Genographic project mtDNA paper, database, and haplogroup predictor

All the information is in the freely available article in PLoS Genetics. Of scientific interest regarding the Neanderthal question:

While all of these five mutations have in fact been observed in our full database of 78,590 samples, no combination of any two of them has appeared in any sample. However, since these six samples may not represent the full diversity of Neanderthal lineages, we have also investigated separately the level of divergence they show from our entire database. No sample in our database is as divergent as these Neanderthal samples, in terms of its distance from its nearest neighbor outside its own Hg, or its distance from the rCRS, which we take to represent a “random” modern human mtDNA (Table S11). We also observe that the most divergent samples in our database all carry well-known HVS-I motifs characteristic of African Hg L branches. While it is difficult to translate these findings into probabilities, it is clear that our results do not support the existence of mtDNA samples of Neanderthal (or other archaic Homo) origin in our database.

PLoS Genetics

The Genographic Project Public Participation Mitochondrial DNA Database

Doron M. Behar et al.

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the Genographic Project, during which we have created the largest standardized human mitochondrial DNA (mtDNA) database ever collected, comprising 78,590 genotypes. Here, we detail our genotyping and quality assurance protocols including direct sequencing of the mtDNA HVS-I, genotyping of 22 coding-region SNPs, and a series of computational quality checks based on phylogenetic principles. This database is very informative with respect to mtDNA phylogeny and mutational dynamics, and its size allows us to develop a nearest neighbor–based methodology for mtDNA haplogroup prediction based on HVS-I motifs that is superior to classic rule-based approaches. We make available to the scientific community and general public two new resources: a periodically updated database comprising all data donated by participants, and the nearest neighbor haplogroup prediction tool.

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mtdna of Hungarians

Acta Biol Hung. 2007 Jun;58(2):245-56.

Comparison of mtdna haplogroups in Hungarians with four other European populations: a small incidence of descents with Asian origin.

Nadasi E, Gyurus P, Czakó M, Bene J, Kosztolányi S, Fazekas S, Dömösi P, Melegh B.

Hungarians are unique among the other European populations because according to history, the ancient Magyars had come from the eastern side of the Ural Mountains and settled down in the Carpathian basin in the 9th century AD. Since variations in the human mitochondrial genome (mtDNA) are routinely used to infer the histories of different populations, we examined the distribution of restriction fragment length polymorphism (RFLP) sites of the mtDNA in apparently healthy, unrelated Hungarian subjects in order to collect data on the genetic origin of the Hungarian population. Among the 55 samples analyzed, the large majority belonged to haplogroups common in other European populations, however, three samples fulfilled the requirements of haplogroup M. Since haplogroup M is classified as a haplogroup characteristic mainly for Asian populations, the presence of haplogroup M found in approximately 5% of the total suggests that an Asian matrilineal ancestry, even if in a small incidence, can be detected among modern Hungarians.

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Sex biased gene flow in Americans

Genet Mol Res. 2007 May 9;6(2):156-61.

Sex-biased gene flow in African Americans but not in American Caucasians.

Gonçalves VF, Prosdocimi F, Santos LS, Ortega JM, Pena SD.

We have previously shown evidence of strong sex-biased genetic blending in the founding and ongoing history of the Brazilian population, with the African and Amerindian contribution being highest from maternal lineages (as measured by mitochondrial DNA) and the European contribution foremost from paternal lineages (estimated from Y-chromosome haplogroups). The same phenomenon has been observed in several other Latin American countries, suggesting that it might constitute a universal characteristic of the Iberian colonization of the Americas. However, it has also recently been detected in the Black population of the United States. We thus wondered if the same could be observed in American Caucasians. To answer that question, we retrieved 1387 hypervariable I Caucasian mitochondrial DNA sequences from the FBI population database and established their haplogroups and continental geographical sources. In sharp contrast with the situation of the Caucasian population of Latin American countries, only 3.1% of the American Caucasian sequences had African and/or Amerindian origin. To explain this discrepancy we propose that the finding of elevated genomic contributions from European males and Amerindian or African females depends not only on the occurrence of directional mating, but also on the "racial" categorization of the children born from these relations. In this respect, social practices in Latin America and in the United States diverge considerably; in the former socially significant "races" are normally designated according to physical appearance, while in the latter descent appears to be the most important factor.

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Y chromosome variation in Europe

The well-known Italian geneticist Andrea Noveletto has written an interesting article on the current knowledge about the European Y chromosome distribution. I heartily recommend that you get a copy of this paper which contains lots of useful summarization of previous work with some new interpretations. An excerpt related to Greece:

Greece and Greek Islands


Greece, Crete and the Aegean Islands is a key area to understand the migrations of early farmers to the rest of Europe. A detailed view of the role of Neolithic processes in shaping the Turkish gene pool has been proposed (Cinnioglu et al. 2004). Together with Turkey, Greece and the Aegean appear clearly as a source for haplogroup J2, but the timing for further movements to the west has not yet been fully established. The well documented expansion of the Ancient Greek world, consisting of repeated colonizations, is an immediate candidate process to have spread in the first millennium BC haplogroups that can be dated to an earlier phase of the Neolithic. This punctuation in the dispersal of 'Neolithic' genes has been hypothesized (Malaspina et al. 2001; Di Giacomo et al. 2003) based on haplogroup J, but further phyletic resolution of other haplogroups is needed. The present-day landscape of Greece is also characterized by a small-scale heterogeneity distinct from the continent-wide clines (Figure 2). This potentially provides the possibility of finding haplogroups or STR haplotypes linking the territories of colonies to those of the respective mother cities, as these relationships are historically known.

Greece and Crete also bring the signature of gene flow from north-eastern Europe, mainly represented by frequencies of R1a like nowhere else in southern Europe. This haplogroup is particularly abundant in Thessaly and underwent a further increase in eastern Crete (Di Giacomo et al. 2003).

and on the Carpathians and Balkans:

It is important to observe that, in spite of a bulk geographic continuity with Greece by land, and through the Ionian Sea, populations of this area display relatively low frequencies of lineages within haplogroup J2 (with the exception of J2e), i.e. little input of what are considered typical markers of the Neolithic diffusion or of post-Neolithic movements ensuing it. Conversely, these haplogroups seem to have undergone a more pronounced entry along the eastern edge of the Balkan peninsula and along the Black Sea coasts.

Ann Hum Biol. 2007 Mar-Apr;34(2):139-72.

Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool


Andrea Novelletto

Abstract

The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.

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mtDNA of Czechs

Hum Biol. 2006 Dec;78(6):681-96.

Mitochondrial DNA variability in the Czech population, with application to the ethnic history of Slavs.

Malyarchuk BA, Vanecek T, Perkova MA, Derenko MV, Sip M.

Mitochondrial DNA (mtDNA) variability was studied in a sample of 179 individuals representing the Czech population of Western Bohemia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding-region haplogroup-specific RFLP markers revealed that most Czech mtDNAs belong to the common West Eurasian mitochondrial haplogroups (H, pre-V HV*, J, T, U, N1, W, and X). However, about 3% of Czech mtDNAs encompass East Eurasian lineages (A, N9a, D4, M*). A comparative analysis with published data showed that different Slavonic populations in Central and Eastern Europe contain small but marked amounts of East Eurasian mtDNAs. We suggest that the presence of East Eurasian mtDNA haplotypes is not an original feature of the gene pool of the proto-Slavs but rather may be mostly a consequence of admixture with Central Asian nomadic tribes, who migrated into Central and Eastern Europe in the early Middle Ages.

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Feast on Food and Sex

A reader sent me this interesting link:

Martin Jones, author of Feast: Why Humans Share Food is the George Pitt-Rivers Professor of Archaeological Science at the University of Cambridge, and specializes in the study of the fragmentary archaeological remains of early food. Feast reconstructs the development of the meal from chimpanzees at a kill to university professors at a formal feast. Jones has a knack for explaining how food has affected both our society and ecology. In the excerpt below he shows how the instinct to share is more biological than we realize.

Toltec Human sacrifice

Ancient Tomb Found in Mexico Reveals Mass Child Sacrifice (National Geographic)

The skeletons of two dozen children killed in an ancient mass sacrifice have been found in a tomb at a construction site in Mexico.

The find reveals new details about the ancient Toltec civilization and adds to an ongoing debate over ritualistic killing in historic Mesoamerica.

Construction crews unearthed the burial chamber this spring near the town of Tula, the ancient Toltec capital, 50 miles (80 kilometers) north of Mexico City (see Mexico map).

The chamber contained 24 skeletons of children believed to have been sacrificed between A.D. 950 and 1150, according to Luis Gamboa, an archaeologist at Mexico's National Institute of Anthropology and History.

Cause of death of Tyrolean Ice Man

It is fascinating how a 5,300-year-old "crime" can be solved using modern forensic technology.

Iceman 'Ötzi's' cause of death proved by researcher at the University of Zurich

An Italian-Swiss research team, including Dr. Frank Rühli of the Institute of Anatomy at the University of Zurich in Switzerland proved the cause of death of the Iceman (“Ötzi,” 3300 BC) by modern X-ray-based technology. A lesion of a close-to-the-shoulder artery has been found thanks to a CT scan or multislice computed tomography, finally clarifying the world-famous glacier mummy’s cause of death. This scientific work appeared online in the Journal of Archaeological Science, published by Elsevier and will be covered in the German and US issues of National Geographic magazine in July.

The Iceman is a uniquely well-preserved late Neolithic glacier mummy, found in 1991 in South Tyrol at 3,210 meters above sea level. He has undergone various scientific examinations, as human bodies are the best source for the study of life conditions in the past as well as the evolution of today’s diseases.

In 2005, the glacier mummy was reinvestigated in South Tyrol by Dr. F. Rühli from the Institute of Anatomy at the University of Zurich in Switzerland, in close collaboration with Dr. Eduard Egarter Vigl of the South Tyrol Museum of Archaeology in Bolzano, Italy, as well as Drs. Patrizia Pernter and Paul Gostner from the Department of Radiology at General Hospital Bolzano, by state-of-the-art multislice computed tomography (CT).

Analysis of the CT images showed a lesion of the dorsal wall of the left subclavian artery, the artery underneath the clavicle, caused by an earlier, already-detected arrowhead that remains in the back. In addition, a large haematoma could be visualized in the surrounding tissue. By incorporating historic as well as modern data on the survival ship of such a severe lesion, the scientists concluded that the Iceman died within a short time due to this lesion.

“Such obvious proof of a vascular lesion in a body of this historic age is unique, and it helped to determine the cause of this extraordinary death without a destructive autopsy. We look forward to further investigating the circumstances surrounding the Iceman’s sudden death,” explains Dr. Dr. Rühli.

Haplogroup R1a1 in prehistoric Southern Siberia

This is an important paper both for making Y-DNA study of ancient remains possible, and also for confirming the late prehistoric presence of the major West Eurasian haplogroup R1a1 in the region of southern Siberia. As I have noted elsewhere, the Caucasoids who bore haplogroup R1a1 in prehistoric times in that part of the world, were later influenced from population movements in the opposite direction, representing the westward push of Mongoloid(-influenced) peoples.

Int J Legal Med. 2007 May 30;

First successful assay of Y-SNP typing by SNaPshot minisequencing on ancient DNA.

Bouakaze C, Keyser C, Amory S, Crubezy E, Ludes B.

Institute of Legal Medicine, EA3428, Strasbourg, France, caroline.bouakaze@ulp.u-strasbg.fr.

In the present study, a set of 13 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) selected for the identification of the most frequent Asian Y-haplogroups was included in an allele-specific primer extension assay. Single nucleotide polymorphism (SNP) genotyping was accomplished by co-amplification of these 13 DNA fragments within 2 multiplex PCRs followed by detection with 1 minisequencing reaction using the SNaPshottrade mark Multiplex kit and analysis of extension products by capillary electrophoresis. First developed on modern samples, the assay was optimized for the analysis of 11 ancient DNA (aDNA) samples from the Krasnoyarsk region (southern Siberia) that were dated from 5,500-1,800 years before present (YBP). SNP typing was successful for most of them, which were all assigned to Y-haplogroup R1a1 except one. These results show that SNPs are well-suited for the analysis of aged and degraded DNA samples. Moreover, we found that the SNaPshot minisequencing methodology is a convenient, robust, and efficient method for SNP typing. To our knowledge, this study reports the first successful investigation of Y-SNPs on aDNA samples. The potential use of Y-SNPs in both evolutionary and forensic fields is also discussed.

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mtDNA variation in France

I had posted before about the paucity of population genetic data from France, perhaps the most under-represented major European nation in human population genetic research. Thankfully, a new study goes some way to rectify this.

Ann Hum Biol. 2007 Jan-Feb;34(1):68-79.

An mtDNA perspective of french genetic variation.

Richard C, Pennarun E, Kivisild T, Tambets K, Tolk HV, Metspalu E, Reidla M, Chevalier S, Giraudet S, Lauc LB, Pericic M, Rudan P, Claustres M, Journel H, Dorval I, Muller C, Villems R, Chaventre A, Moisan JP.

Laboratoire d'Etude du Polymorphisme de l'ADN, Faculte de Medecine, Nantes, France.

BACKGROUND: The French has been insufficiently characterized so far for mitochondrial DNA (mtDNA) diversity. AIMS: The study aimed to enhance the information available for the French mtDNA pool and to explore the potential microgeographical differentiation of two French regions selected for their linguistic and historical idiosyncrasies. SUBJECTS AND METHODS: A total of 868 samples from 12 different locations in France were collected. They were sequenced for the hypervariable segment I (HVS-I) and typed for haplogroup defining markers from the coding region either by restriction fragment length polymorphism (RFLP) or by a new protocol based on the 5' nuclease allelic discrimination. The mtDNA gene pools of French Basques and Bretons were compared in terms of frequency and composition with relevant neighbouring populations. RESULTS: The French Basques' mtDNA pool shares some common features with that of the Spanish Basques, such as the high frequency of haplogroup H. However, the French Basques exhibit a number of distinct features, most notably expressed in the prevalence of haplogroups linked with the Neolithic diffusion in Europe. In Brittany, Finistere shows closer affinities with Britain and Scandinavia than the two other departments of Brittany. CONCLUSION: The mtDNA haplogroup composition of the French does not differ significantly from the surrounding European genetic landscape. At a finer grain, microgeographical differentiation can be revealed, as shown for the French Basque country and for Brittany.

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