July 30, 2007

Click language speakers share deep not recent common ancestry

Mol Biol Evol. 2007 Jul 26; [Epub ahead of print]

History of Click-Speaking Populations of Africa Inferred from mtDNA and Y Chromosome Genetic Variation.

Tishkoff SA et al.

Little is known about the history of click-speaking populations in Africa. Prior genetic studies revealed that the click-speaking Hadza of eastern Africa are as distantly related to click speakers of southern Africa as are most other African populations. The Sandawe, who currently live within 150 km of the Hadza, are the only other population in eastern Africa whose language has been classified as part of the Khoisan language family. Linguists disagree on whether there is any detectable relationship between the Hadza and Sandawe click languages. We characterized both mtDNA and Y chromosome variation of the Sandawe, Hadza, and neighboring Tanzanian populations. New genetic data show that the Sandawe and southern African click speakers share rare mtDNA and Y chromosome haplogroups; however, common ancestry of the two populations dates back >35,000 years. These data also indicate that common ancestry of the Hadza and Sandawe populations dates back >15,000 years. These findings suggest that at the time of the spread of agriculture and pastoralism, the click-speaking populations were already isolated from one another, and are consistent with relatively deep linguistic divergence among the respective click languages.


Ancient Chinese Y chromosomes

Another paper on ancient Y-DNA, it seems like the times where we could only expect to get mtDNA from prehistoric remains is coming to a close.

Hum Genet. 2007 Jul 27; [Epub ahead of print]

Y chromosomes of prehistoric people along the Yangtze River.
Li H et al.

The ability to extract mitochondrial and nuclear DNA from ancient remains has enabled the study of ancient DNA, a legitimate field for over 20 years now. Recently, Y chromosome genotyping has begun to be applied to ancient DNA. The Y chromosome haplogroup in East Asia has since caught the attention of molecular anthropologists, as it is one of the most ethnic-related genetic markers of the region. In this paper, the Y chromosome haplogroup of DNA from ancient East Asians was examined, in order to genetically link them to modern populations. Fifty-six human remains were sampled from five archaeological sites, primarily along the Yangtze River. Strict criteria were followed to eliminate potential contamination. Five SNPs from the Y chromosome were successfully amplified from most of the samples, with at least 62.5% of the samples belonging to the O haplogroup, similar to the frequency for modern East Asian populations. A high frequency of O1 was found in Liangzhu Culture sites around the mouth of the Yangtze River, linking this culture to modern Austronesian and Daic populations. A rare haplogroup, O3d, was found at the Daxi site in the middle reaches of the Yangtze River, indicating that the Daxi people might be the ancestors of modern Hmong-Mien populations, which show only small traces of O3d today. Noticeable genetic segregation was observed among the prehistoric cultures, demonstrating the genetic foundation of the multiple origins of the Chinese Civilization.


July 27, 2007

Phylogeography of African Brazilians

Hum Hered. 2008 Jul 25;65(1):23-32 [Epub ahead of print]

The Phylogeography of African Brazilians.

Gonçalves VF, Carvalho CM, Bortolini MC, Bydlowski SP, Pena SD.

Background/Aims: Approximately four million Africans were taken as slaves to Brazil, where they interbred extensively with Amerindians and Europeans. We have previously shown that while most White Brazilians carry Y chromosomes of European origin, they display high proportions of African and Amerindian mtDNA lineages, because of sex-biased genetic admixture. Methods: We studied the Y chromosome and mtDNA haplogroup structure of 120 Black males from Sao Paulo, Brazil. Results: Only 48% of the Y chromosomes, but 85% of the mtDNA haplogroups were characteristic of sub-Saharan Africa, confirming our previous observation of sexually biased mating. We mined literature data for mtDNA and Y chromosome haplogroup frequencies for African native populations from regions involved in Atlantic Slave Trade. Principal Components Analysis and Bayesian analysis of population structure revealed no genetic differentiation of Y chromosome marker frequencies between the African regions. However, mtDNA examination unraveled considerable genetic structure, with three clusters at Central-West Africa, West Africa and Southeast Africa. A hypothesis is proposed to explain this structure. Conclusion: Using these mtDNA data we could obtain for the first time an estimate of the relative ancestral contribution of Central-West (0.445), West (0.431) and Southeast Africa (0.123) to African Brazilians from Sao Paulo. These estimates are consistent with historical information. Copyright (c) 2008 S. Karger AG, Basel.

July 20, 2007

Genetic structure and suicide risk in Austria

Wien Klin Wochenschr. 2007 Jun;119(11-12):355-360. 

Surname study of suicide in Austria: Differences in regional suicide rates correspond to the genetic structure of the population.

Voracek M, Sonneck G.

OBJECTIVES: There is convergent evidence from adoption, family, geographical, immigrant, molecular genetic, twin and, most recently, surname studies of suicide for genetic contributions to suicide risk. Surnames carry information about genetic relatedness or distance and, in patrilineal surname systems, are a close substitute for Y-chromosome markers and haplotypes, since surname transmission is similar to the transmission of the nonrecombining part of the Y chromosome. This study investigated whether differences in regional suicide rates correspond to the genetic structure of the Austrian population. METHODS: Differences in district-level standardized suicide rates 1988-94 between the five major surname regions identified for Austria were analyzed. The surname regions used in the analysis reflect the contemporary population structure and closely follow the natural borders found in the topography of Austria, less so its administrative division into nine states. RESULTS: Surname region accounted for a significant (P < 0.001) and substantial (38%) portion of the variance in district-level suicide rates. Adjusting the suicide rates for a set of five social and economic indicators that are established ecological correlates of suicide prevalence (income, and rates of the divorced, unemployed, elderly and Roman Catholics) left the results essentially unchanged. CONCLUSIONS: Regional differences in suicide rates within Austria correspond to the genetic structure of the population. The present evidence adds to related findings from geographical and surname studies of suicide that suggest a role for genetic risk factors for suicidal behavior. Genetic differences between subpopulations may partially account for the geography of suicide. Study limitations and directions for future research are discussed.


July 19, 2007

Population bottlenecks in human history (paper in favor of Out of Africa Only theory)

A previous paper by the same author and a story in National Geographic.

The effect of ancient population bottlenecks on human phenotypic variation

Andrea Manica et al.

The origin and patterns of dispersal of anatomically modern humans are the focus of considerable debate1, 2, 3. Global genetic analyses have argued for one single origin, placed somewhere in Africa4, 5, 6, 7. This scenario implies a rapid expansion, with a series of bottlenecks of small amplitude, which would have led to the observed smooth loss of genetic diversity with increasing distance from Africa. Analyses of cranial data, on the other hand, have given mixed results8, 9, 10, 11, 12, and have been argued to support multiple origins of modern humans2, 9, 12. Using a large data set of skull measurements and an analytical framework equivalent to that used for genetic data, we show that the loss in genetic diversity has been mirrored by a loss in phenotypic variability. We find evidence for an African origin, placed somewhere in the central/southern part of the continent, which harbours the highest intra-population diversity in phenotypic measurements. We failed to find evidence for a second origin, and we confirm these results on a large genetic data set. Distance from Africa accounts for an average 19–25% of heritable variation in craniometric measurements—a remarkably strong effect for phenotypic measurements known to be under selection.


Y chromosome differences between southern and northern Altaians

Genetika. 2007 May;43(5):675-87.

[Gene pool differences between northern and southern Altaians inferred from the data on Y-chromosomal haplogroups]

[Article in Russian]

[No authors listed]

Y-chromosomal haplogroups composition and frequencies were analyzed in Northern and Southern Altaians. In the gene pool of Altaians a total of 18 Y-chromosomal haplogroups were identified, including C3xM77, C3c, DxM15, E, F*, J2, I1a, I1b, K*, N*, N2, N3a, O3, P*, Q*, R1*, R1a1, and R1b3. The structured nature of the Altaic gene pool is determined by the presence of the Caucasoid and Mongoloid components, along with the ancient genetic substratum, marked by the corresponding Western and Eastern Eurasian haplogroups. Haplogroup R1a1 prevailed in both ethnic groups, accounting for about 53 and 38% of paternal lineages in Southern and Northern Altaians, respectively. This haplogroup is thought to be associated with the eastward expansion of early Indo-Europeans, and marks Caucasoid element in the gene pools of South Siberian populations. Similarly to haplogroup K*, the second frequent haplogroup Q* represents paleo-Asiatic marker, probably associated with the Ket and Samoyedic contributions to the Altaic gene pool. The presence of lineages N2 and N3a can be explained as the contribution of Finno--Ugric tribes, assimilated by ancient Turks. The presence of haplogroups C3xM77, C3c, N*, and 03 reflects the contribution of Central Asian Mongoloid groups. These haplogroups, probably, mark the latest movements of Mongolian migrants from the territory of contemporary Tuva and Mongolia. The data of factor analysis, variance analysis, cluster analysis, and phylogenetic analysis point to substantial genetic differentiation of Northern and Southern Altaians. The differences between Northern and Southern Altaians in the haplogroup composition, as well as in the internal haplotype structure were demonstrated.


July 18, 2007

Ancient Hungarian mtDNA

See also mtDNA of Hungarians.

Am J Phys Anthropol. 2007 Jul 13; [Epub ahead of print]

Comparison of maternal lineage and biogeographic analyses of ancient and modern Hungarian populations.

Tömöry G et al. 

The Hungarian language belongs to the Finno-Ugric branch of the Uralic family, but Hungarian speakers have been living in Central Europe for more than 1000 years, surrounded by speakers of unrelated Indo-European languages. In order to study the continuity in maternal lineage between ancient and modern Hungarian populations, polymorphisms in the HVSI and protein coding regions of mitochondrial DNA sequences of 27 ancient samples (10th-11th centuries), 101 modern Hungarian, and 76 modern Hungarian-speaking Sekler samples from Transylvania were analyzed. The data were compared with sequences derived from 57 European and Asian populations, including Finno-Ugric populations, and statistical analyses were performed to investigate their genetic relationships. Only 2 of 27 ancient Hungarian samples are unambiguously Asian: the rest belong to one of the western Eurasian haplogroups, but some Asian affinities, and the genetic effect of populations who came into contact with ancient Hungarians during their migrations are seen. Strong differences appear when the ancient Hungarian samples are analyzed according to apparent social status, as judged by grave goods. Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations. Modern Hungarian-speaking populations seem to be specifically European. Our findings demonstrate that significant genetic differences exist between the ancient and recent Hungarian-speaking populations, and no genetic continuity is seen.


July 16, 2007

Genetic heritage of an Afrikaner

I did not have time to read this paper fully, but this may signal the shape of things to come in the field of genetic testing. Until now, people could find something about their individual ancestors in the patrilineal (for men) or matrilineal (for both men and women) line of descent, and they could also get a rough estimate of their ancestral proportions from different population groups. Eventually it may become possible to determine not only the fraction of one's ancestry that derives from some population group but also get an estimate of when and where individual ancestors along all lines of descent lived. Ultimately a mega-genealogical tree for all mankind could -in principle- be constructed.

Ann Hum Genet. 2007 May 22; [Epub ahead of print]

Deconstructing Jaco: Genetic Heritage of an Afrikaner.

Greeff JM.
Department of Genetics, University of Pretoria, Pretoria 0002, South Africa.
It is often assumed that Afrikaners stem from a small number of Dutch immigrants. As a result they should be genetically homogeneous, show founder effects and be rather inbred. By disentangling my own South African pedigree, that is on average 12 generations deep, I try to quantify the genetic heritage of an Afrikaner. As much as 6% of my genes have been contributed by slaves from Africa, Madagascar and India, and a woman from China. This figure compares well to other genetic and genealogical estimates. Seventy three percent of my lineages coalesce into common founders, and I am related in excess of 10 times to 20 founder ancestors (30 times to Willem Schalk van der Merwe). Significant founder effects are thus possible. The overrepresentation of certain founder ancestors is in part explained by the fact that they had more children. This is remarkable given that they lived more than 300 years (or 12 generations) ago. DECONSTRUCT, a new program for pedigree analysis, identified 125 common ancestors in my pedigree. However, these common ancestors are so distant from myself, paths of between 16 and 25 steps in length, that my inbreeding coefficient is not unusually high (f (approx) 0.0019).


July 11, 2007

Origin and spread of haplogroup M1

I had written about the origin of haplogroup M1 before regarding this article. A new paper on the subject has now appeared which solves some of the mysteries involved while creating new ones (i.e. the early (?) appearance of M1 in Basques).

BMC Genomics. 2007 Jul 9;8(1):223

Mitochondrial lineage M1 traces an early human backflow to Africa.

Gonzalez AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM.

ABSTRACT: BACKGROUND: The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out. RESULTS: The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated. CONCLUSIONS: This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.


Spanish mtDNA

Leg Med (Tokyo). 2007 Jul 4; [Epub ahead of print]

Characterization of human control region sequences for Spanish individuals in a forensic mtDNA data set.

Alvarez JC et al.

Population data on the hypervariable regions of the mitochondrial DNA (mtDNA) genome are used to convey the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, mtDNA profiles of Spanish individuals (n=312) were analyzed to describe haplogroup distributions and to determine relevant single nucleotide polymorphisms (SNPs) of those haplogroups. All nine common European haplogroups were observed in the sample, and these were divided into subgroups when possible. Haplogroup H was the most common haplogroup. The haplogroups U, J, T, and V were the next most frequent groups, each occurring at a frequency of 6.4% or greater. In addition, African and Asian sequences were present though rare in the samples. The data were compared with and found to be similar to other published data sets. There were 109 SNPs observed in the data set, including 10 positions not previously reported. The most variable sites are consistent with other studies.


July 09, 2007

ASPM and the alphabet

Peter Frost who had proposed in the past a model for the evolution of light pigmentation in northern Europeans has come up with a new hypothesis linking the spread of the notorious ASPM gene variant with the spread of alphabetical writing.

Med Hypotheses. 2007 Jun 27; [Epub ahead of print]

The spread of alphabetical writing may have favored the latest variant of the ASPM gene.

Frost P.

Anthropology Department, C/o Bernard Saladin d’Anglure, Université Laval, Québec, Canada G1K 7P4.

ASPM, a gene that regulates brain growth, has evolved considerably in the primate lineage that leads to humans. It continued to evolve even after the emergence of modern humans, with the latest ASPM variant arising about 6000 years ago somewhere in the Middle East. The new variant then proliferated within and outside this region, reaching higher incidences in the Middle East (37-52%) and in Europe (38-50%) than in East Asia (0-25%). Despite its apparent selective advantage, this variant does not seem to improve cognitive performance, at least not on standard IQ tests. At present, we can only say that it probably assists performance on a task that exhibited the same geographic expansion from a Middle Eastern origin roughly 6000 years ago. The closest match seems to be the invention of alphabetical writing, specifically the task of transcribing speech and copying texts into alphabetical script. Though more easily learned than ideographs, alphabetical characters place higher demands on mental processing, especially under premodern conditions (continuous text with little or no punctuation, real-time stenography, absence of automated assistance for publishing or copying, etc.). This task was largely delegated to scribes of various sorts who enjoyed privileged status and probably superior reproductive success. Such individuals may have served as vectors for spreading the new ASPM variant.


July 05, 2007

Ancient Chinese mtDNA

American Journal of Physical Anthropology (early view)

Tracing the genetic history of the Chinese people: Mitochondrial DNA analysis of aneolithic population from the Lajia site

Shi-Zhu Gao et al.

Ancient DNA analysis was conducted on the dental remains of specimens from the Lajia site, dating back 3,800-4,000 years. The Lajia site is located in Minhe county, Qinghai province, in northwestern China. Archaeological studies link Lajia to the late period of the Qijia culture, one of the most important Neolithic civilizations of the upper Yellow River region, the cradle of Chinese civilization. Excavations at the site revealed that the inhabitants died in their houses as the result of a sudden flood. The Lajia site provides a rare chance to study the putative families, all of whom died at the same instant. Possible maternal familial relationships were investigated through mitochondrial DNA (mtDNA) sequence analysis. Twelve sequences from individuals found in one house were assigned to only five haplotypes, consistent with a possible close kinship. Results from analyses of RFLP typing and HVI motifs suggest that the Lajia people belonged to the haplogroups B, C, D, M*, and M10. This study, combined with archaeological and anthropological investigations, provides a better understanding of the genetic history of the Chinese people.


Ancient Iberian mtDNA

They are referring to this paper on early Neolithic farmers from Central Europe. The discovery that Neolithic Iberians were more similar to modern Iberians compared to Neolithic and modern Central Europeans is not very surprising; remember the recent finding that
"The surprise is that the Neolithic peoples of Europe and their Bronze Age successors are not closely related to the modern inhabitants, although the prehistoric/modern ties are somewhat more apparent in southern Europe."
Proc Biol Sci. 2007 Jun 26; [Epub ahead of print]

Palaeogenetic evidence supports a dual model of Neolithic spreading into Europe.

Sampietro ML, Lao O, Caramelli D, Lari M, Pou R, Martí M, Bertranpetit J, Lalueza-Fox C.

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.