Tomaž Skrbinšek

Recovery of large carnivores in Europe’s modern human-dominated landscapes

The conservation of large carnivores is a formidable challenge for biodiversity conservation. Using a data set on the past and current status of brown bears (Ursus arctos), Eurasian lynx (Lynx lynx), gray wolves (Canis lupus), and wolverines (Gulo gulo) in European countries, we show that roughly one-third of mainland Europe hosts at least one large carnivore species, with stable or increasing abundance in most cases in 21st-century records. The reasons for this overall conservation success include protective legislation, supportive public opinion, and a variety of practices making coexistence between large carnivores and people possible. The European situation reveals that large carnivores and people can share the same landscape. Many populations of brown bears, lynx, grey wolves, and wolverines persist successfully outside protected areas in Europe. Success for Europes large carnivores? Despite pessimistic forecasts, Europes large carnivores are making a comeback. Chapron et al. report that sustainable populations of brown bear, Eurasian lynx, gray wolf, and wolverine persist in one-third of mainland Europe. Moreover, many individuals and populations are surviving and increasing outside protected areas set aside for wildlife conservation. Coexistence alongside humans has become possible, argue the authors, because of improved public opinion and protective legislation. Science, this issue p. 1517

Monitoring the effective population size of a brown bear (Ursus arctos) population using new single-sample approaches.

The effective population size (Ne) could be the ideal parameter for monitoring populations of conservation concern as it conveniently summarizes both the evolutionary potential of the population and its sensitivity to genetic stochasticity. However, tracing its change through time is difficult in natural populations. We applied four new methods for estimating Ne from a single sample of genotypes to trace temporal change in Ne for bears in the Northern Dinaric Mountains. We genotyped 510 bears using 20 microsatellite loci and determined their age. The samples were organized into cohorts with regard to the year when the animals were born and yearly samples with age categories for every year when they were alive. We used the Estimator by Parentage Assignment (EPA) to directly estimate both Ne and generation interval for each yearly sample. For cohorts, we estimated the effective number of breeders (Nb) using linkage disequilibrium, sibship assignment and approximate Bayesian computation methods and extrapolated these estimates to Ne using the generation interval. The Ne estimate by EPA is 276 (183–350 95% CI), meeting the inbreeding‐avoidance criterion of Ne > 50 but short of the long‐term minimum viable population goal of Ne > 500. The results obtained by the other methods are highly consistent with this result, and all indicate a rapid increase in Ne probably in the late 1990s and early 2000s. The new single‐sample approaches to the estimation of Ne provide efficient means for including Ne in monitoring frameworks and will be of great importance for future management and conservation.

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.

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.

Highly efficient multiplex PCR of noninvasive DNA does not require pre-amplification

Among the key issues determining success of a study employing molecular genetics tools in wildlife monitoring or research is a large enough set of highly informative genetic markers and a reliable, cost effective method for their analysis. While optimized commercial genotyping kits have been developed for humans and domestic animals, such protocols are rare in wildlife research. We developed a highly optimized multiplex PCR that genotypes 12 microsatellite loci and a sex determination locus in brown bear (Ursus arctos) faecal samples in a single multiplex PCR and a single sequencer run. We used this protocol to genotype 1053 faecal samples of bears from the Dinaric population, and obtained useful genotypes for 88% of the samples, a very high success rate. The new protocol outperformed the multiplex pre‐amplification strategy used in a previous study of 473 faecal samples with a 78.4% success rate. On a subset of 182 samples we directly compared the performance of both approaches, and found no advantage of the multiplex pre‐amplification. While pre‐amplification protocols might still improve PCR success and reliability on a small fraction of low‐quality samples, the higher costs and workload do not justify their use when analysing reasonably fresh non‐invasive material. Moreover, the high number of multiplexed loci in the new protocol makes it comparable to commercially developed genotyping kits developed for domestic animals and humans.

Illegal killings may hamper brown bear recovery in the Eastern Alps

Abstract Illegal killings are a major threat to wildlife conservation worldwide. Combating illegal killings and understanding the motives behind them are among the top challenges for the conservation of controversial species such as large carnivores. In Europe, the Eastern Alps are a focal area for many active brown bear (Ursus arctos) conservation and restoration projects. The wider public generally has a positive attitude toward bears and bear restoration, but some hunters and farmers seem less supportive. The extent this opposition can reach was demonstrated by the well documented illegal killing of a bear in the three-country triangle of Slovenia, Italy, and Austria in June 2009. We provide detailed background information and discuss this case within the context of the lack of a northward expansion of the Dinaric–Pindos bear population and the failed bear re-introduction in central Austria.

Distribution and genetic status of brown bears in FYR Macedonia: implications for conservation

Conservation and management of large carnivores is often hampered by the lack of information of basic biological parameters. This is particularly true for brown bears (Ursus arctos) in the Former Yugoslav Republic (FYR) of Macedonia. The bear population in this country is important, as it links bear populations of the central part of the Dinaric–Pindos population and the endangered population to the south in Greece. The aim of this study was to assess bear presence in FYR Macedonia and to provide the first evaluation of the genetic status of the species in this country. Bear presence was assessed through a questionnaire and sign surveys, while the genetic status of the species was evaluated through noninvasive genetic sampling from power poles and microsatellite analysis. The results of the study indicate the continuous and permanent presence of brown bears in FYR Macedonia from the border to Kosovo in the northwest, along the border to Albania and Greece in the south; bear presence around Mount Kožuf in the south of the country was seasonal. High levels of genetic diversity were recorded, and it appears that this bear population is currently not threatened by low genetic variability. Cross-border movements of bears between FYR Macedonia and Greece were documented, indicating the presence of an interconnected population and outlining the necessity for a coordinated international approach in the monitoring and conservation of the species in southeastern Europe.

Combining phylogenetic and demographic inferences to assess the origin of the genetic diversity in an isolated Wolf population

The survival of isolated small populations is threatened by both demographic and genetic factors. Large carnivores declined for centuries in most of Europe due to habitat changes, overhunting of their natural prey and direct persecution. However, the current rewilding trends are driving many carnivore populations to expand again, possibly reverting the erosion of their genetic diversity. In this study we reassessed the extent and origin of the genetic variation of the Italian wolf population, which is expanding after centuries of decline and isolation. We genotyped wolves from Italy and other nine populations at four mtDNA regions (control-region, ATP6, COIII and ND4) and 39 autosomal microsatellites. Results of phylogenetic analyses and assignment procedures confirmed in the Italian wolves a second private mtDNA haplotype, which belongs to a haplogroup distributed mostly in southern Europe. Coalescent analyses showed that the unique mtDNA haplotypes in the Italian wolves likely originated during the late Pleistocene. ABC simulations concordantly showed that the extant wolf populations in Italy and in south-western Europe started to be isolated and declined right after the last glacial maximum. Thus, the standing genetic variation in the Italian wolves principally results from the historical isolation south of the Alps.

Population genetic parameters of brown bears in western Serbia: implications for research and conservation

Abstract The Alps–Dinaric–Pindos (ADP) bear population is considered to be one of the largest populations remaining in Europe. Despite its international importance for large-scale bear conservation, detailed and accurate information about the genetic and conservation status of some of its sub-populations is lacking. Serbia is located in the geographic center of the ADP bear population, and is of special importance because it connects this population to bear populations in southeastern Europe. Our aim was to establish a research protocol for genetic monitoring and provide information on genetic parameters of brown bears in western Serbia. From hair samples collected non-invasively from hair traps and 2 live-captures, we identified 10 individual bears; a comparison to other bear populations in Europe suggests a favorable genetic status (i.e., increased genetic diversity) of bears in this part of the country. The close geographic proximity of bears in western Serbia to bear populations in adjacent countries, and our results, suggest that the ADP population is interconnected in this region. We recommend a coordinated, multi-national approach for the monitoring and conservation of bears in southeastern Europe, for example, through the establishment of a common genetic database.

Partial genomic survival of cave bears in living brown bears

Although many large mammal species went extinct at the end of the Pleistocene epoch, their DNA may persist due to past episodes of interspecies admixture. However, direct empirical evidence of the persistence of ancient alleles remains scarce. Here, we present multifold coverage genomic data from four Late Pleistocene cave bears (Ursus spelaeus complex) and show that cave bears hybridized with brown bears (Ursus arctos) during the Pleistocene. We develop an approach to assess both the directionality and relative timing of gene flow. We find that segments of cave bear DNA still persist in the genomes of living brown bears, with cave bears contributing 0.9 to 2.4% of the genomes of all brown bears investigated. Our results show that even though extinction is typically considered as absolute, following admixture, fragments of the gene pool of extinct species can survive for tens of thousands of years in the genomes of extant recipient species.Palaeogenomic data from four Late Pleistocene cave bears reveals that cave bears admixed with brown bears in the Pleistocene epoch, and despite cave bears going extinct during the Last Glacial Maximum, extant brown bears maintain a genomic contribution from cave bears.