Conservation genetics of the Far Eastern leopard (Panthera pardus orientalis)

The Far Eastern or Amur leopard (Panthera pardus orientalis) survives today as a tiny relict population of 25-40 individuals in the Russian Far East. The population descends from a 19th-century northeastern Asian subspecies whose range extended over southeastern Russia, the Korean peninsula, and northeastern China. A molecular genetic survey of nuclear microsatellite and mitochondrial DNA (mtDNA) sequence variation validates subspecies distinctiveness but also reveals a markedly reduced level of genetic variation. The amount of genetic diversity measured is the lowest among leopard subspecies and is comparable to the genetically depleted Florida panther and Asiatic lion populations. When considered in the context of nonphysiological perils that threaten small populations (e.g., chance mortality, poaching, climatic extremes, and infectious disease), the genetic and demographic data indicate a critically diminished wild population under severe threat of extinction. An established captive population of P. p. orientalis displays much higher diversity than the wild population sample, but nearly all captive individuals are derived from a history of genetic admixture with the adjacent Chinese subspecies, P. p. japonensis. The conservation management implications of potential restoration/augmentation of the wild population with immigrants from the captive population are discussed.     

Genetic diversity and differentiation of Kermode bear populations

The Kermode bear is a white phase of the North American black bear that occurs in low to moderate frequency on British Columbia's mid-coast. To investigate the genetic uniqueness of populations containing the white phase, and to ascertain levels of gene flow among populations, we surveyed 10 highly polymorphic microsatellite loci, assayed from trapped bear hairs. A total of 216 unique bear genotypes, 18 of which were white, was sampled among 12 localities. Island populations, where Kermodes are most frequent, show approximately 4% less diversity than mainland populations, and the island richest in white bears (Gribbell) exhibited substantial genetic isolation, with a mean pairwise FST of 0.14 with other localities. Among all localities, FST for the molecular variant underlying the coat-colour difference (A893G) was 0.223, which falls into the 95th percentile of the distribution of FST values among microsatellite alleles, suggestive of greater differentiation for coat colour than expected under neutrality. Control-region sequences confirm that Kermode bears are part of a coastal or western lineage of black bears whose existence predates the Wisconsin glaciation, but microsatellite variation gave no evidence of past population expansion. We conclude that Kermodism was established and is maintained in populations by a combination of genetic isolation and somewhat reduced population sizes in insular habitat, with the possible contribution of selective pressure and/or nonrandom mating.     

Genetic structure of the asiatic black bear in Japan using mitochondrial DNA analysis

The genetic structure of the Asiatic black bear (Ursus thibetanus) in Japan was studied to understand the events that occurred during its evolution. The left domain of the mitochondrial control region (about 240 bp) was sequenced, defining 27 haplotypes that consisted of 23 haplotypes from 333 bears in Japan and 22 bears in the Asian continent. The network tree of the control region indicated that the Japanese population formed a distinct clade from the continental population. The phylogeographic analysis of the haplotypes indicated that the Shikoku and Kii Hanto populations had diverged during the initial phase from the ancestral population. After the 3 dominant haplotypes were rapidly distributed throughout Japan in the early stage of the population dispersal, the Japanese population diverged into eastern and western populations. Using the entire mitochondrial cytochrome b sequence, divergence time between the Japanese and the Continental populations suggested that the Japanese population might have colonized into Japan through the land bridge from the Korean Peninsula around 500 ka, which is consistent with paleontological evidence. Our finding that bears in western Japan exhibit lower genetic diversity and higher levels of genetic differentiation than bears in eastern Japan provides a vital contribution to conservation policy for these isolated populations.     

Ten novel tetranucleotide microsatellite DNA markers from Asiatic black bear, Ursus thibetanus

Ten polymorphic microsatellite markers were developed for the endangered Formosan black bear (Ursus thibetanus formosanus) from a partial genomic library enriched for GAAA repeat. Polymorphism of these loci was evaluated in 27 Formosan black bear specimens of unknown relationship. The number of alleles per locus ranged from 5 to 15 and the observed heterozygosity of each locus ranged from 0.556 to 0.889. These loci should provide useful molecular tools to study conservation genetics of the Formosan black bear and other Asiatic black bears.     

Admixture and Gene Flow from Russia in the Recovering Northern European Brown Bear (Ursus arctos)

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise F_ST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.     

Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas

We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise F_ST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise F_ST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.     

Mitochondrial cytochrome b gene variation in brown bear (Ursus arctos Linnaeus, 1758) from southern part of Russian Far East

The genetic variability of brown bear Ursus arctos from the southern part of the Russian Far East was first examined based on the variations in the mitochondrial DNA cytochrome b sequence. The presence of two phylogenetic groups of haplotypes described previously for other parts of the species range was demonstrated. Part of the samples belonged to the haplotype group distributed across the whole range, while another part belonged to the rare group previously only reported for Japan and Alaska. These findings partially clarify the pattern of brown-bear colonization on the territory of the Russian Far East and Japan.     

Influence of fruit on habitat selection of Asian bears in a tropical forest

Wild bear populations in Southeast Asia are threatened with extinction, but the ecology and distribution of the 2 species occurring in the region's protected areas is poorly known, so there is little scientific basis underlying conservation strategies. We used bear signs, primarily claw marks on climbed trees, to study habitat selection and distribution of Asiatic black bear (Ursus thibetanus) and sun bear (Helarctos malayanus) across Khao Yai National Park, Thailand from March to December 2008. We found black bear claw marks in 24 of 30 random sample blocks (80%), indicating that this species was widely distributed across Khao Yai. Sun bear signs were much scarcer: their claw marks occurred in 11 blocks (37%); data were too sparse for sun bear so we limited our focus to Asiatic black bear. Using logistic regression, we found that fruit abundance best explained variation in presence of black bear, whereas human disturbance, distance to park edge, elevation, and ground cover had little influence. Fruits appear to be a key resource for Asiatic black bears, and factors affecting fruit abundance or shifts in seasonality (e.g., climate change) will impact bear populations. Knowledge of this relationship will allow managers to be more proactive in managing bears. We recommend using sign surveys for monitoring changes in black bear occupancy as they are inexpensive, efficient, and can be conducted by trained park rangers. © 2011 The Wildlife Society.     

Subspecific affinity of black bears in the White River National Wildlife Refuge.

The black bear population of the White River National Wildlife Refuge (NWR) is adjacent to populations of black bear in Louisiana (Urusus americanus luteolus) which are listed as threatened under the U.S. Endangered Species Act. Wildlife management plans can pose restrictions on bear harvests and timber extraction; therefore the management plan for the White River NWR is sensitive to subspecific classification of its bear population. The objective of this study was to analyze genetic variation in the White River NWR and seven adjacent populations of black bears to assess the subspecific affinity of the White River NWR population. Here we report the variation at seven microsatellite DNA loci among eight black bear populations. The patterns of genetic variation gave strong support for distinguishing a southern group of black bears comprised of the White River, Arkansas; Tensas River, Louisiana; Upper Atchafalaya, Louisiana; Lower Atchafalaya, Louisiana; and Alabama/Mississippi populations. Phylogenetic analysis of individual variation suggested that historical black bear introductions into Arkansas and Louisiana affected gene pools of certain southern receiving populations, but did not significantly change interpopulation relatedness. Phylogenetic inferences at both the population and individual levels support the hypothesis that the White River NWR population of black bears belongs to the U. a. luteolus subspecies.     

Unraveling the mystery of the glacier bear: Genetic population structure of black bears (Ursus americanus) within the range of a rare pelage type

Glacier bears are a rare grey color morph of American black bear (Ursus americanus) found only in northern Southeast Alaska and a small portion of western Canada. We examine contemporary genetic population structure of black bears within the geographic extent of glacier bears and explore how this structure relates to pelage color and landscape features of a recently glaciated and highly fragmented landscape. We used existing radiocollar data to quantify black bear home‐range size within the geographic range of glacier bears. The mean home‐range size of female black bears in the study area was 13 km² (n = 11), whereas the home range of a single male was 86.9 km². We genotyped 284 bears using 21 microsatellites extracted from noninvasively collected hair as well as tissue samples from harvested bears. We found ten populations of black bears in the study area, including several new populations not previously identified, divided largely by geographic features such as glaciers and marine fjords. Glacier bears were assigned to four populations found on the north and east side of Lynn Canal and the north and west side of Glacier Bay with a curious absence in the nonglaciated peninsula between. Lack of genetic relatedness and geographic continuity between black bear populations containing glacier bears suggest a possible unsampled population or an association with ice fields. Further investigation is needed to determine the genetic basis and the adaptive and evolutionary significance of the glacier bear color morph to help focus black bear conservation management to maximize and preserve genetic diversity.     

Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes

The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ two nuclear single-copy gene segments, the partial exon 1 from gene encoding interphotoreceptor retinoid binding protein (IRBP) and the complete intron 1 from transthyretin (TTR) gene, in conjunction with previously published mt data, to clarify these enigmatic problems. The combined analyses of nuclear IRBP and TTR datasets not only corroborated prior hypotheses, positioning the spectacled bear most basally and grouping the brown and polar bear together but also provided new insights into the bear phylogeny, suggesting the sister-taxa association of sloth bear and sun bear with strong support. Analyses based on combination of nuclear and mt genes differed from nuclear analysis in recognizing the sloth bears as the earliest diverging species among the subfamily ursine representatives while the exact placement of the sun bear did not resolved. Asiatic and American black bears clustered as sister group in all analyses with moderate levels of bootstrap support and high posterior probabilities. Comparisons between the nuclear and mtDNA findings suggested that our combined nuclear dataset have the resolving power comparable to mtDNA dataset for the phylogenetic interpretation of the bear family. As can be seen from present study, the unanimous phylogeny for this recently derived family was still not produced and additional independent genetic markers were in need.     

DNA-Based Population Demographics of Black Bears in Coastal North Carolina and Virginia

ABSTRACT Noninvasive genetic sampling has become a popular method for obtaining population parameter estimates for black (Ursus americanus) and brown (U. arctos) bears. These estimates allow wildlife managers to develop appropriate management strategies for populations of concern. Black bear populations at Great Dismal Swamp (GDSNWR), Pocosin Lakes (PLNWR), and Alligator River (ARNWR) National Wildlife Refuges in coastal Virginia and North Carolina, USA, were perceived by refuge biologists to be at or above cultural and perhaps biological carrying capacity, but managers had no reliable abundance estimates upon which to base population management. We derived density estimates from 3,150 hair samples collected noninvasively at each of the 3 refuges, using 6–7 microsatellite markers to obtain multilocus genotypes for individual bears. We used Program MARK to calculate population estimates from capture histories at each refuge. We estimated densities using both traditional buffer strip methods and Program DENSITY. Estimated densities were some of the highest reported in the literature and ranged from 0.46 bears/km² at GDSNWR to 1.30 bears/km² at PLNWR. Sex ratios were male-biased at all refuges. Our estimates can be directly utilized by biologists to develop effective strategies for managing and maintaining bears at these refuges, and noninvasive methods may also be effective for monitoring bear populations over the long term.     

A multi‐genome analysis approach enables tracking of the invasion of a single Russian wheat aphid (Diuraphis noxia) clone throughout the New World

This study investigated the population genetics, demographic history and pathway of invasion of the Russian wheat aphid (RWA) from its native range in Central Asia, the Middle East and Europe to South Africa and the Americas. We screened microsatellite markers, mitochondrial DNA and endosymbiont genes in 504 RWA clones from nineteen populations worldwide. Following pathway analyses of microsatellite and endosymbiont data, we postulate that Turkey and Syria were the most likely sources of invasion to Kenya and South Africa, respectively. Furthermore, we found that one clone transferred between South Africa and the Americas was most likely responsible for the New World invasion. Finally, endosymbiont DNA was found to be a high‐resolution population genetic marker, extremely useful for studies of invasion over a relatively short evolutionary history time frame. This study has provided valuable insights into the factors that may have facilitated the recent global invasion by this damaging pest.     

Genetic population structure of the Fire-bellied toad <Emphasis Type="Italic">Bombina bombina</Emphasis> in an area of high population density: implications for conservation

In this study, we report the genetic population structure of the Fire-bellied toad Bombina bombina in Brandenburg (East Germany) in the context of conservation. We analysed 298 samples originating from 11 populations in Brandenburg using mitochondrial control region sequences and six polymorphic microsatellite loci. For comparison, we included one population each from Poland and Ukraine into our analysis. Within Brandenburg, we detected a moderate variability in the mitochondrial control region (19 different haplotypes) and at microsatellite loci (9–12 alleles per locus). These polymorphisms revealed a clear population structure among toads in Brandenburg, despite a relatively high overall population density and the moderate size of single populations (100–2000 individuals). The overall genetic population structure is consistent with a postglacial colonization from South East-Europe and a subsequent population expansion. Based on genetic connectivity, we infer Management Units (MUs) as targets for conservation. Our genetic survey identified MUs, within which human infrastructure is currently preventing any genetic exchange. We also detect an unintentional translocation from South East to North West Brandenburg, presumably in the course of fish stocking activities. Provided suitable conservation measures are taken, Brandenburg should continue to harbor large populations of this critically endangered species.     

Genetic diversity,effective population size,and structure among black bear populations in the Lower Mississippi Alluvial Valley,USA

Multiple small populations of American black bears Ursus americanus, including the recently delisted Louisiana black bear subspecies U. a. luteolus, occupy a fragmented landscape in the Lower Mississippi Alluvial Valley, USA (LMAV). Populations include bears native to the LMAV, bears translocated from Minnesota during the 1960s, and recently reintroduced and colonizing populations sourced from within the LMAV. We estimated population structure, gene flow, and genetic parameters important to conservation of small populations using genotypes at 23 microsatellite markers for 265 bears from seven populations. We inferred five genetic clusters corresponding to the following populations: White River and western Mississippi, Tensas River and Three Rivers, Upper Atchafalaya, Lower Atchafalaya, and Minnesota. Upper Atchafalaya was suggested as the product of Minnesota-sourced translocations, but those populations have since diverged, likely because of a founder effect followed by genetic drift and isolation. An admixture zone recently developed in northeastern Louisiana and western Mississippi between migrants from White River and Tensas River, resulting in a Wahlund effect. However, gene flow among most populations has been limited and considerable genetic differentiation accumulated (global F_ST?=?0.22), particularly among the three Louisiana black bear populations that existed when federal listing occurred. Consistent with previous bottlenecks, founder effects, and persisting isolation, all LMAV bear populations had low genetic diversity (A_R?=?2.08–4.81; H_E?=?0.36–0.63) or small effective population size (N_E?=?3–49). Translocating bears among populations as part of a regional genetic restoration program may help improve genetic diversity and increase effective population sizes.     

Black bears in Southeast Alaska: the fate of two ancient lineages in the face of contemporary movement

Biodiversity across a landscape is a product of both historical events and ongoing contemporary forces. The past and present factors that influence black bear Ursus americanus diversity on the Alexander Archipelago and mainland of Southeast Alaska were investigated by assessing nuclear genetic variation. The natural fragmentation of the region, the high vagility of black bears and their possible recent post-Pleistocene colonization to Southeast Alaska allowed us to discern between past and present forces characterizing diversity. Two known black bear lineages, estimated previously with mitochondrial DNA to have diverged 1.8 million years ago, remained evident in data from more rapidly evolving nuclear genetic markers. Two nuclear genetic clusters geographically correspond to the lineages, suggesting that contemporary movement since colonization (likely beginning 18 000 cybp) has not been sufficient to eliminate genetic differences between the highly divergent lineages. Concomitantly, the clearest pattern of genetic diversity is related to contemporary geographic patterns; contemporary geography differs from geography immediately after deglaciation due to sea-level change. Narrow saltwater straits, expansive ice fields, narrow beach fringes and saltwater inland bays separate genetically distinct groupings of black bears.     

Genetic variation of <Emphasis Type="Italic">Picea jezoensis</Emphasis> populations in South Korea revealed by chloroplast,mitochondrial and nuclear DNA markers

Genetic variation associated with Picea jezoensis populations of South Korea was investigated using chloroplast (cp), mitochondrial (mt) and nuclear DNA markers. In South Korea, P. jezoensis is distributed across a very restricted area, being found on the summits of three mountains: Mts. Jiri, Dokyu and Gyebang. Examination of five region restriction enzyme combinations for mtDNA and four for cpDNA revealed haplotypes endemic to South Korea. The Gyebang population, the most northerly and most isolated, was genetically distinct from the other populations. Nuclear microsatellite markers indicated, overall, a low level of genetic diversity (H _e = 0.406) in South Korea; this could be attributed to genetic drift and/or founder effects associated with historical events. The Wilcoxon sign-rank test did not indicate a recent bottleneck in any of the populations irrespective of the model considered (infinite allele model, two-phased model of mutation, and stepwise mutation model). Microsatellite markers also demonstrated that the Gyebang population was distinct from the others. The results of this study could be used as the basis for conservation guidelines for the management of this species in South Korea.     

Inferences on the population structure and colonization process of the invasive oriental fruit fly, Bactrocera dorsalis (Hendel)

The phytophagous insects of the Tephritidae family offer different case histories of successful invasions. An example is Bactrocera dorsalis sensu stricto, the oriental fruit fly which has been recognized as a key pest of Asia and the Pacific. It is known to have the potential to establish adventive populations in various tropical and subtropical areas. Despite the economic risk associated with a putative stable presence of this fly, the genetic aspects of its invasion process have remained relatively unexplored. Using microsatellite markers we have investigated the population structure and genetic variability in 14 geographical populations across the four areas of the actual species range: Far East Asia, South Asia, Southeast Asia and the Pacific Area. Results of clustering and admixture, associated with phylogenetic and migration analyses, were used to evaluate the changes in population genetic structure that this species underwent during its invasion process and establishment in the different areas. The colonization process of this fly is associated with a relatively stable population demographic structure, especially in an unfragmented habitat, rich in intensive cultivation such as in Southeast Asia. In this area, the results suggest a lively demographic history, characterized by evolutionary recent demographic expansions and no recent bottlenecks. Cases of genetic isolation attributable to geographical factors, fragmented habitats and/or fruit trade restrictions were observed in Bangladesh, Myanmar and Hawaii. Regarding the pattern of invasion, the overall genetic profile of the considered populations suggests a western orientated migration route from China to the West.     

Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa

Aim  Middle East brown bears ( Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species.
Location  Middle East region of south-western Asia.
Methods  We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed.
Results  Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals.
Main conclusion  This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations.     

A microsatellite guided insight into the genetic status of adi, an isolated hunting-gathering tribe of northeast India

Tibeto-Burman populations of India provide an insight into the peopling of India and aid in understanding their genetic relationship with populations of East, South and Southeast Asia. The study investigates the genetic status of one such Tibeto-Burman group, Adi of Arunachal Pradesh based on 15 autosomal microsatellite markers. Further the study examines, based on 9 common microsatellite loci, the genetic relationship of Adi with 16 other Tibeto-Burman speakers of India and 28 neighboring populations of East and Southeast Asia. Overall, the results support the recent formation of the Adi sub-tribes from a putative ancestral group and reveal that geographic contiguity is a major influencing factor of the genetic affinity among the Tibeto-Burman populations of India.