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An Alternative Model for the Early Peopling of Southern South America Revealed by Analyses of Three Mitochondrial DNA Haplogroups  [PDF]
Michelle de Saint Pierre, Claudio M. Bravi, Josefina M. B. Motti, Noriyuki Fuku, Masashi Tanaka, Elena Llop, Sandro L. Bonatto, Mauricio Moraga
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0043486
Abstract: After several years of research, there is now a consensus that America was populated from Asia through Beringia, probably at the end of the Pleistocene. But many details such as the timing, route(s), and origin of the first settlers remain uncertain. In the last decade genetic evidence has taken on a major role in elucidating the peopling of the Americas. To study the early peopling of South America, we sequenced the control region of mitochondrial DNA from 300 individuals belonging to indigenous populations of Chile and Argentina, and also obtained seven complete mitochondrial DNA sequences. We identified two novel mtDNA monophyletic clades, preliminarily designated B2l and C1b13, which together with the recently described D1g sub-haplogroup have locally high frequencies and are basically restricted to populations from the extreme south of South America. The estimated ages of D1g and B2l, about ~15,000 years BP, together with their similar population dynamics and the high haplotype diversity shown by the networks, suggests that they probably appeared soon after the arrival of the first settlers and agrees with the dating of the earliest archaeological sites in South America (Monte Verde, Chile, 14,500 BP). One further sub-haplogroup, D4h3a5, appears to be restricted to Fuegian-Patagonian populations and reinforces our hypothesis of the continuity of the current Patagonian populations with the initial founders. Our results indicate that the extant native populations inhabiting South Chile and Argentina are a group which had a common origin, and suggest a population break between the extreme south of South America and the more northern part of the continent. Thus the early colonization process was not just an expansion from north to south, but also included movements across the Andes.
The Peopling of Europe from the Mitochondrial Haplogroup U5 Perspective  [PDF]
Boris Malyarchuk,Miroslava Derenko,Tomasz Grzybowski,Maria Perkova,Urszula Rogalla,Tomas Vanecek,Iosif Tsybovsky
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010285
Abstract: It is generally accepted that the most ancient European mitochondrial haplogroup, U5, has evolved essentially in Europe. To resolve the phylogeny of this haplogroup, we completely sequenced 113 mitochondrial genomes (79 U5a and 34 U5b) of central and eastern Europeans (Czechs, Slovaks, Poles, Russians and Belorussians), and reconstructed a detailed phylogenetic tree, that incorporates previously published data. Molecular dating suggests that the coalescence time estimate for the U5 is ~25–30 thousand years (ky), and ~16–20 and ~20–24 ky for its subhaplogroups U5a and U5b, respectively. Phylogeographic analysis reveals that expansions of U5 subclusters started earlier in central and southern Europe, than in eastern Europe. In addition, during the Last Glacial Maximum central Europe (probably, the Carpathian Basin) apparently represented the area of intermingling between human flows from refugial zones in the Balkans, the Mediterranean coastline and the Pyrenees. Age estimations amounting for many U5 subclusters in eastern Europeans to ~15 ky ago and less are consistent with the view that during the Ice Age eastern Europe was an inhospitable place for modern humans.
High frequencies of Y-chromosome haplogroup O2b-SRY465 lineages in Korea: a genetic perspective on the peopling of Korea
Soon-Hee Kim, Ki-Cheol Kim, Dong-Jik Shin, Han-Jun Jin, Kyoung-Don Kwak, Myun-Soo Han, Joon-Myong Song, Won Kim, Wook Kim
Investigative Genetics , 2011, DOI: 10.1186/2041-2223-2-10
Abstract: In general, we found East Asian populations to be characterized by male haplogroup homogeneity, showing major Y-chromosomal expansions of haplogroup O-M175 lineages. Interestingly, a high frequency (31.4%) of haplogroup O2b-SRY465 (and its sublineage) is characteristic of male Koreans, whereas the haplogroup distribution elsewhere in East Asian populations is patchy. The ages of the haplogroup O2b-SRY465 lineages (~9,900 years) and the pattern of variation within the lineages suggested an ancient origin in a nearby part of northeastern Asia, followed by an expansion in the vicinity of the Korean Peninsula. In addition, the coalescence time (~4,400 years) for the age of haplogroup O2b1-47z, and its Y-STR diversity, suggest that this lineage probably originated in Korea. Further studies with sufficiently large sample sizes to cover the vast East Asian region and using genomewide genotyping should provide further insights.These findings are consistent with linguistic, archaeological and historical evidence, which suggest that the direct ancestors of Koreans were proto-Koreans who inhabited the northeastern region of China and the Korean Peninsula during the Neolithic (8,000-1,000 BC) and Bronze (1,500-400 BC) Ages.The Koreans are geographically a Northeast Asian group, who are thought to be most closely related to Altaic language-speaking populations. Anthropological and archaeological evidence suggests that the early Korean population was related to Mongolian ethnic groups, who inhabited the general area of the Altai Mountains and the Lake Baikal regions of southeastern Siberia [1]. Based on archaeological data, the earliest modern human lithic cultures date from 25,000 to 45,000 years ago in the Altai Mountains and southeastern Siberia and the Korean Peninsula [2,3]. According to Korea's founding myths, the Gojoseon (the first state-level society) was established around 2,333 BC in the region of southern Manchuria, but later stretched from the northeastern region of
Population Genetic Structure of Carassius auratus (Pisces: Cypriniformes) in South Korea Inferred from AFLP Markers: Discordance with Mitochondrial Genetic Structure  [PDF]
Jongwoo Jung
Animal Systematics, Evolution and Diversity , 2013, DOI: http://dx.doi.org/10.5635/ased.2013.29.1.18
Abstract: A recent study on the mitochondrial genetic variation of the Carassius auratus population in South Korea suggested that there are 3 distinct mitochondrial lineages in the country, and that they are geographically separated between westward rivers and southward rivers, respectively. In this study, the population genetic structure of amplified fragment length polymorphism (AFLP) of Carassius auratus was investigated. The results of analysis of molecular variance (AMOVA) supported the geographic distinction between westward and southward river populations, but only 3.66% of total genetic variance lies among these populations. The panmicticity of the AFLP genetic variation is backed up by the results of the neighbor-joining dendrogram drawn from a linearized pairwise FST matrix and Bayesian clustering analysis. The discordance of genetic structure between mitochondrial and AFLP genetic variation may come from difference in effective population size between these markers and/or gene flow between westward and southward river populations through river capture events.
The origin of Eastern European Jews revealed by autosomal, sex chromosomal and mtDNA polymorphisms
Avshalom Zoossmann-Diskin
Biology Direct , 2010, DOI: 10.1186/1745-6150-5-57
Abstract: According to the autosomal polymorphisms the investigated Jewish populations do not share a common origin, and EEJ are closer to Italians in particular and to Europeans in general than to the other Jewish populations. The similarity of EEJ to Italians and Europeans is also supported by the X chromosomal haplogroups. In contrast according to the Y-chromosomal haplogroups EEJ are closest to the non-Jewish populations of the Eastern Mediterranean. MtDNA shows a mixed pattern, but overall EEJ are more distant from most populations and hold a marginal rather than a central position. The autosomal genetic distance matrix has a very high correlation (0.789) with geography, whereas the X-chromosomal, Y-chromosomal and mtDNA matrices have a lower correlation (0.540, 0.395 and 0.641 respectively).The close genetic resemblance to Italians accords with the historical presumption that Ashkenazi Jews started their migrations across Europe in Italy and with historical evidence that conversion to Judaism was common in ancient Rome. The reasons for the discrepancy between the biparental markers and the uniparental markers are discussed.This article was reviewed by Damian Labuda (nominated by Jerzy Jurka), Kateryna Makova and Qasim Ayub (nominated by Dan Graur).The genetic affinities of the Jewish populations have been studied since the early days of genetics, yet the origin of these populations is still obscure. Some of the studies, trying to establish the origins of the Jewish populations with autosomal markers, claimed that the Jewish populations have a common origin, but others concluded that the Jews are a very diverse group. This corpus of studies has already been critically reviewed [1].The origin of Eastern European Jews, (EEJ) by far the largest and most important Ashkenazi population, and their affinities to other Jewish and European populations are still not resolved. Studies that compared them by genetic distance analysis of autosomal markers to European Mediterranean pop
Geographical origin of Plasmodium vivax in the Republic of Korea: haplotype network analysis based on the parasite's mitochondrial genome
Moritoshi Iwagami, Seung-Young Hwang, Megumi Fukumoto, Toshiyuki Hayakawa, Kazuyuki Tanabe, So-Hee Kim, Weon-Gyu Kho, Shigeyuki Kano
Malaria Journal , 2010, DOI: 10.1186/1475-2875-9-184
Abstract: A haplotype network analysis based on P. vivax mitochondrial (mt) DNA sequences was conducted on 11 P. vivax isolates from South Korea and another 282 P. vivax isolates collected worldwide.The network analysis of P. vivax mtDNA sequences showed that the coexistence of two different groups (A and B) in South Korea. Groups A and B were identical or close to two different populations in southern China.Although the direct introduction of the two P. vivax populations in South Korea were thought to have been from North Korea, the results of this analysis suggest the genealogical origin to be the two different populations in southern China.Malaria is distributed not only in tropical and subtropical areas but also in some temperate areas of the world. Plasmodium falciparum, which is distributed in tropical and subtropical areas, accounts for 90% of malaria cases. Like P. falciparum, Plasmodium vivax is distributed in tropical and subtropical areas, but its range extends to some temperate areas. In Asian and South American countries, the proportion of P. falciparum cases is gradually decreasing due to global malaria controls programmes, such as The Roll Back Malaria Partnership and The Global Fund. On the other hand, the proportion of P. vivax cases is gradually increasing [1]. Therefore, P. vivax should be given greater attention than it has received.The Republic of Korea (South Korea) is one of the countries where vivax malaria had been successfully eradicated by the late 1970s. This was due to an effective national eradication programme conducted by the National Malaria Eradication Service under the operation of the South Korean government with the support of the WHO [2-4]. However, in 1993, the first case of indigenous vivax malaria after the eradication program was reported from the border area between North and South Korea in the western Demilitarized Zone (DMZ) [5]. The number of cases steadily increased until 2000 (4,142 cases), at which point they began to gradually
Lack of Mitochondrial DNA Sequence Divergence between Two Subspecies of the Siberian Weasel from Korea: Mustela sibirica coreanus from the Korean Peninsula and M. s. quelpartis from Jeju Island  [PDF]
Hung Sun Koh,Kyung Hee Jang,Jang Geun Oh,Eui Dong Han
Animal Systematics, Evolution and Diversity , 2012, DOI: http://dx.doi.org/10.5635/ased.2012.28.2.133
Abstract: The objective of this study was to determine the degree of mitochondrial DNA (mtDNA) divergence between two subspecies of Mustela sibirica from Korea (M. s. coreanus on the Korean Peninsula and M. s. quelpartis on Jeju Island) and to examine the taxonomic status of M. s. quelpartis. Thus, we obtained complete sequences of mtDNA cytochrome b gene (1,140 bp) from the two subspecies, and these sequences were compared to a corresponding haplotype of M. s. coreanus, downloaded from GenBank. From this analysis, it was observed that the sequences from monogenic M. s. quelpartis on Jeju Island were identical to the sequences of four M. s. coreanus from four locations across the Korean Peninsula, and that the two subspecies formed a single clade; the average nucleotide distance between the two subspecies was 0.26% (range, 0.00 to 0.53%). We found that the subspecies quelpartis is not genetically distinct from the subspecies coreanus, and that this cytochrome b sequencing result does not support the current classification, distinguishing these two subspecies by pelage color. Further systematic analyses using morphometric characters and other DNA markers are necessary to confirm the taxonomic status of M. s. quelpartis.
Microsatellite DNA Analysis Revealed a Drastic Genetic Change of Plasmodium vivax Population in the Republic of Korea During 2002 and 2003  [PDF]
Moritoshi Iwagami,Seung-Young Hwang,So-Hee Kim,So-Jung Park,Ga-Young Lee,Emilie Louise Akiko Matsumoto-Takahashi,Weon-Gyu Kho ,Shigeyuki Kano
PLOS Neglected Tropical Diseases , 2013, DOI: 10.1371/journal.pntd.0002522
Abstract: Background Vivax malaria was successfully eliminated in the Republic of Korea (South Korea) in the late 1970s, but it was found to have re-emerged from 1993. In order to control malaria and evaluate the effectiveness of malaria controls, it is important to develop a spatiotemporal understanding of the genetic structure of the parasite population. Here, we estimated the population structure and temporal dynamics of the transmission of Plasmodium vivax in South Korea by analyzing microsatellite DNA markers of the parasite. Methodology/Principal Findings We analyzed 14 microsatellite DNA loci of the P. vivax genome from 163 South Korean isolates collected from 1994 to 2008. Allelic data were used to analyze linkage disequilibrium (LD), genetic differentiation and population structure, in order to make a detailed estimate of temporal change in the parasite population. The LD analysis showed a gradual decrease in LD levels, while the levels of genetic differentiation between successive years and analysis of the population structure based on the Bayesian approach suggested that a drastic genetic change occurred in the South Korean population during 2002 and 2003. Conclusions/Significance Although relapse and asymptomatic parasite carriage might influence the population structure to some extent, our results suggested the continual introduction of P. vivax into South Korea through other parasite population sources. One possible source, particularly during 2002 and 2003, is North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and temporal dynamics of parasite transmission; information that can assist in the elimination of vivax malaria in endemic areas.
Culture creates genetic structure in the Caucasus: Autosomal, mitochondrial, and Y-chromosomal variation in Daghestan
Elizabeth E Marchani, W Scott Watkins, Kazima Bulayeva, Henry C Harpending, Lynn B Jorde
BMC Genetics , 2008, DOI: 10.1186/1471-2156-9-47
Abstract: We found that the highland Daghestani populations had contrasting histories for the mitochondrial DNA and Y-chromosome data sets. Y-chromosomal haplogroup diversity was reduced among highland Daghestani populations when compared to other populations and to highland Daghestani mitochondrial DNA haplogroup diversity. Lowland Daghestani populations showed Turkish and Central Asian affinities for both mitochondrial and Y-chromosomal data sets. Autosomal population histories are strongly correlated to the pattern observed for the mitochondrial DNA data set, while the correlation between the mitochondrial DNA and Y-chromosome distance matrices was weak and not significant.The reduced Y-chromosomal diversity exhibited by highland Daghestani populations is consistent with genetic drift caused by patrilocal endogamy. Mitochondrial and Y-chromosomal phylogeographic comparisons indicate a common Near Eastern origin of highland populations. Lowland Daghestani populations show varying influence from Near Eastern and Central Asian populations.The populations of the Caucasus region have complex histories of isolation and gene flow. The region as a whole has served as a gateway between continents, with waves of human migration leaving rich cultural and linguistic diversity in their wake [1,2]. The Caucasus Mountains have shaped the routes of migrating populations and military invasions, diverting these travellers away from the remote highlands and into the more easily accessible lowlands. Differences between highland and lowland populations are exaggerated by the marriage practices of highland populations: wives move to the home of their husbands, while husbands remain in the land of their forefathers for generations [3,4].We have identified five populations from Daghestan that have been influenced by both physical and cultural barriers to gene flow. Three are highland isolates, while two lowland populations represent admixed groups influenced by Turkic and Mongolian migrants. We i
Updated Three-Stage Model for the Peopling of the Americas  [PDF]
Connie J. Mulligan, Andrew Kitchen, Michael M. Miyamoto
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003199
Abstract: Background We re-assess support for our three stage model for the peopling of the Americas in light of a recent report that identified nine non-Native American mitochondrial genome sequences that should not have been included in our initial analysis. Removal of these sequences results in the elimination of an early (i.e. ~40,000 years ago) expansion signal we had proposed for the proto-Amerind population. Methodology/Findings Bayesian skyline plot analysis of a new dataset of Native American mitochondrial coding genomes confirms the absence of an early expansion signal for the proto-Amerind population and allows us to reduce the variation around our estimate of the New World founder population size. In addition, genetic variants that define New World founder haplogroups are used to estimate the amount of time required between divergence of proto-Amerinds from the Asian gene pool and expansion into the New World. Conclusions/Significance The period of population isolation required for the generation of New World mitochondrial founder haplogroup-defining genetic variants makes the existence of three stages of colonization a logical conclusion. Thus, our three stage model remains an important and useful working hypothesis for researchers interested in the peopling of the Americas and the processes of colonization.
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