Phylogeographic analysis of pigtail macaque populations (Macaca nemestrina) inferred from mitochondrial DNA

Mitochondrial DNA variation was surveyed in nine populations of the pigtail macaque (Macaca nemestrina), covering all three recognized subspecies in Southeast Asia. To do this, a 2,300 base pair fragment spanning the mitochondrial NAD 3 and NAD 4 genes and flanking tRNA subunits leucine and glycine was targeted for amplification and digested with a battery of 16 restriction endonucleases. Out of a total of 107 individuals, 32 unique haplotypes could be distinguished. Parsimony and neighbor-joining analyses grouped the haplotypes into five strongly supported assemblages representing China/Thailand, Malaysia, Sumatra, Borneo, and Siberut. These results indicate that the mainland and island mtDNA haplotypes are strictly and uniquely limited to the geographic ranges of the recognized morphological subspecies. Cladistic and neighbor-joining analyses indicate that inferred phylogenies of mtDNA haplotypes are congruent with subspecies designations. Furthermore, in support of morphological studies, results indicate that the Mentawai macaque is most likely not a distinct species but a subspecies of M. nemestrina. Am J Phys Anthropol 104:35–45, 1997. © 1997 Wiley-Liss, Inc.     

Comparative analysis of mitochondrial DNA of Yakuts and other Asian populations

Mitochondrial DNA of Yakuts has been compared to those of other Asian populations that belong to the Turkic, Mongolic, and Manchu-Tungusic linguistic groups. Haplogroups C and D proved to be the most frequent ones in Yakuts. In contrast to other Asian populations, subcluster D5a is major in Yakuts. The results have demonstrated that Yakuts are close to Tuvinians and Altaians in maternal lineage.     

Comparative analysis of mitochondrial DNA of Yakuts and other Asian populations

Mitochondrial DNA of Yakuts has been compared to those of other Asian populations that belong to the Turkic, Mongolic, and Manchu-Tungusic linguistic groups. Haplogroups C and D proved to be the most frequent ones in Yakuts. In contrast to other Asian populations, subcluster D5a is major in Yakuts. The results have demonstrated that Yakuts are close to Tuvinians and Altaians in maternal lineage.     

Phylogeographic differentiation of mitochondrial DNA in Han Chinese

To characterize the mitochondrial DNA (mtDNA) variation in Han Chinese from several provinces of China, we have sequenced the two hypervariable segments of the control region and the segment spanning nucleotide positions 10171-10659 of the coding region, and we have identified a number of specific coding-region mutations by direct sequencing or restriction-fragment-length-polymorphism tests. This allows us to define new haplogroups (clades of the mtDNA phylogeny) and to dissect the Han mtDNA pool on a phylogenetic basis, which is a prerequisite for any fine-grained phylogeographic analysis, the interpretation of ancient mtDNA, or future complete mtDNA sequencing efforts. Some of the haplogroups under study differ considerably in frequencies across different provinces. The southernmost provinces show more pronounced contrasts in their regional Han mtDNA pools than the central and northern provinces. These and other features of the geographical distribution of the mtDNA haplogroups observed in the Han Chinese make an initial Paleolithic colonization from south to north plausible but would suggest subsequent migration events in China that mainly proceeded from north to south and east to west. Lumping together all regional Han mtDNA pools into one fictive general mtDNA pool or choosing one or two regional Han populations to represent all Han Chinese is inappropriate for prehistoric considerations as well as for forensic purposes or medical disease studies.     

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

Indian subcontinent harbours both the human mtDNA macrohaplogroups M and N, of which M is the most prevalent. In this study, we discuss the overall distribution of the various haplogroups and sub-haplogroups of M among the different castes and tribes to understand their diverse pattern with respect to geographical location and linguistic affiliation of the populations. An overview of about 170 studied populations, belonging to four distinct linguistic families and inhabiting different geographic zones, revealed wide diversity of about 22 major haplogroups of M. The tribal populations belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro-Asiatic speakers) exhibited differences in their haplogroup diversity. The northern and southern region castes showed greater diversity than the castes of other regions.     

Genetic history of Southeast Asian populations as revealed by ancient and modern human mitochondrial DNA analysis

The 360 base-pair fragment in HVS-1 of the mitochondrial genome were determined from ancient human remains excavated at Noen U-loke and Ban Lum-Khao, two Bronze and Iron Age archaeological sites in Northeastern Thailand, radio-carbon dated to circa 3,500-1,500 years BP and 3,200-2,400 years BP, respectively. These two neighboring populations were parts of early agricultural communities prevailing in northeastern Thailand from the fourth millennium BP onwards. The nucleotide sequences of these ancient samples were compared with the sequences of modern samples from various ethnic populations of East and Southeast Asia, encompassing four major linguistic affiliations (Altaic, Sino-Tibetan, Tai-Kadai, and Austroasiatic), to investigate the genetic relationships and history among them. The two ancient samples were most closely related to each other, and next most closely related to the Chao-Bon, an Austroasiatic-speaking group living near the archaeological sites, suggesting that the genetic continuum may have persisted since prehistoric times in situ among the native, perhaps Austroasiatic-speaking population. Tai-Kadai groups formed close affinities among themselves, with a tendency to be more closely related to other Southeast Asian populations than to populations from further north. The Tai-Kadai groups were relatively distant from all groups that have presumably been in Southeast Asia for longer-that is, the two ancient groups and the Austroasiatic-speaking groups, with the exception of the Khmer group. This finding is compatible with the known history of the Thais: their late arrival in Southeast Asia from southern China after the 10th-11th century AD, followed by a period of subjugation under the Khmers.     

Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe

With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.     

Frequency of a 9-bp deletion in the mitochondrial DNA among Asian populations.

Individuals of the following Asian populations were surveyed for the presence of a 9-base-pair deletion of mitochondrial DNA (mtDNA): Ainu, Japanese, Korean, Negrito, and Vedda. Although the variation was detected in every population except the Vedda, the frequencies of the variation differed widely among the populations, suggesting a geographic cline.     

Phylogeographic signal variation in mitochondrial DNA among geographically isolated grassland butterflies

Aim We surveyed mitochondrial DNA (mtDNA) sequence variation among regionally isolated populations of 10 grassland‐associated butterfly species to determine: (1) the utility of phylogeographic comparisons among multiple species for assessing recent evolutionary patterns, and (2) the respective roles of isolation attributable to range disjunction versus isolation attributable solely to geographic distance in establishing divergence patterns. Location The Peace River grasslands of northern Alberta and British Columbia, Canada, which are isolated by 300+ km from similar communities to the south. Methods We sequenced mtDNA (1420 bp of cytochrome c oxidase subunit I) from five grassland‐restricted butterfly species that have geographically disjunct populations and from five ecologically broader species that have more continuous distributions across the same regions. Using analysis of molecular variance (AMOVA), Mantel and partial Mantel tests, and haplotype networks, we compared population structure within and between species in order to assess the validity of single‐species phylogeographic characterizations. We then contrasted variance components between disjunct and continuously distributed species to assess whether divergences were correlated more with disjunction or with geographic distance. Results Single‐species analyses varied substantially within both the disjunct and the continuous groups. One species in each of these groups had mtDNA with unusually deep intraspecific mitochondrial lineage divergences. On the whole, however, the five species with disjunct ranges exhibited greater divergence between geographically distant populations than did the five species with continuous distributions. Comparison of variance components between disjunct and continuous species indicated that isolation attributable only to geographic distance was responsible for up to half of the total sequence variation between disjunct populations of grassland butterflies. Main conclusions Our findings show that single‐species phylogeographic analyses of post‐Pleistocene butterfly distributions are inadequate for characterizing regional biogeographic divergence histories. However, comparison of mtDNA sequence divergences between groups of disjunct and continuously distributed species can allow isolation attributable to range interruption to be quantitatively distinguished from isolation attributable solely to gene flow attenuation over the same geographic area.     

Phylogeographic study of brown trout from Serbia,based on mitochondrial DNA control region analysis

In order to illuminate the phylogeography of brown trout (Salmo trutta) populations in the Balkan state of Serbia, the 561 bp 5''-end of mtDNA control region of 101 individuals originating from upland tributaries of the Danubian, Aegean and Adriatic drainages were sequenced and compared to corresponding brown trout sequences obtained in previous studies. Among 15 haplotypes found, 14 were considered native, representing the Danubian and Adriatic lineages of the brown trout, while one haplotype (ATcs1), found only in two individuals originating from two stocked rivers, corresponded to the Atlantic lineage and was considered introduced. Native haplotypes exhibited a strong geographic pattern of distribution: the Danubian haplotypes were strictly confined to the Danubian drainage, while the Adriatic haplotypes dominated in the Aegean and Adriatic drainages; most of the total molecular variance (69%) was attributed to differences among the drainages. Phylogenetic reconstruction, supplemented with seven haplotypes newly described in this study, suggested a sister position of the Atlantic-Danubian and Adriatic-Mediterranean-marmoratus ("southern") phylogenetic group, and pointed to the existence of a distinct clade, detected within the "southern" group. The data obtained confirmed our expectation of the existence of high genetic diversity in Balkan trout populations, and we recommend more widespread surveys covering trout stocks from the region.     

Phylogenic and geographic analysis of chum salmon Oncorhynchus keta (Walbaum) in Asian populations based on mitochondrial DNA variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993-2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

Mitochondrial DNA diversity in Southeast Asian populations

In a previous study of Southeast Asian genetic variation, we characterized mitochondrial DNAs (mtDNAs) from six populations through high-resolution restriction fragment length polymorphism (RFLP) analysis. Our analysis revealed that these Southeast Asian populations were genetically similar to each other, suggesting they had a common origin. However, other patterns of population associations also emerged. Haplotypes from a major founding haplogroup in Papua New Guinea were present in Malaysia; the Vietnamese and Malaysian aborigines (Orang Asli) had high frequencies of haplogroup F, which was also seen in most other Southeast Asian populations; and haplogroup B, defined by the Region V 9-base-pair deletion, was present throughout the region. In addition, the Malaysian and Sabah (Borneo) aborigine populations exhibited a number of unique mtDNA clusters that were not observed in other populations. Unfortunately, it has been difficult to compare these patterns of genetic diversity with those shown in subsequent studies of mtDNA variation in Southeast Asian populations because the latter have typically sequenced the first hypervariable segment (HVS-I) of the control region (CR) sequencing rather than used RFLP haplotyping to characterize the mtDNAs present in them. For this reason, we sequenced the HVS-I of Southeast Asian mtDNAs that had previously been subjected to RFLP analysis, and compared the resulting data with published information from other Southeast Asian and Oceanic groups. Our findings reveal broad patterns of mtDNA haplogroup distribution in Southeast Asia that may reflect different population expansion events in this region over the past 50,000-5,000 years.     

Phylogeographic relationships within the Mediterranean turbot inferred by mitochondrial DNA haplotype variation

The Mediterranean turbot Psetta maxima consists of two main genetically distinct lineages (western Mediterranean and 'eastern secluded Mediterranean' basins) as investigated by mitochondrial DNA analysis. Within the latter lineage, most haplotypes from the Sea of Azov were endemic and more than half of them derived from a single ancestral haplotype shared among all the eastern Mediterranean areas. There was no relation between morphotype variation in bony tubercles and mitochondrial genealogy.     

Differentiation and levels of genetic variation in northern European lynx (Lynx lynx) populations revealed by microsatellites and mitochondrial DNA analysis

The European lynx (Lynx lynx) hasexperienced significant decline in populationnumbers over large parts of its formerdistribution area in central and northernEurope. In Scandinavia (Sweden and Norway), thespecies has been subject to intense hunting and inthe early 20th century the population size mayhave been as low as about 100 animals. Duringthe rest of the century there have beenalternating periods of restricted hunting andtotal protection. Future management of theScandinavian lynx population will requireinsight into what effects demographicbottlenecks may have had on genetic variabilityand structure. For this purpose, 276 lynxesfrom Sweden, Norway, Finland, Estonia andLatvia were analysed for polymorphism at 11feline microsatellite loci and at themitochondrial DNA (mtDNA) control region.Scandinavian lynxes were found to be fixed fora single mtDNA haplotype, while this and threeadditional haplotypes were seen in Finland andthe Baltic States (Estonia and Latvia); thehaplotypes were all very similar, onlydiffering at 1–4 sites within a 700 bp regionsequenced. Microsatellite variability wasmoderate (H_e = 0.51–0.62) with lowerheterozygosity and fewer alleles in Scandinaviathan in Finland and the Baltic States together,though significant so only for the latter.Heterozygosity data in Scandinavia wereconsistent with a recent population bottleneck.Various analyses (e.g. F_st, individual-basedtree, assignment test) revealed distinctgenetic differentiation between Scandinavianlynxes and animals from Finland and the BalticStates. Some structure was evident withinScandinavia as well, suggesting an isolation bydistance. The observed partition of geneticvariability between Scandinavia and the easterncountries thereof indicates that lynxpopulations from the two regions may need to beseparately managed. We discuss what factors canhave contributed to the population geneticstructure seen in northern European lynxpopulations of today.     

Phylogeographic history of mitochondrial haplogroup J in Scandinavia

Background

Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach.

Methods

Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates.

Results

Haplogroup J originated approximately 42.6 kya (95% CI: 30.0–64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers.

Conclusions

Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.

     

基于线粒体COⅡ基因序列推测黄脊竹蝗谱系地理结构

黄脊竹蝗是危害我国南方竹林的重要害虫。该蝗虫的幼虫和成虫主要以竹叶为食,经常引起大面积的竹林死亡,导致毛竹产量锐减。尽管人们对其生物学特性已经有了较为深入的了解,然而,关于其种群遗传结构以及种群发生、发展和迁移的历史研究极少,这对其灾害的预测十分不利。因此,我们研究黄脊竹蝗不同地理种群的遗传变异,探讨其遗传多样性和种群遗传结构。线粒体细胞色素C氧化酶亚基Ⅱ(COⅡ)是在系统发生学和系统地理学研究中最受欢迎的分子标记之一,本研究即应用线粒体COⅡ基因作为遗传标记对中国黄脊竹蝗分布范围内的种群进行了初步的谱系地理学分析,以期对今后该物种的生物防治提供基础资料。研究结果显示:1)AMOVA分析表明黄脊竹蝗存在明显的种群遗传结构;2)黄脊竹蝗经历了一个近期集群和种群扩张,种群扩张时间估计为0.014百万年前,这处于末次冰期Ⅲ和新冰期Ⅰ之间的间冰期;3)系统发生树与中间-连接网络图的结果相一致,即大部分地理距离较近的种群,在系统发生树中聚集为一支,亲缘关系相近;4)本研究获得的具有浅显世系关系的系统发生分析结果,是邻近区域之间的高迁移率、集群过程和长距离迁移的证据。第四纪盛冰期阶段的气候和生态或环境状况的巨大波动可能对该蝗的遗传多样性和种群动态具有重要影响。     

Mitochondrial DNA polymorphism among five Asian populations

Mitochondrial DNA (mtDNA) polymorphisms were detected using 13 restriction enzymes on the total DNA obtained from blood samples of five Asian populations: Japanese and Ainu of northern Japan, Korean, Negrito (Aeta) of the Philippines, and Vedda of Sri Lanka. Of a total of 28 restriction-enzyme morphs detected, eight had not been reported previously. By combining the morphs, we were able to classify mtDNAs of 243 individuals into 20 mtDNA types. Phylogenetic analyses using maximum parsimony and genetic distance methods both showed that the Japanese, Ainu, and Korean populations were closely related to each other. Aeta was found to show a relatively close relationship to these three populations, confirming the conclusion from previous studies of blood markers. In contrast, Vedda was quite different from the other four populations.     

The divergence of the dolly varden char Salvelinus malma in Asian Northern Pacific populations inferred from the PCR-RFLP analysis of the mitochondrial DNA

Genetic differentiation of the dolly varden char Salvelinus malma Walbaum was studied in five populations from the western part of the Northern Pacific. Using restriction analysis (RFLP), we examined polymorphism of three mitochondrial DNA (mtDNA) fragments amplified in polymerase chain reaction (PCR). MtDNA haplotypes were shown to fall into two phylogenetic groups, which probably reflect the existence of two previously described subspecies of Asian dolly varden, S. malma malma and S. malma krascheninnikovi. The divergence of mtDNA nucleotide sequences in the dolly varden subspecies (about 4%) corresponds to the differences between the valid char species from the genus Salvelinus.     

Species identification of Chilean Artemia populations based on mitochondrial DNA RFLP analysis

Aim Two species of the brine shrimp, namely Artemia franciscana Kellogg and A. persimilis Piccinelli and Prosdocimi, inhabit Chile. Most studies so far have shown that A. franciscana is the most widely distributed species in Chile, with A. persimilis present only in Chilean Patagonia. In general, there is good agreement between morphological and genetic comparisons of Chilean populations with respect to species discrimination. However, a number of results indicate an overlap with some populations tending to diverge from A. franciscana and/or resembling A. persimilis. Prior to the mid 90's the use of DNA markers in Artemia was rather limited, despite their successful application in numerous other species. In this study, we investigate whether the conclusions drawn from traditional comparative tools are congruent with the pattern of genetic divergence depicted by DNA analysis at the mitochondrial level. Location Eight sites in Chile and two reference samples of A. franciscana and A. persimilis from San Francisco Bay (USA) and Buenos Aires (Argentina), respectively. Methods Restriction fragment length polymorphism (RFLP) analysis of a 535 bp segment of the mitochondrial 16S rRNA gene with nine restriction enzymes in 240 individuals. Results No haplotype was shared between the two species. Five restriction enzymes produced species‐specific patterns, enabling the unambiguous assignment of populations to species. Very high (100%) bootstrap values supported the clustering of haplotypes in two groups corresponding to the two species. The two species were clearly differentiated with average sequence divergence of 12.3%. High genetic differentiation was also found among con‐specific populations of A. franciscana with an F_ST estimate of 91%. Main conclusions The mitochondrial DNA (mtDNA) results of this study show a broadly similar pattern to those of previous allozyme and nuclear DNA analyses, with the two New World species appearing as highly divergent. The presence of A. persimilis in southern Chile (Chilean Patagonia) was confirmed. Hence, a species previously regarded as geographically restricted mainly to Argentina, appears to have expanded its range. Populations of A. franciscana appear highly structured with a level of inter‐population genetic differentiation much higher for mtDNA than previously reported with allozymes. Clustering of these populations does not follow a clear geographic pattern. The identification of population‐specific genetic markers for A. persimilis and A. franciscana will help to tackle further aspects of the speciation patterns of these species.