Genetic diversity, population structure, effective population size and demographic history of the Finnish wolf population

Centrality to the metapopulation is more important for population genetic diversity than habitat area or fragmentation

Drift and gene flow affect genetic diversity. Given that the strength of genetic drift increases as population size decreases, management activities have focused on increasing population size through preserving habitats to preserve genetic diversity. Few studies have empirically evaluated the impacts of drift and gene flow on genetic diversity. Kryptolebias marmoratus, henceforth 'rivulus', is a small killifish restricted to fragmented New World mangrove forests with gene flow primarily associated with ocean currents. Rivulus form distinct populations across patches, making them a well-suited system to test the extent to which habitat area, fragmentation and connectivity are associated with genetic diversity. Using over 1000 individuals genotyped at 32 microsatellite loci, high-resolution landcover data and oceanographic simulations with graph theory, we demonstrate that centrality (connectivity) to the metapopulation is more strongly associated with genetic diversity than habitat area or fragmentation. By comparing models with and without centrality standardized by the source population's genetic diversity, our results suggest that metapopulation centrality is critical to genetic diversity regardless of the diversity of adjacent populations. While we find evidence that habitat area and fragmentation are related to genetic diversity, centrality is always a significant predictor with a larger effect than any measure of habitat configuration.

Patterns of Wolf Dispersal Respond to Harvest Density across an Island Complex

Wolves are highly mobile predators and can disperse across a variety of habitats and over long distances. However, less is known about dispersal capabilities across water and among islands. The biogeography of island systems fosters spatially structured local populations, and their degree of connectivity may influence the dynamics and long-term viability of the regional population. We sought to quantify wolf dispersal rate, distance, and dispersal sex bias throughout Prince of Wales Island, a 6670 km2 island in southeast Alaska, and the surrounding islands that constitute the wildlife management unit (9025 km2). We also investigated patterns of dispersal in relation to hunting and trapping intensity and wolf population density. We used DNA data collected during 2012-2021 long-term monitoring efforts and genotyped 811 wolves, 144 of which (18%) were dispersers. Annual dispersal rates were 9-23% and had a weakly positive relationship with wolf density. Wolves dispersed 41.9 km on average (SD = 23.7 km), and males and females did not disperse at different rates. Of the dispersing wolves, 107 died, and the majority (n = 81) died before they were able to settle. The leading manner of death was trapping (97% of mortalities), and wolves tended to disperse from areas with low harvest density to areas where harvest density was relatively higher. Dispersal occurred both to and from small islands and the larger Prince of Wales Island, indicating bidirectional as opposed to asymmetrical movement, and the genetic overlap of wolf groups demonstrates connectivity throughout this naturally patchy system. Island ecosystems have different predator-prey dynamics and recolonization processes than large, intact systems due to their isolation and restricted sizes; thus, a better understanding of the degree of population connectivity including dispersal patterns among islands in the Prince of Wales archipelago could help inform the management and research strategies of these wolves.

A universal panel of STR loci for the study of polymorphism of the species Canis lupus and forensic identification of dog and wolf

Commercial panels of microsatellite (STR) loci are intended for DNA analysis of the domestic dog (Canis lupus familiaris) and, therefore, when genotyping the Grey wolf (Canis lupus lupus), most markers reveal significant deviations from the Hardy-Weinberg equilibrium and have a low informative value, which complicates their use in a forensic examination. The aim of this study was to select STR markers that equally effectively reflect population polymorphism in the wolf and the dog, and to create a universal panel for the identification of individuals in forensic science. Based on the study of polymorphisms of 34 STR loci, a CPlex panel of 15 autosomal loci and two sex loci was developed, which is equally suitable for identifying wolfs and dogs. Analysis of molecular variance (AMOVA) between samples revealed significant differentiation values (FST = 0.0828, p < 0.05), which allows the panel to be used for differentiating between wolf and dog samples. For the first time in the forensic examination of objects of animal origin in the Republic of Belarus, population subdivision coefficients (θ-values) were calculated for each of the 15 STR loci of the test system being reported. It was shown that the values of the genotype frequency, when averaged over all studied animals without and with considering the θ-value, differ by three orders of magnitude (3.39 · 10-17 and 4.71 · 10-14, respectively). The use of population subdivision coefficients will provide the researcher with the most relevant results of an expert identification study. The test system was validated in accordance with the protocol of the Scientific Working Group on DNA Analysis Methods. A computational tool was developed to automate the analysis of genetic data on the wolf and dog in the forensic examination; two guides were approved for practicing forensic experts. This methodology is being successfully used in expert practice in investigating cases of illegal hunting, animal abuse and other offenses in the Republic of Belarus.

Saving the overlooked mangrove horseshoe crabs-A perspective from enhancing mangrove ecosystem conservation

Despite being widely distributed in Asia, Carcinoscorpius rotundicauda is often overlooked and, its population status remains unclear. Moreover, it is threatened by illegal harvesting and degradation of mangrove ecosystems. Protecting its habitat is essential for population and biodiversity conservation, as mangroves provide nursery grounds and food supply for C. rotundicauda. This review discusses the biological characteristics of C. rotundicauda, including ecology, nutrition, life history, toxicology, and immunology. It also presents information about its distribution and population status. The review emphasizes the challenges faced by C. rotundicauda and proposes a conservation framework that involves the participation of local residents to facilitate conservation efforts. Collaboration between local residents and communities is proposed to protect and monitor the mangrove ecosystem. Additionally, this framework can support field research, protect C. rotundicauda juveniles and other species, and ensure the livelihood of local residents through participation in carbon trading markets and eco-industries such as eco-farming and eco-tourism.

Wolf genetic diversity compared across Europe using the yardstick method

Integrating data across studies with traditional microsatellite genetic markers requires careful calibration and represents an obstacle for investigation of wide-ranging species where populations require transboundary management. We used the "yardstick" method to compare results published across Europe since 2002 and new wolf (Canis lupus) genetic profiles from the Carpathian Mountains in Central Europe and the Dinaric Mountains in Southeastern Europe, with the latter as our reference population. We compared each population with Dinaric wolves, considering only shared markers (range 4-17). For each population, we calculated standard genetic diversity indices plus calibrated heterozygosity (Hec) and allelic richness (Ac). Hec and Ac in Dinaric (0.704 and 9.394) and Carpathian wolves (0.695 and 7.023) were comparable to those observed in other large and mid-sized European populations, but smaller than those of northeastern Europe. Major discrepancies in marker choices among some studies made comparisons more difficult. However, the yardstick method, including the new measures of Hec and Ac, provided a direct comparison of genetic diversity values among wolf populations and an intuitive interpretation of the results. The yardstick method thus permitted the integration of diverse sources of publicly available microsatellite data for spatiotemporal genetic monitoring of evolutionary potential.

The first assessment of the genetic diversity and structure of the endangered West Indian manatee in Cuba

The coastal waters of Cuba are home to a small, endangered population of West Indian manatee, which would benefit from a comprehensive characterization of the population's genetic variation. We conducted the first genetic assessment of Cuban manatees to determine the extent of the population's genetic structure and characterize the neutral genetic diversity among regions within the archipelago. We genotyped 49 manatees at 18 microsatellite loci, a subset of 27 samples on 1703 single nucleotide polymorphisms (SNPs), and sequenced 59 manatees at the mitochondrial control region. The Cuba manatee population had low nuclear (microsatellites H_E = 0.44, and SNP H_E = 0.29) and mitochondrial genetic diversity (h = 0.068 and π = 0.00025), and displayed moderate departures from random mating (microsatellite F_IS = 0.12, SNP F_IS = 0.10). Our results suggest that the western portion of the archipelago undergoes periodic exchange of alleles based on the evidence of shared ancestry and low but significant differentiation. The southeast Guantanamo Bay region and the western portion of the archipelago were more differentiated than southwest and northwest manatees. The genetic distinctiveness observed in the southeast supports its recognition as a demographically independent unit for natural resource management regardless of whether it is due to historical isolation or isolation by distance. Estimates of the regional effective population sizes, with the microsatellite and SNP datasets, were small (all N_e < 60). Subsequent analyses using additional samples could better examine how the observed structure is masking simple isolation by distance patterns or whether ecological or biogeographic forces shape genetic patterns.

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 diversity and mate selection in a reintroduced population of gray wolves

The genetic composition of an individual can markedly affect its survival, reproduction, and ultimately fitness. As some wildlife populations become smaller, conserving genetic diversity will be a conservation challenge. Many imperiled species are already supported through population augmentation efforts and we often do not know if or how genetic diversity is maintained in translocated species. As a case study for understanding the maintenance of genetic diversity in augmented populations, I wanted to know if genetic diversity (i.e., observed heterozygosity) remained high in a population of gray wolves in the Rocky Mountains of the U.S. > 20 years after reintroduction. Additionally, I wanted to know if a potential mechanism for such diversity was individuals with below average genetic diversity choosing mates with above average diversity. I also asked whether there was a preference for mating with unrelated individuals. Finally, I hypothesized that mated pairs with above average heterozygosity would have increased survival of young. Ultimately, I found that females with below average heterozygosity did not choose mates with above average heterozygosity and wolves chose mates randomly with respect to genetic relatedness. Pup survival was not higher for mated pairs with above average heterozygosity in my models. The dominant variables predicting pup survival were harvest rate during their first year of life and years pairs were mated. Ultimately, genetic diversity was relatively unchanged > 20 years after reintroduction. The mechanism for maintaining such diversity does not appear related to individuals preferentially choosing more genetically diverse mates. Inbreeding avoidance, however, appears to be at least one mechanism maintaining genetic diversity in this population.

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.

Genetic Differentiation of Reintroduced Père David's Deer (Elaphurus davidianus) Based on Population Genomics Analysis

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David's deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David's deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David's deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David's deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David's deer, and low levels of genome-wide genetic diversity were observed in Père David's deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David's deer, especially between the captive population in Beijing Père David's deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David's deer started to decline ~25.8ka, and the similar levels of three populations' LD reflected the genetic impacts of long-term population bottlenecks in the Père David's deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.

Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Background

Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples.

Results

Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations.

Conclusions

We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07761-5.

Population genetics of the wolverine in Finland: the road to recovery?

After decades, even centuries of persecution, large carnivore populations are widely recovering in Europe. Considering the recent recovery of the wolverine (Gulo gulo) in Finland, our aim was to evaluate genetic variation using 14 microsatellites and mtDNA control region (579 bp) in order (1) to determine whether the species is represented by a single genetic population within Finland, (2) to quantify the genetic diversity, and (3) to estimate the effective population size. We found two major genetic clusters divided between eastern and northern Finland based on microsatellites (FST = 0.100) but also a significant pattern of isolation by distance. Wolverines in western Finland had a genetic signature similar to the northern cluster, which can be explained by former translocations of wolverines from northern to western Finland. For both main clusters, most estimates of the effective population size Ne were below 50. Nevertheless, the genetic diversity was higher in the eastern cluster (HE = 0.57, AR = 4.0, AP = 0.3) than in the northern cluster (HE = 0.49, AR = 3.7, AP = 0.1). Migration between the clusters was low. Two mtDNA haplotypes were found: one common and identical to Scandinavian wolverines; the other rare and not previously detected. The rare haplotype was more prominent in the eastern genetic cluster. Combining all available data, we infer that the genetic population structure within Finland is shaped by a recent bottleneck, isolation by distance, human-aided translocations and postglacial recolonization routes.

Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across the Indian subcontinent

Background

Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline.

Methods

We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities.

Results

Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India.

Conclusions

Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.

Alternated selection mechanisms maintain adaptive diversity in different demographic scenarios of a large carnivore

Background

Different population trajectories are expected to impact the signature of neutral and adaptive processes at multiple levels, challenging the assessment of the relative roles of different microevolutionary forces. Here, we integrate adaptive and neutral variability patterns to disentangle how adaptive diversity is driven under different demographic scenarios within the Iberian wolf (Canis lupus) range. We studied the persistent, the expanding and a small, isolated group within the Iberian wolf population, using 3 MHC class II genes (DRB1, DQA1, and DQB1), which diversity was compared with 39 microsatellite loci.

Results

Both the persistent and the expanding groups show evidence of balancing selection, revealed by a significant departure from neutrality at MHC loci, significant higher observed and expected heterozygosity and lower differentiation at MHC than at neutral loci, and signs of positive selection. However, despite exhibiting a significantly higher genetic diversity than the isolated group, the persistent group did not show significant excess of MHC heterozygotes. The expanding group, while showing a similar level of genetic diversity than the persistent group, displays by contrast a significant excess of MHC heterozygotes, which is compatible with the heterozygote advantage mechanism. Results are not clear regarding the role of drift and selection in the isolated group due to the small size of this population. Although diversity indices of MHC loci correspond to neutral expectations in the isolated group, accelerated MHC divergence, revealed by a higher differentiation at MHC than neutral loci, may indicate diversifying selection.

Conclusion

Different selective pressures were observed in the three different demographic scenarios, which are possibly driven by different selection mechanisms to maintain adaptive diversity.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1420-5) contains supplementary material, which is available to authorized users.

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.

Cryptic population structure reveals low dispersal in Iberian wolves

Highly mobile mammalian carnivores are expected to have the capability to maintain high levels of gene flow across large geographic scales. Nonetheless, surprising levels of genetic structure have been found in many such populations. We combined genetic and spatial behavioural information from wolves (Canis lupus) in the Iberian Peninsula (Western Europe) during the last two decades to present a particular case of low dispersal levels in a large carnivore population persisting in human-dominated landscapes. We found an exceptionally reticulated pattern of cryptic population structure emerging at two hierarchical levels, in which four or eleven meaningful genetic clusters can be recognized, respectively. These clusters were characterized by moderate-high levels of differentiation (average pairwise F_ST = 0.09–0.19), low levels of admixture and varying degrees of genetic diversity. The number of dispersers identified among the 11 clusters was very low (<4% out of 218 wolves). Spatial information of tracked wolves further confirmed the geographical genetic patterns (only 2 out of 85 collared wolves overlapped with more than one genetic cluster). The high levels of genetic structure in this population may be determined by the recent demographic history of this population, among other factors. The identification of meaningful genetic clusters has implications for the delineation of conservation units and, consequently, on the conservation and management actions for Iberian wolves.

Demographic mechanisms underpinning genetic assimilation of remnant groups of a large carnivore

Current range expansions of large terrestrial carnivores are occurring following human-induced range contraction. Contractions are often incomplete, leaving small remnant groups in refugia throughout the former range. Little is known about the underlying ecological and evolutionary processes that influence how remnant groups are affected during range expansion. We used data from a spatially explicit, long-term genetic sampling effort of grizzly bears (Ursus arctos) in the Northern Continental Divide Ecosystem (NCDE), USA, to identify the demographic processes underlying spatial and temporal patterns of genetic diversity. We conducted parentage analysis to evaluate how reproductive success and dispersal contribute to spatio-temporal patterns of genetic diversity in remnant groups of grizzly bears existing in the southwestern (SW), southeastern (SE) and east-central (EC) regions of the NCDE. A few reproductively dominant individuals and local inbreeding caused low genetic diversity in peripheral regions that may have persisted for multiple generations before eroding rapidly (approx. one generation) during population expansion. Our results highlight that individual-level genetic and reproductive dynamics play critical roles during genetic assimilation, and show that spatial patterns of genetic diversity on the leading edge of an expansion may result from historical demographic patterns that are highly ephemeral.

Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.

Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management

The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.

Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine

Geological and ecological features restrict dispersal and gene flow, leading to isolated populations. Dispersal barriers can be obvious physical structures in the landscape; however microgeographic differences can also lead to genetic isolation. Our study examined dispersal barriers at both macro- and micro-geographical scales in the black-capped chickadee, a resident North American songbird. Although birds have high dispersal potential, evidence suggests dispersal is restricted by barriers. The chickadee's range encompasses a number of physiological features which may impede movement and lead to divergence. Analyses of 913 individuals from 34 sampling sites across the entire range using 11 microsatellite loci revealed as many as 13 genetic clusters. Populations in the east were largely panmictic whereas populations in the western portion of the range showed significant genetic structure, which often coincided with large mountain ranges, such as the Cascade and Rocky Mountains, as well as areas of unsuitable habitat. Unlike populations in the central and southern Rockies, populations on either side of the northern Rockies were not genetically distinct. Furthermore, Northeast Oregon represents a forested island within the Great Basin; genetically isolated from all other populations. Substructuring at the microgeographical scale was also evident within the Fraser Plateau of central British Columbia, and in the southeast Rockies where no obvious physical barriers are present, suggesting additional factors may be impeding dispersal and gene flow. Dispersal barriers are therefore not restricted to large physical structures, although mountain ranges and large water bodies do play a large role in structuring populations in this study.

Estimation of Effective Population Size in the Sapsaree: A Korean Native Dog (Canis familiaris)

Effective population size (N_e) is an important measure to understand population structure and genetic variability in animal species. The objective of this study was to estimate N_e in Sapsaree dogs using the information of rate of inbreeding and genomic data that were obtained from pedigree and the Illumina CanineSNP20 (20K) and CanineHD (170K) beadchips, respectively. Three SNP panels, i.e. Sap134 (20K), Sap60 (170K), and Sap183 (the combined panel from the 20K and 170K), were used to genotype 134, 60, and 183 animal samples, respectively. The N_e estimates based on inbreeding rate ranged from 16 to 51 about five to 13 generations ago. With the use of SNP genotypes, two methods were applied for N_e estimation, i.e. pair-wise r² values using a simple expectation of distance and r² values under a non-linear regression with respective distances assuming a finite population size. The average pair-wise N_e estimates across generations using the pairs of SNPs that were located within 5 Mb in the Sap134, Sap60, and Sap183 panels, were 1,486, 1,025 and 1,293, respectively. Under the non-linear regression method, the average N_e estimates were 1,601, 528, and 1,129 for the respective panels. Also, the point estimates of past N_e at 5, 20, and 50 generations ago ranged between 64 to 75, 245 to 286, and 573 to 646, respectively, indicating a significant N_e reduction in the last several generations. These results suggest a strong necessity for minimizing inbreeding through the application of genomic selection or other breeding strategies to increase N_e, so as to maintain genetic variation and to avoid future bottlenecks in the Sapsaree population.

Causes and consequences of fine-scale population structure in a critically endangered freshwater seal

Background

Small, genetically uniform populations may face an elevated risk of extinction due to reduced environmental adaptability and individual fitness. Fragmentation can intensify these genetic adversities and, therefore, dispersal and gene flow among subpopulations within an isolated population is often essential for maintaining its viability. Using microsatellite and mtDNA data, we examined genetic diversity, spatial differentiation, interregional gene flow, and effective population sizes in the critically endangered Saimaa ringed seal (Phoca hispida saimensis), which is endemic to the large but highly fragmented Lake Saimaa in southeastern Finland.

Results

Microsatellite diversity within the subspecies (H_E = 0.36) ranks among the lowest thus far recorded within the order Pinnipedia, with signs of ongoing loss of individual heterozygosity, reflecting very low effective subpopulation sizes. Bayesian assignment analyses of the microsatellite data revealed clear genetic differentiation among the main breeding areas, but interregional structuring was substantially weaker in biparentally inherited microsatellites (F_ST = 0.107) than in maternally inherited mtDNA (F_ST = 0.444), indicating a sevenfold difference in the gene flow mediated by males versus females.

Conclusions

Genetic structuring in the population appears to arise from the joint effects of multiple factors, including small effective subpopulation sizes, a fragmented lacustrine habitat, and behavioural dispersal limitation. The fine-scale differentiation found in the landlocked Saimaa ringed seal is especially surprising when contrasted with marine ringed seals, which often exhibit near-panmixia among subpopulations separated by hundreds or even thousands of kilometres. Our results demonstrate that population structures of endangered animals cannot be predicted based on data on even closely related species or subspecies.

Living on the edge: reconstructing the genetic history of the Finnish wolf population

Background

Many western European carnivore populations became almost or completely eradicated during the last ~200 years, but are now recovering. Extirpation of wolves started in Finland in the 19th century, and for more than 150 years the population size of wolves has remained small. To investigate historical patterns of genetic variation, we extracted DNA from 114 wolf samples collected in zoological museums over the last ~150 years. Fifteen microsatellite loci were used to look at genotypic variation in this historical sample. Additionally, we amplified a 430 bp sequence of mtDNA control region from the same samples. Contemporary wolf samples (N = 298) obtained after the population recovery in the mid-1990s, were used as a reference.

Results

Our analyses of mtDNA revealed reduced variation in the mtDNA control region through the loss of historical haplotypes observed prior to wolf declines. Heterozygosity at autosomal microsatellite loci did not decrease significantly. However, almost 20% of microsatellite alleles were unique to wolves collected before the 1960s. The genetic composition of the population changed gradually with the largest changes occurring prior to 1920. Half of the oldest historical samples formed a distinguishable genetic cluster not detected in the modern-day Finnish or Russian samples, and might therefore represent northern genetic variation lost from today’s gene pool. Point estimates of N_e were small (13.2 and 20.5) suggesting population fragmentation. Evidence of a genetic population bottleneck was also detected.

Conclusions

Our genetic analyses confirm changes in the genetic composition of the Finnish wolf population through time, despite the geographic interconnectivity to a much larger population in Russia. Our results emphasize the need for restoration of the historical connectivity between the present wolf populations to secure long-term viability. This might be challenging, however, because the management policies between Western and Eastern Europe often differ greatly. Additionally, wolf conservation is still a rather controversial issue, and anthropogenic pressure towards wolves remains strong.

Multilocus detection of wolf x dog hybridization in italy, and guidelines for marker selection

Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past generation backcrosses is always uncertain, and a larger number of ancestry-informative markers is needed.

Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus) population in north-eastern Europe

Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus) population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

Demographic loss, genetic structure and the conservation implications for Indian tigers

India is home to approximately 60 per cent of the world's remaining wild tigers, a species that has declined in the last few centuries to occupy less than 7 per cent of its former geographical range. While Indian tiger numbers have somewhat stabilized in recent years, they remain low and populations are highly fragmented. Therefore, the application of evidence-based demographic and genetic management to enhance the remaining populations is a priority. In this context, and using genetic data from historical and modern tigers, we investigated anthropogenic impacts on genetic variation in Indian tigers using mitochondrial and nuclear genetic markers. We found a very high number of historical mitochondrial DNA variants, 93 per cent of which are not detected in modern populations. Population differentiation was higher in modern tigers. Simulations incorporating historical data support population decline, and suggest high population structure in extant populations. Decreased connectivity and habitat loss as a result of ongoing fragmentation in the Indian subcontinent has therefore resulted in a loss of genetic variants and increased genetic differentiation among tiger populations. These results highlight that anthropogenic fragmentation and species-specific demographic processes can interact to alter the partitioning of genetic variation over very short time scales. We conclude that ongoing strategies to maximize the size of some tiger populations, at the expense of losing others, is an inadequate conservation strategy, as it could result in a loss of genetic diversity that may be of adaptive significance for this emblematic species.

Variation of genetic diversity in a rapidly expanding population of the greater long-tailed hamster (Tscherskia triton) as revealed by microsatellites

Genetic diversity is essential for persistence of animal populations over both the short- and long-term. Previous studies suggest that genetic diversity may decrease with population decline due to genetic drift or inbreeding of small populations. For oscillating populations, there are some studies on the relationship between population density and genetic diversity, but these studies were based on short-term observation or in low-density phases. Evidence from rapidly expanding populations is lacking. In this study, genetic diversity of a rapidly expanding population of the Greater long-tailed hamsters during 1984–1990, in the Raoyang County of the North China Plain was studied using DNA microsatellite markers. Results show that genetic diversity was positively correlated with population density (as measured by % trap success), and the increase in population density was correlated with a decrease of genetic differentiation between the sub-population A and B. The genetic diversity tended to be higher in spring than in autumn. Variation in population density and genetic diversity are consistent between sub-population A and B. Such results suggest that dispersal is density- and season-dependent in a rapidly expanding population of the Greater long-tailed hamster. For typically solitary species, increasing population density can increase intra-specific attack, which is a driving force for dispersal. This situation is counterbalanced by decreasing population density caused by genetic drift or inbreeding as the result of small population size. Season is a major factor influencing population density and genetic diversity. Meanwhile, roads, used to be considered as geographical isolation, have less effect on genetic differentiation in a rapidly expanding population. Evidences suggest that gene flow (Nm) is positively correlated with population density, and it is significant higher in spring than that in autumn.

Genetic diversity of the Eurasian Otter (Lutra lutra) population in Israel

The Israeli population of Eurasian otter (Lutra lutra) marks the Palearctic southern boundary of the species' distribution in the Levant. During the 20th century, the otter population in Israel experienced a dramatic decline due to anthropogenic habitat alterations. Currently, the otter population in Israel is estimated at about 100 individuals and defined as "Critically Endangered". The aim of this research was to characterize the Israeli otter population in order to determine its genetic diversity and fragmentation state for conservation purposes. Monitoring spraint sites during 2000-2011 along active and historic otter distribution regions indicate both stable and unstable otter subpopulations, mainly along the Jordan River. Four otter subpopulations, representing 57 individuals, were characterized by 12 microsatellites, previously used to characterize the European otter populations. The genetic results indicated three subpopulations correlating with three geographical regions: the Hula Valley, Sea of Galilee, and the Harod Valley. A moderate genetic diversity (F (st) = 0.087-0.123) was found among the subpopulations, suggesting sporadic interactions between individuals from distinct geographical locations along the Jordan Rift Valley. The Israeli otter population was found to be very small, demographically remote and genetically distinct, harboring unique alleles absent from the studied European populations. Therefore, immediate conservation actions are recommended to prevent the deterioration of the isolated, unique, and critically endangered otter population in Israel.

Can genetic estimators provide robust estimates of the effective number of breeders in small populations?

The effective population size (N(e)) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N(e). Because geckos have overlapping generations, our goal was to demographically estimate N(bI), the inbreeding effective number of breeders and to calculate the N(bI)/N(a) ratio (N(a) =number of adults) for four populations. Demographically estimated N(bI) ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N(bI)/N(a)) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N(bI(gen)) and the variance effective populations size N(eV(gen)) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14-55 and 24-48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N(bI) for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.

MHC variability supports dog domestication from a large number of wolves: high diversity in Asia

The process of dog domestication is still somewhat unresolved. Earlier studies indicate that domestic dogs from all over the world have a common origin in Asia. So far, major histocompatibility complex (MHC) diversity has not been studied in detail in Asian dogs, although high levels of genetic diversity are expected at the domestication locality. We sequenced the second exon of the canine MHC gene DLA-DRB1 from 128 Asian dogs and compared our data with a previously published large data set of MHC alleles, mostly from European dogs. Our results show that Asian dogs have a higher MHC diversity than European dogs. We also estimated that there is only a small probability that new alleles have arisen by mutation since domestication. Based on the assumption that all of the currently known 102 DLA-DRB1 alleles come from the founding wolf population, we simulated the number of founding wolf individuals. Our simulations indicate an effective population size of at least 500 founding wolves, suggesting that the founding wolf population was large or that backcrossing has taken place.