Phylogeography of field voles (Microtus agrestis) in Eurasia inferred from mitochondrial DNA sequences

In a distribution-wide phylogeographic survey of the field vole (Microtus agrestis), 75 specimens from 56 localities across Eurasia were examined for DNA sequence variation along the whole 1140 base pair (bp) mitochondrial (mt) cytochrome b gene. The species is subdivided into three main mtDNA phylogeographic groups - western, eastern and southern - with largely allopatric distributions. The western phylogeographical group is found in west and central Europe and spread most probably from a glacial refugium in the Carpathians. The eastern group covers a large range from Lithuania to central Asia, and probably originated from a southeast European source (e.g. the southern Urals or the Caucasus). The southern group occupies an area from Portugal to Hungary, with division into two distinct mtDNA sublineages that presumably derive from separate glacial refugia in the Iberian Peninsula. Molecular clock estimates suggest that the western and eastern field vole populations separated during the last glaciation, whereas the southern population dates back 0.5-0.9 Myr. High levels of mtDNA variation indicate relatively large population sizes and subdivisions within phylogeographic groups during the last glaciation. We report a possible new suture zone in east Europe.     

The western and eastern roots of the Saami--the story of genetic "outliers" told by mitochondrial DNA and Y chromosomes

The Saami are regarded as extreme genetic outliers among European populations. In this study, a high-resolution phylogenetic analysis of Saami genetic heritage was undertaken in a comprehensive context, through use of maternally inherited mitochondrial DNA (mtDNA) and paternally inherited Y-chromosomal variation. DNA variants present in the Saami were compared with those found in Europe and Siberia, through use of both new and previously published data from 445 Saami and 17,096 western Eurasian and Siberian mtDNA samples, as well as 127 Saami and 2,840 western Eurasian and Siberian Y-chromosome samples. It was shown that the “Saami motif” variant of mtDNA haplogroup U5b is present in a large area outside Scandinavia. A detailed phylogeographic analysis of one of the predominant Saami mtDNA haplogroups, U5b1b, which also includes the lineages of the “Saami motif,” was undertaken in 31 populations. The results indicate that the origin of U5b1b, as for the other predominant Saami haplogroup, V, is most likely in western, rather than eastern, Europe. Furthermore, an additional haplogroup (H1) spread among the Saami was virtually absent in 781 Samoyed and Ob-Ugric Siberians but was present in western and central European populations. The Y-chromosomal variety in the Saami is also consistent with their European ancestry. It suggests that the large genetic separation of the Saami from other Europeans is best explained by assuming that the Saami are descendants of a narrow, distinctive subset of Europeans. In particular, no evidence of a significant directional gene flow from extant aboriginal Siberian populations into the haploid gene pools of the Saami was found.     

Mitochondrial DNA variations in Russian and Belorussian populations

The sequence of the first hypervariable segment (HVS-I) of mitochondrial DNA (mtDNA) was determined in 251 individuals from three eastern Slavonic populations, two Russian and one Belorussian. Within HVS-I, 78 polymorphic positions were revealed. Within-population diversity of HVS-I varies slightly among three samples; its estimates do not differ strongly from those for European populations. Haplotype diversity for three populations calculated in this study is 0.949; mean pairwise differences estimate is 3.59. To assign mtDNA sequences to major phylogenetic clusters, haplogroup-specific restriction polymorphisms were selectively typed in most samples. The haplogroup distribution in the total Eastern Slavonic sample is similar to that reported for the European sample. However, the separate consideration of three Slavonic samples reveals the complicated structure of the mitochondrial gene pool in the Eastern European area. Data of this study support the proposed model of the origin of modern Eastern Slavs, which implies the admixture of ancient Slavonic tribes with pre-Slavonic populations of Eastern Europe. These data should contribute to general studies of mitochondrial DNA variations in Europe.     

Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective

More than a third of the European pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroup (hg) H, the most frequent hg throughout western Eurasia. Although there has been considerable recent progress in studying mitochondrial genome variation in Europe at the complete sequence resolution, little data of comparable resolution is so far available for regions like the Caucasus and the Near and Middle East-areas where most of European genetic lineages, including hg H, have likely emerged. This gap in our knowledge causes a serious hindrance for progress in understanding the demographic prehistory of Europe and western Eurasia in general. Here we describe the phylogeography of hg H in the populations of the Near East and the Caucasus. We have analyzed 545 samples of hg H at high resolution, including 15 novel complete mtDNA sequences. As in Europe, most of the present-day Near Eastern-Caucasus area variants of hg H started to expand after the last glacial maximum (LGM) and presumably before the Holocene. Yet importantly, several hg H subclades in Near East and Southern Caucasus region coalesce to the pre-LGM period. Furthermore, irrespective of their common origin, significant differences between the distribution of hg H sub-hgs in Europe and in the Near East and South Caucasus imply limited post-LGM maternal gene flow between these regions. In a contrast, the North Caucasus mitochondrial gene pool has received an influx of hg H variants, arriving from the Ponto-Caspian/East European area.     

The macrohaplogroup U structure in Russians

The structure and diversity of mitochondrial DNA (mtDNA) macrohaplogroup U lineages in Russians from Eastern Europe are studied on the basis of analysis of variation of nucleotide sequences of complete mitochondrial genomes. In total, 132 mitochondrial genomes belonging to haplogroups U1, U2e, U3, U4, U5, U7, U8a, and K are characterized. Results of phylogeographic analysis show that the mitochondrial gene pool of Russians contains mtDNA haplotypes belonging to subhaplogroups that are characteristic only of Russians and other Eastern Slavs (13.7%), Slavs in general (11.4%), Slavs and Germans (17.4%), and Slavs, Germans, and Baltic Finns (9.8%). Results of molecular dating show that ages of mtDNA subhaplogroups to which Russian mtDNA haplotypes belong vary in a wide range, from 600 to 17000 years. However, molecular dating results for Slavic and Slavic-Germanic mtDNA subhaplogroups demonstrate that their formation mainly occurred in the Bronze and Iron Ages (1000–5000 years ago). Only some instances (for subhaplogroups U5b1a1 and U5b1e1a) are characterized by a good agreement between molecular dating results and the chronology of Slavic ethnic history based on historical and archaeological data.     

Genetic polymorphism of mitochondrial DNA HVS-I and HVS-Ⅱ of Chinese Tu ethnic minority group

We analyzed the two hypervariable segments HVS-Ⅰ and HVS-Ⅱ of 108 Chinese Tu ethnic minority group samples for forensic and population genetics purposes.Comparing with Anderson sequence,79 polymorphic loci in HVS-Ⅰ and 40 in HVS-Ⅱ were found in Chi-nese Tu ethnic minority group mtDNA sequences,and 90 and 64 haplotypes were then defined.Haplotype diversity and the mean pair-wise differences were 0.9903±0.0013 and 5.7785 in HVS-Ⅰ,and 0.9777±0.0013 and 3.5819 in HVS-Ⅱ,respectively.By analyzing the hypervariable domain from nucleotide 1,6180 to 1,6193 in HVS-Ⅰ,we defined some new types of sequence variations.We also compared the relationship between Tu population and other populations using mtDNA HVS-Ⅰ sequences.According to Rst genetic distances,the phylogenetic tree showed that the Tu population,the Xi'an Han population,the Chinese Korean,and the Mongol ethnic group were in a clade.This indicated a close genetic relationship between them.There were far relations between the Tu population and other Chinese southern Han populations,Siberian,European,African,and other foreign populations.The results suggest that Tu population has a multi-origin and has also merged with other local populations.     

Mitochondrial DNA phylogeography in northern grasshopper mice (Onychomys leucogaster) — the influence of Quaternary climatic oscillations on population dispersion and divergence

The details of mitochondrial DNA (mtDNA) phylogenetic structure of the northern grasshopper mouse Onychomys leucogaster were examined using populations from a postulated area of endemism that includes three arid regions (Colorado Plateaus, Interior Plains, and Wyoming Basins) in western North America. Fifteen tetra- and heptanucleotide restriction enzymes were used to assay restriction-site variation in a 2150-bp PCR-amplified fragment of mtDNA representing the ND2 and part of the COI gene regions. A total of 18 mtDNA haplotypes were detected. Although overall genetic divergence among these haplotypes was low (average = 1.1%), phylogeographic structuring was apparent. Notably, a clear phylogenetic split separated one group of haplotypes restricted to the Wyoming Basins from all others. This phylogenetic split was further corroborated by examination of nucleotide sequence variation from a 270-bp stretch of the mtDNA cytochrome b gene. Overall geographic and phylogenetic patterns suggest a complex history of geographic structuring and subsequent mixing of populations of grasshopper mice throughout the late Pleistocene. These patterns of variation are evaluated relative to alternative hypotheses about biotic responses to Quaternary climatic oscillations in western North American arid regions.     

Indian Signatures in the Westernmost Edge of the European Romani Diaspora: New Insight from Mitogenomes

In agreement with historical documentation, several genetic studies have revealed ancestral links between the European Romani and India. The entire mitochondrial DNA (mtDNA) of 27 Spanish Romani was sequenced in order to shed further light on the origins of this population. The data were analyzed together with a large published dataset (mainly hypervariable region I [HVS-I] haplotypes) of Romani (N = 1,353) and non-Romani worldwide populations (N>150,000). Analysis of mitogenomes allowed the characterization of various Romani-specific clades. M5a1b1a1 is the most distinctive European Romani haplogroup; it is present in all Romani groups at variable frequencies (with only sporadic findings in non-Romani) and represents 18% of their mtDNA pool. Its phylogeographic features indicate that M5a1b1a1 originated 1.5 thousand years ago (kya; 95% CI: 1.3–1.8) in a proto-Romani population living in Northwest India. U3 represents the most characteristic Romani haplogroup of European/Near Eastern origin (12.4%); it appears at dissimilar frequencies across the continent (Iberia: ∼31%; Eastern/Central Europe: ∼13%). All U3 mitogenomes of our Iberian Romani sample fall within a new sub-clade, U3b1c, which can be dated to 0.5 kya (95% CI: 0.3–0.7); therefore, signaling a lower bound for the founder event that followed admixture in Europe/Near East. Other minor European/Near Eastern haplogroups (e.g. H24, H88a) were also assimilated into the Romani by introgression with neighboring populations during their diaspora into Europe; yet some show a differentiation from the phylogenetically closest non-Romani counterpart. The phylogeny of Romani mitogenomes shows clear signatures of low effective population sizes and founder effects. Overall, these results are in good agreement with historical documentation, suggesting that cultural identity and relative isolation have allowed the Romani to preserve a distinctive mtDNA heritage, with some features linking them unequivocally to their ancestral Indian homeland.     

Comparative analysis of the hypervariable segment 1 mutational spectra in human mitochondrial DNA phylogeographic groups

Variability of the mtDNA hypervariable segment 1 (HVS 1) nucleotide sequences belonging to 88 phylogeographic clusters characteristic for human populations of Africa, West and East Eurasia was analyzed. Statistically significant differences between distribution of mutations in mitochondrial gene pools of the human continental groups were revealed. The list of the HVS 1 nucleotide positions characterizing by instability explained by the model of mtDNA strands dislocation during the replication process is suggested. It was shown that DNA strands dislocation during mtDNA replication is one of the key mechanisms of the context-dependent mtDNA mutagenesis during the regional differentiation of human populations.     

Phylogeny of mitochondrial DNA macrohaplogroup N in India, based on complete sequencing: implications for the peopling of South Asia

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse subset of 75 macrohaplogroup N lineages was chosen for complete sequencing from a collection of >800 control-region sequences sampled across India. We identified five new autochthonous haplogroups (R7, R8, R30, R31, and N5) and fully characterized the autochthonous haplogroups (R5, R6, N1d, U2a, U2b, and U2c) that were previously described only by first hypervariable segment (HVS-I) sequencing and coding-region restriction-fragment-length polymorphism analysis. Our findings demonstrate that the Indian mtDNA pool, even when restricted to macrohaplogroup N, harbors at least as many deepest-branching lineages as the western Eurasian mtDNA pool. Moreover, the distribution of the earliest branches within haplogroups M, N, and R across Eurasia and Oceania provides additional evidence for a three-founder-mtDNA scenario and a single migration route out of Africa.     

A signal, from human mtDNA, of postglacial recolonization in Europe

Mitochondrial HVS-I sequences from 10,365 subjects belonging to 56 populations/geographical regions of western Eurasia and northern Africa were first surveyed for the presence of the T-->C transition at nucleotide position 16298, a mutation which has previously been shown to characterize haplogroup V mtDNAs. All mtDNAs with this mutation were then screened for a number of diagnostic RFLP sites, revealing two major subsets of mtDNAs. One is haplogroup V proper, and the other has been termed "pre*V," since it predates V phylogenetically. The rather uncommon pre*V tends to be scattered throughout Europe (and northwestern Africa), whereas V attains two peaks of frequency: one situated in southwestern Europe and one in the Saami of northern Scandinavia. Geographical distributions and ages support the scenario that pre*V originated in Europe before the Last Glacial Maximum (LGM), whereas the more recently derived haplogroup V arose in a southwestern European refugium soon after the LGM. The arrival of V in eastern/central Europe, however, occurred much later, possibly with (post-)Neolithic contacts. The distribution of haplogroup V mtDNAs in modern European populations would thus, at least in part, reflect the pattern of postglacial human recolonization from that refugium, affecting even the Saami. Overall, the present study shows that the dissection of mtDNA variation into small and well-defined evolutionary units is an essential step in the identification of spatial frequency patterns. Mass screening of a few markers identified using complete mtDNA sequences promises to be an efficient strategy for inferring features of human prehistory.     

Phylogeny of east Asian mitochondrial DNA lineages inferred from complete sequences

The now-emerging mitochondrial DNA (mtDNA) population genomics provides information for reconstructing a well-resolved mtDNA phylogeny and for discerning the phylogenetic status of the subcontinentally specific haplogroups. Although several major East Asian mtDNA haplogroups have been identified in studies elsewhere, some of the most basal haplogroups, as well as numerous minor subhaplogroups, were not yet determined or fully characterized. To fill the lacunae, we selected 48 mtDNAs from >2,000 samples across China for complete sequencing that cover virtually all (sub)haplogroups discernible to date in East Asia. This East Asian mtDNA phylogeny can henceforth serve as a solid basis for phylogeographic analyses of mtDNAs, as well as for studies of mitochondrial diseases in East and Southeast Asia.     

Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: comparison with other Asian,European, and North American populations

To illustrate phylogeography of red deer (Cervus elaphus) populations of Xinjiang, we determined their mitochondrial DNA (mtDNA) control region sequences, and then investigated geographic variations and phylogenetic relationships between Xinjiang populations and other populations from Asia, Europe, and North America. The C. elaphus mtDNA control region shared different copy numbers of tandem repeats of 38 to 43-bp motifs which clearly distinguished the Western lineage from the Eastern lineage of this species in Eurasia. The western lineage comprised the Tarim populations from southern Xinjiang and the European populations, all of which had four copies of the motifs. By contrast, the Eastern lineage consisted of populations from northern Xinjiang (Tianshan and Altai Mountains), other Asian areas (Alashan, Gansu, Tibet, Mongolia, and northeastern China), and North America, all of which shared six copies of the motifs. MtDNA phylogenetic trees showed that there are two major clusters of haplotypes which referred to the Western and Eastern lineages, and that subgroupings of haplotypes in each cluster were congruent with their geographic distributions. The present study revealed that a boundary separating the Western lineage from the Eastern lineage occurs between Tarim Basin and Tianshan Mountains in Xinjiang. Meanwhile, North American populations were genetically closer to those of northern Xinjiang, northeastern China, and Mongolia, supporting that C. elaphus immigrated from northeastern Eurasia to North America through the glacier-induced land-bridge (Beringia) which had formed between the two continents after Late Pleistocene.     

The Caucasus as an asymmetric semipermeable barrier to ancient human migrations

The Caucasus, inhabited by modern humans since the Early Upper Paleolithic and known for its linguistic diversity, is considered to be important for understanding human dispersals and genetic diversity in Eurasia. We report a synthesis of autosomal, Y chromosome, and mitochondrial DNA (mtDNA) variation in populations from all major subregions and linguistic phyla of the area. Autosomal genome variation in the Caucasus reveals significant genetic uniformity among its ethnically and linguistically diverse populations and is consistent with predominantly Near/Middle Eastern origin of the Caucasians, with minor external impacts. In contrast to autosomal and mtDNA variation, signals of regional Y chromosome founder effects distinguish the eastern from western North Caucasians. Genetic discontinuity between the North Caucasus and the East European Plain contrasts with continuity through Anatolia and the Balkans, suggesting major routes of ancient gene flows and admixture.     

Mitochondrial DNA perspective of Serbian genetic diversity

Although south‐Slavic populations have been studied to date from various aspects, the population of Serbia, occupying the central part of the Balkan Peninsula, is still genetically understudied at least at the level of mitochondrial DNA (mtDNA) variation. We analyzed polymorphisms of the first and the second mtDNA hypervariable segments (HVS‐I and HVS‐II) and informative coding‐region markers in 139 Serbians to shed more light on their mtDNA variability, and used available data on other Slavic and neighboring non‐Slavic populations to assess their interrelations in a broader European context. The contemporary Serbian mtDNA profile is consistent with the general European maternal landscape having a substantial proportion of shared haplotypes with eastern, central, and southern European populations. Serbian population was characterized as an important link between easternmost and westernmost south‐Slavic populations due to the observed lack of genetic differentiation with all other south‐Slavic populations and its geographical positioning within the Balkan Peninsula. An increased heterogeneity of south Slavs, most likely mirroring turbulent demographic events within the Balkan Peninsula over time (i.e., frequent admixture and differential introgression of various gene pools), and a marked geographical stratification of Slavs to south‐, east‐, and west‐Slavic groups, were also found. A phylogeographic analyses of 20 completely sequenced Serbian mitochondrial genomes revealed not only the presence of mtDNA lineages predominantly found within the Slavic gene pool (U4a2a*, U4a2a1, U4a2c, U4a2g, HV10), supporting a common Slavic origin, but also lineages that may have originated within the southern Europe (H5*, H5e1, H5a1v) and the Balkan Peninsula in particular (H6a2b and L2a1k). Am J Phys Anthropol 156:449–465, 2015. © 2014 Wiley Periodicals, Inc.     

The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool

Complete sequencing of 62 mitochondrial DNAs (mtDNAs) belonging (or very closely related) to haplogroup H revealed that this mtDNA haplogroup--by far the most common in Europe--is subdivided into numerous subhaplogroups, with at least 15 of them (H1-H15) identifiable by characteristic mutations. All the haplogroup H mtDNAs found in 5,743 subjects from 43 populations were then screened for diagnostic markers of subhaplogroups H1 and H3. This survey showed that both subhaplogroups display frequency peaks, centered in Iberia and surrounding areas, with distributions declining toward the northeast and southeast--a pattern extremely similar to that previously reported for mtDNA haplogroup V. Furthermore, the coalescence ages of H1 and H3 (~11,000 years) are close to that previously reported for V. These findings have major implications for the origin of Europeans, since they attest that the Franco-Cantabrian refuge area was indeed the source of late-glacial expansions of hunter-gatherers that repopulated much of Central and Northern Europe from ~15,000 years ago. This has also some implications for disease studies. For instance, the high occurrence of H1 and H3 in Iberia led us to re-evaluate the haplogroup distribution in 50 Spanish families affected by nonsyndromic sensorineural deafness due to the A1555G mutation. The survey revealed that the previously reported excess of H among these families is caused entirely by H3 and is due to a major, probably nonrecent, founder event.     

华南西部及海南岛美丽小条鳅种群遗传变异与亲缘地理

通过分析108尾采自华南西部12条水系的美丽小条鳅(Micronemacheilus pulcher)mtDNA 细胞色素b (cyt b) 基因全序列,研究其种群遗传变异和亲缘生物地理格局.美丽小条鳅的cyt b序列包含138个核苷酸变异位点(占全序列12.11%).分子变异分析(AMOVA)显示,分子遗传变异主要来自种群内(58.53%)和地理区内种群间(42.84%).采用邻接法构建的39个单倍型的NJ系统树显示,12条水系的美丽小条鳅聚成两支.其中,广西沿海诸独立水系(防城河、峒中河、北仑河、南流江)和横穿广东和广西的西江水系与广东漠阳江和潭江水系关系密切;而海南岛万泉河和南渡江与广东鉴江水系关系密切. 根据嵌套进化枝系地理分析(NCPA)推测,与越南毗邻的防城河周边地区可能是美丽小条鳅的扩散中心,该物种可由此区域通过两条途径扩散:1)沿西江水系向广西沿海独立水系至广东漠阳江和潭江水系扩散;2)向海南岛诸水系再至雷州半岛的鉴江水系扩散.在演化过程中,曾发生片断化事件、长距离建群和持续的分布区扩张.     

Molecular differentiation within European <Emphasis Type="Italic">Cratoneuron filicinum</Emphasis>, and differences from Asiatic and American populations

Variation in ITS and the two chloroplast markers rpl16 and tRNA-Gly was studied to explore phylogeographic patterns in, especially, western Eurasiatic Cratoneuron filicinum (Hedw.) Spruce. ITS and chloroplast data yield incongruent results and are therefore analysed separately; recombination is indicated for ITS. For both data sets one group of haplotypes is widespread in western Eurasia. Another is found in the Mediterranean region and occurs in southern Scandinavia (ITS) or large portions of northern Europe, but is missing in central Europe. It is suggested that the northern populations of the latter haplotypes have dispersed from eastern or south-eastern glacial refugia. At the continental scale, south-east Asiatic populations differ from those in western Eurasia, with an apparent meeting zone west of the Himalayas. American haplotypes are most similar to some European ones according to ITS, but to south-east Asiatic ones according to chloroplast data.     

The phylogeographic pattern of mitochondrial DNA variation in the Dall's porpoise Phocoenoides dalli

We used 11 restriction endonucleases to study mtDNA variation in 101 Dall's porpoises Phocoenoides dalli from the Bering Sea and western North Pacific. There was little phylogeographic patterning among the 34 mtDNA haplotypes identified in this analysis, suggesting a strong historical connection among populations across this region. Nonetheless, mtDNA variation does not appear to be randomly distributed in this species. Both G_ST and AMOVA uncovered significant differences in the distribution of mtDNA variation between the Bering Sea and western North Pacific populations. These mtDNA results, coupled with differences in allozyme variation and parasite infestation, support the demographic distinctiveness of Bering Sea and western North Pacific stocks of Dall's porpoise. The lack of a strong phylogeographic orientation of mtDNA haplotypes within the Dall's porpoise is similar to the pattern reported in other vertebrates such as coyotes, blackbirds, chickadees, marine catfish, and catadromous eels. Like Dall's porpoise, these species are broadly distributed, and have large populations linked by moderate to high levels of gene flow. However, the more complex, deeply branched phylogenetic network of mtDNA haplotypes within Dall's porpoise, relative to these other vertebrates, suggests important differences between these species in the forces shaping mtDNA variation. One such force is the effective size of female populations, which appears to have been comparatively large and stable in Dall's porpoise.     

GLOBAL MITOCHONDRIAL DNA PHYLOGEOGRAPHY OF HOLARCTIC BREEDING DUNLINS (CALIDRIS ALPINA)

Comparison of mitochondrial DNA (mtDNA) control-region sequences of 155 dunlins from 15 breeding populations confirmed the existence of five major phylogeographic groups in the circumpolar breeding range of this migratory shorebird species. Time estimates of the origin of groups, based on sequence divergences and a molecular clock for birds, suggest a scenario of repeated fragmentation of populations in isolated tundra refugia during the late Pleistocene. The distribution of about three-quarters of all detected molecular variance between phylogeographic groups attests to the strongly subdivided genetic population structure in dunlins that is being maintained by natal philopatry. Each mtDNA phylogeographic group can be related to a morphometrically defined subspecies, but several other recognized subspecies are not supported by monophyletic mtDNA lineages within their purported ranges. More detailed analysis of several European populations reveals low amounts of gene flow and the partitioning of a substantial fraction of molecular variance between them. This ongoing evolution of population-genetic structuring within the European phylogeographic group most likely started with the last retreat of the ice sheets some 10,000 years ago. Dunlins thus provide one of the clearest examples of the linkage between historical and contemporary components of mtDNA phylogeographic structuring in birds.