Genetic Chaos

Thursday, April 28, 2005

Y-Chromosome Lineages Trace Diffusion of People and Languages in Southwestern Asia

The origins and dispersal of farming and pastoral nomadism in southwestern Asia are complex, and there is controversy about whether they were associated with cultural transmission or demic diffusion. In addition, the spread of these technological innovations has been associated with the dispersal of Dravidian and Indo-Iranian languages in southwestern Asia. Here we present genetic evidence for the occurrence of two major population movements, supporting a model of demic diffusion of early farmers from southwestern Iran—and of pastoral nomads from western and central Asia—into India, associated with Dravidian and Indo-European–language dispersals, respectively.

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Genetic Evidence Concerning the Origins of South and North Ossetians

Ossetians are a unique group in the Caucasus, in that they are the only ethnic group found on both the north and south slopes of the Caucasus, and moreover they speak an Indo-European language in contrast to their Caucasian-speaking neighbours. We analyzed mtDNA HV1 sequences, Y chromosome binary genetic markers, and Y chromosome short tandem repeat (Y-STR) variability in three North Ossetian groups and compared these data to published data for two additional North Ossetian groups and for South Ossetians. The mtDNA data suggest a common origin for North and South Ossetians, whereas the Y-haplogroup data indicate that North Ossetians are more similar to other North Caucasian groups, and South Ossetians are more similar to other South Caucasian groups, than to each other. Also, with respect to mtDNA, Ossetians are significantly more similar to Iranian groups than to Caucasian groups. We suggest that a common origin of Ossetians from Iran, followed by subsequent male-mediated migrations from their Caucasian neighbours, is the most likely explanation for these results. Thus, genetic studies of such complex and multiple migrations as the Ossetians can provide additional insights into the circumstances surrounding such migrations.

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Thursday, April 14, 2005

Y Chromosomes Traveling South: The Cohen Modal Haplotype and the Origins of the Lemba-the "Black Jews of Southern Africa"

The Lemba are a traditionally endogamous group speaking a variety of Bantu languages who live in a number of locations in southern Africa. They claim descent from Jews who came to Africa from "Sena." "Sena" is variously identified by them as Sanaa in Yemen, Judea, Egypt, or Ethiopia. A previous study using Y-chromosome markers suggested both a Bantu and a Semitic contribution to the Lemba gene pool, a suggestion that is not inconsistent with Lemba oral tradition. To provide a more detailed picture of the Lemba paternal genetic heritage, we analyzed 399 Y chromosomes for six microsatellites and six biallelic markers in six populations (Lemba, Bantu, Yemeni-Hadramaut, Yemeni-Sena, Sephardic Jews, and Ashkenazic Jews). The high resolution afforded by the markers shows that Lemba Y chromosomes are clearly divided into Semitic and Bantu clades. Interestingly, one of the Lemba clans carries, at a very high frequency, a particular Y-chromosome type termed the "Cohen modal haplotype," which is known to be characteristic of the paternally inherited Jewish priesthood and is thought, more generally, to be a potential signature haplotype of Judaic origin. The Bantu Y-chromosome samples are predominantly (>80%) YAP+ and include a modal haplotype at high frequency. Assuming a rapid expansion of the eastern Bantu, we used variation in microsatellite alleles in YAP+ sY81-G Bantu Y chromosomes to calculate a rough date, 3,000-5,000 years before the present, for the start of their expansion.

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Tracking the genetic imprints of lost Jewish tribes among the gene pool of Kuki-Chin-Mizo population of India


The Kuki-Chin-Mizo population comprising traditionally endogamous tribal groups residing in the state of Mizoram, India claim their descent from the ten lost tribes of Israel that were exiled by the Assyrians. To ascertain their oral history, we analysed DNA markers comprising 15 autosomal microsatellite markers, 5 biallelic and 20 microsatellite markers on Y-chromosome and the maternally inherited mitochondrial DNA sequence variations on 414 individuals belonging to 5 tribal communities from Mizoram (Hmar, Kuki, Mara, Lai and Lusei). The genetic profiles obtained were compared either with populations sharing Jewish ancestry or with local populations along the probable route of migration of the Jewish ancestry claimant Mizoram tribes.


Y-STR analyses showed absence of the Cohen Modal Haplotype, the genetic signature of Cohanim origin. Y-chromosomal biallelic marker analyses revealed the presence of East and Southeast Asian-specific lineages and absence of haplogroup J predominant among Jewish populations. The mitochondrial DNA sequence analyses however revealed traces of genetic relatedness between the Jewish ancestry claimant Mizoram tribes and Near Eastern lineages. Autosomal analyses showed moderate degree of genetic differentiation among the different Mizoram tribes.


Migration of the lost tribes through China resulting in subsequent genetic admixture over a long period of time has probably diluted the extant gene pool of the Kuki-Chin-Mizo population. Although their paternal lineages do not exhibit any trace of Jewish ancestry, incidence of maternal Near Eastern lineages among the Mizoram tribals suggests their claim to Jewish ancestry cannot be excluded.

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Tuesday, April 12, 2005

A Y Chromosome Census of the British Isles

The degree of population replacement in the British Isles associated with cultural changes has been extensively debated. Recent work has demonstrated that comparisons of genetic variation in the British Isles and on the European Continent can illuminate specific demographic processes in the history of the British Isles. For example, Wilson et al. used the similarity of Basque and Celtic Y chromosomes to argue for genetic continuity from the Upper Palaeolithic to the present in the paternal history of these populations. Differences in the Y chromosome composition of these groups also suggested genetic signatures of Norwegian influence in the Orkney Islands north of the Scottish mainland, an important center of Viking activities between 800 and 1300 A.D. More recently, Weale et al. argued for substantial Anglo-Saxon male migration into central England based on the analysis of eight British sample sets collected on an east-west transect across England and Wales. To provide a more complete assessment of the paternal genetic history of the British Isles, we have compared the Y chromosome composition of multiple geographically distant British sample sets with collections from Norway (two sites), Denmark, and Germany and with collections from central Ireland, representing, respectively, the putative invading and the indigenous populations. By analyzing 1772 Y chromosomes from 25 predominantly small urban locations,we found that different parts of the British Isles have sharply different paternal histories; the degree of population replacement and genetic continuity shows systematic variation across the sampled areas.

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Supplemental material

Additional data

Y Chromosome Evidence for Anglo-Saxon Mass Migration

British history contains several periods of major cultural change. It remains controversial as to how much these periods coincided with substantial immigration from continental Europe, even for those that occurred most recently. In this study, we examine genetic data for evidence of male immigration at particular times into Central England and North Wales. To do this, we used 12 biallelic polymorphisms and six microsatellite markers to define high resolution Y chromosome haplotypes in a sample of 313 males from seven towns located along an east-west transect from East Anglia to North Wales. The Central English towns were genetically very similar, whereas the two North Welsh towns differed significantly both from each other and from the Central English towns. When we compared our data with an additional 177 samples collected in Friesland and Norway, we found that the Central English and Frisian samples were statistically indistinguishable. Using novel population genetic models that incorporate both mass migration and continuous gene flow, we conclude that these striking patterns are best explained by a substantial migration of Anglo-Saxon Y chromosomes into Central England (contributing 50%–100% to the gene pool at that time) but not into North Wales.

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Genetic evidence for different male and female roles during cultural transitions in the British Isles

Human history is punctuated by periods of rapid cultural change. Although archeologists have developed a range of models to describe cultural transitions, in most real examples we do not know whether the processes involved the movement of people or the movement of culture only. With a series of relatively well defined cultural transitions, the British Isles present an ideal opportunity to assess the demographic context of cultural change. Important transitions after the first Paleolithic settlements include the Neolithic, the development of Iron Age cultures, and various historical invasions from continental Europe. Here we show that patterns of Y-chromosome variation indicate that the Neolithic and Iron Age transitions in the British Isles occurred without large-scale male movements. The more recent invasions from Scandinavia, on the other hand, appear to have left a significant paternal genetic legacy. In contrast, patterns of mtDNA and X-chromosome variation indicate that one or more of these pre-Anglo-Saxon cultural revolutions had a major effect on the maternal genetic heritage of the British Isles.

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Evidence of Admixture from Haplotyping in an Epidemiological Study of UK Caucasian Males: Implications for Association Analyses

Objective: Cohort and case-control genetic association studies offer the greatest power to detect small genotypic influences on disease phenotypes, relative to family-based designs. However, genetic subdivisions could confound studies involving unrelated individuals, but the topic has been little investigated. We examined geographical and interallelic association of SNP and microsatellite haplotypes of the Y chromosome, of regions of chromosome 11, and of autosomal SNP genotypes relevant to cardiovascular risk traits in a UK-wide epidemiological survey. Results: We show evidence (p = 0.00001) of the Danelaw history of the UK, marked by a two-fold excess of a Viking Y haplotype in central England. We also found evidence for a (different) single-centre geographical over-representation of one haplotype, both for APOC3-A4-A5 and for IGF2. The basis of this remains obscure but neither reflect genotyping error nor correlate with the phenotypic associations by centre of these markers. A panel of SNPs relevant to cardiovascular risks traits showed neither association with geographical location nor with Y haplotypes. Conclusion: Combinations of Y haplotyping, autosomal haplotyping, and genome-wide SNP typing, taken together with phenotypic2 associations, should improve epidemiological recognition and interpretation of possible confounding by genetic subdivision.

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Genetic evidence for a family-based Scandinavian settlement of Shetland and Orkney during the Viking periods

The Viking age witnessed the expansion of Scandinavian invaders across much of northwestern Europe. While Scandinavian settlements had an enduring cultural impact on North Atlantic populations, the nature and extent of their genetic legacy in places such as Shetland and Orkney is not clear. In order to explore this question further, we have made an extensive survey of both Y-chromosomal and mitochondrial DNA (mtDNA) variation in the North Atlantic region. Our findings indicate an overall Scandinavian ancestry of ~44% for Shetland and ~30% for Orkney, with approximately equal contributions from Scandinavian male and female subjects in both cases. This contrasts with the situation for the Western Isles, where the overall Scandinavian ancestry is less (~15%) and where there is a disproportionately high contribution from Scandinavian males. In line with previous studies, we find that Iceland exhibits both the greatest overall amount of Scandinavian ancestry (55%) and the greatest discrepancy between Scandinavian male and female components. Our results suggest that while areas close to Scandinavia, such as Orkney and Shetland, may have been settled primarily by Scandinavian family groups, lone Scandinavian males, who later established families with female subjects from the British Isles, may have been prominent in areas more distant from their homeland.

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Friday, April 08, 2005

The Emerging Tree of West Eurasian mtDNAs: A Synthesis of Control-Region Sequences and RFLPs

Variation in the human mitochondrial genome (mtDNA) is now routinely described and used to infer the histories of peoples, by means of one of two procedures, namely, the assaying of RFLPs throughout the genome and the sequencing of parts of the control region (CR). Using 95 samples from the Near East and northwest Caucasus, we present an analysis based on both systems, demonstrate their concordance, and, using additional available information, present the most refined phylogeny to date of west Eurasian mtDNA. We describe and apply a nomenclature for mtDNA clusters. Hypervariable nucleotides are identified, and the relative mutation rates of the two systems are evaluated. We point out where ambiguities remain. The identification of signature mutations for each cluster leads us to apply a hierarchical scheme for determining the cluster composition of a sample of Berber speakers, previously analyzed only for CR variation. We show that the main indigenous North African cluster is a sister group to the most ancient cluster of European mtDNAs, from which it diverged ~50,000 years ago.

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The origins of southern and western Eurasian populations: an mtDNA study

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The topology of the network of western Eurasian mitochondrial DNA (mtDNA) lineage clusters in the context of their expansion and spread in this geographic area is analysed. Special attention is devoted to the inner nods of the reconstructed median network tree, ancestral to mtDNA lineage clusters H and V, to the Caucasus and Trans-Caucasus area populations and to the problem of timing of the expansion of the Caucasoid-specific mtDNA lineage clusters in western Europe versus in the Trans-Caucasus. It appears on several examples that typical for Western Europe mtDNA lineage clusters exhibit significantly earlier expansion in the Trans-Caucasus area. Furthermore, the lineage cluster, radiating from the pre-HV node, is significantly more frequent and divergent in the Trans-Caucasus populations than it is in Europe. Meanwhile, a comparison of the Central Asian and the Trans-Caucasus area populations shows that the former have a significant share of eastern Asian-specific mtDNA lineages, which are almost absent in the latter. Finally, a picture starts to emerge, revealing an ancient Indian—Trans-Caucasian—European continuum of a significant proportion of human maternal lineage clusters, dating back to the period between the Upper and Lower Pleniglacials.

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A comprehensive analysis of Arabs and Berbers maternal lineages in Morocco

Morocco is situated on the Northwestern Africa. As far as the genetics of the present-day Moroccan populations is concerned, one may say that both its geography and history point to a possible influence from the Iberian Peninsula, northwestern Africa, the near East and sub-Saharan Africa. The two major ethnics populations of Morocco are the Arabs and the Berbers. Fossil evidences suggests that anatomically modern humans inhabited this area as early as 40,000 years ago. Around 22 000 years ago, the Iberomaurusians, Cro-Magnon hunters type, started to succeed the previous populations. The Berbers have been regarded as aboriginal North Africans (Brett and Fentress, 1996) descendents of the Iberomaurusians people. On the other hand, during the historical time, North Africa had been under several waves of east-west invasions. Several empires spread their kingdom as far as Morocco. However, it is not at all obvious how significant was their contributions to the local gene pool, especially as far as maternally inherited mtDNA is concerned. It is often speculated that one of the major events that might have had a significant impact on the Moroccan population could be the Islamic expansion some 1300 years ago, bringing, inter alia, Araics language to the area and introducing the current division of people to Berbers and Arabs. Yet again, there has been no serious study addressing genetics of this scenario. Here, we report the results of our analysis of the mtDNA pool in the Moroccan population: in Arabs and in Berbers. Although maternal lineages do not tell the full story, they can speak about important part of it- and in a rather clear way.

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Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages


Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India.


The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub- lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports.


This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non-existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.

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