Current Genetic Diversity Research Articles

Genetic Variation and Structure within 3 Endangered Calanthe Species (Orchidaceae) from Korea: Inference of Population-Establishment History and Implications for Conservation

It is thought that the warm-temperate vegetation of Korea, which at present is limited to southern coastal areas, was founded by individuals from glacial refugia putatively located in southern Japan and/or southern China. Two scenarios of postglacial recolonization can be hypothesized: 1) extant Korean populations are derived from multiple source populations or, 2) they originated from a single source. To test which of these scenarios is more likely, we surveyed patterns of genetic diversity in 3 congeneric terrestrial orchids that are typical of Korean warm-temperate vegetation, Calanthe discolor, C. sieboldii, and C. reflexa. In total, we studied 14 populations with 17 allozyme loci. To complement the study, we also tested the 2 scenarios with previous population-genetics data reported for other warm-temperate plant species native to Korea. Levels of genetic variation in the 3 Calanthe species were substantially higher than those typical of allozyme-based studies in other terrestrial orchid species, which clearly suggest a pattern of postglacial recolonization fitting the first scenario. However, previous studies with native Korean species showed equivocal patterns and suggest conflicting scenarios. The Calanthe species studied here and the previous genetic surveys conducted on other species indicate that the establishment of contemporary warm-temperate vegetation in Korea has been diverse since deglaciation. From a conservation perspective, C. reflexa should be regarded as endangered in Korea, needing special attention to preserve its current genetic diversity and to prevent further decreases in population sizes.

Genetic relationships among Italian and Croatian Podolian cattle breeds assessed by microsatellite markers

As recent findings supported new hypotheses regarding the origin and spreading of Podolian breeds, the objectives of the present study were to assess the current genetic diversity and the population structure of five Italian Podolian breeds, and to explore their genetic relationships with the Istrian Cattle (IST) population of Croatia, as Istria peninsula represents the passage between Italian and Balcanic Peninsulas. A total of 373 animals were analyzed using 20 microsatellite markers. The individuals were from seven different breeds: IST (n=113), Romagnola (ROM, n=53), Marchigiana (MAC, n=32), Chianina (CHI, n=30), Maremmana (MAM, n=51), Podolica (POD, n=38), and a reference breed, the Brown Swiss (BRO, n=56). The MAM breed showed the highest gene diversity over all loci (0.726), followed by the POD (0.719) and IST (0.659). The mean observed heterozygosity was 0.580 and it was lower than expected in all breeds. The IST breed appeared genetically very close to the Italian breeds, more similar to Podolian stereotype (POD and MAM; the genetic distances were 0.058 and 0.080, respectively) than to the geographically closer beef type breeds (CHI, MAC, and ROM), suggesting possible ancient trade of animals through the Adriatic Sea. Our results emphasize the importance of monitoring genetic variability in native populations both for conservation purposes and to maintain breed identity and genetic diversity.

Low Within Population Genetic Variation and High Among Population Differentiation inCyrtomium falcatum(L.f.) C. Presl (Dryopteridaceae) in Southern Korea: Inference of Population-Establishment History

Abstract In the Korean Peninsula, the current distribution of the warm-temperate and subtropical vegetation (including many homosporous ferns) is limited to southern coastal areas. Paleoecological data suggest that during the Last Glacial Maximum this vegetation retreated to glacial refugia putatively located in southern Japan and/or southern China, followed by a post-glacial recolonization. Two broad scenarios of post-glacial recolonization could be hypothesized: extant Korean populations are derived from multiple source populations (i.e., from multiple refugia); alternatively, they originate from a single refugium. To test which of these scenarios is more likely, we surveyed patterns of genetic diversity in eight (n = 307) populations of Cyrtomium falcatum from southern Korea. We found extremely low levels of allozyme variation within populations coupled with high among-population differentiation. These data best support the second hypothesis, and indicate that the current genetic diversity may be a c...

Commentary on Sokal's "Ancient Movement Patterns Determine Modern Genetic Variances in Europe" (1991)

Commentary on Sokal's "Ancient Movement Patterns Determine Modern Genetic Variances in Europe" (1991) Jean-Pierre Bocquet-Appel Correction: Due to an error at the printer, the original article page range (551–552) was incorrect. The correct pagination is 553–554 and is reflected in this updated article. Click here for the corrected PDF. In his work on quantitative systematics, Robert Reuven Sokal introduced the idea of spatialization in the late 1970s. After his studies on metapopulations of red flour beetles, house-flies, and cottonwood gall (Bell 2012), he became interested in human metapopulations in the 1980s. This genre had been somewhat neglected, probably because of the shadow cast by the outcomes of eugenics in the earlier half of the twentieth century. As an Austrian Jew who took refuge in China to escape Nazi eugenics, Bob Sokal was perhaps the right man to venture into the field of biological anthropology, armed with the theoretical tools of systematic zoology, in which beast and Man are equal. To analyze the allele or haplotypic frequencies of classic genetic markers, the approach then emerging was to consider these frequencies as samples of surfaces of biological variables on the map, then represented in two dimensions by their so-called principal components (Menozzi et al. 1978). To understand the hypothetical cause(s) that generated geographical patterns of human population, it was (and is) natural to bring in prehistoric and historic sources that provide information on population biology. Based on the similarity between the geographical pattern of a large fraction of allele frequencies and the Neolithic expansion from the Levant, Ammerman and Cavalli-Sforza (1984), as we know, attributed the founding impact of the current genetic structure of European populations to the latter. But the history of European genetic structure was shaped not only by the long, quiet flow of the Neolithic, but also by subsequent "partial migration to, expanding into, settling in, conquering, attacking the area militarily without settling there, naval attacks, etc." (Sokal 1991: 592). In this article, Bob Sokal innovates on two points: Instead of focusing on allele frequencies, understood only as sampled values of the continuum at different localities, he turned to local variations in these frequencies, as estimated in each square of a grid. In theory, it seems obvious that localities that came to be of historical importance—as expressed by the movements of populations in these localities either as places of departure (sources) or places of arrival (targets)—would have high within-locality genetic variance, while localities that did not have this importance would have low or nil genetic variance. Therefore, a positive correlation would be expected between the intensity of population movements within localities and their respective genetic variances. The same would be [End Page 553] true for genetic similarities between localities, which should be correlated with the directional intensity of exchanges between them (as sources or as targets). The second innovation in this article by Bob Sokal is the creation of an ethnohistorical database used to quantify the multitude of population movements in localities on the map. This ethnohistorical database covers the same geographic reference frame as the genetic data. It reflects population movements after the Neolithic expansion from 2000 BC to 1970 AD, that is to say, after the founding impact that shaped the structure of European genetics. (The ethnohistorical database is still downloadable at http://life.bio.sunysb.edu/ee/msr/Ethno/.) The results of this vast work show, apparently and despite the article's title, a very modest influence of historical movements on the modern genetic structure, more modest than Gustave Malecot's "isolation by distance," expressing the limited geographical mobility of individuals in the populations. But the scientific requirement to bring out the impact of population movements in the last 4,000 years on today's population structure, both conceptually— quantitative and now geographical systematics—and in terms of data, was taken by Bob Sokal to a level that became a model for many subsequent studies, regarding the origins of current genetic diversity and its correlates in several world regions (Barbujani and Pilastro 1993; Calafell et al. 1996; Harich et al. 2002; Hunley et al. 2008) and in spatial analysis of human variation (Barbujani and...

Biogeographical Study of Plateau PikasOchotona curzoniae(Lagomorpha, Ochotonidae)

We reconstructed the demographic history of the plateau pika (Ochotona curzoniae) on the Qinghai-Tibetan plateau by using genetic variation data obtained from spatially distributed populations across much of the plateau. We obtained sequence data, including cob (1,140 bp) and D-loop sequences (732 bp), from 144 individuals at sites ranging from the high-altitude interior to the relatively low-altitude northeastern plateau, and identified 37 and 42 unique haplotypes, respectively. Phylogenetic analysis and haplotype networks based on the individual and the combined datasets of cob and D-loop sequences clustered all populations into four well-supported major groups, and the interaction between vicariance, dispersal, and habitat fragmentation resulted in the current geographical distribution and genetic diversity of O. curzoniae on the plateau. Analysis of molecular variance (AMOVA) and mismatch distribution suggested that the recent continuous uplifts of the plateau contributed to the radiation and diversification of the O. curzoniae populations occurring there.

Conservation genetics and phylogeography of the poorly known Middle Eastern terrapin Mauremys caspica (Testudines: Geoemydidae)

The West Asian stripe-necked terrapin Mauremys caspica is widespread throughout the Middle East—a region for which only few phylogeographic studies are available. Due to landscape alteration, pollution and intensification of water management, M. caspica is increasingly threatened. However, genetic diversity among and within populations is poorly known, impeding the identification of management units. Using a nearly rangewide sampling, we analyzed 14 microsatellite loci and mtDNA sequences in order to gain insight into the population structure and history of M. caspica. In agreement with a previous study, we found two clusters of mitochondrial haplotypes, with one cluster distributed in the east and the other in the west of the range. However, our microsatellite data suggested a more pronounced geographical structuring. When null alleles were coded as recessive with structure 2.3.2, three clusters were revealed, with one cluster matching roughly the range of the western mitochondrial cluster, and the composite ranges of the two other microsatellite clusters correspond to the distribution of the eastern mitochondrial cluster. Naive structure analyses without correction for null alleles were congruent with respect to the two eastern microsatellite clusters, but subdivided the western cluster into two units, with an additional geographical divide corresponding to the ‘Anatolian diagonal’—a well-known high mountain barrier impeding exchange between western and eastern taxa. In naive analyses, the westernmost microsatellite cluster (from Central Anatolia) is quite isolated from the others, and its distinctness is also supported by fixation indices resembling the values among the other three clusters. One of the two eastern clusters is distributed in the Caucasus region plus Iran, and terrapins from Saudi Arabia and Bahrain constitute the second eastern cluster, supporting the view that these endangered populations are native. Coalescent-based analyses of our microsatellite data reveal for all four clusters bottlenecks 4,000–20,000 years ago, suggesting that climatic fluctuations of the Late Pleistocene and Holocene played an important role in shaping current genetic diversity. We propose that each of the four identified clusters, including the Central Anatolian one, should be treated as a distinct management unit. The presence of non-native terrapins in the animal trade of Bahrain highlights the danger of genetic pollution of the endangered Arabian populations. Further sampling is needed to elucidate the situation in southern and central Iran and Iraq. Our results confirm that genetic data do not support the validity of any of the three morphologically defined subspecies of M. caspica, and we propose that their usage be abandoned.

Historical habitat connectivity affects current genetic structure in a grassland species

Many recent studies have explored the effects of present and past landscape structure on species distribution and diversity. However, we know little about the effects of past landscape structure on distribution of genetic diversity within and between populations of a single species. Here we describe the relationship between present and past landscape structure (landscape connectivity and habitat size estimated from historical maps) and current genetic structure in a perennial herb, Succisa pratensis. We used allozymes as co-dominant markers to estimate genetic diversity and deviation from Hardy-Weinberg equilibrium in 31 populations distributed within a 5 km(2) agricultural landscape. The results showed that current genetic diversity of populations was related to habitat suitability, habitat age, habitat size and habitat connectivity in the past. The effects of habitat age and past connectivity on genetic diversity were in most cases also significant after taking the current landscape structure into account. Moreover, current genetic similarity between populations was affected by past connectivity after accounting for current landscape structure. In both cases, the oldest time layer (1850) was the most informative. Most populations showed heterozygote excess, indicating disequilibrium due to recent gene flow or selection against homozygotes. These results suggest that habitat age and past connectivity are important determinants of distribution of genetic diversity between populations at a scale of a few kilometres. Landscape history may significantly contribute to our understanding of distribution of current genetic structure within species and the genetic structure may be used to better understand landscape history, even at a small scale.

Low genetic diversity and local adaptive divergence ofDracaena cambodiana(Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long‐lived tree endemic to Hainan Island, China

Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D.cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D.cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D.cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D.cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.

Genomic Ancestry of North Africans Supports Back-to-Africa Migrations

North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by characterizing the effect of hypothesized migrations from the Near East, Europe, and sub-Saharan Africa on current genetic diversity. We present dense, genome-wide SNP genotyping array data (730,000 sites) from seven North African populations, spanning from Egypt to Morocco, and one Spanish population. We identify a gradient of likely autochthonous Maghrebi ancestry that increases from east to west across northern Africa; this ancestry is likely derived from “back-to-Africa” gene flow more than 12,000 years ago (ya), prior to the Holocene. The indigenous North African ancestry is more frequent in populations with historical Berber ethnicity. In most North African populations we also see substantial shared ancestry with the Near East, and to a lesser extent sub-Saharan Africa and Europe. To estimate the time of migration from sub-Saharan populations into North Africa, we implement a maximum likelihood dating method based on the distribution of migrant tracts. In order to first identify migrant tracts, we assign local ancestry to haplotypes using a novel, principal component-based analysis of three ancestral populations. We estimate that a migration of western African origin into Morocco began about 40 generations ago (approximately 1,200 ya); a migration of individuals with Nilotic ancestry into Egypt occurred about 25 generations ago (approximately 750 ya). Our genomic data reveal an extraordinarily complex history of migrations, involving at least five ancestral populations, into North Africa.

Temporal Analysis of mtDNA Variation Reveals Decreased Genetic Diversity in Least Terns

Abstract. The Least Tern (Sternula antillarum) has undergone large population declines over the last century as a result of direct and indirect anthropogenic factors. The genetic implications of these declines are unknown. We used historical museum specimens (pre-1960) and contemporary (2001–2005) samples to examine range-wide phylogeographic patterns and investigate potential loss in the species' genetic variation. We obtained sequences (522 bp) of the mitochondrial gene for NADH dehydrogenase subunit 6 (ND6) from 268 individuals from across the species' range. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. However, we detected potential reductions in genetic diversity in contemporary samples from California and the Atlantic coast Least Tern from that in historical samples, suggesting that current genetic diversity in Least Tern populations is lower than in their pre-1960 counterparts. Our results offer unique insights into changes in the Least Ter...

The Colonization History of Juniperus brevifolia (Cupressaceae) in the Azores Islands

BackgroundA central aim of island biogeography is to understand the colonization history of insular species using current distributions, fossil records and genetic diversity. Here, we analyze five plastid DNA regions of the endangered Juniperus brevifolia, which is endemic to the Azores archipelago.Methodology/Principal FindingsThe phylogeny of the section Juniperus and the phylogeographic analyses of J. brevifolia based on the coalescence theory of allele (plastid) diversity suggest that: (1) a single introduction event likely occurred from Europe; (2) genetic diversification and inter-island dispersal postdated the emergence of the oldest island (Santa Maria, 8.12 Ma); (3) the genetic differentiation found in populations on the islands with higher age and smaller distance to the continent is significantly higher than that on the younger, more remote ones; (4) the high number of haplotypes observed (16), and the widespread distribution of the most frequent and ancestral ones across the archipelago, are indicating early diversification, demographic expansion, and recurrent dispersal. In contrast, restriction of six of the seven derived haplotypes to single islands is construed as reflecting significant isolation time prior to colonization.Conclusions/SignificanceOur phylogeographic reconstruction points to the sequence of island emergence as the key factor to explain the distribution of plastid DNA variation. The reproductive traits of this juniper species (anemophily, ornithochory, multi-seeded cones), together with its broad ecological range, appear to be largely responsible for recurrent inter-island colonization of ancestral haplotypes. In contrast, certain delay in colonization of new haplotypes may reflect intraspecific habitat competition on islands where this juniper was already present.

Genetic Diversity Despite Population Collapse in a Critically Endangered Marine Fish: The Smalltooth Sawfish (Pristis pectinata)

Sawfish (family Pristidae) are among the most critically endangered marine fish in the world, yet very little is known about how genetic bottlenecks, genetic drift, and inbreeding depression may be affecting these elasmobranchs. In the US Atlantic, the smalltooth sawfish (Pristis pectinata) has declined to 1-5% of its abundance in the 1900s, and its core distribution has contracted to southwest Florida. We used 8 polymorphic microsatellite markers to show that this remnant population still exhibits high genetic diversity in terms of average allelic richness (18.23), average alleles per locus (18.75, standard deviation [SD] 6.6) and observed heterozygosity (0.43-0.98). Inbreeding is rare (mean individual internal relatedness = -0.02, SD 0.14; F(IS) = -0.011, 95% confidence interval [CI] = -0.039 to 0.011), even though the estimated effective population size (N(e)) is modest (250-350, 95% CI = 142-955). Simulations suggest that the remnant smalltooth sawfish population will probably retain >90% of its current genetic diversity over the next century even at the lower estimate of N(e). There is no evidence of a genetic bottleneck accompanying last century's demographic bottleneck, and we discuss hypotheses that could explain this. We also discuss features of elasmobranch life history and population biology that could make them less vulnerable than other large marine vertebrates to genetic change associated with reduced population size.

Genetic evaluation of a reintroduced population of black-footed ferrets (Mustela nigripes)

The black-footed ferret (Mustela nigripes) went extinct in the wild when the last 18 known ferrets were captured for a captive-breeding program. Following the success of the captive-breeding program, 146 genetically nonessential ferrets were released at the Conata Basin, South Dakota, from 1996 to 1999. We conducted a genetic analysis of the Conata Basin black-footed ferret population from 2001 to 2003 to determine if genetic variation had been lost since the cessation of reintroductions and if demographic- and genetic-based estimates of effective population size (Ne) accurately predicted observed levels of heterozygosity. We used DNA from wild-born kits (n = 254) in the Conata Basin population (2001–2003) to calculate current genetic diversity levels. Both allelic diversity (A = 2, both subpopulations) and mean heterozygosity were low for both subpopulations—0.39 ± 0.12 SE in Agate-Sage Creek and 0.39 ± 0.16 SE in Heck Table—but not significantly different from estimates made in 1999. We found no significant difference between observed and expected heterozygosity levels. Demographic-based estimates of Ne were an order of magnitude higher than genetic-based estimates of Ne, but the 2 estimates provide a range of Ne values for the population. This study shows that the Conata Basin ferret population is able to maintain its genetic diversity over time despite its population history.

Old problems on a new playing field: Helminth zoonoses transmitted among dogs, wildlife, and people in a changing northern climate

Although surveillance is limited, indigenous residents at latitudes ranging from 53 to 73°N in Canada appear to have a higher occurrence of infection with some zoonotic parasites than the general population. Conversely, they are relatively naïve to other zoonotic parasites that have previously been unable to establish at northern latitudes. For those parasites that circulate among dogs, wildlife, and people, potential risk factors in the North include limited availability of veterinary services, presence of free-roaming dog populations, and consumption of locally harvested fish and wildlife. These regions are also experiencing some of the greatest impacts of climate change in North America, including increased temperature, precipitation, and frequency and severity of extreme weather. We review the current taxonomy, genetic diversity, host and geographic distributions, epidemiology and risk factors for 3 genera of helminths (Diphyllobothrium spp., Echinococcus spp., and Toxocara sp.) in Canada's North in order to identify climate-sensitive aspects of their ecology. Free-living stages of parasitic zoonoses endemic in the Arctic (such as Diphyllobothrium dendriticum, the cervid strain of Echinococcus granulosus, and Arctic strains of Echinococcus multilocularis) will experience trade-offs between enhanced survival under wetter conditions and increased mortality under warmer conditions. Climate change might also lead to the introduction and establishment in the Arctic of parasitic zoonoses previously restricted to the sub-Arctic, such as Diphyllobothrium latum, Toxocara canis, and the prairie strain of E. multilocularis. Molecular techniques applied in broad geographic surveys are needed to address critical knowledge gaps in the geographic distribution, genetic diversity, and public health significance of zoonotic helminths already in the circumpolar North, and to determine the current barriers to range expansion of temperate-adapted parasites into the North. Dogs will continue to play important roles in the North, including that of a “bridging” host between sylvatic cycles and human communities. In a warming north, increased opportunities for business, agriculture, and tourism favor importation of dogs and their parasites into a newly suitable environment. Collaborations among veterinarians, public health personnel, and policy-makers are needed to enhance surveillance and mitigate for dog-transmitted parasitic zoonoses in a changing North.

Molecular evidence for Pleistocene refugia at the eastern edge of the Tibetan Plateau

The role of the Quaternary ice ages in forming the contemporary genetic structure of populations has been well studied in a number of global regions. However, due to the different nature of glaciations and complex topography, their role in shaping eastern Eurasian genetic diversity, particular in areas surrounding the Tibetan Plateau have remained largely unstudied. We aimed to address this question by examining the genetic structure of an alpine forest-associated taxon, the blood pheasant (Ithaginis cruentus) to infer its phylogeographic history. We detected three phylogenetic lineages and four current population groups. By comparing molecular and palaeovegetation data, we found that major glaciations during the Pleistocene have had a major impact upon the current genetic diversity of this species. Coalescent simulations indicate that the populations retreated to different refugia during some glacial periods in the Pleistocene, but persisted through the last glacial maximum (LGM). The most significant recent population expansion was found to have occurred before the LGM, during which palaeoclimatic data indicate that the climate was both warmer and wetter than today. In contrast, during the LGM populations may have adopted an altitudinal shift strategy in order to track changes in alpine glaciers, exemplifying a general response for montane species in the region where alpine glaciations were not large enough to cause qualitative changes in vegetation. Although analysis based on a plumage related gene showed that divergent selection may have contributed to current patterns of intra-specific diversity, demographic isolation is inferred to have played a more dominant role.

Southern European glacial refugia: A tale of tales

AbstractInterpretations of current diversity patterns based on the contraction/expansion model forced by climatic oscillations during the last two million years are commonplace in phylogeographic literature. Of the wealth of scientific studies accumulated during the past two decades in Europe, the ones we understand best are those mostly from higher latitudes, probably because patterns were simplified to a great extent by major losses of diversity during glacial periods. In Southern European regions (or in general, in those places where ice effects were less severe) the situation is quite different and to some extent opposite. These regions are referred to as refugia because they are known to contain more genetic diversity than elsewhere. This is not only due to preservation of genotypes that went extinct in other places, however, but also to the intensity and accumulation of a number of processes in a patchy landscape across a varied topography. A lack of general phylogeographic patterns in these regions is one consequence. Speaking of a single refugium to refer to each of the peninsulas, however, is an oversimplification. Even speaking of multiple unconnected refugia does not adequately reflect the complexity of the processes that shaped the current genetic and specific diversity.

Genetic Diversity Measures of 8 Local Sheep Breeds in Northwest of China for Genetic Resource Conservation

The aim of this study was to evaluate, through the use of microsatellite markers, the current genetic diversity and the relationships of 375 individuals from 8 local sheep breeds reared in typical breeding farms in the northwest of China, and moreover, to offer a contribution towards genetic conservation decisions for the studied breeds. The expected heterozygosities and allelic richness for the 8 breeds varied from 0.474 to 0.623 and from 3.8 to 5.4, respectively. All the populations showed a significant deficit in heterozygosity and a relatively low level of genetic diversity. Furthermore, the high positive F IS value (ranging from 0.255 to 0.556) indicated inbreeding to be one of the main causes for high genetic homogeneity and lack of heterozygosity in all breeds. The clustering analysis performed with the DISPAN package showed that Aletai, Kazak, Bashibai and Bayinbuluke were grouped together, and Hetian, Qira black and Duolang were grouped together, which indicated that the relationship among breeds displayed some degree of consistency with their geographical distribution, production and origin. These findings indicate that improved conservation measures must be undertaken to avoid further losses of genetic diversity and minimize inbreeding represented by these breeds.

Comparison of phylogeographic structure and population history of two Phrynocephalus species in the Tarim Basin and adjacent areas

An aridification of the Tarim Basin and adjacent areas since middle Pleistocene has produced significant genetic structuring of the local fauna. We examined the phylogeographic patterns, population structure and history of Phrynocephalus axillaris and Phrynocephalus forsythii using a mitochondrial fragment ND4-tRNA LEU. Phylogenetic hypotheses were constructed using maximum parsimony and Bayesian inference, and the divergence times of major lineages were estimated by BEAST. Population structure and history were inferred by nested clade analysis, neutrality tests, mismatch distribution, and isolation by distance analysis. The two species might have experienced different evolutionary history throughout their current distribution. For P. forsythii, a vicariant event, as a consequence of geological isolation and desert expansion, might have produced the significant divergence between the Tarim and the Yanqi populations. For P. axillaris, populations of the Yanqi, Turpan and Hami Basins might have been established through dispersal during demographic expansion. Climatic fluctuations caused alternate expansion and shrinkage of rivers and oases several times, which likely led to habitat fragmentation for both species. Interaction between vicariance, dispersal and habitat fragmentation produced the current distribution and genetic diversity. The observed difference between the two species may be due partially to their different reproductive modes (ovoviviparous vs. oviparous).

Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene

Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.

Eastern Beringian biogeography: historical and spatial genetic structure of singing voles in Alaska

AbstractAim Pleistocene climatic cycles have left marked signatures in the spatial and historical genetic structure of high‐latitude organisms. We examine the mitochondrial (cytochrome b) genetic structure of the singing vole, Microtus miurus (Rodentia: Cricetidae: Arvicolinae), a member of the Pleistocene Beringian fauna, and of the insular vole, Microtus abbreviatus, its putative sister species found only on the St Matthew Archipelago. We reconstruct the phylogenetic and phylogeographical structure of these taxa, characterize their geographical partitioning and date coalescent and cladogenetic events in these species. Finally, we compare the recovered results with the phylogenetic, coalescent and spatial genetic patterns of other eastern Beringian mammals and high‐latitude arvicoline rodents.Location Continental Alaska (alpine and arctic tundra) and the St Matthew Archipelago (Bering Sea).Methods We generated and analysed cytochrome b sequences of 97 singing and insular voles (M. miurus and M. abbreviatus) from Alaska. Deep evolutionary structure was inferred by phylogenetic analysis using parsimony, maximum likelihood and Bayesian approaches; the geographical structure of genetic diversity was assessed using analysis of molecular variance and network analysis; ages of cladogenetic and coalescent events were estimated using a relaxed molecular clock model with Bayesian approximation.Results Regional nucleotide diversity in singing voles is higher than in other high‐latitude arvicoline species, but intra‐population diversity is within the observed range of values for arvicolines. Microtus abbreviatus specimens are phylogenetically nested within M. miurus. Molecular divergence date estimates indicate that current genetic diversity was formed in the last glacial (Wisconsinan) and previous interglacial (Sangamonian) periods, with the exception of a Middle Pleistocene split found between samples collected in the Wrangell Mountains region and all other singing vole samples.Main conclusions High levels of phylogenetic and spatial structure are observed among analysed populations. This pattern is consistent with that expected for a taxon with a long history in Beringia. The spatial genetic structure of continental singing voles differs in its northern and southern ranges, possibly reflecting differences in habitat distribution between arctic and alpine tundra. Our phylogenetic results support the taxonomic inclusion of M. miurus in its senior synonym, M. abbreviatus.