A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes

The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a non-uniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity, which appears to be partially related to the geography. In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population and geographic structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo–speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y-chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon.

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The T Allele of a Single-Nucleotide Polymorphism 13.9 kb Upstream of the Lactase Gene (LCT) (C513.9kbT) Does Not Predict or Cause the Lactase-Persistence Phenotype in Africans

The ability to digest the milk sugar lactose as an adult (lactase persistence) is a variable genetic trait in human populations. The lactase-persistence phenotype is found at low frequencies in the majority of populations in sub-Saharan Africa that have been tested, but, in some populations, particularly pastoral groups, it is significantly more frequent. Recently, a CT polymorphism located 13.9 kb upstream of exon 1 of the lactase gene (LCT) was shown in a Finnish population to be closely associated with the lactase-persistence phenotype (Enattah et al. 2002). We typed this polymorphism in 1,671 individuals from 20 distinct cultural groups in seven African countries. It was possible to match seven of the groups tested with groups from the literature for whom phenotypic information is available. In five of these groups, the published frequencies of lactase persistence are equal or greater than 25%. We found the T allele to be so rare that it cannot explain the frequency of the lactase-persistence phenotype throughout Africa. By use of a statistical procedure to take phenotyping and sampling errors into account, the T-allele frequency was shown to be significantly different from that predicted in five of the African groups. Only the Fulbe and Hausa from Cameroon possessed the T allele at a level consistent with phenotypic observations (as well as an Irish sample used for comparison). We conclude that the C513.9kbT polymorphism is not a predictor of lactase persistence in sub-Saharan Africans. We also present Y-chromosome data that are consistent with previously reported evidence for a back-migration event into Cameroon, and we comment on the implications for the introgression of the 513.9kb*T allele.

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African Y Chromosome and mtDNA Divergence Provides Insight into the History of Click Languages

Background: About 30 languages of southern Africa, spoken by Khwe and San, are characterized by a repertoire of click consonants and phonetic accompaniments. The Jumid R:'hoansi (!Kung) San carry multiple deeply coalescing gene lineages. The deep genetic diversity of the San parallels the diversity among the languages they speak. Intriguingly, the language of the Hadzabe of eastern Africa, although not closely related to any other language, shares click consonants and accompaniments with languages of Khwe and San.

Results: We present original Y chromosome and mtDNA variation of Hadzabe and other ethnic groups of Tanzania and Y chromosome variation of San and peoples of the central African forests: Biaka, Mbuti, and Lisongo. In the context of comparable published data for other African populations, analyses of each of these independently inherited DNA segments indicate that click-speaking Hadzabe and Jumid R:'hoansi are separated by genetic distance as great or greater than that between any other pair of African populations. Phylogenetic tree topology indicates a basal separation of the ancient ancestors of these click-speaking peoples. That genetic divergence does not appear to be the result of recent gene flow from neighboring groups.

Conclusions: The deep genetic divergence among click-speaking peoples of Africa and mounting linguistic evidence suggest that click consonants date to early in the history of modern humans. At least two explanations remain viable. Clicks may have persisted for tens of thousands of years, independently in multiple populations, as a neutral trait. Alternatively, clicks may have been retained, because they confer an advantage during hunting in certain environments.

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Supplementary Material

A Walk in the Garden of Eden: Genetic Trails into our African Past

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Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan

A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.

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Where West Meets East: The Complex mtDNA Landscape of the Southwest and Central Asian Corridor

The southwestern and Central Asian corridor has played a pivotal role in the history of humankind, witnessing numerous waves of migration of different peoples at different times. To evaluate the effects of these population movements on the current genetic landscape of the Iranian plateau, the Indus Valley, and Central Asia, we have analyzed 910 mitochondrial DNAs (mtDNAs) from 23 populations of the region. This study has allowed a re-finement of the phylogenetic relationships of some lineages and the identification of new haplogroups in the southwestern and Central Asian mtDNA tree. Both lineage geographical distribution and spatial analysis of molecular variance showed that populations located west of the Indus Valley mainly harbor mtDNAs of western Eurasian origin, whereas those inhabiting the Indo-Gangetic region and Central Asia present substantial proportions of lineages that can be allocated to three different genetic components of western Eurasian, eastern Eurasian, and south Asian origin. In addition to the overall composite picture of lineage clusters of different origin, we observed a number of deep-rooting lineages, whose relative clustering and coalescent ages suggest an autochthonous origin in the southwestern Asian corridor during the Pleistocene. The comparison with Y-chromosome data revealed a highly complex genetic and demographic history of the region, which includes sexually asymmetrical mating patterns, founder effects, and female-specific traces of the East African slave trade.

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Investigation of the mitochondrial haplogroups M, BM, N, J, K and their frequencies in five regions in Iran

The frequencies of the Asian (M, BM) and European (N, J, K) mtDNA haplogroups in five major regions of Iran was investigated. Unexpectedly, the frequencies of the Asian haplogroups M and BM were low in Iran (2.34% for haplogroup M; 17.6% for haplogroup BM and 80.06% for haplogroup N). Almost identical frequencies for haplogroups J and K were found in the present study (10.81% and 10.14% for haplogroups J and K, respectively). On the other hand, the frequencies of haplogroups M and BM in Eastern regions were more than their frequencies in Western regions of the country. In contrast, the frequencies of haplogroups J and K in Western regions were more than their frequencies in Eastern regions of Iran. As a result, this study gives evidence for similarity between Iranian population ethnic groups and people from Northwest Asia and Southeast Europe. Our data suggest that Iranian tribes probably played a remarkable role in the formation of these ethnic groups. It gives the indication that the haplogroup J may be older than 6000-10000 years, and probably developed in Iran, and then expanded to different regions in Europe and Northwest Asia. On the other hand, it seems that the super-haplogroup M has developed after the inhabitants of Iran moved to Eastern Asia or this group migrated from Southern Iran/North of Arabian halve O to Pakistan and then to Asia.

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Concomitant Replacement of Language and mtDNA in South Caspian Populations of Iran

The Gilaki and Mazandarani occupy the South Caspian region of Iran and speak languages belonging to the North-Western branch of Iranian languages. It has been suggested that their ancestors came from the Caucasus region, perhaps displacing an earlier group in the South Caspian. Linguistic evidence supports this scenario, in that the Gilaki and Mazandarani languages (but not other Iranian languages) share certain typological features with Caucasian languages. We analyzed patterns of mtDNA and Y chromosome variation in the Gilaki and Mazandarani. Based on mtDNA HV1 sequences, the Gilaki and Mazandarani most closely resemble their geographic and linguistic neighbors, namely other Iranian groups. However, their Y chromosome types most closely resemble those found in groups from the South Caucasus. A scenario that explains these differences is a south Caucasian origin for the ancestors of the Gilaki and Mazandarani, followed by introgression of women (but not men) from local Iranian groups, possibly because of patrilocality. Given that both mtDNA and language are maternally transmitted, the incorporation of local Iranian women would have resulted in the concomitant replacement of the ancestral Caucasian language and mtDNA types of the Gilaki and Mazandarani with their current Iranian language and mtDNA types. Concomitant replacement of language and mtDNA may be a more general phenomenon than previously recognized.

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Tracing European Founder Lineages in the Near Eastern mtDNA Pool

Founder analysis is a method for analysis of non-recombining DNA sequence data, with the aim of identification and dating of migrations into new territory. The method picks out founder sequence types in potential source populations and dates lineage clusters deriving from them in the settlement zone of interest. Here, using mtDNA, we apply the approach to the colonization of Europe, to estimate the proportion of modern lineages whose ancestors arrived during each major phase of settlement. To estimate the Palaeolithic and Neolithic contributions to European mtDNA diversity more accurately than was previously achievable, we have now extended the Near Eastern, European, and northern-Caucasus databases to 1,234, 2,804, and 208 samples, respectively. Both back-migration into the source population and recurrent mutation in the source and derived populations represent major obstacles to this approach. We have developed phylogenetic criteria to take account of both these factors, and we suggest a way to account for multiple dispersals of common sequence types. We conclude that (i) there has been substantial back-migration into the Near East, (ii) the majority of extant mtDNA lineages entered Europe in several waves during the Upper Palaeolithic, (iii) there was a founder effect or bottleneck associated with the Last Glacial Maximum, 20,000 years ago, from which derives the largest fraction of surviving lineages, and (iv) the immigrant Neolithic component is likely to comprise less than one-quarter of the mtDNA pool of modern Europeans.

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Phylogeographic Analysis of Mitochondrial DNA in the Nogays: A Strong Mixture of Maternal Lineages from Eastern and Western Eurasia

Analysis of mtDNA markers in a population of the Nogays (n = 206), the people inhabiting the North Caucasus and speaking a Turkic language of the Altaic linguistic family, has revealed a high level of genetic diversity (H = 0.99). The identified haplotypes include all major West Eurasian haplogroups, with the prevalence of H and U clusters (22 and 21%, respectively), but the percentage of lineages specific for East Eurasian populations is the highest (40%). Some other mtDNA variants in the Nogay population belong to the M1 haplogroups typical of northeastern Africa and U2 characteristic of Indian populations. Thus, components of different origin have contributed to the gene pool of Nogays.

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Estimating the impact of prehistoric admixture on the genome of Europeans

We inferred past admixture processes in the European population from genetic diversity at eight loci, including autosomal, mitochondrial and Y-linked polymorphisms. Admixture coefficients were estimated from multilocus data, assuming that most current populations can be regarded as the result of a hybridization process among four or less potential parental populations. Two main components are apparent in the Europeans' genome, presumably corresponding to the contributions of the first, Paleolithic Europeans, and of the early, Neolithic farmers dispersing from the Near East. In addition, only a small fraction of the European alleles seems to come from North Africa, and a fourth component reflecting gene flow from Northern Asia is largely restricted to the northeast of the continent. The estimated Near Eastern contribution decreases as one moves from east to west, in agreement with the predictions of a model in which (Neolithic) immigrants from the Near East contributed a large share of the alleles in the genome of current Europeans. Several tests suggest that probable departures from the admixture models, due to factors such as choice of the putative parental populations and more complex demographic scenarios, may have affected our main estimates only to a limited extent.

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Effects of Purifying and Adaptive Selection on Regional Variation in Human mtDNA

A phylogenetic analysis of 1125 global human mitochondrial DNA (mtDNA) sequences permitted positioning of all nucleotide substitutions according to their order of occurrence. The relative frequency and amino acid conservation of internal branch replacement mutations was found to increase from tropical Africa to temperate Europe and arctic northeastern Siberia. Particularly highly conserved amino acid substitutions were found at the roots of multiple mtDNA lineages from higher latitudes. These same lineages correlate with increased propensity for energy deficiency diseases as well as longevity. Thus, specific mtDNA replacement mutations permitted our ancestors to adapt to more northern climates, and these same variants are influencing our health today.

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Positive Selection on MMP3 Regulation Has Shaped Heart Disease Risk

BACKGROUND: The evolutionary forces of mutation, natural selection, and genetic drift shape the pattern of phenotypic variation in nature, but the roles of these forces in defining the distributions of particular traits have been hard to disentangle. To better understand the mechanisms contributing to common variation in humans, we investigated the evolutionary history of a functional polymorphism in the upstream regulatory region of the MMP3 gene. This single base pair insertion/deletion variant, which results in a run of either 5 or 6 thymidines 1608 bp from the transcription start site, alters transcription factor binding and influences levels of MMP3 mRNA and protein. The polymorphism contributes to variation in arterial traits and to the risk of coronary heart disease and its progression.

RESULTS: Phylogenetic and population genetic analysis of primate sequences indicate that the binding site region is rapidly evolving and has been a hot spot for mutation for tens of millions of years. We also find evidence for the action of positive selection, beginning approximately 24,000 years ago, increasing the frequency of the high-expression allele in Europe but not elsewhere. Positive selection is evident in statistical tests of differentiation among populations and haplotype diversity within populations. Europeans have greater arterial elasticity and suffer dramatically fewer coronary heart disease events than they would have had this selection not occurred.

CONCLUSIONS: Locally elevated mutation rates and strong positive selection on a cis-regulatory variant have shaped contemporary phenotypic variation and public health.

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Different genetic components in the Norwegian population revealed by the analysis of mtDNA and Y chromosome polymorphisms

The genetic composition of the Norwegian population was investigated by analysing polymorphisms associated with both the mitochondrial DNA (mtDNA) and Y chromosome loci in a sample of 74 Norwegian males. The combination of their uniparental mode of inheritance and the absence of recombination make these haplotypic stretches of DNA the tools of choice in evaluating the different components of a population’s gene pool. The sequencing of the Dloop and two diagnostic RFLPs (AluI 7025 and HinfI at 12 308) allowed us to classify the mtDNA molecules in 10 previously described groups. As for the Y chromosome the combination of binary markers and microsatellites allowed us to compare our results to those obtained elsewhere in Europe. Both mtDNA and Y chromosome polymorphisms showed a noticeable genetic affinity between Norwegians and central Europeans, especially Germans. When the phylogeographic analysis of the Y chromosome haplotypes was attempted some interesting clues on the peopling of Norway emerged. Although Y chromosome binary and microsatellite data indicate that 80% of the haplotypes are closely related to Central and western Europeans, the remainder share a unique binary marker (M17) common in eastern Europeans with informative microsatellite haplotypes suggesting a different demographic history. Other minor genetic influences on the Norwegian population from Uralic speakers and Mediterranean populations were also highlighted.

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Geographical heterogeneity of Y-chromosomal lineages in Norway

Y-chromosomal variation at five biallelic markers (Tat, YAP, 12f2, SRY10831 and 92R7) and nine multiallelic short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II and DYS388) in a Norwegian population sample are presented. The material consists of 1766 unrelated males of Norwegian origin. The geographical distribution of the population sample reflects fairly well the population distribution around the year 1942, which is the median birth year of the index persons. Seven hundred and twenty-one different Y-STR haplotypes but 726 different lineages (Y-STRs plus biallelic markers) were encountered. We observed six known (P*(xR1a), BR(xDE, J, N3, P), R1a, N3, DE, J), and one previously undescribed haplogroup (probably a subgroup within haplogroup P*(xR1a)). Four of the haplogroups (P*(xR1a), BR(xDE, J, N3, P), R1a and N3) represented about 98% of the population sample. The analysis of population pairwise differences indicates that the Norwegian Y-chromosome distribution most closely resembles those observed in Iceland, Germany, the Netherlands and Denmark. Within Norway, geographical substructuring was observed between regions and counties. The substructuring reflects to some extent the European Y-chromosome gradients, with higher frequency of P*(xR1a) in the south-west and of R1a in the east. Heterogeneity in major founder groups, geographical isolation, severe epidemics, historical trading links and population movements may have led to population stratification and have most probably contributed to the observed regional differences in distribution of haplotypes within two of the major haplogroups.

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Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population

In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (Phi(ST)=-0.0008, P>0.5), a highly significant difference (Phi(ST)=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.

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Y Chromosome and Mitochondrial DNA Variation in Lithuanians

The genetic composition of the Lithuanian population was investigated by analysing mitochondrial DNA hypervariable region 1, RFLP polymorphisms and Y chromosomal biallelic and STR markers in six ethnolinguistic groups of Lithuanians, to address questions about the origin and genetic structure of the present day population. There were no significant genetic differences among ethnolinguistic groups, and an analysis of molecular variance confirmed the homogeneity of the Lithuanian population. MtDNA diversity revealed that Lithuanians are close to both Slavic (Indo-European) and Finno-Ugric speaking populations of Northern and Eastern Europe. Y-chromosome SNP haplogroup analysis showed Lithuanians to be closest to Latvians and Estonians. Significant differences between Lithuanian and Estonian Y chromosome STR haplotypes suggested that these populations have had different demographic histories. We suggest that the observed pattern of Y chromosome diversity in Lithuanians may be explained by a population bottleneck associated with Indo-European contact. Different Y chromosome STR distributions in Lithuanians and Estonians might be explained by different origins or, alternatively, be the result of some period of isolation and genetic drift after the population split.

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Mitochondrial DNA Sequence Analysis in the Lithuanian Population

Analysis of mitochondrial DNA (mtDNA) diversity has proved to be a useful tool in our understanding of the origin and history of human populations and also provided insights into the pathophysiology of mitochondrial disease. In order to investigate the genetic composition of the Lithuanian population, we have analysed mtDNA variation in 180 individuals from six Lithuanian ethnolinguistic subgroups. The sequencing of the first hypervariable segment (HV1) in the control region of the mtDNA and restriction fragment length polymorphism typing allowed us to classify mtDNA molecules to previously described haplogroups. This analysis revealed the presence of all major European mtDNA haplogroups (H, V, U, K, J, T, I, W, X) in the Lithuanian sample. Haplogroup H was the most common in Lithuanians, comprising 46% of all sequences. The frequencies of the rest haplogroups ranged from 1% to 20%. No significant differences, which could indicate influence of different Baltic tribes, were detected among ethnolinguistic subgroups of Lithuanians. The analysis of molecular variance (AMOVA) further confirmed the absence of internal genetic structuring in the Lithuanian population. Comparisons with other European populations demonstrated that the Lithuanian mtDNA gene pool is more closely related to the mtDNA gene pool of Northern European populations, while molecular diversity indices (gene diversity 0.971 ± 0.008, nucleotide diversity 0.012 ± 0.007 and the mean number of pairwise differences between sequences 4.41 ± 2.19) indicate that the Lithuanians are among the more diverse populations in Europe.

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The Balts and the Finns in historical perspective: a multidisciplinary approach

Introduction. Ethnic history of human populations is a too complicated phenomenon to elucidate it on the basis of several gene frequencies. It is obligatory to compile all data on molecular genetics and serology, to add new ones, to request services of paleopopulation comparisons, facts of anthropological odontology, craniology, and anthropology of the modern population of the area as well as linguistic and archaeological information. A multidisciplinary approach to elucidating historical relations between the Balts and the Finns is the goal of the present report. Materials and methods. Approx. 800 blood samples from Lithuania were examined in order to investigate Lithuanian population according to different genetic markers. Discrete cranial traits of 6,426 skulls from Lithuania and adjacent territories as well as 3,734 skulls belonging to the Neolithic, Bronze Age, 2,000 YBP and 1,000 YBP were investigated. We disposed of data on the ethnic odontology of 4,993 modern Lithuanians as well as of 1446 skulls dated to 2,000 YBP and 1,000 YBP. Results. Two separate clusters consisting consequently of four Baltic and two Finnish groups emerged in the dendrogram (Fig. 1).The mesocranial Mesolithic population in Lithuania might be related to the Middle-European kernel of mesocranes. The Middle-European orientation of the Neolithic and Bronze Age Lithuanian population is evident. The influx from the eastern part of the ancient Baltic area was detected in the 2,000 YBP population. The Lithuanian 1,000 YBP population was more homogeneous than the inhabitants of Latvia (Fig. 2). The Y chromosome haplogroups 1 and 9 show complementary clines from southeast to northwest of Europe, the Baltic peoples (Latvians and Lithuanians) demonstrating a mixture of western and eastern genetic traits (Fig. 3). In Northern Europe, strong geographical, linguistic and cultural barriers can be identified. Three main migration directions could have a real influence on the formation of the Lithuanian gene pool. Conclusions. Anthropological, archaeological and linguistic data demonstrate that there was no common ancestry of the Balts and the Finns. Genetic and phenetical similarities might occur due to gene exchange between adjacent populations on the northern and eastern borderlines of the ancient Baltic area that took place from the Mesolithic time. It is impossible to date the emergence of some genetic and anthropological similarities between the Balts and the Finns.

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Regional differences among the Finns: A Y-chromosomal perspective

Twenty-two Y-chromosomal markers, consisting of fourteen biallelic markers (YAP/DYS287, M170, M253, P37, M223, 12f2, M9, P43, Tat, 92R7, P36, SRY-1532, M17, P25) and eight STRs (DYS19, DYS385a/b, DYS388, DYS389I/II, DYS390, DYS391, DYS392, DYS393), were analyzed in 536 unrelated Finnish males from eastern and western subpopulations of Finland. The aim of the study was to analyze regional differences in genetic variation within the country, and to analyze the population history of the Finns. Our results gave further support to the existence of a sharp genetic border between eastern and western Finns so far observed exclusively in Y-chromosomal variation. Both biallelic haplogroup and STR haplotype networks showed bifurcated structures, and similar clustering was evident in haplogroup and haplotype frequencies and genetic distances. These results suggest that the western and eastern parts of the country have been subject to partly different population histories, which is also supported by earlier archaeological, historical and genetic data. It seems probable that early migrations from Finno-Ugric sources affected the whole country, whereas subsequent migrations from Scandinavia had an impact mainly on the western parts of the country. The contacts between Finland and neighboring Finno-Ugric, Scandinavian and Baltic regions are evident. However, there is no support for recent migrations from Siberia and Central Europe. Our results emphasize the importance of incorporating Y-chromosomal data to reveal the population substructure which is often left undetected in mitochondrial DNA variation. Early assumptions of the homogeneity of the isolated Finnish population have now proven to be false, which may also have implications for future association studies.

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