Microsatellite diversity and structure of Carpathian brown bears (Ursus arctos): consequences of human caused fragmentation

Evidence of population genetic structure in Ecuadorian Andean bears

Wildlife conservation in Andean countries is a global priority because of the high levels of biodiversity and endemism. Historically, these countries have had limited resources to monitor wildlife (e.g., through genetic tools) and establish conservation programs. Focusing on the study and emblematic use of a few charismatic species has been a strategic approach to direct efforts for conservation and development planning. Consequently, the Andean bear is a flagship and umbrella species for highly biodiverse Andean countries like Ecuador. The few studies exploring the population genetics of this species have concluded that it has low genetic diversity and few units for conservation as populations appear to be well connected. However, these results might be attributed to ascertainment bias as studies have been performed with heterologous molecular markers. Here, using both mtDNA sequences and species-specific microsatellite markers, we show that Andean bears in Ecuador have population structure. Additionally, we found through the study of three Ecuadorian populations that the species might have a higher genetic diversity than we previously thought. These results could support the revision of research priorities, conservation, and planning strategies to improve connectivity for this species which occurs in crucial biodiversity hotspots.

Exploring 15 years of brown bear (Ursus arctos)-vehicle collisions in northwestern Greece

Road networks provide several benefits to human societies; however, they are also one of the major drivers of fragmentation and habitat degradation. Their negative effects include wildlife-vehicle collisions which are associated with increased barrier effects, restricted gene flow, and increased local extinction risk. Large carnivores, such as the brown bear (Ursus arctos), are vulnerable to road mortality while they also put human safety at risk in every collision. We recorded approximately 100 bear-vehicle collisions during the last 15 years (2005–2020) in northwestern Greece and identified common aspects for collisions, i.e., spatial, or temporal segregation of collision events, road features, and age or sex of the involved animals. We recorded collisions in both the core distribution area of brown bears, as well as at the periphery, where few individuals, mostly males, disperse. According to our findings, there are four collision hotspots which include ca. 60% of total collisions. Bear-vehicle collisions occurred mostly in periods of increased animal mobility, under poor light conditions and low visibility. In most cases, we deem that a collision was unavoidable at the time of animal detection, because the driver could not have reacted in time to avoid it. Appropriate fencing, in combination with the retention of safe passages for the animals, can minimize collisions. Therefore, such mitigation measures, wildlife warning signs and other collision prevention systems, such as animal detection systems, should be adopted to decrease the number of bear-vehicle collisions and improve road safety.

Population and landscape genetic analysis of the Malayan sun bear Helarctos malayanus

Conservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.

Predicting species occurrences with habitat network models

Biodiversity conservation requires modeling tools capable of predicting the presence or absence (i.e., occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity [wc]), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modeling approach, which aims to predict species occurrence-state in habitat patches using readily available presence-only records.For the tree frog Hyla arborea in the Swiss Plateau, we delineated habitat network nodes from an ensemble habitat suitability model and used different cost surfaces to generate the edges of three networks: one limited only by dispersal distance (Uniform), another incorporating traffic, and a third based on inverse habitat suitability. For each network, we calculated explanatory variables representing the three categories (lh, wc, and nt). The response variable, occurrence-state, was parametrized by a sampling intensity procedure assessing observations of comparable species over a threshold of patch visits. The explanatory variables from the three networks and an additional non-topological model were related to the response variable with boosted regression trees.The habitat network models had a similar fit; they all outperformed the non-topological model. Habitat suitability index (lh) was the most important predictor in all networks, followed by third-order neighborhood (nt). Patch size (lh) was unimportant in all three networks.We found that topological variables of habitat networks are relevant for the prediction of species occurrence-state, a step-forward from models considering only local habitat characteristics. For any habitat patch, occurrence-state is most prominently influenced by its habitat suitability and then by the number of patches in a wide neighborhood. Our approach is generic and can be applied to multiple species in different habitats.

Inferring fine-scale spatial structure of the brown bear (Ursus arctos) population in the Carpathians prior to infrastructure development

Landscape genetics is increasingly being used in landscape planning for biodiversity conservation by assessing habitat connectivity and identifying landscape barriers, using intraspecific genetic data and quantification of landscape heterogeneity to statistically test the link between genetic variation and landscape variability. In this study we used genetic data to understand how landscape features and environmental factors influence demographic connectedness in Europe’s largest brown bear population and to assist in mitigating planned infrastructure development in Romania. Model-based clustering inferred one large and continuous bear population across the Carpathians suggesting that suitable bear habitat has not become sufficiently fragmented to restrict movement of individuals. However, at a finer scale, large rivers, often located alongside large roads with heavy traffic, were found to restrict gene flow significantly, while eastern facing slopes promoted genetic exchange. Since the proposed highway infrastructure development threatens to fragment regions of the Carpathians where brown bears occur, we develop a decision support tool based on models that assess the landscape configuration needed for brown bear conservation using wildlife corridor parameters. Critical brown bear corridors were identified through spatial mapping and connectivity models, which may be negatively influenced by infrastructure development and which therefore require mitigation. We recommend that current and proposed infrastructure developments incorporate these findings into their design and where possible avoid construction measures that may further fragment Romania’s brown bear population or include mitigation measures where alternative routes are not feasible.

Genetic turnovers and northern survival during the last glacial maximum in European brown bears

The current phylogeographic pattern of European brown bears (Ursus arctos) has commonly been explained by postglacial recolonization out of geographically distinct refugia in southern Europe, a pattern well in accordance with the expansion/contraction model. Studies of ancient DNA from brown bear remains have questioned this pattern, but have failed to explain the glacial distribution of mitochondrial brown bear clades and their subsequent expansion across the European continent. We here present 136 new mitochondrial sequences generated from 346 remains from Europe, ranging in age between the Late Pleistocene and historical times. The genetic data show a high Late Pleistocene diversity across the continent and challenge the strict confinement of bears to traditional southern refugia during the last glacial maximum (LGM). The mitochondrial data further suggest a genetic turnover just before this time, as well as a steep demographic decline starting in the mid-Holocene. Levels of stable nitrogen isotopes from the remains confirm a previously proposed shift toward increasing herbivory around the LGM in Europe. Overall, these results suggest that in addition to climate, anthropogenic impact and inter-specific competition may have had more important effects on the brown bear's ecology, demography, and genetic structure than previously thought.

Identifying attributes associated with brown bear (Ursus arctos) road-crossing and roadkill sites

Habitat fragmentation caused by transportation infrastructure is an issue of growing concern worldwide. We show how secondary roads may affect landscape permeability for brown bears (Ursus arctos Linnaeus, 1758). We focused on identifying environmental variables that govern the selection of road-crossing zones by bears (crossing model). We also investigated whether variables that characterize road-crossing zones differ from those that are typical for bear–vehicle collision sites (collision model). The study area was located in north-central Slovakia. To identify road-crossing sites, we used the GPS fixes of 27 bears and identified 35 bear–vehicle collision sites from a different data set. We used mixed-effects logistic regression to model resource selection at road-crossing sites and to compare bear-crossing sites with bear-kill sites. The crossing model showed that the traffic volume with distance to forest and grassland were the most influential factors in bear selection of road-crossing sites. Results of the collision model indicated that successful road crossings by bears were located at different road sections from vehicle collisions, which differed by a traffic volume of 5000 vehicles/24 h. The outcomes of this study can facilitate improved mitigation measures on secondary roads.

Genetic differentiation and asymmetric gene flow among Carpathian brown bear (Ursus arctos) populations-Implications for conservation of transboundary populations

The abundance and distribution of large carnivores in Europe have been historically reduced. Their recovery requires multilevel coordination, especially regarding transboundary populations. Here, we apply nuclear and mitochondrial genetic markers to test for admixture level and its impact on population genetic structure of contemporary brown bears (Ursus arctos) from the Eastern, Southern, and Western Carpathians. Carpathian Mountains (Europe). Nearly 400 noninvasive brown bear DNA samples from the Western (Poland) and Eastern Carpathians (Bieszczady Mountains in Poland, Slovakia, Ukraine) were collected. Together with DNA isolates from Slovakia and Romania, they were analyzed using the set of eight microsatellite loci and two mtDNA regions (control region and cytochrome b). A set of 113 individuals with complete genotypes was used to investigate genetic differentiation across national boundaries, genetic structuring within and between populations, and movement between populations. Transboundary brown bear subpopulations (Slovakia and Poland) did not show significant internal genetic structure, and thus were treated as cohesive units. All brown bears from the Western Carpathians carried mitochondrial haplotypes from the Eastern lineage, while the Western lineage prevailed in the brown bears from the Bieszczady Mountains. Despite similar levels of microsatellite variability, we documented significant differentiation among the studied populations for nuclear markers and mtDNA. We also detected male-biased and asymmetrical movement into the Bieszczady Mountains population from the Western Carpathians. Our findings suggest initial colonization of the Western Carpathians by brown bears possessing mtDNA from the Eastern lineage. Genetic structuring among populations at microsatellite loci could be a result of human-mediated alterations. Detected asymmetric gene flow suggests ongoing expansion from more abundant populations into the Bieszczady Mountains and thus supports a metapopulation model. The knowledge concerning this complex pattern can be implemented in a joint Carpathian brown bear management plan that should allow population mixing by dispersing males.

Population genetics of the main population of brown bears in southwest Asia

Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.

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.

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.

Genetic and demographic recovery of an isolated population of brown bear Ursus arctos L., 1758

The brown bear Ursus arctos L., 1758 population of the Cantabrian Mountains (northwestern Spain) became isolated from other bear populations in Europe about 500 years ago and has declined due to hunting and habitat degradation. At the beginning of the 20th century, the Cantabrian population split into eastern and western subpopulations, and genetic exchange between them ceased. In the early 1990s, total population size was estimated to be < 100 bears. Subsequently, reduction in human-caused mortality has brought about an increase in numbers, mainly in the western subpopulation, likely promoting male-mediated migration and gene flow from the western nucleus to the eastern. To evaluate the possible genetic recovery of the small and genetically depauperate eastern subpopulation, in 2013 and 2014 we genotyped hair and faeces samples (116 from the eastern subpopulation and 36 from the western) for 18 microsatellite markers. Data from the annual count of females with cubs of the year (COY) during the past twenty-six years was used to analyze demographic changes. The number of females with COY fell to a minimum of seven in the western and three in eastern subpopulations in the biennium 1993-1994 and reached a respective maximum of 54 and 10 individuals in 2013-2014. We also observed increased bear dispersal and gene flow, mainly from the western to the eastern subpopulation. Of the 26 unique genotypes detected in the eastern subpopulation, 14 (54%) presented an admixture composition, and seven (27%) were determined to be migrants from the western subpopulation. Hence, the two separated and clearly structured subpopulations identified in the past currently show some degree of genetic admixture. This research shows the partial demographic recovery and a change in genetic composition due to migration process in a population of bears that has been isolated for several centuries.

North-South differentiation and a region of high diversity in European wolves (Canis lupus)

European wolves (Canis lupus) show population genetic structure in the absence of geographic barriers, and across relatively short distances for this highly mobile species. Additional information on the location of and divergence between population clusters is required, particularly because wolves are currently recolonizing parts of Europe. We evaluated genetic structure in 177 wolves from 11 countries using over 67K single nucleotide polymorphism (SNP) loci. The results supported previous findings of an isolated Italian population with lower genetic diversity than that observed across other areas of Europe. Wolves from the remaining countries were primarily structured in a north-south axis, with Croatia, Bulgaria, and Greece (Dinaric-Balkan) differentiated from northcentral wolves that included individuals from Finland, Latvia, Belarus, Poland and Russia. Carpathian Mountain wolves in central Europe had genotypes intermediate between those identified in northcentral Europe and the Dinaric-Balkan cluster. Overall, individual genotypes from northcentral Europe suggested high levels of admixture. We observed high diversity within Belarus, with wolves from western and northern Belarus representing the two most differentiated groups within northcentral Europe. Our results support the presence of at least three major clusters (Italy, Carpathians, Dinaric-Balkan) in southern and central Europe. Individuals from Croatia also appeared differentiated from wolves in Greece and Bulgaria. Expansion from glacial refugia, adaptation to local environments, and human-related factors such as landscape fragmentation and frequent killing of wolves in some areas may have contributed to the observed patterns. Our findings can help inform conservation management of these apex predators and the ecosystems of which they are part.

Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear

In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a 'yardstick' to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this data set to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed throughout a species range.