analysing the expected N_e in complex, subdivided populations have previously not been available. We recently developed such analytical theory and central parts of that work have now been incorporated into a freely available software tool presented here. gesp (Genetic Effective population size, inbreeding and divergence in Substructured Populations) is R‐based and designed to model short‐ and long‐term patterns of genetic differentiation and effective population size of subdivided populations. The algorithms performed by gesp allow exact computation of global and local inbreeding and eigenvalue effective population size, predictions of genetic divergence among populations (G_ST) as well as departures from random mating (F_IS, F_IT) while varying (i) subpopulation census and effective size, separately or including trend of the global population size, (ii) rate and direction of migration between all pairs of subpopulations, (iii) degree of relatedness and divergence among subpopulations, (iv) ploidy (haploid or diploid) and (v) degree of selfing. Here, we describe gesp and exemplify its use in conservation genetics modelling.