The genetical history of an isolated population of the endangered grey wolf Canis lupus: a study of nuclear and mitochondrial polymorphisms

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.

Dental and Temporomandibular Joint Pathology of the Grey Wolf (Canis lupus)

Skulls from 392 grey wolves (Canis lupus) were examined macroscopically according to predefined criteria. Two hundred and seven skulls were included in this study, comprised of 124 young adults (59.9%) and 83 adults (40.1%); of these, 65 (31.4%) specimens were from male wolves and 104 (50.3%) were from females, with 38 (18.4%) of unknown sex. Out of 8,694 possible teeth, 8,339 (95.9%) were present for evaluation. Fifty-five teeth (15.5%) were absent congenitally, 30 (8.5%) were lost during life and 270 (76.1%) were lost artefactually post mortem. Skeletal or dental malocclusion was present in 37 specimens (17.9%), with level bite being the most commonly encountered malocclusion. Enamel hypoplasia was present in five skulls (2.4%), affecting eight teeth (0.1%) in total. An abnormal number of roots was found on 23 teeth (0.3%) on 13 skulls (6.3%). Persistent deciduous teeth occurred in two (1.0%) specimens, affecting one (0.01%) tooth each. Fenestration or dehiscence was found associated with 203 teeth (2.4%) in 72 skulls (34.8%). Periodontitis was noted on 115 skulls (55.6%) and 1,000 teeth (11.5%), affecting significantly more adults (n = 63, 75.0%) than young adults (n = 52, 41.9%; P <0.0001). One hundred and sixty-one skulls (77.8%) showed signs of endodontal disease, including attrition or abrasion on 144 skulls (69.6%) and 2,522 teeth (30.2%) and 424 fractured teeth (5.1%) on 103 skulls (49.8%). Both lesions affected significantly more adults than young adults. Overt periapical disease was associated with six teeth (0.1%) distributed across five skulls (2.4%). A carious lesion was present on one tooth (0.01%) of one specimen (0.5%). Lesions consistent with temporomandibular joint (TMJ) osteoarthritis were found in 24 specimens (11.6%), affecting 38 joints (9.2%). Trauma to the skull, such as bite marks, bullet holes or blunt trauma, was noted in 44 skulls (21.2%). The grey wolf and the domestic dog (Canis lupus familiaris) share common dental diseases; however, the proportion and severity may vary. Although the clinical significance of dental and TMJ pathology in the grey wolf remains unknown, based on the impact of these disorders on the domestic dog, the occurrence and severity of these lesions are likely to play an important role in the morbidity and mortality of this wild canid species.

New insights into the genetic composition and phylogenetic relationship of wolves and dogs in the Iberian Peninsula

This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I. Our data reveal new variants for the molecular markers and confirm significant genetic differentiation between Iberian wolf and native domestic dogs from Portugal. Based on our sampling, no signs of recent introgression between the two subspecies were detected. Y chromosome data do not reveal genetic differentiation among the analyzed dog breeds, suggesting they share the same patrilineal origin. Moreover, the genetic distinctiveness of the Iberian wolf from other wolf populations is further confirmed with the description of new mtDNA variants for this endemism. Our research also discloses new molecular markers for wolf and dog subspecies assignment, which might become particularly relevant in the case of forensic or noninvasive genetic studies. The Iberian wolf represents a relic of the once widespread wolf population in Europe and our study reveals that it is a reservoir of unique genetic diversity of the grey wolf, Canis lupus. These results stress the need for conservation plans that will guarantee the sustainability of this threatened top predator in Iberia.

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.

Field studies in absentia: counting and monitoring from a distance as technologies of government in Norwegian wolf management (1960s-2010s)

The article investigates how national and international measures to protect wolves turned the whole of Norway into a field of study for wildlife biologists, and how the extensiveness of this "field" prompted a transformation in the methods employed to count and monitor wolves. As it was not possible to conduct traditional field studies throughout the whole of Norway, the biologists constructed an extensive infrastructure, which I have termed a "counting complex," in order to count wolves from a distance. The article identifies three decisive periods in the construction of this complex: the 1960s, the 1980s, and the first decade of the new millennium. During the first two periods, biologists used the infrastructure to mobilize ordinary people's observations; they did this by first searching through newspaper notes, then enrolling people more directly through local committees of game management. However, the public's observations often turned out to be unreliable, and, in the 2000s, molecular biologists helped to incorporate genetic techniques into the counting complex. By using the infrastructure to mobilize wolf scat, rather than observations, and by constructing DNA profiles for individual wolves, the molecular biologists enabled research that I have termed "nationwide field studies in absentia." The article argues that the biologists' main motive for constructing and refining the counting complex was to make wolves amenable to government, as they considered this a vital premise for the successful practice of protecting wolves. The increased intensity in monitoring in the last period, however, was also driven by international conventions and detailed regulations.

Reconstructing the colonization history of lost wolf lineages by the analysis of the mitochondrial genome

The grey wolves (Canis lupus) originally inhabited major parts of the Northern hemisphere, but many local populations became extinct. Two lineages of wolves in Japan, namely, Japanese or Honshu (C. l. hodophilax) and Ezo or Hokkaido (C. l. hattai) wolves, rapidly went extinct between 100 and 120years ago. Here we analyse the complete mitochondrial genome sequences from ancient specimens and reconstruct the colonization history of the two extinct subspecies. We show a unique status of Japanese wolves in wolf phylogeny, suggesting their long time separation from other grey wolf populations. Japanese wolves appeared to have colonized the Japanese archipelago in the Late Pleistocene (ca. 25,000-125,000years ago). By contrast, Ezo wolves, which are clearly separated from Japanese wolves in phylogeny, are likely to have arrived at Japan relatively recently (<14,000years ago). Interestingly, their colonization history to Japan tallies well with the dynamics of wolf populations in Europe and America during the last several millennia. Our analyses suggest that at least several thousands of wolves once inhabited in the Japanese archipelago. Our analyses also show that an enigmatic clade of domestic dogs is likely to have originated from rare admixture events between male dogs and female Japanese wolves.

First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes ( Canis latrans)

Previous genetic studies of eastern coyotes ( Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

Wolf body mass, skull morphology, and mitochondrial DNA haplotypes in the Riding Mountain National Park region of Manitoba, Canada

Two types of wolves, gray ( Canis lupus L., 1758) and eastern ( Canis lupus lycaon Schreber, 1775 or Canis lycaon ) or Great Lakes wolves, representing Old World (OW) and New World (NW) mitochondrial DNA (mtDNA) haplotypes, have been reported in eastern Canada and the Great Lakes region. Both haplotypes were found in Duck Mountain Provincial Park and Forest, Manitoba. Only OW haplotypes have been reported from the isolated Riding Mountain National Park (RMNP), 30 km to the south. Wolves with NW haplotypes hybridize with C. lupus and coyotes ( Canis latrans Say, 1823) and could mediate gene flow between canids. We examined available data on wolf body mass, skull morphology, and mtDNA from the RMNP region, as well as mtDNA from Manitoba and Saskatchewan, to assess the occurrence of NW haplotypes in wolves and possible canid hybridization. Mean body mass of female (n = 54) and male (n = 42) RMNP wolves during 1985–1987 was higher than that of females (n = 12) and males (n = 8) during 1999–2004. Thirteen skull measures from 29 wolf skulls did not suggest significant differences between RMNP and Duck Mountain wolves. Nineteen of 20 RMNP samples had OW haplotypes, whereas one clustered together with NW haplotypes.

Population genomics of the inbred Scandinavian wolf

The Scandinavian wolf population represents one of the genetically most well-characterized examples of a severely bottlenecked natural population (with only two founders), and of how the addition of new genetic material (one immigrant) can at least temporarily provide a 'genetic rescue'. However, inbreeding depression has been observed in this population and in the absence of additional immigrants, its long-term viability is questioned. To study the effects of inbreeding and selection on genomic diversity, we performed a genomic scan with approximately 250 microsatellite markers distributed across all autosomes and the X chromosome. We found linkage disequilibrium (LD) that extended up to distances of 50 Mb, exceeding that of most outbreeding species studied thus far. LD was particularly pronounced on the X chromosome. Overall levels of observed genomic heterozygosity did not deviate significantly from simulations based on known population history, giving no support for a general selection for heterozygotes. However, we found evidence supporting balancing selection at a number of loci and also evidence suggesting directional selection at other loci. For markers on chromosome 23, the signal of selection was particularly strong, indicating that purifying selection against deleterious alleles may have occurred even in this very small population. These data suggest that population genomics allows the exploration of the effects of neutral and non-neutral evolution on a finer scale than what has previously been possible.

The genealogy and genetic viability of reintroduced Yellowstone grey wolves

The recovery of the grey wolf in Yellowstone National Park is an outstanding example of a successful reintroduction. A general question concerning reintroduction is the degree to which genetic variation has been preserved and the specific behavioural mechanisms that enhance the preservation of genetic diversity and reduce inbreeding. We have analysed 200 Yellowstone wolves, including all 31 founders, for variation in 26 microsatellite loci over the 10-year reintroduction period (1995-2004). The population maintained high levels of variation (1995 H(0) = 0.69; 2004 H(0) = 0.73) with low levels of inbreeding (1995 F(IS) = -0.063; 2004 F(IS) = -0.051) and throughout, the population expanded rapidly (N(1995) = 21; N(2004) = 169). Pedigree-based effective population size ratios did not vary appreciably over the duration of population expansion (1995 N(e)/N(g) = 0.29; 2000 N(e)/N(g) = 0.26; 2004 N(e)/N(g) = 0.33). We estimated kinship and found only two of 30 natural breeding pairs showed evidence of being related (average r = -0.026, SE = 0.03). We reconstructed the genealogy of 200 wolves based on genetic and field data and discovered that they avoid inbreeding through a wide variety of behavioural mechanisms including absolute avoidance of breeding with related pack members, male-biased dispersal to packs where they breed with nonrelatives, and female-biased subordinate breeding. We documented a greater diversity of such population assembly patterns in Yellowstone than previously observed in any other natural wolf population. Inbreeding avoidance is nearly absolute despite the high probability of within-pack inbreeding opportunities and extensive interpack kinship ties between adjacent packs. Simulations showed that the Yellowstone population has levels of genetic variation similar to that of a population managed for high variation and low inbreeding, and greater than that expected for random breeding within packs or across the entire breeding pool. Although short-term losses in variation seem minimal, future projections of the population at carrying capacity suggest significant inbreeding depression will occur without connectivity and migratory exchange with other populations.

Frequency and distribution of alleles of canine MHC-II DLA-DQB1, DLA-DQA1 and DLA-DRB1 in 25 representative American Kennel Club breeds

The frequency and distribution of dog leucocyte antigens (DLA) class II -DQA1, -DQB1 and -DRB1 alleles were determined for 25 American Kennel Club (AKC) registered dog breeds, representing 360 dogs from each of the seven major performance categories. Six to twenty-eight (average n=11) dogs were studied per group, with the exception of the Akita dog (n=94). All dogs were unrelated with no common grandparents based on AKC pedigree records (F-value <0.125). DLA class II allelic diversity was broad across breeds; 31/61 published DLA-DRB1 alleles, 11/18 published DLA-DQA1 alleles and 31/47 published DLA-DQB1 alleles were found among the 25 breeds. However, allelic diversity was severely limited within a breed. Seventeen of the DLA-DRB1 alleles were each found in only a single breed, and only seven alleles were shared by seven or more breeds. DLA-DRB1*00101 and DLA-DRB1*01501 were shared by 16 and 19 breeds, respectively. DLA-DQA1*00101 and DLA-DQA1*00601 alleles were shared by many breeds. The Rough Collie (DLA-DQA1*00901), English Setter (DLA-DQA1*00101) and Scottish Terrier (DLA-DQA1*00101) were monoallelic for DLA-DQA1. Eleven DLA-DQB1 alleles were each found only in a single breed and only seven alleles were shared by six or more breeds. DLA-DQB1*00201 and DLA-DQB1*02301 were shared by 17 and 18 breeds, respectively. Forty per cent of dogs typed were homozygous at DLA-DRB1, 52% at DLA-DQA1 and 44% at DLA-DQB1. Nine new DLA class II alleles were identified; three for DRB1 and six for DQB1. Comparison of our study of North American purebred dogs to previous European DLA surveys showed a similar use of common alleles consistent with known founder effects. However, more alleles were detected in European breeds, compared to their North American descendents, indicating that additional DLA class II diversity was lost when European breeds were established in North America.

SNPs in ecological and conservation studies: a test in the Scandinavian wolf population

Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.

A temporal analysis shows major histocompatibility complex loci in the Scandinavian wolf population are consistent with neutral evolution

The major histocompatibility complex (MHC) has an integral role in the immune system, and hence diversity at its genes may be of particular importance for the health of populations. In large populations, balancing selection maintains diversity in MHC genes, but theoretical expectations indicate that this form of selection is absent or inefficient in small populations. We examine the level of diversity at three MHC class II loci in the wolf population of Scandinavia, a population naturally recolonized with a genetic contribution from as few as three founders, and in four neighbouring wolf populations. In the Scandinavian wolf population, two alleles were found for each locus and the distribution of alleles is compatible with their linkage into two haplotypes. Changes in the level of heterozygosity over time since recolonization demonstrate the effects of the proposed arrival of an immigrant wolf. The maintenance of diversity is shown to be compatible with a neutral, random allocation of alleles, in conjunction with crossing between packs. A total of 15 DRB1, seven DQA and 10 DQB1 alleles are found in four neighbouring wolf populations, with substantial sharing across populations. Even in these larger populations, bottlenecks and fragmentation with consequent genetic drift are likely to have resulted in few indicators for balancing selection and significant differentiation of populations.

Identification of Atlantic hake species by a simple PCR-based methodology employing microsatellite loci

Three Atlantic hake species (Merluccius merluccius, M. bilinearis, and M. hubbsi) were PCR typed for two microsatellite loci. A blind survey of the markers in samples of the three species determined the suitability of microsatellite loci for identification of hake product. All the analyzed samples were correctly assigned to the corresponding species. Typing of processed products (fish fingers, preprocessed frozen pieces) employing an automated sequencer was successful. This simple (PCR + fragment size) automated determination method is faster than any other method yet described for identification of hake commercial products.

AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites

Individual-based population assignment tests have thus far mainly relied on the use of microsatellite loci. However, the logistic difficulty of screening large numbers of loci required to reach sufficient statistical power hampers the usefulness of microsatellites in situations of weak population structuring. Amplified fragment length polymorphisms (AFLP) represents an alternative for overcoming this logistical issue as the technique allows the user to characterize a much larger number of loci with a comparable analytical effort. In this study, an assignment test based on maximum likelihood for dominant markers was used to investigate the potential usefulness of AFLP for population assignment. We also compared assignment success achieved with AFLP with that obtained using microsatellites in a case study of low population differentiation involving whitefish (Coregonus clupeaformis) sympatric ecotypes. The analytical investigation showed that the minimum number of AFLP loci required to reach an assignment success of 95% stood within values that are easily achievable in many situations. This also showed how assignment success varied according to the number of AFLP loci used, their absolute frequency and their frequency differential and sampling errors, as well as the number of putative source populations. The case study showed that given a comparable analytical effort in the laboratory, AFLP were much more efficient than the microsatellite loci in discriminating the source of an individual among putative populations. AFLP resulted in higher assignment success at all levels of stringency and the log-likelihood differences between populations obtained with AFLP for each individual were much larger than those obtained with microsatellites. These results indicate that research involving individual-based population assignment methods should benefit importantly from the use of AFLP markers, especially in systems characterized by weak population structuring.

Mitochondrial DNA extracted from eastern North American wolves killed in the 1800s is not of gray wolf origin

We analysed the mitochondrial DNA (mtDNA) from two historical samples of eastern North American wolves: the last wolf reported to have been killed in northern New York State (ca. 1890s) and a wolf killed in Maine in the 1880s. These wolves represent eastern wolves, presently classified as the gray wolf (Canis lupus) subspecies Canis lupus lycaon, which were present well before the expansion of western coyotes (Canis latrans) into these regions. We show the absence of gray wolf mtDNA in these wolves. They both contain New World mtDNA, supporting previous findings of a North American evolution of the eastern timber wolf (originally classified as Canis lycaon) and red wolf (Canis rufus) independently of the gray wolf, which originated in Eurasia. The presence of a second wolf species in North America has important implications for the conservation and management of wolves. In the upper Great Lakes region, wolves of both species may exist in sympatry or interbreed with each other, which impacts the accuracy of estimates of numbers of wolves of each species within this geographic region. Furthermore, the historical distribution of the eastern timber wolf (C. lycaon), as revealed by these skin samples, has important implications for the reintroduction of wolves into the northeastern U.S. states, such as New York and Maine.

Two centuries of the Scandinavian wolf population: patterns of genetic variability and migration during an era of dramatic decline

The grey wolf (Canis lupus) was numerous on the Scandinavian peninsula in the early 19th century. However, as a result of intense persecution, the population declined dramatically and was virtually extinct from the peninsula by the 1960s. We examined historical patterns of genetic variability throughout the period of decline, from 1829 to 1979. Contemporary Finnish wolves, considered to be representative of a large eastern wolf population, were used for comparison. Mitochondrial DNA (mtDNA) variability among historical Scandinavian wolves was significantly lower than in Finland while Y chromosome variability was comparable between the two populations. This may suggest that long-distance migration from the east has been male-biased. Importantly though, as the historical population was significantly differentiated from contemporary Finnish wolves, the overall immigration rate to the Scandinavian peninsula appears to have been low. Levels of variability at autosomal microsatellite loci were high by the early 1800s but declined considerably towards the mid-20th century. At this time, approximately 40% of the allelic diversity and 30% of the heterozygosity had been lost. After 1940, however, there is evidence of several immigration events, coinciding with episodes of marked population increase in Russian Karelia and subsequent westwards migration.

Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant

The fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for the rescue of small and inbred populations. However, the relevance of such migration events to genetically depauperate natural populations is not supported by empirical data. We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals, was recovered by the arrival of a single immigrant. Before the arrival of this immigrant, for several generations the population comprised only a single breeding pack, necessarily involving matings between close relatives and resulting in a subsequent decline in individual heterozygosity. With the arrival of just a single immigrant, there is evidence of increased heterozygosity, significant outbreeding (inbreeding avoidance), a rapid spread of new alleles and exponential population growth. Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations.

Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf-dog hybrids

The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the direction of hybridization. We used these three types of markers to genetically characterize one possible wolf-dog hybrid in the endangered Scandinavian wolf population. We first characterized the variability of mtDNA and Y chromosome markers in Scandinavian wolves as well as in neighboring wolf populations and in dogs. While the mtDNA data suggested that the target sample could correspond to a wolf, its Y chromosome type had not been observed before in Scandinavian wolves. We compared the genotype of the target sample at 18 autosomal microsatellite markers with those expected in pure specimens and in hybrids using assignment tests. The combined results led to the conclusion that the animal was a hybrid between a Scandinavian female wolf and a male dog. This finding confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations. A possible correlation between hybridization and wolf population density and disturbance deserves further research.

Y chromosome haplotyping in Scandinavian wolves (Canis lupus) based on microsatellite markers

The analysis of mitochondrial DNA sequences has for a long time been the most extensively used genetic tool for phylogenetic, phylogeographic and population genetic studies. Since this approach only considers female lineages, it tends to give a biased picture of the population history. The use of protein polymorphisms and microsatellites has helped to obtain a more unbiased view, but complementing population genetic studies with Y chromosome markers could clarify the role of each sex in natural processes. In this study we analysed genetic variability at four microsatellite loci on the canid Y chromosome. With these four microsatellites we constructed haplotypes and used them to study the genetic status of the Scandinavian wolf population, a population that now contains 60-70 animals but was thought to have been extinct in the 1970s. In a sample of 100 male wolves from northern Europe we found 17 different Y chromosome haplotypes. Only two of these were found in the current Scandinavian population. This indicates that there should have been at least two males involved in the founding of the Scandinavian wolf population after the bottleneck in the 1970s. The two Scandinavian Y chromosome haplotypes were not found elsewhere in northern Europe, which indicates low male gene flow between Scandinavia and the neighbouring countries.

The recovery, distribution, and population dynamics of wolves on the Scandinavian peninsula, 1978-1998

In 1966 the gray wolf (Canis lupus) was regarded as functionally extinct in Norway and Sweden (the Scandinavian peninsula). In 1978 the first confirmed reproduction on the peninsula in 14 years was recorded. During 20 successive winters, from 1978–1979 to 1997–1998, the status, distribution, and dynamics of the wolf population were monitored by snow-tracking as a cooperative Swedish–Norwegian project. After the 1978 reproduction in northern Sweden, all new pairs and packs were located in south-central parts of the Scandinavian peninsula. Between 1983 and 1990 wolves reproduced each year except 1986, but in only one territory. There was no population growth during this period and the population never exceeded 10 animals. In 1991 reproduction was recorded in two territories. After that there were multiple reproductions each year and the population started growing. In 1998 there were 50–72 wolves and six reproducing packs on the peninsula. Between 1991 and 1998 the annual growth rate was 1.29 ± 0.035 (mean ± SD). A minimum of 25 litters were born during the study period. The early-winter size of packs reproducing for the first time was 6.2 ± 1.4 wolves (n = 9), and this decreased with time during the study. The size of packs that had reproduced more than once was 6.4 ± 1.8 wolves (n = 12), and this increased with time over the study period. All but 1 of 30 reported wolf deaths were human-caused. The annual mortality rate was 0.13 ± 0.11, and this decreased with time during the study period. The minimum dispersal distance was 323 ± 212 km for males and 123 ± 67 km for females. Of 10 new wolf territories where breeding occurred, only 1 bordered other, existing territories. The distance from newly established wolf pairs to the nearest existing packs was 119 ± 73 km. Simulation of population growth based on known reproductions and mortalities showed a close similarity to the results from population censuses up to the mid-1990s. To what extent this population is genetically isolated is at present unclear.

Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps

The genetic structure of the Alpine marmot, Marmota marmota, was studied by an analysis of five polymorphic microsatellite loci. Eight locations were sampled in the French Alps, one from Les Ecrins valley (n = 160), another from La Sassière valley (n = 289) and the six others from the Maurienne valley (n = 139). Information on social group structure was available for both Les Ecrins and La Sassière but not for the other samples. The high levels of genetic diversity observed are at odds with the results obtained using microsatellites, minisatellites and allozymes on Alpine marmots from Germany, Austria and Switzerland. Strong deficits in heterozygotes were found in Les Ecrins and La Sassière. They are caused by a Wahlund effect due to the family structure (i.e. differentiation between the family groups). The family groups exhibit excess of heterozygotes rather than deficits. This may be caused by outbreeding and this is compatible with recent results from the genetics of related social species when information on the social structure is taken into account. The observed outbreeding could be the result of females mating with transient males or males coming from neighbouring colonies. Both indicate that the species may not be as monogamous as is usually believed. The results are also compatible with a male-biased dispersal but do not allow us to exclude some female migration. We also found a significant correlation between geographical and genetic distance indicating that isolation by distance could be an issue in marmots. This study is the first that analysed populations of marmots taking into account the social structure within populations and assessing inbreeding at different levels (region, valley, population, and family groups). Our study clearly demonstrated that the sampling strategy and behavioural information can have dramatic effects on both the results and interpretation of the genetic data.

DNA profiles of the eastern Canadian wolf and the red wolf provide evidence for a common evolutionary history independent of the gray wolf

The origin and taxonomy of the red wolf (Canis rufus) have been the subject of considerable debate and it has been suggested that this taxon was recently formed as a result of hybridization between the coyote and gray wolf. Like the red wolf, the eastern Canadian wolf has been characterized as a small "deer-eating" wolf that hybridizes with coyotes (Canis latrans). While studying the population of eastern Canadian wolves in Algonquin Provincial Park we recognized similarities to the red wolf, based on DNA profiles at 8 microsatellite loci. We examined whether this relationship was due to similar levels of introgressed coyote genetic material by comparing the microsatellite alleles with those of other North American populations of wolves and coyotes. These analyses indicated that it was not coyote genetic material which led to the close genetic affinity between red wolves and eastern Canadian wolves. We then examined the control region of the mitochondrial DNA (mtDNA) and confirmed the presence of coyote sequences in both. However, we also found sequences in both that diverged by 150 000 - 300 000 years from sequences found in coyotes. None of the red wolves or eastern Canadian wolf samples from the 1960s contained gray wolf (Canis lupus) mtDNA sequences. The data are not consistent with the hypothesis that the eastern Canadian wolf is a subspecies of gray wolf as it is presently designated. We suggest that both the red wolf and the eastern Canadian wolf evolved in North America sharing a common lineage with the coyote until 150 000 - 300 000 years ago. We propose that it retain its original species designation, Canis lycaon.

Mitochondrial DNA phylogeography and population history of the grey wolf canis lupus

The grey wolf (Canis lupus) and coyote (C. latrans) are highly mobile carnivores that disperse over great distances in search of territories and mates. Previous genetic studies have shown little geographical structure in either species. However, population genetic structure is also influenced by past isolation events and population fluctuations during glacial periods. In this study, control region sequence data from a worldwide sample of grey wolves and a more limited sample of coyotes were analysed. The results suggest that fluctuating population sizes during the late Pleistocene have left a genetic signature on levels of variation in both species. Genealogical measures of nucleotide diversity suggest that historical population sizes were much larger in both species and grey wolves were more numerous than coyotes. Currently, about 300 000 wolves and 7 million coyotes exist. In grey wolves, genetic diversity is greater than that predicted from census population size, reflecting recent historical population declines. By contrast, nucleotide diversity in coyotes is smaller than that predicted by census population size, reflecting a recent population expansion following the extirpation of wolves from much of North America. Both species show little partitioning of haplotypes on continental or regional scales. However, a statistical parsimony analysis indicates local genetic structure that suggests recent restricted gene flow.

Inbreeding and relatedness in Scandinavian grey wolves Canis lupus

Management of small and threatened populations may require detailed knowledge about the genetic status of individuals and the genetic relatedness between individuals. I show here that individual heterozygosity at a set of 29 microsatellite loci correlates closely to the degree of inbreeding in a captive grey wolf population. Microsatellite allele sharing similarly correlates closely to known relatedness between pairs of individuals. Genotyping the same markers in a small (60-70 individuals) natural population of grey wolves in Sweden, low individual heterozygosities and high values of allele sharing between some animals were found. Since inbreeding depression has been documented in a captive grey wolf population of Scandinavian origin, the results point out an additional risk for the small Swedish wild population.

Conservation genetics of Nordic carnivores: lessons from zoos

This paper summarizes results from genetic studies of Nordic carnivore populations bred in captivity. The conservation genetic implications of those results for the management of wild populations of the same species are discussed. Inbreeding depression has been documented in the brown bear (Ursus arctos), wolf (Canis lupus), and lynx (Lynx lynx) populations held in Nordic zoos. The characters negatively affected by inbreeding include litter size (brown bear and wolf), longevity (lynx and wolf), female reproduction, and weight (wolf). In addition, hereditary defects caused by single autosomal alleles occur in the wolf and brown bear populations. These deleterious alleles cause blindness (wolf) and albinism (brown bear) in the homozygous state. The amount of inbreeding depression observed in Nordic carnivores are similar to that documented in other species. The captive populations have the same genetic background as the current wild ones and inbreeding depression is therefore a potential threat to wild carnivore populations in Sweden. This threat is presently not being adequately recognized in the management of these species. Frequently occurring misunderstandings regarding the kind of conclusions that can be drawn from the presented genetic observations are also discussed.

Potential of microsatellites for individual assignment: the North Atlantic redfish (genus Sebastes) species complex as a case study

We used the four redfish taxa (genus Sebastes) from the North Atlantic to evaluate the potential of multilocus genotype information obtained from microsatellites in assigning individuals at two different levels of group divergence. We first tested the hypothesis that microsatellites can diagnostically discriminate individual redfish from different groups. Second, we compared two different methods to quantify the effect of number of loci and likelihood stringency levels on the power of microsatellites for redfish group membership. The potential of microsatellites to discriminate individuals from different taxa was illustrated by a shared allele distance tree in which four major clusters corresponding to each taxa were defined. Concomitant with this strong discrimination, microsatellites also proved to be powerful in reclassifying specimens to the taxon of origin, using either an empirical or simulated method of estimating assignment success. By testing for the effect of both the number of loci and the level of stringency on the assignment success, we found that 95% of all specimens were still correctly reclassified with only four loci at the most commonly used criterion of log0. In contrast, the results obtained at the population level within taxa highlighted several problems of assignment that may occur at low levels of divergence. Namely, a drastic decrease of success with increasing stringency illustrated the lack of power of our set of loci. Strong discrepancy was observed between results obtained from the empirical and simulated methods. Finally, the highest assignment success was obtained when reducing the number of loci used, an observation previously reported in studies of human populations.