A mitochondrial DNA phylogeny of the endangered vipers of the Vipera ursinii complex

The last two populations of the Hungarian meadow viper Vipera ursinii rakosiensis were thought to persist in the steppe fragments of Hungary until meadow vipers were discovered in central Romania (Transylvania), suggesting a possible existence of remnant populations elsewhere. We assessed the phylogenetic position of the Transylvanian vipers using 2030 bp of mitochondrial DNA sequence. We showed that they were closely related to the Hungarian vipers, while those from northeastern Romania (Moldavia) and Danube Delta belonged to the subspecies Vipera ursinii moldavica. Montane subspecies from Europe (Vipera ursinii ursinii and Vipera ursinii macrops) formed a sister clade to the two lowland subspecies. Vipera renardi formed a sister clade to V. ursinii, with populations from the Greater Caucasus (Vipera renardi lotievi) and Tien Shan (Vipera renardi tienshanica) as the sister group to Vipera renardi renardi, and Vipera renardi eriwanensis from the Lesser Caucasus as the most basal taxon in the species. Our results illustrate that the divergence between the lowland and montane populations occurred separately in each species and several times in V. renardi. We demonstrated that the recently discovered Transylvanian population is the third surviving population of V. u. rakosiensis and the only known population outside of Hungary.     

Genetic variability of brown bear (<Emphasis Type="Italic">Ursus arctos</Emphasis> L., 1758)

We perform an analysis of the diversity of the control region fragment (570 bp) and ten nuclear microsatellite loci for 36 specimens of the brown bear (Ursus arctos) from several regions of the Caucasus. Four mitochondrial haplogroups that significantly differ from each other are revealed. An assumption of reiterative brown bear colonization of the Caucasus is made. Microsatellite data analysis shows a medium level of heterozygosity and clear differentiation between Caucasian and European bears combined with a slight distinction between the Caucasian regions.     

Genomic Evidence for Island Population Conversion Resolves Conflicting Theories of Polar Bear Evolution

Despite extensive genetic analysis, the evolutionary relationship between polar bears (Ursus maritimus) and brown bears (U. arctos) remains unclear. The two most recent comprehensive reports indicate a recent divergence with little subsequent admixture or a much more ancient divergence followed by extensive admixture. At the center of this controversy are the Alaskan ABC Islands brown bears that show evidence of shared ancestry with polar bears. We present an analysis of genome-wide sequence data for seven polar bears, one ABC Islands brown bear, one mainland Alaskan brown bear, and a black bear (U. americanus), plus recently published datasets from other bears. Surprisingly, we find clear evidence for gene flow from polar bears into ABC Islands brown bears but no evidence of gene flow from brown bears into polar bears. Importantly, while polar bears contributed <1% of the autosomal genome of the ABC Islands brown bear, they contributed 6.5% of the X chromosome. The magnitude of sex-biased polar bear ancestry and the clear direction of gene flow suggest a model wherein the enigmatic ABC Island brown bears are the descendants of a polar bear population that was gradually converted into brown bears via male-dominated brown bear admixture. We present a model that reconciles heretofore conflicting genetic observations. We posit that the enigmatic ABC Islands brown bears derive from a population of polar bears likely stranded by the receding ice at the end of the last glacial period. Since then, male brown bear migration onto the island has gradually converted these bears into an admixed population whose phenotype and genotype are principally brown bear, except at mtDNA and X-linked loci. This process of genome erosion and conversion may be a common outcome when climate change or other forces cause a population to become isolated and then overrun by species with which it can hybridize.     

The role of western Mediterranean islands in the evolutionary diversification of the spotted flycatcher Muscicapa striata,a long‐distance migratory passerine species

We investigated the evolutionary history of the spotted flycatcher Muscicapa striata, a long distance migratory passerine having a widespread range, using mitochondrial markers and nuclear introns. Our mitochondrial results reveal the existence of one insular lineage restricted to the western Mediterranean islands (Balearics, Corsica, Sardinia) and possibly to the Tyrrhenian coast of Italy that diverged from the mainland lineages around 1 Mya. Mitochondrial genetic distance between insular and mainland lineages is around 3.5%. Limited levels of shared nuclear alleles among insular and mainland populations further support the genetic distinctiveness of insular spotted flycatchers with respect to their mainland counterparts. Moreover, lack of mitochondrial haplotypes sharing between Balearic birds (M. s. balearica) and Corso‐Sardinian birds (M. s. tyrrhenica) suggest the absence of recent matrilineal gene flow between these two insular subspecies. Accordingly, we suggest that insular spotted flycatchers could be treated as one polytypic species (Muscicapa tyrrhenica) that differs from M. striata in morphology, migration, mitochondrial and nuclear DNA and comprises two subspecies (the nominate and M. t. balearica) that diverged recently phenotypically and in mitochondrial DNA and but still share the same nuclear alleles. This study provides an interesting case‐study illustrating the crucial role of western Mediterranean islands in the evolution of a passerine showing high dispersal capabilities. Our genetic results highlight the role of glacial refugia of these islands that allowed initial allopatric divergence of insular populations. We hypothesize that differences in migratory and breeding phenology may prevent any current gene flow between insular and mainland populations of the spotted flycatcher that temporarily share the same insular habitats during the spring migration.     

Variability of the upper incisors in the cave bears (Carnivora,Ursidae) from the Caucasus and Urals

Morphometric and morphotypic variability of the cave bear upper incisors from two different geographic regions (Caucasus and Urals), different stratigraphic periods (middle and late Pleistocene), and bearing different mitochondrial haplogroups (kudarensis and ingressus) was studied. The specific diet of the cave bears, i.e. hard vegetables, led to noticeable differences between their incisors and the incisors of the brown bear (Ursus arctos). It was found that the upper incisors of the Caucasian cave bears from different stratigraphic periods demonstrate consistent development of their morphology. The late Pleistocene cave bears from the Urals show a greater similarity to the Caucasian cave bears from earlier periods than with the cave bears from later periods. Our results suggest that the incisor morphology has evolved independently in the Caucasian and Ural cave bears as they belong to different phylogenetic lineages and display different ways of adaptation to local environmental conditions.     

Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos)

In the 1930s, the Scandinavian brown bear was close to extinction due to vigorous extermination programmes in Norway and Sweden. Increased protection of the brown bear in Scandinavia has resulted in the recovery of four subpopulations, which currently contain close to 1000 individuals. Effective conservation and management of the Scandinavian brown bear requires knowledge of the current levels of genetic diversity and gene flow among the four subpopulations. Earlier studies of mitochondrial DNA (mtDNA) diversity revealed extremely low levels of genetic variation, and population structure that grouped the three northern subpopulations in one genetic clade and the southernmost subpopulation in a second highly divergent clade. In this study, we extended the analysis of genetic diversity and gene flow in the Scandinavian brown bear using data from 19 nuclear DNA microsatellite loci. Results from the nuclear loci were strikingly different than the mtDNA results. Genetic diversity levels in the four subpopulations were equivalent to diversity levels in nonbottlenecked populations from North America, and significantly higher than levels in other bottlenecked and isolated brown bear populations. Gene flow levels between subpopulations ranged from low to moderate and were correlated with geographical distance. The substantial difference in results obtained using mtDNA and nuclear DNA markers stresses the importance of collecting data from both types of genetic markers before interpreting data and making recommendations for the conservation and management of natural populations. Based on the results from the mtDNA and nuclear DNA data sets, we propose one evolutionarily significant unit and four management units for the brown bear in Scandinavia.     

Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals?

The brown bear has proved a useful model for studying Late Quaternary mammalian phylogeography. However, information is lacking from northern continental Eurasia, which constitutes a large part of the species' current distribution. We analysed mitochondrial DNA sequences (totalling 1943 bp) from 205 bears from northeast Europe and Russia in order to characterize the maternal phylogeography of bears in this region. We also estimated the formation times of the sampled brown bear lineages and those of its extinct relative, the cave bear.
Four closely related haplogroups belonging to a single mitochondrial subclade were identified in northern continental Eurasia. Several haplotypes were found throughout the whole study area, while one haplogroup was restricted to Kamchatka. The haplotype network, estimated divergence times and various statistical tests indicated that bears in northern continental Eurasia recently underwent a sudden expansion, preceded by a severe bottleneck. This brown bear population was therefore most likely founded by a small number of bears that were restricted to a single refuge area during the last glacial maximum. This pattern has been described previously for other mammal species and as such may represent one general model for the phylogeography of Eurasian mammals. Bayesian divergence time estimates are presented for different brown and cave bear clades. Moreover, our results demonstrate the extent of substitution rate variation occurring throughout the phylogenetic tree, highlighting the need for appropriate calibration when estimating divergence times.     

Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (<Emphasis Type="Italic">Dicerorhinus sumatrensis</Emphasis>)

The Sumatran rhinoceros (Dicerorhinus sumatrensis) is the smallest and one of the most endangered rhinoceros species, with less than 100 individuals estimated to live in the wild. It was originally divided into three subspecies but only two have survived, D. sumatrensis sumatrensis (Sumatran subspecies), and D. s. harrissoni (Bornean). Questions regarding whether populations of the Sumatran rhinoceros should be treated as different management units to preserve genetic diversity have been raised, particularly in light of its severe decline in the wild and low breeding success in captivity. This work aims to characterize genetic differentiation between Sumatran rhinoceros subspecies using complete mitochondrial genomes, in order to unravel their maternal evolutionary history and evaluate their status as separate management units. We identified three major phylogenetic groups with moderate genetic differentiation: two distinct haplogroups comprising individuals from both the Malay Peninsula and Sumatra, and a third group from Borneo. Estimates of divergence time indicate that the most recent common ancestor of the Sumatran rhinoceros occurred approximately 360,000 years ago. The three mitochondrial haplogroups showed a common divergence time about 80,000 years ago corresponding with a major biogeographic event in the Sundaland region. Patterns of mitochondrial genetic differentiation may suggest considering Sumatran rhinoceros subspecies as different conservation units. However, the management of subspecies as part of a metapopulation may appear as the last resource to save this species from extinction, imposing a conservation dilemma.     

Ancestral Polymorphisms and Sex-Biased Migration Shaped the Demographic History of Brown Bears and Polar Bears

Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA) and matrilineal mitochondrial DNA (mtDNA). Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA) or more than 14 times (mtDNA) larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.     

Morphological and microsatellite differentiation in Melospiza melodia (Aves) at a microgeographic scale

Geographical variation in microsatellite allele frequencies and morphology were compared for five subspecies of Melospiza melodia (song sparrow; M. m. samuelis, M. m. maxillaris, M. m. pusillula, M. m. gouldii, and M. m. heermanni) in 14 populations in the San Francisco Bay region to (a) assess divergence based on these estimates and (b) test the hypothesis that drift is responsible for morphological and genetic divergence. Morphological differentiation between subspecies was high despite low differentiation at microsatellite loci, indicating high gene flow and large effective population sizes. Low concordance of morphological and genetic estimates of divergence suggests that selection or phenotypic plasticity in morphology has caused morphological differentiation among the subspecies.     

Microevolution of the mitochondrial DNA control region in the Japanese brown bear (Ursus arctos) population.

We investigated nucleotide sequences of the mitochondrial DNA control region to describe natural genetic variations and to assess the relationships between subpopulations of the brown bear Ursus arctos on Hokkaido Island, Japan. Using the polymerase chain reaction product-direct sequencing technique, partial sequences (about 930 bases) of the control region were determined for 56 brown bears sampled throughout Hokkaido Island. A sequence alignment revealed that the brown bear control region included a variable sequence on the 5' side and a repetitive region on the 3' side. Phylogenetic trees reconstructed from the 5' variable region (696-702 bases) exhibited 17 haplotypes, which were clustered into three groups (Clusters A, B, and C). The distribution of each group did not overlap with those of the others, and the three different areas were located in separate mountainous forests of Hokkaido Island. Furthermore, most of the phylogenetically close haplotypes within each group were distributed geographically close to each other. In addition, the 3' repetitive region (arrays of 10 bases) exhibited a much faster mutation rate than the 5' variable region, resulting in heteroplasmy. Such mitochondrial DNA divergence in each group could have occurred after the brown bears migrated from the continent to Hokkaido and became fixed in the different areas.     

Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico

The fossil record indicates that the brown bear (Ursus arctos) colonized North America from Asia over 50 000 years ago. The species historically occupied the western United States and northern Mexico but has been extirpated from over 99% of this range in the last two centuries. To evaluate colonization hypotheses, subspecific classifications, and historical patterns and levels of genetic diversity in this region, we sequenced 229 nucleotides of the mitochondrial DNA control region in 108 museum specimens. The work was set in a global context by synthesizing all previous brown bear control region sequences from around the world. In mid-latitude North America a single moderately diverse clade is observed, represented by 23 haplotypes with up to 3.5% divergence. Only eight of 23 haplotypes (35%) are observed in the extensively sampled extant populations suggesting a substantial loss of genetic variability. The restriction of all haplotypes from mid-latitude North America to a single clade suggests that this region was founded by bears with a similar maternal ancestry. However, the levels and distributions of diversity also suggest that the colonizing population was not a small founder event, and that expansion occurred long enough ago for local mutations to accrue. Our data are consistent with recent genetic evidence that brown bears were south of the ice prior to the last glacial maximum. There is no support for previous subspecies designations, although bears of the southwestern United States may have had a distinctive, but recent, pattern of ancestry.     

Colonisation and Diversification of the Zenaida Dove (Zenaida aurita) in the Antilles: Phylogeography,Contemporary Gene Flow and Morphological Divergence

Caribbean avifaunal biogeography has been mainly studied based on mitochondrial DNA. Here, we investigated both past and recent island differentiation and micro-evolutionary changes in the Zenaida Dove (Zenaida aurita) based on combined information from one mitochondrial (Cytochrome c Oxydase subunit I, COI) and 13 microsatellite markers and four morphological characters. This Caribbean endemic and abundant species has a large distribution, and two subspecies are supposed to occur: Z. a. zenaida in the Greater Antilles (GA) and Z. a. aurita in the Lesser Antilles (LA). Doves were sampled on two GA islands (Puerto Rico and the British Virgin Islands) and six LA islands (Saint Barthélemy, Guadeloupe, Les Saintes, Martinique, Saint Lucia and Barbados). Eleven COI haplotypes were observed that could be assembled in two distinct lineages, with six specific to GA, four to LA, the remaining one occurring in all islands. However, the level of divergence between those two lineages was too moderate to fully corroborate the existence of two subspecies. Colonisation of the studied islands appeared to be a recent process. However, both phenotypic and microsatellite data suggest that differentiation is already under way between all of them, partly associated with the existence of limited gene flow. No isolation by distance was observed. Differentiation for morphological traits was more pronounced than for neutral markers. These results suggest that despite recent colonisation, genetic drift and/or restricted gene flow are promoting differentiation for neutral markers. Variation in selective pressures between islands may explain the observed phenotypic differentiation.     

Population Genetic Structuring in <Emphasis Type="Italic">Acanthopagrus butcheri</Emphasis> (Pisces: Sparidae): Does Low Gene Flow Among Estuaries Apply to Both Sexes?

Acanthopagrus butcheri completes its entire life history within estuaries and coastal lakes of southern Australia, although adults occasionally move between estuaries via the sea. Consequently, it is expected that populations of A. butcheri in different estuaries will be genetically distinct, with the magnitude of genetic divergence increasing with geographic isolation. However, previous genetic studies of A. butcheri from southeast Australia yielded conflicting results; allozyme variation exhibited minimal spatial structuring (θ = 0.012), whereas mitochondrial DNA distinguished the majority of populations analyzed (θ = 0.263) and genetic divergence was positively correlated with geographic isolation. This discrepancy could reflect high male gene flow, which impacts nuclear but not mitochondrial markers. Here we estimated allele frequencies at five nuclear microsatellite loci across 11 southeast Australian populations (595 individuals). Overall structuring of microsatellite variation was weaker (θ = 0.088) than that observed for mitochondrial DNA, but was able to distinguish a greater number of populations and was positively correlated with geographic distance. Therefore, we reject high male gene flow and invoke a stepping-stone model of infrequent gene flow among estuaries for both sexes. Likewise, management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries for both sexes. The lack of allozyme structuring in southeast Australia reflects either the large variance in structuring expected among loci under neutral conditions and the low number of allozymes surveyed or a recent colonization of estuaries such that some but not all nuclear loci have approached migration-drift equilibrium.     

POPULATION STRUCTURE AND GENETIC DIFFERENTIATION IN NATIVE AND INTRODUCED POPULATIONS OF DESCHAMPSIA CAESPITOSA (POACEAE) IN THE COLORADO ALPINE

Deschampsia caespitosa is a widespread grass common in moist areas of the alpine tundra of the Rocky Mountains. Enzyme electrophoresis was used to examine population genetic structure along two soil moisture gradients in Rocky Mountain National Park, Colorado. Introduced plants used in a revegetation project were also sampled at one of the sites. At both sites, there were significant differences among subpopulations in allele frequencies, but these differences were distributed in a patchy fashion and were not correlated with the apparent soil moisture gradients. The degree of genetic subdivision differed between the two sites. At one site, gene flow appeared to be high and differences in allele frequencies are attributed to selection in a mosaic environment. At the other site, gene flow appeared more restricted and differences in allele frequencies between subpopulations are attributed to selection and limited gene flow acting simultaneously. Overall, 15% of the genetic variability is between subpopulations and gene flow is high, even between subpopulations separated by up to 1.5 km, but local conditions can apparently limit gene flow and increase the degree of genetic subdivision. The mean genetic distance between introduced plants and the native subpopulations was significantly higher than the mean genetic distance between all other subpopulations. Despite the high gene flow apparent in alpine tundra subpopulations of Deschampsia caespitosa, significant genetic structuring of these subpopulations has developed.     

Potential distribution under different climatic scenarios of climate change of the vulnerable Caucasian salamander (<Emphasis Type="Italic">Mertensiella caucasica</Emphasis>): A case study of the Caucasus Hotspot

Amphibians are strongly affected by climate change like many vertebrate animals. To address this problematic situation, we examined the potential effect of climate change on the distribution of Mertensiella caucasica (Waga, 1876) that is the best known species in Caucasus hotspot using future distribution modelling (average for 2041–2060 and 2061–2080) under RCP 4.5 and RCP 8.5 emission scenarios. According to our model, the future distribution showed a remarkable expansion towards the northwest part of the Greater Caucasus whereas it indicated a regression from the West of the western Lesser Caucasus up to the Greater Caucasus. Our results indicated that most habitat loss seems to occur in the West Lesser Caucasus including the northeast of Turkey and the East Lesser Caucasus. Moreover, habitat suitability for M. caucasica showed trends towards local extinction in the future. In the Caucasus hotspot, the expected distribution range of M. caucasica will decrease with the risk of local extinction. Therefore, we recommend that its status in IUCN Red List should be reconsidered again.     

Migration distance rather than migration rate explains genetic diversity in human patrilocal groups

In patrilocal groups, females preferentially move to join their mate’s paternal relatives. The gender‐biased gene flow generated by this cultural practice is expected to affect genetic diversity across human populations. Greater female than male migration is predicted to result in a larger decrease in between‐group differentiation for mitochondrial DNA (mtDNA) than for the non‐recombining part of the Y chromosome (NRY). We address the question of how patrilocality affects the distribution of genetic variation in human populations controlling for confounding factors such as ethno‐linguistic heterogeneity and geographic distance which possibly explain the contradictory results observed in previous studies. By combining genetic and bio‐demographic data from Lesotho and Spain, we show that preferential female migration over short distances appears to minimize the impact of a generally higher female migration rate in patrilocal communities, suggesting patrilocality might influence genetic variation only at short ranges.     

Mitochondrial haplogroup T is negatively associated with the status of elite endurance athlete

Mitochondrial function is absolutely necessary to supply the energy required for muscles, and germ line mutations in mitochondrial genes have been related with impaired cardiac function and exercise intolerance. In addition, alleles at several polymorphic sites in mtDNA define nine common haplogroups, and some of these haplogroups have been implicated in the risk of developing several diseases. In this study, we analysed the association between mtHaplogroups and the capacity to reach the status of elite endurance athlete. DNA was obtained from blood leukocytes of 95 Spanish elite endurance athletes and 250 healthy male population controls. We analysed eight mitochondrial polymorphisms and the frequencies were statistically compared between elite athletes and controls. Haplogroup T, specifically defined by 13368A, was significantly less frequent among elite endurance athletes (p =0.012, Fisher's exact test). Our study suggests that allele 13368A and mitochondrial haplogroup T might be a marker negatively associated with the status of elite endurance athlete. This mitochondrial variant could be related with a lower capacity to respond to endurance training, through unknown mechanisms involving a less efficient mitochondrial workload.     

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

The formerly large, continuous brown bear population of the Carpathians has experienced a radical decrease in population size due to human activities which have resulted in splitting the population into the larger Eastern Carpathian and the smaller Western Carpathian subpopulations. In the Western Carpathians, brown bears came close to extinction at the beginning of 1930s, but thanks to both conservation and management efforts the bear population has begun to recover. In contrast, the Eastern Carpathian subpopulation in Romania has never dropped below 800 individuals, potentially preserving the original amount of genetic variation. In this paper we present results of a genetic study of brown bear subpopulations distributed in the Slovak and Romanian sections of the Carpathians using 13 nuclear microsatellites. The documented level of genetic differentiation between the Western and Eastern Carpathian subpopulations reflects the isolation which lasted almost 100 years. Furthermore, the existence of two, different, genetic clusters within the Western Carpathians despite close geographic proximity indicates that human-caused fragmentation and isolation have resulted in significant genetic divergence. Although the subpopulations display an indication of genetic bottleneck, the level of genetic diversity is within the range commonly observed in different brown bear populations. The results presented here point out the significance of human exploitation to the population structure of this large carnivore species. Future management efforts should be aimed at securing and restoring the connectivity of forested habitats, in order to preserve the genetic variation of the Carpathian brown bear subpopulations and to support the gene flow between them.