tag:blogger.com,1999:blog-66292172024-03-08T15:55:48.261-05:00Genetic ChaosUsing genetic research to study human migration patterns.Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comBlogger225125tag:blogger.com,1999:blog-6629217.post-1080327790588762432007-07-06T08:41:00.000-04:002007-07-06T08:40:07.375-04:00<strong>Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: evidence for a strong genetic boundary through the Gibraltar Straits</strong><br /><br />An analysis of 11 Alu insertion polymorphisms (ACE, TPA25, PV92, APO, FXIIIB, D1, A25, B65, HS2.43, HS3.23, and HS4.65) has been performed in several NW African (Northern, Western, and Southeastern Moroccans; Saharawi; Algerians; Tunisians) and Iberian (Basques, Catalans, and Andalusians) populations. Genetic distances and principal component analyses show a clear differentiation of NW African and Iberian groups of samples, suggesting a strong genetic barrier matching the geographical Mediterranean Sea barrier. The restriction to gene flow may be attributed to the navigational hazards across the Straits, but cultural factors must also have played a role. Some degree of gene flow from sub-Saharan Africa can be detected in the southern part of North Africa and in Saharawi and Southeastern Moroccans, as a result of a continuous gene flow across the Sahara desert that has created a south-north cline of sub-Saharan Africa influence in North Africa. Iberian samples show a substantial degree of homogeneity and fall within the cluster of European-based genetic diversity.<br /><br /><a href="http://batzerlab.lsu.edu/Publications/Comas%20et%20al.%202000%20Hum%20Genet.pdf">PDF file</a><br /><br /><strong>Mitochondrial DNA Affinities at the Atlantic Fringe of Europe</strong><br /><br />Mitochondrial DNA analysis of Atlantic European samples has detected significant latitudinal clines for several clusters with Paleolithic (H) and Neolithic (J, U4, U5a1, and U5a1a) coalescence ages in Europe. These gradients may be explained as the result of Neolithic influence on a rather homogeneous Paleolithic background. There is also evidence that some Neolithic clusters reached this border by a continental route (J, J1, J1a, U5a1, and U5a1a), whereas others (J2) did so through the Mediterranean coast. An important gene flow from Africa was detected in the Atlantic Iberia. Specific sub-Saharan lineages appeared mainly restricted to southern Portugal, and could be attributed to historic Black slave trade in the area and to a probable Saharan Neolithic influence. In fact, U6 haplotypes of specific North African origin have only been detected in the Iberian peninsula northwards from central Portugal. Based on this peculiar distribution and the high diversity pi value (0.014 +/- 0.001) in this area compared to North Africa (0.006 +/- 0.001), we reject the proposal that only historic events such as the Moslem occupation are the main cause of this gene flow, and instead propose a pre-Neolithic origin for it.<br /><br /><a href="http://www.uma.pt/abrehm/v1.1/docs/downloads/pdfs/Gonzalez_mtDNAPortugal_AJPA2003.pdf">PDF file</a><br /><br /><strong>The place of the Basques in the European Y-chromosome diversity landscape</strong><br /><br />There is a trend to consider the gene pool of the Basques as a 'living fossil' of the earliest modern humans that colonized Europe. To investigate this assumption, we have typed 45 binary markers and five short tandem repeat loci of the Y chromosome in a set of 168 male Basques. Results on these combined haplotypes were analyzed in the context of matching data belonging to approximately 3000 individuals from over 20 European, Near East and North African populations, which were compiled from the literature. Our results place the low Y-chromosome diversity of Basques within the European diversity landscape. This low diversity seems to be the result of a lower effective population size maintained through generations. At least some lineages of Y chromosome in modern Basques originated and have been evolving since pre-Neolithic times. However, the strong genetic drift experienced by the Basques does not allow us to consider Basques either the only or the best representatives of the ancestral European gene pool. Contrary to previous suggestions, we do not observe any particular link between Basques and Celtic populations beyond that provided by the Paleolithic ancestry common to European populations, nor we find evidence supporting Basques as the focus of major population expansions.<br /><br /><a href="http://www.nature.com/ejhg/journal/v13/n12/pdf/5201482a.pdf">PDF file</a><br /><br /><strong>Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe</strong><br /><br />The peopling of Europe is a complex process. One of the most dramatic demographic events, the Neolithic agricultural revolution, took place in the Near East roughly 10000 years ago and then spread through the European continent. Nevertheless, the nature of this process (either cultural or demographic) is still a matter of debate among scientists. We have retrieved HVRI mitochondrial DNA sequences from 11 Neolithic remains from Granollers (Catalonia, northeast Spain) dated to 5500 years BP. We followed the proposed authenticity criteria, and we were also able, for the first time, to track down the pre-laboratory-derived contaminant sequences and consequently eliminate them from the generated cloning dataset. Phylogeographic analysis shows that the haplogroup composition of the Neolithic population is very similar to that found in modern populations from the Iberian Peninsula, suggesting a long-time genetic continuity, at least since Neolithic times. This result contrasts with that recently found in a Neolithic population from Central Europe and, therefore, raises new questions on the heterogeneity of the Neolithic dispersals into Europe. We propose here a dual model of Neolithic spread: acculturation in Central Europe and demic diffusion in southern Europe.<br /><br /><a href="http://www.upf.edu/grec/en/0607/docs/neolitic.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-78465029991480084292007-06-22T10:34:00.000-04:002007-06-22T10:33:03.011-04:00<strong>Human X-chromosomal lineages in Europe reveal Middle Eastern and Asiatic contacts</strong><br /><br />Within Europe, classical genetic markers, nuclear autosomal and Y-chromosome DNA polymorphisms display an east-west frequency gradient. This has been taken as evidence for the westward migration of Neolithic farmers from the Middle East. In contrast, most studies of mtDNA variation in Europe and the Middle East have not revealed clinal distributions. Here we report an analysis of dys44 haplotypes, consisting of 35 polymorphisms on an 8 kb segment of the dystrophin gene on Xp21, in a sample of 1203 Eurasian chromosomes. Our results do not show a significant genetic structure in Europe, though when Middle Eastern samples are included a very low but significant genetic structure, rooted in Middle Eastern heterogeneity, is observed. This structure was not correlated to either geography or language, indicating that neither of these factors are a barrier to gene flow within Europe and/or the Middle East. Spatial autocorrelation analysis did not show clinal variation from the Middle East to Europe, though an underlying and ancient east-west cline across the Eurasian continent was detected. Clines provide a strong signal of ancient major population migration(s), and we suggest that the observed cline likely resulted from an ancient, bifurcating migration out of Africa that influenced the colonizing of Europe, Asia and the Americas. Our study reveals that, in addition to settlements from the Near East, Europe has been influenced by other major population movements, such as expansion(s) from Asia, as well as by recent gene flow from within Europe and the Middle East.<br /><br /><a href="http://www.nature.com/ejhg/journal/v12/n4/pdf/5201097a.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-84442972734482071592007-06-19T13:16:00.000-04:002007-06-19T13:14:39.142-04:00<span style="font-weight:bold;">Differential Susceptibility to Hypertension Is Due to Selection during the Out-of-Africa Expansion</span><br /><br />Hypertension is a leading cause of stroke, heart disease, and kidney failure. The genetic basis of blood pressure variation is largely unknown but is likely to involve genes that influence renal salt handling and arterial vessel tone. Here we argue that susceptibility to hypertension is ancestral and that differential susceptibility to hypertension is due to differential exposure to selection pressures during the out-of-Africa expansion. The most important selection pressure was climate, which produced a latitudinal cline in heat adaptation and, therefore, hypertension susceptibility. Consistent with this hypothesis, we show that ecological variables, such as latitude, temperature, and rainfall, explain worldwide variation in heat adaptation as defined by seven functional alleles in five genes involved in blood pressure regulation. The latitudinal cline in heat adaptation is consistent worldwide and is largely unmatched by latitudinal clines in short tandem repeat markers, control single nucleotide polymorphisms, or non-functional single nucleotide polymorphisms within the five genes. In addition, we show that latitude and one of these alleles, GNB3 (G protein β3 subunit) 825T, account for a major portion of worldwide variation in blood pressure. These results suggest that the current epidemic of hypertension is due to exposures of the modern period interacting with ancestral susceptibility. Modern populations differ in susceptibility to these new exposures, however, such that those from hot environments are more susceptible to hypertension than populations from cold environments. This differential susceptibility is likely due to our history of adaptation to climate.<br /><br /><a href="http://genetics.plosjournals.org/archive/1553-7404/1/6/pdf/10.1371_journal.pgen.0010082-L.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083008962441211112007-06-18T08:48:00.000-04:002007-06-18T08:46:38.795-04:00<strong>Genetics of population isolates</strong><br /><br />Genetic isolates, as shown empirically by the Finnish, Old Order Amish, Hutterites, Sardinian and Jewish communities among others, represent a most important and powerful tool in genetically mapping inherited disorders. The main features associated with that genetic power are the existence of multigenerational pedigrees which are mostly descended from a small number of founders a short number of generations ago, environmental and phenotypic homogeneity, restricted geographical distribution, the presence of exhaustive and detailed records correlating individuals in very well ascertained pedigrees, and inbreeding as a norm. On the other hand, the presence of a multifounder effect or admixture among divergent populations in the founder time (e.g. the Finnish and the Paisa community from Colombia) will theoretically result in increased linkage disequilibrium among adjacent loci. The present review evaluates the historical context and features of some genetic isolates with emphasis on the basic population genetic concepts of inbreeding and genetic drift, and also the state-of-the-art in mapping traits, both Mendelian and complex, on genetic isolates.<br /><br /><a href="http://www.med.umich.edu/hg/EDUCATION/COURSES/542/pdfs/Apr12_Arcos.pdf">PDF file</a><br /><br /><strong>Y Chromosome Binary Markers to Study the High Prevalence of Males in Sardinian Centenarians and the Genetic Structure of the Sardinian Population</strong><br /><br />We have analyzed a sample of 40 centenarians and 116 young controls from Sardinia, with a set of new Y chromosome binary markers, to evaluate if Y chromosome genes are involved in the high prevalence of males among centenarian Sardinians (1/2 vs. 1/4 in other populations studied). The results indicate that none of the seven lineages that account for 197% of the Y chromosome diversity in Sardinia provide an advantage with respect to the extreme longevity. However, our results, although based on the male-specific Y chromosome polymorphisms, give a clear profile of the pattern of genetic variability in Sardinia. Indeed they indicate that the Sardinian population had two main founder populations that have evolved in isolation for at least the last 5,000 years. These findings set the stage for future studies on longevity and other complex traits in Sardinia.<br /><br /><a href="http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowPDF&ProduktNr=224250&Ausgabe=227994&ArtikelNr=53368">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-50312851117261547132007-06-05T14:36:00.000-04:002007-06-05T14:36:51.234-04:00<span style="font-weight:bold;">Localizing Recent Adaptive Evolution in the Human Genome</span><br /><br />Identifying genomic locations that have experienced selective sweeps is an important first step toward understanding the molecular basis of adaptive evolution. Using statistical methods that account for the confounding effects of population demography, recombination rate variation, and single-nucleotide polymorphism ascertainment, while also providing fine-scale estimates of the position of the selected site, we analyzed a genomic dataset of 1.2 million human single-nucleotide polymorphisms genotyped in African-American, European-American, and Chinese samples. We identify 101 regions of the human genome with very strong evidence (p < 10<sup>-5</sup>) of a recent selective sweep and where our estimate of the position of the selective sweep falls within 100 kb of a known gene. Within these regions, genes of biological interest include genes in pigmentation pathways, components of the dystrophin protein complex, clusters of olfactory receptors, genes involved in nervous system development and function, immune system genes, and heat shock genes. We also observe consistent evidence of selective sweeps in centromeric regions. In general, we find that recent adaptation is strikingly pervasive in the human genome, with as much as 10% of the genome affected by linkage to a selective sweep.<br /><br /><a href="http://genetics.plosjournals.org/archive/1553-7404/3/6/pdf/10.1371_journal.pgen.0030090-L.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083084016647339972007-05-04T20:43:00.000-04:002007-05-04T08:43:01.150-04:00<strong>Lactase Haplotype Diversity in the Old World</strong><br /><br />Lactase persistence, the genetic trait in which intestinal lactase activity persists at childhood levels into adulthood, varies in frequency in different human populations, being most frequent in northern Europeans and certain African and Arabian nomadic tribes, who have a history of drinking fresh milk. Selection is likely to have played an important role in establishing these different frequencies since the development of agricultural pastoralism ~9,000 years ago. We have previously shown that the element responsible for the lactase persistence/nonpersistence polymorphism in humans is <em>cis</em>-acting to the lactase gene and that lactase persistence is associated, in Europeans, with the most common 70-kb lactase haplotype, A. We report here a study of the 11-site haplotype in 1,338 chromosomes from 11 populations that differ in lactase persistence frequency. Our data show that haplotype diversity was generated both by point mutations and recombinations. The four globally common haplotypes (A, B, C, and U) are not closely related and have different distributions; the A haplotype is at high frequencies only in northern Europeans, where lactase persistence is common; and the U haplotype is virtually absent from Indo-European populations. Much more diversity is seen in sub-Saharan Africans than in non-Africans, consistent with an "Out of Africa" model for peopling of the Old World. Analysis of recent recombinant haplotypes by allele-specific PCR, along with deduction of the root haplotype from chimpanzee sequence, allowed construction of a haplotype network that assisted in evaluation of the relative roles of drift and selection in establishing the haplotype frequencies in the different populations. We suggest that genetic drift was important in shaping the general pattern of non-African haplotype diversity, with recent directional selection in northern Europeans for the haplotype associated with lactase persistence.<br /><br /><a href="http://www.journals.uchicago.edu/AJHG/journal/issues/v68n1/002187/002187.web.pdf">PDF file</a><br /><br /><strong>Absence of the lactase-persistence-associated allele in early Neolithic Europeans</strong><br /><br />Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.<br /><br /><a href="http://www.ucl.ac.uk/tcga/tcgapdf/Burger_etal_PNAS07_LCT-aDNA.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-28026240756062950032007-05-02T09:04:00.000-04:002007-05-02T09:04:08.783-04:00<strong>Global variation in copy number in the human genome</strong><br /><br />Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.<br /><br /><a href="http://www.nature.com/nature/journal/v444/n7118/pdf/nature05329.pdf">PDF file</a><br /><br /><strong>Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms</strong><br /><br /><em>Background</em><br />Recent studies have shown that when individuals are grouped on the basis of genetic similarity, group membership corresponds closely to continental origin. There has been considerable debate about the implications of these findings in the context of larger debates about race and the extent of genetic variation between groups. Some have argued that clustering according to continental origin demonstrates the existence of significant genetic differences between groups and that these differences may have important implications for differences in health and disease. Others argue that clustering according to continental origin requires the use of large amounts of genetic data or specifically chosen markers and is indicative only of very subtle genetic differences that are unlikely to have biomedical significance.<br /><br /><em>Results</em><br />We used small numbers of randomly selected single nucleotide polymorphisms (SNPs) from the International HapMap Project to train naïve Bayes classifiers for prediction of ancestral continent of origin. Predictive accuracy was tested on two independent data sets. Genetically similar groups should be difficult to distinguish, especially if only a small number of genetic markers are used. The genetic differences between continentally defined groups are sufficiently large that one can accurately predict ancestral continent of origin using only a minute, randomly selected fraction of the genetic variation present in the human genome. Genotype data from only 50 random SNPs was sufficient to predict ancestral continent of origin in our primary test data set with an average accuracy of 95%. Genetic variations informative about ancestry were common and widely distributed throughout the genome.<br /><br /><em>Conclusion</em><br />Accurate characterization of ancestry is possible using small numbers of randomly selected SNPs. The results presented here show how investigators conducting genetic association studies can use small numbers of arbitrarily chosen SNPs to identify stratification in study subjects and avoid false positive genotype-phenotype associations. Our findings also demonstrate the extent of variation between continentally defined groups and argue strongly against the contention that genetic differences between groups are too small to have biomedical significance.<br /><br /><a href="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1828730&blobtype=pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-28427780721645161302007-04-06T14:30:00.000-04:002007-04-06T14:28:18.270-04:00<strong>Was the C282Y mutation an Irish Gaelic mutation that the Vikings help disseminate?</strong><br /><br />The C282Y mutation is held to have arisen in either a Celtic or a Viking ancestor some 60 generations ago. While the Scandinavians have a high frequency of C282Y, the Irish have the highest frequency of the C282Y mutation in the world. However testing of the Irish people for C282Y has been patchy. The true frequency of the C282Y mutation in Ireland and specifically in the relatively isolated western province of Connaught is unknown. Establishment of the C282Y frequency in the Irish male population of Connaught with traditional Irish surnames, a group which has a virtual fixation for Y chromosome R1b3, could help establish C282Y as an Irish mutation. Elucidation of greater C282Y haplotype diversity for the Irish as opposed to the Scandinavians would indicate the Irish as the likely source population for C282Y. Taken together, linking of C282Y to the Irish Gaelic male population of Connaught and establishment of an Irish origin of the C282Y mutation would point to dissemination of the C282Y mutation by Viking raiders and colonizers.<br /><br /><a href="http://vetinari.sitesled.com/vikings.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-88949425467883501352007-04-06T13:59:00.000-04:002007-04-06T13:57:00.918-04:00<strong>No signature of Y chromosomal resemblance between possible descendants of the Cimbri in Denmark and Northern Italy</strong><br /><br />Two European populations are believed to be related to the ancient Germanic tribe Cimbri: one living in Northern Italy, the other living in Jutland, Denmark. The people called Cimbri are documented in the ancient Roman historical record. Arriving from the far north their movements can be tracked from successive battles with the Romans. The Cimbri finally entered Italy from the northeast and were defeated at Vercellae (present day Vercelli) in 101 BC by Gaius Marius and his professional legions. Classical sources from the first centuries AD relate the homeland of the Cimbri to the coasts around the Elb estuary (northern Germany) or specifically towards the north (Himmerland in northern Jutland). In the alpine parts of Veneto, northeast of the historical battlefield, local traditions dating back to late medieval time, identify a local population as Cimbri living in Terra dei Cimbri. They are considered the descendents of the Germanic combatants that fled the battlefield at Vercelli. As the defeated Cimbri that possibly fled to the mountains of Northern Italy most likely would have been male (warriors), the present study investigated the possible Y chromosomal diversity of the two present populations using microsatellite markers and single nucleotide polymorphisms. While Cimbri from Himmerland resembled their geographical neighbors from Denmark for the Y-chromosome markers, Cimbri from Italy were significantly differentiated both from Cimbri from Himmerland and from Danes. Therefore, we were not able to show any biological relationship for uniparentally transmitted markers.<br /><br /><a href="http://vetinari.sitesled.com/cimbri.pdf">PDF file</a><br /><br /><strong>Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic–Neolithic encounter</strong><br /><br />The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North–South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy. <br /><br /><a href="http://vetinari.sitesled.com/meso.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1084215200395247582007-04-05T09:36:00.000-04:002007-04-05T09:36:03.371-04:00<strong>Y chromosome haplotypes reveal prehistorical migrations to the Himalayas</strong><br /><br />By using 19 Y chromosome biallelic markers and 3 Y chromosome microsatellite markers, we analyzed the genetic structure of 31 indigenous Sino-Tibetan speaking populations (607 individuals) currently residing in East, Southeast, and South Asia. Our results showed that a T to C mutation at locus M122 is highly prevalent in almost all of the Sino-Tibetan populations, implying a strong genetic affinity among populations in the same language family. Furthermore, the extremely high frequency of H8, a haplotype derived from M122C, in the Sino-Tibetan speaking populations in the Himalayas including Tibet and northeast India indicated a strong bottleneck effect that occurred during a westward and then southward migration of the founding population of Tibeto-Burmans. We, therefore, postulate that the ancient people, who lived in the upper-middle Yellow River basin about 10,000 years ago and developed one of the earliest Neolithic cultures in East Asia, were the ancestors of modern Sino-Tibetan populations.<br /><br /><a href="http://hpgl.stanford.edu/publications/HG_2000_v107_p582.pdf">PDF file</a><br /><br /><strong>Analyses of Genetic Structure of Tibeto-Burman Populations Reveals Sex-Biased Admixture in Southern Tibeto-Burmans</strong><br /><br />An unequal contribution of male and female lineages from parental populations to admixed ones is not uncommon in the American continents, as a consequence of directional gene flow from European men into African and Hispanic Americans in the past several centuries. However, little is known about sex-biased admixture in East Asia, where substantial migrations are recorded. Tibeto-Burman (TB) populations were historically derived from ancient tribes of northwestern China and subsequently moved to the south, where they admixed with the southern natives during the past 2,600 years. They are currently extensively distributed in China and Southeast Asia. In this study, we analyze the variations of 965 Y chromosomes and 754 mtDNAs in 120 TB populations from China. By examining the haplotype group distributions of Y-chromosome and mtDNA markers and their principal components, we show that the genetic structure of the extant southern Tibeto-Burman (STB) populations were primarily formed by two parental groups: northern immigrants and native southerners. Furthermore, the admixture has a bias between male and female lineages, with a stronger influence of northern immigrants on the male lineages (~62%) and with the southern natives contributing more extensively to the female lineages (~56%) in the extant STBs. This is the first genetic evidence revealing sex-biased admixture in STB populations, which has genetic, historical, and anthropological implications.<br /><br /><a href="http://www.journals.uchicago.edu/AJHG/journal/issues/v74n5/40779/40779.web.pdf">PDF file</a><br /><br /><strong>The Northeast Indian Passageway: A Barrier or Corridor for Human Migrations?</strong><br /><br />The northeast Indian passageway connecting the Indian subcontinent to east/southeast Asia is thought to have been a major corridor for human migrations. Because it is also an important linguistic contact zone, it is predicted that northeast India has witnessed extensive population interactions, thus leading to high genetic diversity within groups and heterogeneity among groups. To test this prediction, we analyzed 14 bi-allelic and 5 short tandem repeat Y-chromosome markers and hypervariable region 1 mtDNA sequence variation in 192 northeast Indians. We find that both northeast Indian Y-chromosomes and mtDNAs consistently show strikingly high homogeneity among groups and strong affinities to east Asian groups. We detect virtually no Y-chromosome and mtDNA admixture between northeast and other Indian groups. Northeast Indian groups are also characterized by a greatly reduced Y-chromosome diversity, which contrasts with extensive mtDNA diversity. This is best explained by a male founder effect during the colonization of northeast India that is estimated to have occurred within the last 4,000 years. Thus, contrary to the prediction, these results provide strong evidence for a genetic discontinuity between northeast Indian groups and other Indian groups. We therefore conclude that the northeast Indian passageway acted as a geographic barrier rather than as a corridor for human migrations between the Indian subcontinent and east/southeast Asia, at least within the last millennia and possibly for several tens of thousand years, as suggested by the overall distinctiveness of the Indian and east Asian Y-chromosome and mtDNA gene pools.<br /><br /><a href="http://www.eva.mpg.de/genetics/pdf/CordauxMBE2004.pdf">PDF file</a><br /><br /><strong>The Himalayas as a Directional Barrier to Gene Flow</strong><br /><br />High-resolution Y-chromosome haplogroup analyses coupled with Y–short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal—including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)—as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman–speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134–derived chromosomes, whose Y-STR–based age (±SE) was estimated at 8.1 ± 2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives—namely, D1-M15 and D3-P47 in Tibet—involved two different demographic events (5.1 ± 1.8 and 11.3 ± 3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.<br /><br /><a href="http://vetinari.sitesled.com/Himalayas.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083605991622164802007-03-29T10:48:00.000-04:002007-03-29T10:46:08.767-04:00<strong>Y-Chromosome Mismatch Distributions in Europe</strong><br /><br />Ancient demographic events can be inferred from the distribution of pairwise sequence differences (or mismatches) among individuals. We analyzed a database of 3,677 Y chromosomes typed for 11 biallelic markers in 48 human populations from Europe and the Mediterranean area. Contrary to what is observed in the analysis of mitochondrial polymorphisms, Tajima’s test was insignificant for most Y-chromosome samples, and in 47 populations the mismatch distributions had multiple peaks. Taken at face value, these results would suggest either (1) that the size of the male population stayed essentially constant over time, while the female population size increased, or (2) that different selective regimes have shaped mitochondrial and Y-chromosome diversity, leading to an excess of rare alleles only in the mitochondrial genome. An alternative explanation would be that the 11 variable sites of the Y chromosome do not provide sufficient statistical power, so a comparison with mitochondrial data (where more than 200 variable sites are studied in Europe) is impossible at present. To discriminate between these possibilities, we repeatedly analyzed a European mitochondrial database, each time considering only 11 variable sites, and we estimated mismatch distributions in stable and growing populations, generated by simulating coalescent processes. Along with theoretical considerations, these tests suggest that the difference between the mismatch distributions inferred from mitochondrial and Y-chromosome data are not a statistical artifact. Therefore, the observed mismatch distributions appear to reflect different underlying demographic histories and/or selective pressures for maternally and paternally transmitted loci.<br /><br /><a href="http://mbe.oupjournals.org/cgi/reprint/18/7/1259.pdf">PDF file</a><br /><br /><strong>European Population Substructure: Clustering of Northern and Southern Populations</strong><br /><br />The development of methodologies for defining population genetic structure has provided the ability to identify the major ethnic contributions in individual subjects in diverse populations. Using a genome-wide SNP panel we observe population structure in a diverse group of Europeans and European Americans. Under a variety of conditions and tests there is a consistent and reproducible distinction between "northern" and "southern" European population groups: most individual subjects with southern European ancestry (Italian, Spanish, Portuguese, and Greek) have >85% membership in the "south" population; and most northern, western, eastern and central Europeans have >90% in the "north" population group. Ashkenazi Jewish as well as Sephardic Jewish origin also showed >85% membership in the "south" population consistent with a later Mediterranean origin of these ethnic groups. Based on this work, we have developed a core set of informative SNP markers that can control for this partition in European population structure in a variety of clinical and genetic studies.<br /><br /><a href="http://genetics.plosjournals.org/archive/1553-7404/2/9/pdf/10.1371_journal.pgen.0020143-L.pdf">PDF file</a><br /><br /><strong>Measuring European Population Stratification with Microarray Genotype Data</strong><br /><br />A proper understanding of population genetic stratification - differences in individual ancestry within a population - is crucial in attempts to find genes for complex traits through association mapping. We report on genomewide typing of ~10,000 single-nucleotide polymorphisms in 297 individuals, to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most prominently in a northern-southeastern trend, but also along an east-west axis. We also demonstrate the selection and application of EuroAIMs (European ancestry informative markers) for ancestry estimation and correction. The Coriell Caucasian and CEPH (Centre d'Étude du Polymorphisme Humain) Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent's ancestry.<br /><br /><a href="http://vetinari.sitesled.com/euroaims.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-71669003813008866282007-02-07T08:54:00.001-05:002007-02-07T08:54:00.647-05:00<strong>Thomas Jefferson's Y chromosome belongs to a rare European lineage</strong><br /><br />We have characterized the Y chromosome carried by President Thomas Jefferson, the general rarity of which supported the idea that he, or a patrilineal relative, fathered the last son of his slave Sally Hemings. It belongs to haplogroup K2, a lineage representing only ~1% of chromosomes worldwide, and most common in East Africa and the Middle East. Phylogenetic network analysis of its Y-STR (short tandem repeat) haplotype shows that it is most closely related to an Egyptian K2 haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with Jefferson's patrilineage belonging to an ancient and rare indigenous European type. This is supported by the observation that two of 85 unrelated British men sharing the surname Jefferson also share the President's Y-STR haplotype within haplogroup K2. Our findings represent a cautionary tale in showing the difficulty of assigning individual ancestry based on a Y-chromosome haplotype, particularly for rare lineages where population data are scarce. <br /><br /><a href="http://vetinari.sitesled.com/k2.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-87397844283484708612006-12-15T16:09:00.000-05:002006-12-15T16:06:32.126-05:00<strong>Genetic stratification of pathogen-response-related and other variants within a homogeneous Caucasian Irish population</strong><br /><br />Selection pressures from pathogens impact on the worldwide geographic distribution of polymorphisms in certain pathogen-response-associated genes. Such gene-specific effects could lead to confounding by geographic disease associations. We wished to determine if such constraints impinge on the genetic structure of a population of Irish patients and whether variants associated with responses to pathogens showed greater stratification. The counties of origin of each subject's grandparents were used as the geographic variable. F(st), proportional to the extent of population structure, was low (mean F(st)=0.004 across 25 SNPs, range 0.001-0.008) and it was not significantly higher for pathogen response SNPs (F(st)=0.004) than for other SNPs (F(st)=0.003, P=0.21). Correspondence analysis revealed weak trends primarily in approximately northeast to southwest and secondarily in northwest to southeast directions. One-dimensional spatial autocorrelation analysis revealed a weak (Moran's I autocorrelation of -0.10) tendency for SNP frequencies to diverge with greater distance. Two-dimensional autocorrelation indicated a northeast to southwest gradient that was similar for both the pathogen response and other SNPs. The southeastern county, Wexford, showed a distinctive pattern, perhaps consistent with Anglo-Norman settlements. In conclusion, these results indicate that pathogen response SNPs do not exhibit significantly more population structure than other SNPs within this Caucasian population. This suggests that the specific population structure of particular genes may not typically be a cause of strong confounding in genetic studies where population structure is controlled.<br /><br /><a href="http://www.kbioscience.co.uk/genotyping/Genetic%20stratification%20of%20pathogen-response-related%20and%20other%20variants%20within%20a%20homogeneous%20Caucasian%20Irish%20population.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-38147331551958230132006-12-15T15:58:00.000-05:002006-12-15T15:54:45.968-05:00<strong>Sub-populations within the major European and African derived haplogroups R1b3 and E3a are differentiated by previously phylogenetically undefined Y-SNPs</strong><br /><br />Single nucleotide polymorphisms on the Y chromosome (Y-SNPs) have been widely used in the study of human migration patterns and evolution. Potential forensic applications of Y-SNPs include their use in predicting the ethnogeographic origin of the donor of a crime scene sample, or exclusion of suspects of sexual assaults (the evidence of which often comprises male/female mixtures and may involve multiple perpetrators), paternity testing, and identification of non- and half-siblings. In this study, we used a population of 118 African- and 125 European-Americans to evaluate 12 previously phylogenetically undefined Y-SNPs for their ability to further differentiate individuals who belong to the major African (E3a)- and European (R1b3, I)-derived haplogroups. Ten of these markers define seven new sub-clades (equivalent to E3a7a, E3a8, E3a8a, E3a8a1, R1b3h, R1b3i, and R1b3i1 using the Y Chromosome Consortium nomenclature) within haplogroups E and R. Interestingly, during the course of this study we evaluated M222, a sub-R1b3 marker rarely used, and found that this sub-haplogroup in effect defines the Y-STR Irish Modal Haplotype (IMH). The new bi-allelic markers described here are expected to find application in human evolutionary studies and forensic genetics.<br /><br /><a href="http://vetinari.sitesled.com/r1b3.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-51278716876123652952006-12-15T14:48:00.000-05:002006-12-15T14:45:14.656-05:00<strong>The mtDNA Legacy of the Levantine Early Upper Palaeolithic in Africa</strong><br /><br />Sequencing of 81 entire human mitochondrial DNAs (mtDNAs) belonging to haplogroups M1 and U6 reveals that these predominantly North African clades arose in southwestern Asia and moved together to Africa about 40,000 to 45,000 years ago. Their arrival temporally overlaps with the event(s) that led to the peopling of Europe by modern humans and was most likely the result of the same change in climate conditions that allowed humans to enter the Levant, opening the way to the colonization of both Europe and North Africa. Thus, the early Upper Palaeolithic population(s) carrying M1 and U6 did not return to Africa along the southern coastal route of the “out of Africa” exit, but from the Mediterranean area; and the North African Dabban and European Aurignacian industries derived from a common Levantine source.<br /><br /><a href="http://vetinari.sitesled.com/levantine.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1101745370156251062006-11-28T10:07:00.000-05:002006-11-28T10:07:37.776-05:00<strong>Modern Humans Did Not Admix with Neanderthals during Their Range Expansion into Europe</strong><br /><br />The process by which the Neanderthals were replaced by modern humans between 42,000 and 30,000 before present is still intriguing. Although no Neanderthal mitochondrial DNA (mtDNA) lineage is found to date among several thousands of Europeans and in seven early modern Europeans, interbreeding rates as high as 25% could not be excluded between the two subspecies. In this study, we introduce a realistic model of the range expansion of early modern humans into Europe, and of their competition and potential admixture with local Neanderthals. Under this scenario, which explicitly models the dynamics of Neanderthals’ replacement, we estimate that maximum interbreeding rates between the two populations should have been smaller than 0.1%. We indeed show that the absence of Neanderthal mtDNA sequences in Europe is compatible with at most 120 admixture events between the two populations despite a likely cohabitation time of more than 12,000 y. This extremely low number strongly suggests an almost complete sterility between Neanderthal females and modern human males, implying that the two populations were probably distinct biological species.<br /><br /><a href="http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=532389&action=stream&blobtype=pdf">PDF file</a><br /><br /><strong>Evidence that the adaptive allele of the brain size gene microcephalin introgressed into Homo sapiens from an archaic Homo lineage</strong><br /><br />At the center of the debate on the emergence of modern humans and their spread throughout the globe is the question of whether archaic Homo lineages contributed to the modern human gene pool, and more importantly, whether such contributions impacted the evolutionary adaptation of our species. A major obstacle to answering this question is that low levels of admixture with archaic lineages are not expected to leave extensive traces in the modern human gene pool because of genetic drift. Loci that have undergone strong positive selection, however, offer a unique opportunity to identify low-level admixture with archaic lineages, provided that the introgressed archaic allele has risen to high frequency under positive selection. The gene microcephalin (MCPH1) regulates brain size during development and has experienced positive selection in the lineage leading to Homo sapiens. Within modern humans, a group of closely related haplotypes at this locus, known as haplogroup D, rose from a single copy ~37,000 years ago and swept to exceptionally high frequency (~70% worldwide today) because of positive selection. Here, we examine the origin of haplogroup D. By using the interhaplogroup divergence test, we show that haplogroup D likely originated from a lineage separated from modern humans ~1.1 million years ago and introgressed into humans by ~37,000 years ago. This finding supports the possibility of admixture between modern humans and archaic Homo populations (Neanderthals being one possibility). Furthermore, it buttresses the important notion that, through such adminture, our species has benefited evolutionarily by gaining new advantageous alleles. The interhaplogroup divergence test developed here may be broadly applicable to the detection of introgression at other loci in the human genome or in genomes of other species.<br /><br /><a href="http://www.pnas.org/cgi/reprint/0606966103v1.pdf">PDF file</a><br /><br /><strong>Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens</strong><br /><br />The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the coexistence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.<br /><br /><a href="http://www.biochemsoctrans.org/bst/033/0582/0330582.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083605184135535062006-11-03T14:59:00.000-05:002006-11-03T15:02:37.650-05:00<strong>Geographical, Linguistic, and Cultural Influences on Genetic Diversity: Y-Chromosomal Distribution in Northern European Populations</strong><br /><br />We analyzed 10 Y-chromosomal binary markers in 363 males from 8 populations in Northern Europe and 5 Y microsatellites in 346 of these individuals. These populations can be grouped according to cultural, linguistic, or geographical criteria, and the groupings are different in each case. We can therefore ask which criterion best corresponds to the distribution of genetic variation. In an AMOVA analysis using the binary markers, 13% of the Y variation was found between populations, indicating a high level of differentiation within this small area. No significant difference was seen between the traditionally nomadic Saami and the neighboring, historically farming, populations. When the populations were divided into Uralic speakers and Indo-European speakers, 8% of the variation was found between groups, but when they were divided according to geographical location, 14% of the variation was between groups. Geographical factors have thus been the most important in limiting gene flow between these populations, but linguistic differences have also been important in the east.<br /><br /><a href="http://mbe.oupjournals.org/cgi/reprint/18/6/1077.pdf">PDF file</a><br /><br /><strong>Y-chromosome diversity in Sweden – A long-time perspective</strong><br /><br />Sixteen Y-chromosomal binary markers and nine Y-chromosome short tandem repeats were analyzed in a total of 383 unrelated males from seven different Swedish regions, one Finnish region and a Swedish Saami population in order to address questions about the origin and genetic structure of the present day population in Sweden. Haplogroup I1a* was found to be the most common haplogroup in Sweden and accounted, together with haplogroups R1b3, R1a1 and N3, for over 80% of the male lineages. Within Sweden, a minor stratification was found in which the northern region Va¨sterbotten differed significantly (Po0.05) from the other Swedish regions. A flow of N3 chromosomes into Vasterbotten mainly from Saami and Finnish populations could be one explanation for this stratification. However, the demographic history of Vasterbotten involving a significant male absence during the 17th Century may also have had a large impact. Immigration of young men from elsewhere to Varmland at the same time, can be responsible for a similar deviation with I1a* haplotypes. Y chromosomes within haplogroup R1b3 were found to have the highest STR variation among all haplogroups and could thus be considered to be one of the earliest major male lineages present in Sweden. Regional haplotype variation, within R1b3, also showed a difference between two regions in the south of Sweden. This can also be traced from historical time and is visible in archaeological material. Overall this Y chromosome study provides interesting information about the genetic patterns and demographic events in the Swedish population.<br /><br /><a href="http://vetinari.sitesled.com/sweden.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1162567816249194572006-11-03T10:29:00.000-05:002006-11-03T14:48:07.726-05:00<strong>Y-Chromosomal Variation in the Czech Republic</strong><br /><br />To analyze the contribution of the Czech population to the Y-chromosome diversity landscape of Europe and to reconstruct past demographic events, we typed 257 males from five locations for 21 UEPs. Moreover, 141 carriers of the three most common haplogroups were typed for 10 microsatellites and coalescent analyses applied. Sixteen Hg's characterized by derived alleles were identified, the most common being R1a-SRY10831 and P-DYS257*(xR1a). The pool of haplogroups within I-M170 represented the third most common clade. Overall, the degree of population structure was low. The ages for Hg I-M170, P-DYS257*(xR1a), and R1a-SRY10831 ap peared to be comparable and compatible with their presence during or soon after the LGM. A signal of population growth beginning in the first millennium B.C. was detected. Its similarity among the three most common Hg's indicated that growth was characteristic for a gene pool that already contained all of them. The Czech population appears to be influenced, to a very moderate extent, by genetic inputs from outside Europe in the post-Neolithic and historical times. Population growth postdated the archaeologically documented introduction of Neolithic technology and the estimated central value coincides with a period of repeated changes driven by the development of metal technologies and the associated social and trade organization.<br /><br /><a href="http://vetinari.sitesled.com/czech.pdf">PDF file</a><br /><br /><strong>Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis</strong><br /><br />To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n = 913) and 11 from Germany (n = 1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r = 0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations. By means of analysis of the molecular variance (AMOVA) we observed a large and statistically significant proportion of 14% (for Y-SNPs) and 15% (for Y-STRs) of the respective total genetic variation being explained between both countries. The same population differentiation was detected using Monmonier's algorithm, with a resulting genetic border between Poland and Germany that closely resembles the course of the political border between both countries. The observed genetic differentiation was mainly, but not exclusively, due to the frequency distribution of two Y-SNP haplogroups and their associated Y-STR haplotypes: R1a1*, most frequent in Poland, and R1*(xR1a1), most frequent in Germany. We suggest here that the pronounced population differentiation between the two geographically neighbouring countries, Poland and Germany, is the consequence of very recent events in human population history, namely the forced human resettlement of many millions of Germans and Poles during and, especially, shortly after World War II. In addition, our findings have consequences for the forensic application of Y-chromosome markers, strongly supporting the implementation of population substructure into forensic Y chromosome databases, and also for genetic association studies.<br /><br /><a href="http://vetinari.sitesled.com/poland.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1081873485926871262006-10-26T12:59:00.000-04:002006-10-26T13:03:01.076-04:00<strong>Population structure and history in East Asia</strong><br /><br />Archaeological, anatomical, linguistic, and genetic data have suggested that there is an old and significant boundary between the populations of north and south China. We use three human genetic marker systems and one human-carried virus to examine the north/south distinction. We find no support for a major north/south division in these markers; rather, the marker patterns suggest simple isolation by distance.<br /><br /><a href="http://harpend.dsl.xmission.com/Documents/ding.china.pnas.pdf">PDF file</a><br /><br /><strong>Evidence for Archaic Asian Ancestry on the Human X Chromosome</strong><br /><br />The human RRM2P4 pseudogene has a pattern of nucleotide polymorphism that is unlike any locus published to date. A gene tree constructed from a 2.4-kb fragment of the RRM2P4 locus sequenced in a sample of 41 worldwide humans clearly roots in East Asia and has a most-recent common ancestor approximately 2 Myr before present. The presence of this basal lineage exclusively in Asia results in higher nucleotide diversity among non-Africans than among Africans. A global survey of a single-nucleotide polymorphism that is diagnostic for the basal, Asian lineage in 570 individuals shows that it occurs at frequencies up to 53% in south China, whereas only one of 177 surveyed Africans carries this archaic lineage. We suggest that this ancient lineage is a remnant of introgressive hybridization between expanding anatomically modern humans emerging from Africa and archaic populations in Eurasia.<br /><br /><a href="http://hammerlab.biosci.arizona.edu/Publications/Garrigan_2005_2.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083257163240789922006-10-17T16:13:00.000-04:002006-11-03T18:17:36.490-05:00<strong>Analysis of Mitochondrial DNA Lineages in Yakuts</strong><br /><br />To study the mitochondrial gene pool structure in Yakuts, polymorphism of mtDNA hypervariable segment I (16,024–16,390) was analyzed in 191 people sampled from the indigenous population of the Sakha Republic. In total, 67 haplotypes of 14 haplogroups were detected. Most (91.6%) haplotypes belonged to haplogroups A, B, C, D, F, G, M*, and Y, which are specific for East Eurasian ethnic groups; 8.4% haplotypes represented Caucasian haplogroups H, HV1, J, T, U, and W. A high frequency of mtDNA types belonging to Asian supercluster M was peculiar for Yakuts: mtDNA types belonging to haplogroup C, D, or G and undifferentiated mtDNA types of haplogroup M (M*) accounted for 81% of all haplotypes. The highest diversity was observed for haplogroups C and D, which comprised respectively 22 (44%) and 18 (30%) haplotypes. Yakuts showed the lowest genetic diversity (H= 0.964) among all Turkic ethnic groups. Phylogenetic analysis testified to common genetic substrate of Yakuts, Mongols, and Central Asian (Kazakh, Kyrgyz, Uighur) populations. Yakuts proved to share 21 (55.5%) mtDNA haplotypes with the Central Asian ethnic groups and Mongols. Comparisons with modern Paleoasian populations (Chukcha, Itelmen, Koryaks) revealed three (8.9%) haplotypes common for Yakuts and Koryaks. The results of mtDNA analysis disagree with the hypothesis of an appreciable Paleoasian contribution to the modern Yakut gene pool.<br /><br /><a href="http://evolutsioon.ut.ee/publications/Fedorova2003.pdf">PDF file</a><br /><br /><strong>Mitochondrial DNA evidence for admixed origins of central Siberian populations</strong><br /><br />The Yakuts of northeastern Siberia are a Turkic-speaking population of horse- and cattle-breeders surrounded by Tungusic-speaking reindeer-herders and hunter-gatherers. Archaeological and ethnohistorical data suggest that Yakuts stem from a common ancestral population with the Buryats living near Lake Baikal. To address this hypothesis, we obtained sequences of the first hypervariable segment (HV1) of the mitochondrial DNA control region from Yakuts and Buryats and compared these with sequences from other Eurasian populations. The mtDNA results show that the Buryats have close affinities with both Central Asian Turkic groups and Mongols, while the Yakuts have close affinities with northeastern Siberian, Tungusic-speaking Evenks and south Siberian, Turkic-speaking Tuvans. This different ancestry of the Yakuts and the Tuvans (compared with other Turkic-speaking groups) most likely reflects extensive admixture that occurred between Turkic-speaking steppe groups and Evenks as the former migrated into Siberia. Moreover, the Yakuts are unique among Siberian populations in having a high number of haplotypes shared exclusively with Europeans, suggesting, contrary to the historical record, that occasionally Yakut men took Russian women as wives.<br /><br /><a href="http://www.eva.mpg.de/genetics/pdf/Pakendorf.AJPA.2003.pdf">PDF file</a><br /><br /><strong>Investigating the effects of prehistoric migrations in Siberia: genetic variation and the origins of Yakuts</strong><br /><br />The Yakuts (also known as Sakha), Turkic-speaking cattle- and horse-breeders, inhabit a vast territory in Central and northeastern Siberia. On the basis of the archaeological, ethnographic and linguistic evidence, they are assumed to have migrated north from their original area of settlement in the vicinity of Lake Baykal in South Siberia under the pressure of the Mongol expansion during the thirteenth to fifteenth century AD. During their initial migration and subsequent expansion, the ancestors of the Yakuts settled in the territory originally occupied by Tungusic- and Uralic-speaking reindeer-herders and hunters. In this paper we use mtDNA and Y-chromosomal analyses to elucidate whether the Yakut immigration and expansion was accompanied by admixture with the indigenous populations of their new area of settlement or whether the Yakuts displaced the original inhabitants without intermarriage. The mtDNA results show a very close aYnity of the Yakuts with Central Asian and South Siberian groups, which conWrms their southern origin. There is no conclusive evidence for admixture with indigenous populations, though a small amount cannot be excluded on the basis of the mtDNA data alone. The Y-chromosomal results confirm previous findings of a very strong bottleneck in the Yakuts, the age of which is in good accordance with the hypothesis that the Yakuts migrated north under Mongol pressure. Furthermore, the genetic results show that the Yakuts are a very homogenous population, notwithstanding their current spread over a very large territory. This conWrms the historical accounts that they spread over their current area of settlement fairly recently.<br /><br /><a href="http://www.eva.mpg.de/genetics/pdf/Yakut_article_2006.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1084209670844572172006-10-17T15:52:00.000-04:002006-10-17T15:56:23.603-04:00<strong>An Indian Ancestry: a Key for Understanding Human Diversity in Europe and Beyond</strong><br /><br />A recent African origin of modern humans, although still disputed, is supported now by a majority of genetic studies. To address the question when and where very early diversification(s) of modern humans outside of Africa occurred, we concentrated on the investigation of maternal and paternal lineages of the extant populations of India, southern China, Caucasus, Anatolia and Europe. Through the analyses of about 1000 mtDNA genomes and 400 Y chromosomesfrom various locations in India we reached the following conclusions, relevant to the peopling of Europe in particular and of the Old World in general. First, we found that the node of the phylogenetic tree of mtDNA, ancestral to more than 90 per cent of the present-day typically European maternal lineages, is present in India at a relatively high frequency. Inferred coalescence time of this ancestral node is slightly above 50,000 BP. Second, we found that haplogroup U is the second most abundant mtDNA variety in India as it is in Europe. Summing up, we believe that there are now enough reasons not only to question a 'recent Indo-Aryan invasion' into India some 4000 BP, but alternatively to consider India as a part of the common gene pool ancestral to the diversity of human maternal lineages in Europe. Our results on Y-chromosomal diversity of various Indian populations support an early split between Indian and east of Indian paternal lineages, while on a surface, Indian (Sanskrit as well as Dravidic speakers) and European Y-chromosomal lineages are much closer than the corresponding mtDNA variants.<br /><br /><a href="http://evolutsioon.ut.ee/publications/Kivisild2000.pdf">PDF file</a><br /><br /><strong>Influence of language and ancestry on genetic structure of contiguous populations: A microsatellite based study on populations of Orissa</strong><br /><br /><strong>Background</strong>: We have examined genetic diversity at fifteen autosomal microsatellite loci in seven predominant populations of Orissa to decipher whether populations inhabiting the same geographic region can be differentiated on the basis of language or ancestry. The studied populations have diverse historical accounts of their origin, belong to two major ethnic groups and different linguistic families. Caucasoid caste populations are speakers of Indo-European language and comprise Brahmins, Khandayat, Karan and Gope, while the three Australoid tribal populations include two Austric speakers: Juang and Saora and a Dravidian speaking population, Paroja. These divergent groups provide a varied substratum for understanding variation of genetic patterns in a geographical area resulting from differential admixture between migrants groups and aboriginals, and the influence of this admixture on population stratification.<br /><br /><strong>Results</strong>: The allele distribution pattern showed uniformity in the studied groups with approximately 81% genetic variability within populations. The coefficient of gene differentiation was found to be significantly higher in tribes (0.014) than caste groups (0.004). Genetic variance between the groups was 0.34% in both ethnic and linguistic clusters and statistically significant only in the ethnic apportionment. Although the populations were genetically close (FST = 0.010), the contemporary caste and tribal groups formed distinct clusters in both Principal-Component plot and Neighbor-Joining tree. In the phylogenetic tree, the Orissa Brahmins showed close affinity to populations of North India, while Khandayat and Gope clustered with the tribal groups, suggesting a possibility of their origin from indigenous people.<br /><br /><strong>Conclusions</strong>: The extent of genetic differentiation in the contemporary caste and tribal groups of Orissa is highly significant and constitutes two distinct genetic clusters. Based on our observations, we suggest that since genetic distances and coefficient of gene differentiation were fairly small, the studied populations are indeed genetically similar and that the genetic structure of populations in a geographical region is primarily influenced by their ancestry and not by socio-cultural hierarchy or language. The scenario of genetic structure, however, might be different for other regions of the subcontinent where populations have more similar ethnic and linguistic backgrounds and there might be variations in the patterns of genomic and socio-cultural affinities in different geographical regions.<br /><br /><a href="http://www.biomedcentral.com/content/pdf/1471-2156-6-4.pdf">PDF file</a><br /><br /><strong>Molecular insight into the genesis of ranked caste populations of western India based upon polymorphisms across nonrecombinant and recombinant regions in genome</strong><br /><br /><em>Background</em><br /> <br />Large-scale trade and cultural contacts between coastal populations of western India and Western-Eurasians paved for extensive immigration and genesis of wide spectrum of admixed gene pool. To trace admixture and genesis of caste populations of western India, we have examined polymorphisms across non-recombining 20 Y-SNPs, 20 Y-STRs, 18 mtDNA diagnostic sites, HVS-1 plus HVS-2 regions; and recombining 15 highly polymorphic autosomal STRs in four predominant caste populations- upper-ranking Desasth-brahmin and Chitpavan-brahmin; a middle-ranking Kshtriya Maratha; and a lower-rank peasant Dhangar.<br /><br /><em>Results</em><br /> <br />The generated genomic data was compared with putative parental populations- Central Asians, West Asians and Europeans using AMOVA, PC plot, and admixture estimates. Overall, disparate uniparental ancestries, and l.1% GST value for biparental markers among four studied caste populations linked well with their exchequer demographic histories. Marathi-speaking ancient Desasth-brahmin shows substantial admixture from Central Asian males but Paleolithic maternal component support their Scytho-Dravidian origin. Chitpavanbrahmin demonstrates younger maternal component and substantial paternal gene flow from West Asia, thus giving credence to their recent Irano-Scythian ancestry from Mediterranean or Turkey, which correlated well with European-looking features of this caste. This also explains their untraceable ethno-history before 1000 years, brahminization event and later amalgamation by Maratha. The widespread Palaeolithic mtDNA haplogroups in Maratha and Dhangar highlight their shared Proto-Asian ancestries. Maratha males harboured Anatolian-derived J2 lineage corroborating the blending of farming communities. Dhangar heterogeneity is ascribable to predominantly South-Asian males and West-Eurasian females.<br /><br /><em>Conclusions</em><br /> <br />The genomic data-sets of this study provide ample genomic evidences of diverse origins of four ranked castes and synchronization of caste stratification with asymmetrical gene flows from Indo-European migration during Upper Paleolithic, Neolithic, and later dates. However, subsequent gene flows among these castes living in geographical proximity, have diminished significant genetic differentiation as indicated by AMOVA and structure.<br /><br /><a href="http://kelkar.net/images/Irano-Scythian%20Ancestry%20of%20Chitpavans.pdf">PDF file</a><br /><br /><strong>Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA</strong><br /><br /><em>Background</em>:<br />India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations.<br /><br /><em>Results</em>:<br />No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes.<br /><br /><em>Conclusion</em>: <br />The present study suggests that the vast majority (>98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.<br /><br /><a href="http://www.biomedcentral.com/content/pdf/1471-2156-7-42.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1083866069702923062006-10-17T15:38:00.000-04:002006-10-17T15:41:36.666-04:00<strong>Genetic demography of Antioquia (Colombia) and the Central Valley of Costa Rica</strong><br /><br />We report a comparative genetic characterization of two population isolates with parallel demographic histories: the Central Valley of Costa Rica (CVCR) and Antioquia (in northwest Colombia). The analysis of mtDNA, Y-chromosome and autosomal polymorphisms shows that Antioquia and the CVCR are genetically very similar, indicating that closely related parental populations founded these two isolates. In both populations, the male ancestry is predominantly European, whereas the female ancestry is mostly Amerind. In agreement with their isolation, the Amerindian mtDNA diversity of Antioquia and the CVCR is typical of ethnically-defined native populations and is markedly lower than in other Latin American populations. A comparison of linkage disequilibrium (LD) at 18 marker pairs in Antioquia and the CVCR shows that markers in LD in both populations are located at short genetic distances (<~1 cM), whereas markers separated by greater distances are in LD only in the CVCR. This difference probably reflects stochastic variation of LD at the limited number of genome regions compared. The genetic similarity of the populations from Antioquia and the CVCR together with differences in LD between them should be exploitable for the identification and fine mapping of shared disease-related gene variants.<br /><br /><a href="http://www.ucl.ac.uk/~ucbtarl/HG.pdf">PDF file</a><br /><br /><strong>The Evolution and Genetics of Latin American Populations</strong><br /><br /><a href="http://assets.cambridge.org/052165/2758/sample/0521652758ws.pdf">PDF file</a><br /><br /><strong>Demography, genetic diversity, and population relationships among Argentinean Mapuche Indians</strong><br /><br />Fertility, mortality and migration data from four Mapuche Indian communities located along a 215-km NE-SW linear area in the Province of Río Negro, Argentina, were collated with genetic information furnished by nine blood group systems and by mtDNA haplogroups. The demographic and genetic data indicated a clear dichotomy, which split the four populations into two groups of two. Differing degrees of non-Indian exchanges was probably the main determining factor for this separation. Total genetic variability was very similar in all groups, and the interpopulational variability accounted for only 10% of the total variability. A low prevalence of the Diego(a) antigen among the Mapuche was confirmed. The fact that significant genetic heterogeneity and population clusters were found in such a small territorial region attests to the sensitivity of demographic and genetic approaches in unraveling human history.<br /><br /><a href="http://www.scielo.br/pdf/gmb/v23n3/4340.pdf">PDF file</a><br /><br /><strong>Admixture dynamics in Hispanics: A shift in the nuclear genetic ancestry of a South American population isolate</strong><br /><br />Although it is well established that Hispanics generally have a mixed Native American, African, and European ancestry, the dynamics of admixture at the foundation of Hispanic populations is heterogeneous and poorly documented. Genetic analyses are potentially very informative for probing the early demographic history of these populations. Here we evaluate the genetic structure and admixture dynamics of a province in northwest Colombia (Antioquia), which prior analyses indicate was founded mostly by Spanish men and native women. We examined surname, Y chromosome, and mtDNA diversity in a geographically structured sample of the region and obtained admixture estimates with highly informative autosomal and X chromosome markers. We found evidence of reduced surname diversity and support for the introduction of several common surnames by single founders, consistent with the isolation of Antioquia after the colonial period. Y chromosome and mtDNA data indicate little population substructure among founder Antioquian municipalities. Interestingly, despite a nearly complete Native American mtDNA background, Antioquia has a markedly predominant European ancestry at the autosomal and X chromosome level, which suggests that, after foundation, continuing admixture with Spanish men (but not with native women) increased the European nuclear ancestry of Antioquia. This scenario is consistent with historical information and with results from population genetics theory.<br /><br /><a href="http://www.pnas.org/cgi/reprint/103/19/7234.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1084551924941182892006-09-01T15:54:00.000-04:002006-09-01T15:58:11.283-04:00<strong>Genetic Isolates in East Asia: A Study of Linkage Disequilibrium in the X Chromosome</strong><br /><br />The background linkage disequilibrium (LD) in genetic isolates is of great interest in human genetics. Although many empirical studies have evaluated the background LD in European isolates, such as the Finnish and Sardinians, few data from other regions, such as Asia, have been reported. To evaluate the extent of background LD in East Asian genetic isolates, we analyzed the X chromosome in the Japanese population and in four Mongolian populations (Khalkh, Khoton, Uriankhai, and Zakhchin), the demographic histories of which are quite different from one another. Fisher’s exact test revealed that the Japanese and Khalkh, which are the expanded populations, had the same or a relatively higher level of LD than did the Finnish, European American, and Sardinian populations. In contrast, the Khoton, Uriankhai, and Zakhchin populations, which have kept their population size constant, had a higher background LD. These results were consistent with previous genetic anthropological studies in European isolates and indicate that the Japanese and Khalkh populations could be utilized in the fine mapping of both complex and monogenic diseases, whereas the Khoton, Uriankhai, and Zakhchin populations could play an important role in the initial mapping of complex disease genes.<br /><br /><a href="http://www.journals.uchicago.edu/AJHG/journal/issues/v71n2/023881/023881.web.pdf">PDF file</a><br /><br /><strong>Male Demography in East Asia: A North–South Contrast in Human Population Expansion Times</strong><br /><br />The human population has increased greatly in size in the last 100,000 years, but the initial stimuli to growth, the times when expansion started, and their variation between different parts of the world are poorly understood. We have investigated male demography in East Asia, applying a Bayesian full-likelihood analysis to data from 988 men representing 27 populations from China, Mongolia, Korea, and Japan typed with 45 binary and 16 STR markers from the Y chromosome. According to our analysis, the northern populations examined all started to expand in number between 34 (18-68) and 22 (12-39) thousand years ago (KYA), before the last glacial maximum at 21-18 KYA, while the southern populations all started to expand between 18 (6-47) and 12 (1-45) KYA, but then grew faster. We suggest that the northern populations expanded earlier because they could exploit the abundant megafauna of the "Mammoth Steppe," while the southern populations could increase in number only when a warmer and more stable climate led to more plentiful plant resources such as tubers.<br /><br /><a href="http://www.genetics.org/cgi/reprint/172/4/2431.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1084204100596143832006-09-01T15:40:00.000-04:002006-09-01T15:44:16.770-04:00<strong>Mitochondrial DNA Variation and the Origins of the Aleuts</strong><br /><br />The mitochondrial DNA (mtDNA) variation in 179 Aleuts from<br />five different islands (Atka, Unalaska, Umnak, St. Paul, and St. George) and Anchorage was analyzed to better understand the origins of Aleuts and their role in the peopling of the Americas. Mitochondrial DNA samples were characterized using polymerase chain reaction amplification, restriction fragment length polymorphism analysis, and direct sequencing of the first hypervariable segment (HVS-I) of the control region. This study showed that Aleut mtDNAs belonged to two of the four haplogroups (A and D) common among Native Americans. Haplogroup D occurred at a very high frequency in Aleuts, and this, along with their unique HVS-I sequences, distinguished them from Eskimos, Athapaskan Indians, and other northern Amerindian populations. While sharing several control region sequences (CIR11, CHU14, CIR60, and CIR61) with other circumarctic populations, Aleuts lacked haplogroup A mtDNAs having the 16265G mutation that are specific to Eskimo populations. R-matrix and median network analyses indicated that Aleuts were closest genetically to Chukotkan (Chukchi and Siberian Eskimos) rather than to Native American or Kamchatkan populations (Koryaks and Itel’men). Dating of the Beringian branch of haplogroup A (16192T) suggested that populations ancestral to the Aleuts, Eskimos, and Athapaskan Indians emerged approximately 13,120 years ago, while Aleut-specific A and D sublineages were dated at 6539 ± 3511 and 6035 ± 2885 years, respectively. Our findings support the archaeologically based hypothesis that ancestral Aleuts crossed the Bering Land Bridge or Beringian platform and entered the Aleutian Islands from the east, rather than island hopping from Kamchatka into the western Aleutians. Furthermore, the Aleut migration most likely represents a separate event from those responsible for peopling the remainder of the Americas, meaning that the New World was colonized through multiple migrations.<br /><br /><a href="http://www.ku.edu/~lba/75.6rubicz.pdf">PDF file</a><br /><br /><strong>Analysis of Mitochondrial DNA Diversity in the Aleuts of the Commander Islands and Its Implications for the Genetic History of Beringia</strong><br /><br />The Aleuts are aboriginal inhabitants of the Aleutian archipelago, including Bering and Copper (Medny) Islands of the Commanders, and seem to be the survivors of the inhabitants of the southern belt of the Bering Land Bridge that connected Chukotka/Kamchatka and Alaska during the end of the Ice Age. Thirty mtDNA samples collected in the Commanders, as well as seven mtDNA samples from Sireniki Eskimos in Chukotka who belong to the Beringian-specific subhaplogroup D2, were studied through complete sequencing. This analysis has provided evidence that all 37 of these mtDNAs are closely related, since they share the founding haplotype for subhaplogroup D2. We also demonstrated that, unlike the Eskimos and Na-Dene, the Aleuts of the Commanders were founded by a single lineage of haplogroup D2, which had acquired the novel transversion mutation 8910A. The phylogeny of haplogroup D complete sequences showed that (1) the D2 root sequence type originated among the latest inhabitants of Beringia and (2) the Aleut 8910A sublineage of D2 is a part of larger radiation of rooted D2, which gave rise to D2a (Na-Dene), D2b (Aleut), and D2c (Eskimo) sublineages. The geographic specificity and remarkable intrinsic diversity of D2 lineages support the refugial hypothesis, which assumes that the founding population of Eskimo-Aleut originated in Beringan/southwestern Alaskan refugia during the early postglacial period, rather than having reached the shores of Alaska as the result of recent wave of migration from interior Siberia.<br /><br /><a href="http://www.journals.uchicago.edu/AJHG/journal/issues/v71n2/023874/023874.web.pdf">PDF file</a><br /><br /><strong>Genetic Structure of the Aleuts and Circumpolar Populations Based on Mitochondrial DNA Sequences: A Synthesis</strong><br /><br />The mtDNA variation of 198 Aleuts, as well as North American and Asian populations drawn from the literature, were analyzed to reconstruct the Aleuts' genetic prehistory and to investigate their role in the peopling of the Circumarctic region. From median-joining network analysis, three star-like clusters were identified in the Aleuts within the following subhaplogroups: A3, A7 (an Aleut-specific subclade of A3), and D2. Mismatch analyses, neutrality test scores, and coalescent time estimates for these three components provided evidence of two expansion events, one occurring at approximately 19,900 B.P. and the other at 5,400 B.P. Based on these findings and evidence from the archaeological data, four general models for the genetic prehistory of the Aleutian Island chain are proposed: 1) biological continuity involving a kin-structured peopling of the archipelago; 2) intrusion and expansion of a non-native biface-producing population dominated by subhaplogroup D2; 3) amalgamation of Arctic Small Tool tradition peoples characterized by D2 with an older Anangula substratum; and 4) biological continuity with significant gene flow from neighboring populations of the Alaskan mainland and Kodiak Island. The Aleut mtDNAs are consistent with the Circumarctic pattern by the fixation of A3 and D2, and the exhibition of depressed diversity levels relative to Amerind and Siberian groups. The results of this study indicate a broad postglacial reexpansion of Na-Dene and Esko-Aleuts from reduced populations within northern North America, with D2 representing a later infusion of Siberian mtDNAs into the Beringian gene pool.<br /><br /><a href="http://www2.ku.edu/~lba/Publications/PDF%20files/Zlojutro%20Aleut%202006.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.comtag:blogger.com,1999:blog-6629217.post-1082655776905641372006-08-22T10:01:00.000-04:002006-08-22T10:05:42.976-04:00<strong>Jewish and Middle Eastern non-Jewish populations share a common pool of Y-chromosome biallelic haplotypes</strong><br /><br />Haplotypes constructed from Y-chromosome markers were used to trace the paternal origins of the Jewish Diaspora. A set of 18 biallelic polymorphisms was genotyped in 1,371 males from 29 populations, including 7 Jewish (Ashkenazi, Roman, North African, Kurdish, Near Eastern, Yemenite, and Ethiopian) and 16 non-Jewish groups from similar geographic locations. The Jewish populations were characterized by a diverse set of 13 haplotypes that were also present in non-Jewish populations from Africa, Asia, and Europe. A series of analyses was performed to address whether modern Jewish Y-chromosome diversity derives mainly from a common Middle Eastern source population or from admixture with neighboring non-Jewish populations during and after the Diaspora. Despite their long-term residence in different countries and isolation from one another, most Jewish populations were not significantly different from one another at the genetic level. Admixture estimates suggested low levels of European Y-chromosome gene flow into Ashkenazi and Roman Jewish communities. A multidimensional scaling plot placed six of the seven Jewish populations in a relatively tight cluster that was interspersed with Middle Eastern non-Jewish populations, including Palestinians and Syrians. Pairwise differentiation tests further indicated that these Jewish and Middle Eastern non-Jewish populations were not statistically different. The results support the hypothesis that the paternal gene pools of Jewish communities from Europe, North Africa, and the Middle East descended from a common Middle Eastern ancestral population, and suggest that most Jewish communities have remained relatively isolated from neighboring non-Jewish communities during and after the Diaspora.<br /><br /><a href="http://www.familytreedna.com/pdf/HammerPNAS_2000.pdf">PDF file</a><br /><br /><strong>Y chromosome evidence for a founder effect in Ashkenazi Jews</strong><br /><br />Recent genetic studies, based on Y chromosome polymorphic markers, showed that Ashkenazi Jews are more closely related to other Jewish and Middle Eastern groups than to their host populations in Europe. However, Ashkenazim have an elevated frequency of R-M17, the dominant Y chromosome haplogroup in Eastern Europeans, suggesting possible gene flow. In the present study of 495 Y chromosomes of Ashkenazim, 57 (11.5%) were found to belong to R-M17. Detailed analyses of haplotype structure, diversity and geographic distribution suggest a founder effect for this haplogroup, introduced at an early stage into the evolving Ashkenazi community in Europe. R-M17 chromosomes in Ashkenazim may represent vestiges of the mysterious Khazars.<br /><br /><a href="http://bioanthropology.huji.ac.il/pdf/Nebel%20_2005.pdf">PDF file</a><br /><br /><strong>MtDNA and Y-chromosome Variation in Kurdish Groups</strong><br /><br />In order to investigate the origins and relationships of Kurdish-speaking groups, mtDNA HV1 sequences, eleven Y chromosome bi-allelic markers, and 9 Y-STR loci were analyzed among three Kurdish groups: Zazaki and Kurmanji speakers from Turkey, and Kurmanji speakers from Georgia. When compared with published data from other Kurdish groups and from European, Caucasian, and West and Central Asian groups, Kurdish groups are most similar genetically to other West Asian groups, and most distant from Central Asian groups, for both mtDNA and the Y-chromosome. However, Kurdish groups show a closer relationship with European groups than with Caucasian groups based on mtDNA, but the opposite based on the Y-chromosome, indicating some differences in their maternal and paternal histories. The genetic data indicate that the Georgian Kurdish group experienced a bottleneck effect during their migration to the Caucasus, and that they have not had detectable admixture with their geographic neighbours in Georgia. Our results also do not support the hypothesis of the origin of the Zazaki –speaking group being in northern Iran; genetically they are more similar to other Kurdish groups. Genetic analyses of recent events, such as the origins and migrations of Kurdish-speaking groups, can therefore lead to new insights into such migrations.<br /><br /><a href="http://www.eva.mpg.de/genetics/pdf/Kurds.pdf">PDF file</a><br /><br /><strong>The Matrilineal Ancestry of Ashkenazi Jewry: Portrait of a Recent Founder Event</strong><br /><br />Both the extent and location of the maternal ancestral deme from which the Ashkenazi Jewry arose remain obscure. Here, using complete sequences of the maternally inherited mitochondrial DNA (mtDNA), we show that close to one-half of Ashkenazi Jews, estimated at 8,000,000 people, can be traced back to only 4 women carrying distinct mtDNAs that are virtually absent in other populations, with the important exception of low frequencies among non-Ashkenazi Jews. We conclude that four founding mtDNAs, likely of Near Eastern ancestry, underwent major expansion(s) in Europe within the past millennium.<br /><br /><a href="http://www.familytreedna.com/pdf/43026_Doron.pdf">PDF file</a><br /><br /><strong>LRRK2 G2019S in Families with Parkinson Disease Who Originated from Europe and the Middle East: Evidence of Two Distinct Founding Events Beginning Two Millennia Ago</strong><br /><br />The leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common genetic determinant of Parkinson disease (PD) identified to date. It accounts for 1%–7% of PD in patients of European origin and 20%–40% in Ashkenazi Jews and North African Arabs with PD. Previous studies concluded that patients from these populations all shared a common Middle Eastern founder who lived in the 13th century. We tested this hypothesis by genotyping 25 microsatellite and single-nucleotide–polymorphism markers in 22 families with G2019S and observed two distinct haplotypes. Haplotype 1 was present in 19 families of Ashkenazi Jewish and European ancestry, whereas haplotype 2 occurred in three European American families. Using a maximum-likelihood method, we estimated that the families with haplotype 1 shared a common ancestor 2,250 (95% confidence interval 1,650–3,120) years ago, whereas those with haplotype 2 appeared to share a more recent founder. Our data suggest two separate founding events for G2019S in these populations, beginning at a time that coincides with the Jewish Diasporas.<br /><br /><a href="http://vetinari.sitesled.com/parkin.pdf">PDF file</a>Havelockhttp://www.blogger.com/profile/14363919136262782693noreply@blogger.com