Origins of Mongoloid mtDNA in Slavs

A very interesting article which addresses the issue of the Mongoloid mitochondrial component in Slavs. I like this kind of paper that looks at the minor features of populations, rather than their broad general characteristics that are well known by now, and indeed were known even before genetics came into the picture.

From the paper:

The overwhelming majority of mtDNA clusters, identified in Czechs, were of the western-Eurasian origin. The frequency of eastern-Eurasian (Mongoloid) mtDNA lineages in this population constituted 1.8% (haplogroups A, N9a, and M). African lineage (with the frequency of 0.4%) belonging to haplogroup L2a and marked by the +13803HaeIII variant was also detected.

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Low frequency of Mongoloid mtDNA variant in Letts and Lithuanians suggests that Mongoloid component was probably not typical of Balto-Slavic protogene pool. Thus, it seems reasonable that accumulation of Mongoloid mtDNA lineages in Slavs and their ancestors was intensified only in the last 4000 years.

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The highest frequencies of the Mongoloid component are typical of the Russian populations from Russian Pomor’e and Northwestern region. These populations, however, differ in the mtDNA haplogroup composition. It was established that assimilation of the indigenous pre-Slavic population of Eastern Europe by true Slavs was of great importance to the process of the development of Russian population.

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It is suggested that after the decay of Avar Khaganate the populations included into it were assimilated by Slavic tribes [34]. It is thereby suggested that rather high frequencies of eastern-Eurasian mtDNA lineages observed in the gene pools of some populations of Western and Southern Slavs (especially on the territoryof former Avar Khaganate) can be considered as a consequence of the process described.

Concerning the population of Eastern Europe, it should be noted that the forest zone of Eastern Europe was the area of intense population admixture [35]. It seems likely, that formation of the complex of Mongoloid traits happened not later than in Upper Paleolithic. For this reason, it is suggested that East Siberian populations could have much time for migration to Eastern Europe [35]. The number of such migrations still remains unclear, since in the northwest of Eastern Europe Mongoloid component is detected 10 000–8000 years ago; in Dnepr–Donetsk tribes, 7000–6000 years ago, and on the territory of Ivanovo oblast (Sakhtysh), 6000–5000 years ago [35, 36]. The data on mtDNA variation in Russian populations are consistent with anthropological data, since they point to the substantial differences in the frequencies of Mongoloid mtDNA lineages between the Russian populations of the Russian North, Northwest, and the central/southern regions of the European part of Russia (Table 3). We hope that future investigations would provide
the possibility of analyzing the chronology of the development of the Mongoloid component diversity in the gene pools of Russians and other Slavic populations.

Russian Journal of Genetics, 10.1007/s11177-008-3016-9

On the origin of Mongoloid component in the mitochondrial gene pool of Slavs

B. A. Malyarchuk, M. A. Perkova and M. V. Derenko

Abstract The data on mitochondrial DNA (mtDNA) restriction polymorphism in Czech population (n = 279) are presented. It was demonstrated that in terms of their structure, mitochondrial gene pools of Czechs and other Slavic populations (Russians, Poles, Slovenians, and Bosnians) were practically indistinguishable. In Czechs, the frequency of eastern-Eurasian (Mongoloid) mtDNA lineages constituted 1.8%. The spread of eastern-Eurasian mtDNA lineages belonging to different ethnolinguistic groups in the populations of Europe was examined. Frequency variations of these DNA lineages in different Slavic groups was observed, with the range from 1.2 and 1.6% in Southern and Western Slavs, respectively, to 1.3 to 5.2% in Eastern Slavs, the Russian population of Eastern Europe. The highest frequency of Mongoloid component was detected in the mitochondrial gene pools of Russian populations from the Russian North and the Northwestern region of Russia. This finding can be explained in terms of assimilation of northern-European Finno-Ugric populations during the formation of the Russian population of these regions. The origin of Mongoloid component in the gene pools of different groups of Slavs is discussed.

Link

Geostatistics in biological anthropology of the Irish

American Journal of Physical Anthropology, Volume 136, Issue 1 , Pages 1 - 10

Geostatistics and spatial analysis in biological anthropology

John H. Relethford

Abstract A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology.

Link

HMM-based analysis of polymorphisms in admixed ancestries

New Genomics Software Infers Ancestry With High Accuracy

"With very high accuracy, even for 20 generations, we can trace the populations of those individuals who are indeed represented in your genome," says Stanford computer science Assistant Professor Serafim Batzoglou, who led a team of graduate students to create HAPAA. They include co-lead authors Andreas Sundquist and Eugene Fratkin, as well as Chuong B. Do.

Batzoglou points out that because the HapMap database, a genetic record of 270 individuals of Western European, West African and East Asian ancestry, is very small, HAPAA now can only generate an ethnic profile in terms of these populations.

Fratkin himself was able to verify that he is of European ancestry, but not that he is 1/64th Polish. But more genomics data will become available, the researchers said, which will further expand the software's ability to help people discern their roots.

...

For now the HAPAA software provides proof of this concept but limited utility given the small size of the HapMap database. In the future the software will benefit not only from having more individuals available for comparison, Batzoglou said, but also more detailed data about each individual. Today's genome samples track about 500,000 markers, or common genetic differences, but there are about 10 million candidates. Most individuals have about 3 million such specific differences. As genomics technology improves, he says, so will HAPAA's ability to infer ancestry from the data.

Genome Research, DOI: 10.1101/gr.072850.107

Effect of genetic divergence in identifying ancestral origin using HAPAA

Andreas Sundquist1, Eugene Fratkin1, Chuong B. Do, and Serafim Batzoglou

The genome of an admixed individual with ancestors from isolated populations is a mosaic of chromosomal blocks, each following the statistical properties of variation seen in those populations. By analyzing polymorphisms in the admixed individual against those seen in representatives from the populations, we can infer the ancestral source of the individual’s haploblocks. In this paper we describe a novel approach for ancestry inference, HAPAA (HMM-based analysis of polymorphisms in admixed ancestries), that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy. We also introduce a methodology for evaluating the effect of genetic divergence between ancestral populations and time-to-admixture on inference accuracy. Using HAPAA, we explore the limits of ancestry inference in closely related populations.

Link

PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations

Computer Program Reveals Anyone's Ancestry

"Now that we have found that the program works well, we hope to implement it on a much larger scale, using hundreds of thousands of SNPs and thousands of individuals," said Drineas, who was funded by an NSF CAREER award. "The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways."

Understanding our unique genetic makeup is a crucial step to unraveling the genetic basis for complex diseases. Although the human genome is 99 percent the same from human to human, it is that 1 percent that can have a major impact on our response to diseases, viruses, medications, and toxins. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas said.

This program will help people understand their unique backgrounds and aid historians and anthropologists in their study of where different populations originated and how humans became such a hugely diverse, global society.

The program was more than 99 percent accurate in trials and correctly identified the ancestry of hundreds of individuals. This included people from genetically similar populations (such as Chinese and Japanese) and complex genetic populations like Puerto Ricans who can come from a variety of backgrounds including Native American, European, and African ancestries.

"When we compared our findings to the existing datasets, only one individual was incorrectly identified and his background was almost equally close between Chinese and Japanese," Drineas said. Drineas explains that the results are preliminary, but extremely promising. The team is now working to test their program on a much larger data set.

PLoS Genet 3(9): e160. doi:10.1371/journal.pgen.0030160

PCA-Correlated SNPs for Structure Identification in Worldwide Human Populations

Peristera Paschou1*, Elad Ziv2,3,4, Esteban G. Burchard5,6, Shweta Choudhry7, William Rodriguez-Cintron8, Michael W. Mahoney9, Petros Drineas10

Abstract

Existing methods to ascertain small sets of markers for the identification of human population structure require prior knowledge of individual ancestry. Based on Principal Components Analysis (PCA), and recent results in theoretical computer science, we present a novel algorithm that, applied on genomewide data, selects small subsets of SNPs (PCA-correlated SNPs) to reproduce the structure found by PCA on the complete dataset, without use of ancestry information. Evaluating our method on a previously described dataset (10,805 SNPs, 11 populations), we demonstrate that a very small set of PCA-correlated SNPs can be effectively employed to assign individuals to particular continents or populations, using a simple clustering algorithm. We validate our methods on the HapMap populations and achieve perfect intercontinental differentiation with 14 PCA-correlated SNPs. The Chinese and Japanese populations can be easily differentiated using less than 100 PCA-correlated SNPs ascertained after evaluating 1.7 million SNPs from HapMap. We show that, in general, structure informative SNPs are not portable across geographic regions. However, we manage to identify a general set of 50 PCA-correlated SNPs that effectively assigns individuals to one of nine different populations. Compared to analysis with the measure of informativeness, our methods, although unsupervised, achieved similar results. We proceed to demonstrate that our algorithm can be effectively used for the analysis of admixed populations without having to trace the origin of individuals. Analyzing a Puerto Rican dataset (192 individuals, 7,257 SNPs), we show that PCA-correlated SNPs can be used to successfully predict structure and ancestry proportions. We subsequently validate these SNPs for structure identification in an independent Puerto Rican dataset. The algorithm that we introduce runs in seconds and can be easily applied on large genome-wide datasets, facilitating the identification of population substructure, stratification assessment in multi-stage whole-genome association studies, and the study of demographic history in human populations.

Link

How tall you are may predict how jealous you are

Evolution and Human Behavior
Volume 29, Issue 2, March 2008, Pages 133-139

Height predicts jealousy differently for men and women

Abraham P. Buunk et al.

Abstract

Because male height is associated with attractiveness, dominance, and reproductive success, taller men may be less jealous. And because female height has a curvilinear relationship with health and reproductive success (with average-height females having the advantages), female height may have a curvilinear relationship with jealousy. In Study 1, male height was found to be negatively correlated with self-reported global jealousy, whereas female height was curvilinearly related to jealousy, with average-height women reporting the lowest levels of jealousy. In Study 2, male height was found to be negatively correlated with jealousy in response to socially influential, physically dominant, and physically attractive rivals. Female height was negatively correlated with jealousy in response to physically attractive, physically dominant, and high-social-status rivals; in addition, quadratic effects revealed that approximately average-height women tend to be less jealous of physically attractive rivals but more jealous of rivals with “masculine” characteristics of physical dominance and social status.

Link

Long, but not too long legs are attractive

Evolution and Human Behavior
Volume 29, Issue 2, March 2008, Pages 86-91

Adaptive preferences for leg length in a potential partner

Piotr Sorokowskia, and Boguslaw Pawlowski

Abstract

It has been shown that height is one of the morphological traits that influence a person's attractiveness.next term To date, few studies have addressed the relationship between different components of height and physical previous termattractiveness.next term Here, we study how leg length influences previous termattractivenessnext term in men and women. Stimuli consisted of seven different pictures of a man and seven pictures of a woman in which the ratio between leg length and height was varied from the average phenotype by elongating and shortening the legs. One hundred men and 118 women were asked to assess the previous termattractivenessnext term of the silhouettes using a seven-point scale. We found that male and female pictures with shorter than average legs were perceived as less attractive by both sexes. Although longer legs appeared to be more attractive, this was true only for the slight (5%) leg length increase; excessively long legs decreased body previous termattractivenessnext term for both sexes. Because leg length conveys biological quality, we hypothesize that such preferences reflect the workings of evolved mate-selection mechanisms. Short and/or excessively long legs might indicate maladaptive biological conditions such as genetic diseases, health problems, or weak immune responses to adverse environmental factors acting during childhood and adolescence.

Link

AnthroScape forum

AnthroScape: Human Biodiversity Forum is a new forum in the spirit of the now defunct Dodona forum, founded by Racial Reality.

Computer taught to recognize female attractiveness

Computer Taught To Recognize Attractiveness In Women:

In the first step of the study, 30 men and women were presented with 100 different faces of Caucasian women, roughly of the same age, and were asked to judge the beauty of each face. The subjects rated the images on a scale of 1 through 7 and did not explain why they chose certain scores. Kagian and his colleagues then went to the computer and processed and mapped the geometric shape of facial features mathematically.

Additional features such as face symmetry, smoothness of the skin and hair color were fed into the analysis as well. Based on human preferences, the machine "learned" the relation between facial features and attractiveness scores and was then put to the test on a fresh set of faces.

Says Kagian, "The computer produced impressive results -- its rankings were very similar to the rankings people gave." This is considered a remarkable achievement, believes Kagian, because it's as though the computer "learned" implicitly how to interpret beauty through processing previous data it had received.

Vision Research http://dx.doi.org/10.1016/j.visres.2007.11.007

A machine learning predictor of facial attractiveness revealing human-like psychophysical biases

Amit Kagian et al.

Abstract

Recent psychological studies have strongly suggested that humans share common visual preferences for facial attractiveness. Here, we present a learning model that automatically extracts measurements of facial features from raw images and obtains human-level performance in predicting facial attractiveness ratings. The machine’s ratings are highly correlated with mean human ratings, markedly improving on recent machine learning studies of this task. Simulated psychophysical experiments with virtually manipulated images reveal preferences in the machine’s judgments that are remarkably similar to those of humans. Thus, a model trained explicitly to capture a specific operational performance criteria, implicitly captures basic human psychophysical characteristics.

Link

Austronesian expansion in Admiralty Islands of Melanesia

Molecular Biology and Evolution, doi:10.1093/molbev/msn078

The impact of the Austronesian expansion: evidence from mtDNA and Y-chromosome diversity in the Admiralty Islands of Melanesia

Manfred Kayser et al.

The genetic ancestry of Polynesians can be traced to both Asia and Melanesia, which presumably reflects admixture occurring between incoming Austronesians and resident non-Austronesians in Melanesia before the subsequent occupation of the greater Pacific; however, the genetic impact of the Austronesian expansion to Melanesia remains largely unknown. We therefore studied the diversity of non-recombining Y-chromosomal (NRY) and mitochondrial (mt) DNA in the Admiralty Islands, located north of mainland Papua New Guinea, and updated our previous data from Asia, Melanesia and Polynesia with new NRY markers. The Admiralties are occupied today solely by Austronesian-speaking groups, but their human settlement history goes back 20,000 years prior to the arrival of Austronesians about 3,400 years ago. On the Admiralties we found substantial mtDNA and NRY variation of both Austronesian and non-Austronesian origin, with higher frequencies of Asian mtDNA and Melanesian NRY haplogroups, similar to previous findings in Polynesia, and perhaps as consequence of Austronesian matrilocality. Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity. These results provide further support for the "Slow Boat" model of Polynesian origins, according to which Polynesian ancestors originated from East Asia but genetically mixed with Melanesians before colonizing the Pacific. We also observed that non-Austronesian groups of coastal New Guinea and Island Melanesia had significantly higher frequencies of Asian mtDNA haplogroups than of Asian NRY haplogroups, suggesting sex-biased admixture perhaps as a consequence of non-Austronesian patrilocality. We additionally found that the predominant NRY haplogroup of Asian origin in the Admiralties (O-M110) likely originated in Taiwan, thus providing the first direct Y-chromosome evidence for a Taiwanese origin of the Austronesian expansion. Furthermore, we identified a NRY haplogroup (K-P79, also found on the Admiralties) in Polynesians that most likely arose in the Bismarck Archipelago, providing the first direct link between northern Island Melanesia and Polynesia. These results significantly advance our understanding of the impact of the Austronesian expansion and of human history in the Pacific region.

Link

Ancient mtDNA of northeastern North America

American Journal of Physical Anthropology DOI: 10.1002/ajpa.20835

Using ancient mtDNA to reconstruct the population history of northeastern North America

Beth Alison Schultz Shook et al.

Mitochondrial DNA (mtDNA) was extracted and analyzed from the skeletal remains of 44 individuals, representing four prehistoric populations, and compared to that from two other prehistoric and several contemporary Native American populations to investigate biological relationships and demographic history in northeastern North America. The mtDNA haplogroup frequencies of ancient human remains from the Morse (Red Ocher tradition, 2,700 BP) and Orendorf (Mississippian tradition, 800 BP) sites from the Central Illinois River Valley, and the Great Western Park (Western Basin tradition, 800 BP) and Glacial Kame (2,900 BP) populations from southwestern Ontario, change over time while maintaining a regional continuity between localities. Haplotype patterns suggest that some ancestors of present day Native Americans in northeastern North America have been in that region for at least 3,000 years but have experienced extensive gene flow throughout time, resulting, at least in part, from a demic expansion of ancestors of modern Algonquian-speaking people. However, genetic drift has also been a significant force, and together with a major population crash after European contact, has altered haplogroup frequencies and caused the loss of many haplotypes.

Link

mtDNA haplogroups A2 and B2 in pre-Clovis Americans

Read also, a much related recent study on The phylogeny of Native American mtDNA haplogroups

Researchers, led by UO archaeologist, find pre-Clovis human DNA:

DNA from dried human excrement recovered from Oregon's Paisley Caves is the oldest found yet in the New World -- dating to 14,300 years ago, some 1,200 years before Clovis culture -- and provides apparent genetic ties to Siberia or Asia, according to an international team of 13 scientists.

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The team’s extensively documented analyses on mitochondrial DNA -- genetic material passed on maternally -- removed from long-dried feces, known as coprolites, were published online April 3 in Science Express ahead of regular publication in the journal Science.

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The DNA testing indicated that the feces belonged to Native Americans in haplogroups A2 and B2, haplogroups common in Siberia and east Asia.

Science DOI: 10.1126/science.1154116

DNA from Pre-Clovis Human Coprolites in Oregon, North America

M. Thomas P. Gilbert et al.

The timing of the first human migration into the Americas and its relation to the appearance of the Clovis technological complex in North America ca. 11-10.8 thousand radiocarbon years before present (14C ka B.P.) remains contentious. We establish that humans were present at Paisley 5 Mile Point Caves, south-central Oregon, by 12,300 14C yr. B.P., through recovery of human mtDNA from coprolites, directly dated by accelerator mass spectrometry. The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 14C years earlier than currently accepted dates for the Clovis-complex.

Link

International attitudes towards immigration

Gene Expression points me to an article (pdf) on attitudes in several countries towards immigration; there are quite a few interesting survey questions, which you can read in the freely available paper.

POLITICAL STUDIES: 2008 VOL 56, 33–56

Immigration and the Imagined Community in Europe and the United States

Jack Citrin John Sides

Both Europe and the United States are confronting the challenges of economic and cultural integration posed by immigration. This article uses the ESS and CID surveys to compare transatlantic public opinion about immigrants and immigration.We find more tolerance for cultural diversity in the United States, but we also find that Americans, like Europeans, tend to overestimate the number of immigrants in their countries and tend to favor lower levels of immigration. The underpinnings of individual attitudes are similar in all countries and immigration attitudes are surprisingly unrelated to country-level differences in GDP, unemployment and the number and composition of the foreign born.An implication of these findings is that acceptance of higher levels of immigration, deemed by many to be an economic need, will require both more selective immigration policies and an emphasis on the cultural assimilation of newcomers.

New Y-chromosome haplogroup tree

UPDATE (Apr 2):

The report is now online. Unfortunately, the supplementary information is not yet online.

UPDATE 2:

I think that the Genographic Project has a lot of rewriting to do in their Atlas of the Human Journey given the proposed dates for the major haplogroups. For example, the oft-repeated claim that R1b has something to do with the Cro-Magnons is no longer tenable.

UPDATE 3:

The supplementary material can be found here (pdf).

Genome Research DOI: 10.1101/gr.7172008

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Tatiana M. Karafet et al.

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Link

A new Y-chromosome haplogroup tree will be published in Genome Research. Here is the public release:

The Y chromosome retains a remarkable record of human ancestry, since it is passed directly from father to son. In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.

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Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements. “The major lineages within the most common African haplogroup, E, are now all sorted out, with the topology providing new interpretations on the geographical origin of ancient sub-clades,” describes Hammer. “When one polymorphism formerly described as unique, but recently shown to have reversed was replaced by recently reported markers, a sub-haplogroup of haplogroup O, the most common in China, was considerably rearranged,” explains Fernando Mendez, a co-author of the study.

In addition to improving the resolution of branches, the latest reconstruction of the tree allows estimates of time to the most recent common ancestor of several haplogroups. “The age of [haplogroup] DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” says Hammer, describing an example of the fine resolution of age that is now possible. “Haplogroup E is older than previously estimated, originating approximately 50,000 years ago.”

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”

Guess their origin and rate their attractiveness

Each of these three men is a facial composite of individuals from a single European nation.


UPDATE (Apr 3):

The results of the poll are in:

Who is more attractive: Left: 155 (64%), Middle: 52 (21%), Right: 36 (15%)
The man on the Left is: Germanic: 130 (51%), Finno-Ugrian: 81 (32%), Slavic: 29 (11%), Romance: 11 (4%), Greek: 4 (2%)
The man in the Middle is: Slavic: 56 (26%), Germanic: 45 (21%), Romance: 45 (21%), Finno-Ugrian: 40 (18%), Greek: 31 (14%)
The man on the Right is: Slavic: 115 (53%), Greek: 44 (20%), Romance: 31 (14%), Finno-Ugrian: 14 (6%), Germanic: 14 (6%)

Readers got one of the three right in the majority.

UPDATE (Apr 4): They are Finno-Ugrian, Germanic, Slavic. I won't reveal their nationalities just yet because I plan to do some more comparisons.

mtDNA time depth of humanity more recent than previously thought

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.01.019

A Bayesian Evaluation of Human Mitochondrial Substitution Rates

Phillip Endicott and Simon Y.W. Ho

Accurate estimates of mitochondrial substitution rates are central to molecular studies of human evolution, but meaningful comparisons of published studies are problematic because of the wide range of methodologies and data sets employed. These differences are nowhere more pronounced than among rates estimated from phylogenies, genealogies, and pedigrees. By using a data set comprising mitochondrial genomes from 177 humans, we estimate substitution rates for various data partitions by using Bayesian phylogenetic analysis with a relaxed molecular clock. We compare the effect of multiple internal calibrations with the customary human-chimpanzee split. The analyses reveal wide variation among estimated substitution rates and divergence times made with different partitions and calibrations, with evidence of substitutional saturation, natural selection, and significant rate heterogeneity among lineages and among sites. Collectively, the results support dates for migration out of Africa and the common mitochondrial ancestor of humans that are considerably more recent than most previous estimates. Our results also demonstrate that human mitochondrial genomes exhibit a number of molecular evolutionary complexities that necessitate the use of sophisticated analytical models for genetic analyses.

Link

Y chromosomes of Hungarians

I had blogged about this research in 2005 when it was presented in the ESHG conference. Now there is a full article in Annals of Human Genetics. See also my post on Ancient Hungarian mtDNA. An interesting bit from the paper:

Haplogroup I was detected with almost equal frequency in the two modern populations: 24% in Hungarians and 21.7% in Szeklers. However, two of its major subclades- I1a-M253 and I1b*(xM26) – show an opposite occurrence in the two ethnic groups, 8% and 13%, respectively, in Hungarians, and 16.5% and 5.2% in Szeklers. These are within the range of normal central and eastern European values (Rootsi et al., 2004; Peričić et al., 2005). The elevated frequency of Hg I1a together with higher frequency of R1b-M269 in Szekler population might be the consequence, at least in part, of the genetic impact of people of German origin, who settled in Transylvania from the 12th century onwards (Transylvanian Saxons)(Makkai, 1990; Kristó, 2002).

Also:

The J1-M267 Y-chromosomal lineage is notably frequent in Szeklers (10.3%; a value far above the range for other central and eastern European populations (Semino et al., 2000a, 2004; Di Giacomo et al., 2004), while its frequency in Hungarians (3.0%) is unremarkable.

...

Among these J2-M172 subclades, J2e1-M102 is more frequent in Szeklers (7.2%) than in Hungarians (4.0%), while the undifferentiated J2-M172* Y chromosomes are slightly more common in Hungarian population (8% vs. 3.1%). Both J2f*-M67 and J2f1-M92 lineages were detected in our study in one single individual, in each population.

Interestingly, the two ancient indiviuals harboring Y-haplogroup N3 (anc21 and anc28) were also classified anthropologically as Europo-Mongolid, while anc21 harbored the Caucasoid mtDNA haplogroup H. This is consistent with the notion that the Mongoloid elements in ancient Hungarians fused with Caucasoid elements, although the results from the modern population suggests that the blend was finally overwhelmed by the Caucasoid component.

Annals of Human Genetics doi:10.1111/j.1469-1809.2008.00440.x

Y-Chromosome Analysis of Ancient Hungarian and Two Modern Hungarian-Speaking Populations from the Carpathian Basin

B. Csányi et al.

The Hungarian population belongs linguistically to the Finno-Ugric branch of the Uralic family. The Tat C allele is an interesting marker in the Finno-Ugric context, distributed in all the Finno-Ugric-speaking populations, except for Hungarians. This question arises whether the ancestral Hungarians, who settled in the Carpathian Basin, harbored this polymorphism or not. 100 men from modern Hungary, 97 Szeklers (a Hungarian-speaking population from Transylvania), and 4 archaeologically Hungarian bone samples from the 10^th century were studied for this polymorphism. Among the modern individuals, only one Szekler carries the Tat C allele, whereas out of the four skeletal remains, two possess the allele. The latter finding, even allowing for the low sample number, appears to indicate a Siberian lineage of the invading Hungarians, which later has largely disappeared.

The two modern Hungarian-speaking populations, based on 22 Y-chromosomal binary markers, share similar components described for other Europeans, except for the presence of the haplogroup P*(xM173) in Szekler samples, which may reflect a Central Asian connection, and high frequency of haplogroup J in both Szeklers and Hungarians. MDS analysis based on haplogroup frequency values, confirms that modern Hungarian and Szekler populations are genetically closely related, and similar to populations from Central Europe and the Balkans.

Link