Ancient mtDNA from Sampula population in Xinjiang

From the paper:

Physical anthropology of Shao et al. revealed that the ancient human bones from Sampula exhibited primarily Mongoloid characteristics with certain European features, but Han et al. believed that Sampula populations are mainly of European character and actually are close to that of the Eastern Mediterranean type.

...

In conclusion, the analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population of European and Asian, corresponding to the physical anthopology result of Shao et al.

Progress in Natural Science, Volume 17, Issue 8 August 2007 , pages 927 - 933

Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

Chengzhi Xie et al.

Abstract

The archaeological site fo Sampula cemetery was located about 14 km to the southwest of the Luo County in Xinjiang Khotan, China, belonging to the ancient Yutian kingdom. 14C analysis showed that this cemetery was used from 217 B.C. to 283 A. D. Ancient DNA was analysed by 364 bp of the mitochondrial DNA hypervariable region 1 (mtDNA HVR-1), and by six restriction fragment length polymorphism (RFLP) sites of mtDNA coding region. We successfully extracted and sequenced intact stretches of maternally inherited mtDNA from 13 out of 16 ancient Sampula samples. The analysis of mtDNA haplogroup distribution showed that the ancient Sampula was a complex population with both European and Asian Characteristics. Median joining network of U3 sub-haplogroup and multi-dimensional scaling analysis all showed that the ancient Sampula had maternal relationship with Ossetian and Iranian.

Link

Classifier for 23andMe/deCODEme genotype data

As I mentioned in my previous post, the genotype data provided by companies such as 23andMe and deCODEme allow us to build ancestry assessment tools that use published genotype data from scientific studies.

I have built a simple classifier tool based on the panel of 300 markers of Price et al. (2008), which uses the frequency data supplied in this paper to assess the probability that an individual belongs to the "Northwest European", "Southeast European", or "Ashkenazi Jewish" categories.

The input is genotype values for a number of markers (e.g., the 169/192 markers in common between the deCODEme and 23andMe results) for an individual, and the output is a set of three probabilities for belonging to any of the three groups, summing up to 1.

Using the Greg and Lilly Mendel data that you can download from 23andMe, I came up with the following probabilities (NWE,SEE,AJ):

Greg: 0.89, 0.11, 0
Lilly: 1, 0, 0
(corrected June 15)

23andMe lists the similarity of these individuals to "Northern Europeans","Southern Europeans", and "Near Easterners" as:

Greg: 67.84, 67.74, 67.15
Lilly: 67.85, 67.72, 67.11


So, at least for these two individuals the results of my calculator appear to be analogous to those reported by 23andMe, with Lilly seeming more "Northern" than her husband.

PS: Unfortunately my calculator cannot be released at present, as it's not a standalone program but rather relies on a bunch of different tools with minimum development.

deCODEme, 23andMe SNPs and published Caucasoid substructure studies

Both 23andMe and deCODEme are offering SNP genotyping services which includes an assessment of ancestry. Both companies offer admixture estimates for major continental groups (races), as well as an assessment of similarity with more specific groups: 23andMe uses categories such as Northern European, Southern European, Near Easterner etc. while deCODEme compares clients' profile with "reference individuals" such as Basque, Russian, Tuscan, Orcadian etc. B

Both services seem to use the HGDP populations for the more specific (subracial) similarity assessment. In the last couple of years, there have been a few studies that looked at intra-European or intra-Caucasoid genomic variation, so it might be possible to devise a test using the published results and the SNPs tested by these companies.

deCODEme uses the Illumina 1M BeadChip, while 23andMe uses the Illumina HumanHap550+ BeadChip with an additional custom set of markers. The deCODEme chip measures 1,072,820 SNPs, while 23andME (according to the "Greg Mendel" data you can download from their website) measures 571,754 SNPs.

Price et al. (2008) have identified a set of 300 ancestry informative markers including that distinguishes between NW/SE Europeans and SE Europeans/Ashkenazi Jews. The deCODEme set tests for 192 of these markers, whereas 23andME tests for 169 of them.

Tian et al. (2008) have identified 1,441 European substructure ancestry informative markers (rtf) (ESAIMs). deCODEme tests 1,412 of them, while 23andME tests 1,424 of them. As far as I can tell, the original study did not publish either frequency data or individual genotypes for these markers, so using them to infer ancestry may not be possible. (Let me know if this data exists and I missed it).

(added Jun 12) Bauchet et al. (2007) have identified a panel of 1,200 markers for European population substructure and report frequency data for Southeastern and Northern Europeans (xls). deCODEme tests for 508 of them, and 23andMe tests for 438 of them.

Seldin et al. (2006) have provided frequency data (pdf) in several populations for 5,735 SNPs. markers. deCODEme tests for 3,502 of these, while 23andMe tests for 2,242 of them.

One could also use the 650K SNPs from Stanford. There are 660,755 non-mitochondrial SNPs in the freely available data, all of which are tested by deCODEme; 23andMe which partially funded the study (Li et al. (2008)) tests 549,118 of them.

In conclusion, it seems possible to make your own test using commercially available SNPs and freely available data other than the HGDP populations.

Y chromosomes and mtDNA from Siberian Khanty and Mansi

European Journal of Human Genetics doi: 10.1038/ejhg.2008.101

Northwest Siberian Khanty and Mansi in the junction of West and East Eurasian gene pools as revealed by uniparental markers

Ville N Pimenoff et al.

Abstract

Northwest Siberia is geographically remote territory, which has been settled by indigenous human populations probably since the Upper Paleolithic. To investigate the genetic landscape of Northwest Siberians, we have analyzed mitochondrial and Y chromosome DNA polymorphisms of 169 unrelated individuals from Khanty and Mansi ethnic groups in Northwest Siberia. In addition, HVS-I sequences (N=3522) and Y chromosome SNP data (N=2175), obtained from the literature, were used to elucidate the genetic relationships among the North Eurasian populations. The results show clinal distributions of mtDNA and Y chromosome haplogroups along East–West axis of Northern Eurasia. In this context, the Ugric-speaking Khanty and Mansi appear as unique intermediate populations carrying Upper Paleolithic and more recent haplotypes typical for both West and East Eurasian gene pools. This admixture indicates that the Khanty and Mansi populations have resided in the contact zone of genetically distinguishable eastern and western Eurasia.

Link

Makeup and female Caucasian attractiveness

Int J Cosmet Sci. 2003 Aug;25(4):199-205.

Do cosmetics enhance female Caucasian facial attractiveness?

Mulhern R, Fieldman G, Hussey T, Lévêque JL, Pineau P.

This study sought to investigate whether cosmetics do improve female facial attractiveness, and to determine whether the contribution of different cosmetic products are separable, or whether they function synergistically to enhance female beauty. Ten volunteers were made up by a beautician under five cosmetics conditions: (i) no make-up; (ii) foundation only; (iii) eye make-up only; (iv) lip make-up only; and (v) full facial make-up. Male and female participants were asked to view the 10 sets of five photographs, and rank each set from most attractive to least attractive. As predicted, faces with full make-up were judged more attractive than the same faces with no make-up. Sex differences within the results were also apparent. Women judged eye make-up as contributing most to the attractiveness. Men rated eye make-up and foundation as having a significant impact on the attractiveness of a full facial makeover. Surprisingly, lipstick did not appear to contribute to attractiveness independently.

Link

ESHG 2008 abstracts

The European Society of Human Genetics conference is coming up, and there are some very interesting abstracts.

Note: The ESHG site has updated with a notice that the abstracts are embargoed until their presentation time. Therefore, I have decided to remove the body of this post until then, although I think it is a bit weird to embargo something that one places on the public web. In any case, you can find the abstracts easily by going to the site above. (June 1): post restored.

The peopling of North Asia: Y and X perspectives

V. A. Stepanov, V. Kharkov, I. Khitrinskaya, O. Medvedeva, M. Spiridonova, A. Marusin, V. Puzyrev; Institute for Medical Genetics, Tomsk, Russian Federation.

Presentation Number: P07.056

To reconstruct the origin and evolution of human populations in North Asia we investigated the genetic diversity in 50 population samples (about 2000 individuals totally) using Y and X chromosome lineages. Y-chromosomal haplotypes were constructed with unique event polymorphisms (UEP) and STR markers according to Y Chromosome consortium (YCC) classification. SNP markers in a single 60 kb linkage disequilibrium region of ZFX gene was used to trace the X chromosomal population history. The genetic diversity of Y haplogroups was quite high (0.70 - 0.95) in most populations except few very isolated groups. The proportion of inter-population differences in the total genetic variability measured by Fst statistics is 17% for binary haplogroups and 19% for YSTR. Multidimensional scaling and principal component analysis revealed four major components in North Asian Y gene pool, reflecting the presence of Paleoasiatic (Q), Proto-Uralic (N3, N2), Eastern Asian (O, C), and Western Eurasian (R1, I, J) lineages. X-chromosomal haplotypes in North Asia are less divers (gene diversity within populations 0.65 - 0.80) and less differentiated (Fst = 4%) compared to Y lineages. The population clustering by X and Y gives, to a first approximation, a similar picture, and matrixes of genetic distances between populations for X and Y haplotypes significantly correlates. The age of genetic diversity generation and time of population differentiation demonstrates the Upper Paleolithic origin of major Y and X lineages and post-glacial population expansions. This work is supported by RFBR grants ##06-04-48274 and 07-04-01629.

The following seems to be a very important study; in particular the notion that particular Y chromosome/mtDNA haplogroups may be associated with higher or lower fertility may have implications about their distribution.

UPDATE (May 21): I did a quick and dirty analysis of the Y-haplogroup and mtDNA-haplogroup data from Bosch et al. (2006) (Ann Hum Genet. 2006 Jul;70(Pt 4):459-87.), and there is a -0.43 correlation between Y-haplogroup I and mtDNA-haplogroup H and a +0.46 correlation between Y-haplogroup R1 and mtDNA-haplogroup H. While not significant (with only 10 populations), this is definitely in the right direction for a selection effect for/against specific Y-DNA/mtDNA combinations.

... on the other hand, another quick and dirty analysis of 23 populations from Rootsi's survey on Y-haplogroup I and mtDNA frequencies from AJHG Volume 80, Issue 4, April 2007, Pages 759-768 didn't turn up any correlation. Perhaps, someone can look at possible correlations between Y-chromosome and mtDNA haplogroups in Europe to see if anything interesting turns up.

Male infertility induced by mtDNA/Y unfavorable combination? An association study on human mitochondrial DNA

S. C. Gomes1, S. Fernandes2, R. Gonçalves1, A. T. Fernandes1, A. Barros3, H. Geada4, A. Brehm1; 1Human Genetics Laboratory, University of Madeira, Funchal, Portugal, 2Genetics Department, Faculty of Medicine, University of Porto, Porto, Portugal, 3Centre of Reproductive Genetics A Barros, Porto, Portugal, 4Faculty of Medicine, University of Lisbon, Lisboa, Portugal.

Presentation Number: P07.084

There is growing evidence that certain mtDNA haplogroups determine a genetic susceptibility to various disorders bringing out the interest in the possible role of mtDNA background on the phenotype expression of mitochondrial genetic disorders. An association between haplogroup T and asthenospermia has been reported and several sublineages of haplogroup U were associated with differences in sperm motility and vitality. The deletion of some DAZ copies gene in 10-15% of azoospermic and oligospermic patients has been reported but also present in fertile men belonging to certain Y-haplogroups. The findings of one study have rarely been replicated by studies in other populations and conflicting associations have been reported. Our focus in this case-control study is to investigate the existence of other influences, besides a weak mtDNA background, promoting male infertility. The occurrence of a specific mtDNA variant associated to a certain Y-chromosome haplogroup could represent a vital link that will compromise the sperm function and be responsible for male infertility. A group of 99 infertile men and other one composed by 90 subjects with proven fertility were selected and analysed. The frequency of the combination mtDNA-haplogroup H (especially with the CRS sequence) and Y-haplogroup R was higher in fertile than in infertile men seemingly to be favorable to fertility. On the other hand, a considerable number of infertile men belonging to mtDNA-haplogroup H (CRS) and to Y-haplogroup I, associated to a specific DAZ gene deletion pattern- 2+4d, suggests a non favorable combination to male fertility.

The Bayash Roma: phylogenetic dissection of Eurasian paternal genetic elements

I. Martinovic Klaric, M. Pericic Salihovic, L. Barac Lauc, B. Janicijevic; Institute for Anthropological Research, Zagreb, Croatia.

Presentation Number: P07.110

The Bayash consist of numerous and small Romani groups speaking different dialects of the Romanian language and living dispersedly in Croatia, Hungary, Bosnia and Herzegovina, Serbia, Romania, Bulgaria, and to the lesser extent in Macedonia, Greece, Ukraine, Slovakia and Slovenia. Larger Bayash groups migrated to Croatia most likely during the 19th century, after abolition of slavery in Romania. Molecular architecture and the origin of the Croatian Bayash paternal gene pool was addressed by analysing 151 Bayash Y chromosomes from two Croatian regions, 332 Y chromosomes from Romani populations across Europe, 814 Y-chromosomes from non-Romani host populations living in Southeastern, Southern and Eastern Europe as well as with 1680 Y-chromosomes from South Asian populations. The Bayash in Croatia represent one population of largely shared paternal genetic history characterized by substantial percentage (44%) of common H1-M82 and E3b1-M78 lineages. Relatively ancient expansion signals and limited diversity of Indian specific H1-M82 lineages imply descent from closely related paternal ancestors who could have been settled in the Indian subcontinent between 7th and 9th centuries AD. Minimal time divergence of the Bayash subpopulations is consistent with their putative migratory split within Romania towards Wallachia and Transilvania. Substantial percentage of E3b1 lineages and high associated microsatellite variance in the Bayash men is a reflection of significant admixture with majority populations from the Vardar-Morava-Danube catchment basin - possibly a common paternal signature of Romani populations in Southeastern Europe. Additional traces of admixture are evident in the modest presence of typical European haplogroups.

Are the Moravian Valachs of Czech Republic the Aromuns of Central Europe? Model population for isolation and admixture

E. Ehler1,2, V. Vančata2; 1Department of Anthropology and Human Genetics, Charles University in Prague, Faculty of Science, Prague, Czech Republic, 2Department of Biology and Ecological Education, Charles University in Prague, Faculty of Education, Prague, Czech Republic.

Presentation Number: P07.129

Moravian Valachs of Czech Republic are one of the most distinct ethnic groups from Central Europe. Related to similar populations in Poland and Slovakia, they emerge at the end of 15th century, as the north-westernmost prominence of migration that started 250 years earlier in northern Romania. Being predominately highland sheep herders and of putative Romanian origin, they represent a Central European analogue of Balkan Aromanian populations. We have gathered Y-chromosomal, linguistic, ethnographic and historical data for this population and compared them with surrounding as well as with east European populations. Linguistic data show specific parts of shared vocabulary of Romanian origin between several pastoral groups in Central and Eastern Europe. Comparing genetic and linguistic pairwise distance matrices (Mantel test) in these populations did not revealed any significant correlation. Thus we confirmed that plain geographical distance still plays the major role in genetic distances between populations in Europe. From our further analysis it is clear, that the Moravian Valachs, after at least five centuries of admixture, are not overly genetically different from surrounding populations. On the other hand, from the point of view of intra-population diversity, they are much more similar to isolated Balkan populations (e.g. Aromuns) than to Central European populations.

Phylogeography of the human Y chromosome haplogroup E3a

F. Cruciani1, B. Trombetta1, D. Sellitto2, C. Nodale1, R. Scozzari1; 1Sapienza Università di Roma, Rome, Italy, 2Consiglio Nazionale delle Ricerche, Rome, Italy.

Presentation Number: P07.134

The Y chromosome specific biallelic marker DYS271 defines the most common haplogroup (E3a) currently found in sub-Saharan Africa. A sister clade, E3b (E-M215), is rare in sub-Saharan Africa, but very common in northern and eastern Africa. On the whole, these two clades represent more than 70% of the Y chromosomes of the African continent. A third clade belonging to E3 (E3c or E-M329) has been recently reported to be present only in eastern Africa, at low frequencies. In this study we analyzed more than 1,600 Y chromosomes from 55 African populations, using both new and previously described biallelic markers, in order to refine the phylogeny and the geographic distribution of the E3a haplogroup. The most common E-DYS271 sub-clades (E-DYS271*, E-M191, E-U209) showed a non uniform distribution across sub-Saharan Africa. Most of the E-DYS271 chromosomes found in northern and western Africa belong to the paragroup E-DYS271*, which is rare in central and southern Africa. In these latter regions, haplogroups E-M191 and E-U209 show similar frequency distributions and coalescence ages (13 and 11 kyr, respectively), suggesting their involvement in the same migratory event/s. By the use of two new phylogenetically equivalent markers (V38 and V89), the earlier tripartite structure of E3 haplogroup was resolved in favor of a common ancestor for haplogroups E-DYS271 (formerly E3a) and E-M329 (formerly E3c). The new topology of the E3 haplogroup is suggestive of a relatively recent eastern African origin for the majority of the chromosomes presently found in sub-Saharan Africa.

Y-chromosome lineages in Xhosa and Zulu Bantu speaking populations

R. P. A. Gonçalves, H. Spínola, A. Brehm; Human Genetics Laboratory, Funchal, Portugal.

Presentation Number: P07.137

Y-chromosome Single Nucleotide Polymorphisms have been analysed in Zulu and Xhosa, two southern Africa Bantu speaking populations. These two ethnic groups have their origin on the farmer’s Bantu expansion from Niger-Congo border towards sub-Sahel regions on the southern tip of the continent, during the past 3000 years. Seven different Y-chromosome haplogroups were found in Zulu contrasting with only two in Xhosa. E3a, a common haplogroup among West sub-Saharans associated to Bantu migration was the most prevalent in both populations (56.9% in Zulu and 90% in Xhosa). The second most common haplogroup was E2 (29.3% in Zulu and 10% in Xhosa), present both in West and East African populations. The present-day Zulu and Xhosa paternal legacy is essentially of West sub-Saharan origin. Zulu population shows a most diverse genetic influence comparing to Xhosa, revealing some pre-Bantu expansion markers and East African influences. Zulu presents 8.6% Y-chromosome haplogroups (A, B, J1) of non-Bantu influence that could indicate gene flow from other populations, particularly Khoisan.

Human genetic population structure: Patterns and underlying processes

Presentation Time: Tuesday, 9:15 a.m. - 9:45 a.m.

G. Barbujani; University of Ferrara, Department of Biology and Evolution, Ferrara, Italy.

Presentation Number: S15.2

Classical studies of genetic diversity in humans consistently showed that the largest proportion of human diversity occurs among members of the same population. On average, differences among different populations in the same continent represent 5% of the global human variance, and differences among continents another 10%. Genetic variation is largely discordant across the genome, meaning that different loci show different spatial patterns, and implying that a good description of population structure can only be based on the analysis of multiple loci. Studies of single loci are also unlikely to reasonably identify an individual’s place of origin. A general decline of genetic of genetic diversity with distance from Africa, and a parallel increase in linkage disequilibrium, can be accounted for by the effects of a series of founder effects accompanying the spread of anatomically-modern humans from Africa. Recent DNA analyses at the global level show that most allelic variants are cosmopolitan and only a small percentage are continent-specific, whereas a clearer continental structure emerges when considering composite haplotypes. This suggests that, at the global level, gene flow has had a strong impact on genetic diversity, through both directional dispersal and successive short-range migratory exchanges. At the local level, several factors have contributed to genetic differentiation, and, in particular, language barriers have been shown to be associated with small but non-negligible increases of the genetic differences between neighboring populations.

Hierarchical analysis of 28 Y-chromosome SNP’s in the population of the Republic of Macedonia

P. Noveski, S. Trivodalieva, G. D. Efremov, D. Plaseska-Karanfilska;
Macedonian Academy of Sciences and Arts, Research Centre for Genetic Engineering and Biotechnology, Skopje, Macedonia, The Former Yugoslav Republic of.

Presentation Number: P05.211

Analysis of Y-chromosome haplogroups, defined by single nucleotide polymorphisms (SNP’s), has become a standard approach for studying the origin of human populations and measuring the variability among them. Furthermore, Y-SNP’s represent a new forensic tool, because their population specificity may allow to determine the origin of any male sample of interest for forensic purposes. The aim of this study was to develop a strategy for rapid, simple and inexpensive Y-chromosome SNP’s typing in the population of R. Macedonia. We have studied a total of 343 DNA male samples; 211 Macedonians, 111 Albanians and 21 of other ethnic origin (Roma, Serbs and Turks). Methodology included multiplex PCR and single nucleotide extension reaction by SNaPshot multiplex kit. The set of 28 markers has been grouped in 5 multiplexes in order to determine the most frequent haplogroups using only 1 or 2 multiplexes. Twenty different Y haplogroups were determined among 343 male DNA samples. The finding that five haplogroups (E3b1, I1b1, J2b1a, R1a and R1b) comprise more than 70% of the Y chromosomes is consistent with the typical European Y chromosome gene pool. The distribution of the Y-haplogroups differs between Macedonians and Albanians. The most common Y haplogroup among Macedonians is I1b1 (27.5%), followed by three haplogroups present with similar frequencies E3b1 (15.6%), R1a (14.2%) and R1b (11.4%). Among Albanians the most frequent Y haplogroup is E3b1 (28.8%), followed by R1b (18.0%), J2b1a (13.5%) and R1a (12.6%).

The following paper (probably) refers to a recent study, according to which:

One of the most elevated values of 35delG prevalence corresponds to Greece (1/28); the pattern of various 35delG prevalences is interpretated in the present meta-analysis as the result of Ancient Greek colonizations of the "Magna Grecia" in historical times.

Strong linkage disequilibrium for the frequent GJB2 35delG mutation in the Greek population
H. Kokotas¹, L. Van Laer², M. Grigoriadou¹, V. Iliadou³, J. Economides⁴, S. Pomoni¹, A. Pampanos¹, N. Eleftheriades⁵, E. Ferekidou⁶, S. Korres⁶, A. Giannoulia-Karantana⁷, G. Van Camp², M. B. Petersen¹;
¹Institute of Child Health, Athens, Greece, ²University of Antwerp, Antwerp, Belgium, ³AHEPA Hospital, Thessaloniki, Greece, ⁴‘Aghia Sophia’ Children’s Hospital, Athens, Greece, ⁵St. Loukas Hospital, Thessaloniki, Greece, ⁶Athens University, Athens, Greece, ⁷Athens University Medical School, Athens, Greece.

Presentation Number: P06.080

Approximately one in 1,000 children is affected by severe or profound hearing loss at birth or during early childhood (prelingual deafness). Up to forty percent of autosomal recessive, congenital, severe to profound hearing impairment cases result from mutations in a single gene, GJB2. The 35delG mutation accounts for the majority of GJB2 mutations detected in Caucasian populations and represents one of the most frequent disease mutations identified so far. Some previous studies have assumed that the high frequency of the 35delG mutation reflects the presence of a mutational hot spot, whilst other studies support the theory of a common founder. Greece is amongst the countries presenting high frequency of the 35delG mutation (3.5%), and a recent study raised the hypothesis of the origin of this mutation in ancient Greece. We genotyped 60 Greek deafness patients homozygous for the 35delG mutation for six single nucleotide polymorphisms (SNPs) and two microsatellite markers, mapping within or flanking the GJB2 gene, as compared to 60 Greek hearing controls. A strong linkage disequilibrium was found between the 35delG mutation and markers inside or flanking the GJB2 gene, at distances of 34 kb on the centromeric and 90 kb on the telomeric side of the gene, respectively. Our study supports the hypothesis of a founder effect and we further propose that ethnic groups of Greek ancestry could have propagated the 35delG mutation, as evidenced by historical data beginning from the 15^th century BC.

Skin color evolution in Europeans and Social skin color vs Disease in Puerto Ricans

Science last year (thanks commenter!) had a news story about the evolution of European skin color:

Researchers have disagreed for decades about an issue that is only skin-deep: How quickly did the first modern humans who swept into Europe acquire pale skin? Now a new report on the evolution of a gene for skin color suggests that Europeans lightened up quite recently, perhaps only 6000 to 12,000 years ago. This contradicts a long-standing hypothesis that modern humans in Europe grew paler about 40,000 years ago, as soon as they migrated into northern latitudes. Under darker skies, pale skin absorbs more sunlight than dark skin, allowing ultraviolet rays to produce more vitamin D for bone growth and calcium absorption. "The [evolution of] light skin occurred long after the arrival of modern humans in Europe," molecular anthropologist Heather Norton of the University of Arizona, Tucson, said in her talk.

This seems to be in agreement with accelerating recent selection in the human genome. The Science story is referring to the AAPA 2007 meeting. More from the Science story regarding the SLC24A5 gene:

The genetic origin of the spectrum of human skin colors has been one of the big puzzles of biology. Researchers made a major breakthrough in 2005 by discovering a gene, SLC24A5, that apparently causes pale skin in many Europeans, but not in Asians. A team led by geneticist Keith Cheng of Pennsylvania State University (PSU) College of Medicine in Hershey found two variants of the gene that differed by just one amino acid. Nearly all Africans and East Asians had one allele, whereas 98% of the 120 Europeans they studied had the other (Science, 28 October 2005, p. 601).

This is a wonderful confirmation of Cavalli-Sforza's prediction about recent selection for skin color:

Either way, the implication is that our European ancestors were brown-skinned for tens of thousands of years--a suggestion made 30 years ago by Stanford University geneticist L. Luca Cavalli-Sforza. He argued that the early immigrants to Europe, who were hunter-gatherers, herders, and fishers, survived on ready-made sources of vitamin D in their diet. But when farming spread in the past 6000 years, he argued, Europeans had fewer sources of vitamin D in their food and needed to absorb more sunlight to produce the vitamin in their skin. Cultural factors such as heavier clothing might also have favored increased absorption of sunlight on the few exposed areas of skin, such as hands and faces, says paleoanthropologist Nina Jablonski of PSU in State College.

Perhaps it was the larger population sizes made possible by farming that made it possible for the adaptive mutation to arise in one individual, or the mutation pre-existed in early agriculturalists.

I was looking through the book of abstracts (pdf) of this year's AAPA 2008, and another skin color-related abstract caught my attention:

Social classification, skin color, and genetic ancestry: a bio-cultural analysis of health disparities.

A.L. Non, C.C. Gravlee, C.J. Mulligan. Dept. of Anthropology, University of Florida.

Consistent disparities in health are well documented across racially defined groups for many complex diseases. Researchers have proposed both genetic and socio-cultural hypotheses to explain these disparities, but few studies combine both genetic and sociocultural data to test competing hypotheses directly. Here we address this problem in the context of debate about hypertension in populations of African descent. Some researchers suggest that people of greater African ancestry are genetically predisposed to develop high blood pressure. In support of this hypothesis, some researchers point to preliminary evidence of a modest association between blood pressure and genetic estimates of African ancestry. However, the association between ancestry and disease phenotypes may be due to residual confounding with environmental stressors such as discrimination and poverty. Our study, based on fieldwork in southeastern Puerto Rico, is the first to test these alternatives. We incorporate genetic measures of ancestry, genotyping of candidate genes, and an ethnographically derived measure of social classification that estimates how individuals’ color is perceived in everyday social interactions. We find that social classification of color, but not genetic ancestry, is associated with both systolic and diastolic blood pressure through an interaction with socioeconomic status. These findings emphasize the importance of gathering bociocultural data in studies on health and disease, rather than relying on skin color or genetic ancestry as a proxy for potential disease status.

Remember that while skin color is correlated with ancestry, the correlation is not perfect, i.e., a person with more Caucasoid than Negroid ancestry could in fact be darker than a person with more Negroid than Caucasoid ancestry (*). On top of that, the social perception of skin color may blur the picture even more, since skin color is not value-neutral in most multiracial societies. Thus, "social skin color" is two levels removed from "ancestry". What this abstract suggests is that "social skin color", rather than "ancestry" is the culprit for the disease discrepancies. Hopefully a paper on this will follow.

(*) "More" within reason, e.g., a 100% Caucasoid will be almost always lighter than a 100% Negroid.

Origins of the Uighur

Interesting bit from the paper:

Notably, the distribution of admixture proportions among UIG individuals is relatively even, with 48.7% the lowest admixture from European ancestry and the highest 62.2%. The standard deviation is only 3.8%, which is much smaller than the estimation for the African-American (AfA) population,58 suggesting a much longer history of admixture events for the Uyghur population compared with the AfA population.

The American Journal of Human Genetics, doi:10.1016/j.ajhg.2008.01.017

Analysis of Genomic Admixture in Uyghur and Its Implication in Mapping Strategy

Shuhua Xu et al.

Abstract

The Uyghur (UIG) population, settled in Xinjiang, China, is a population presenting a typical admixture of Eastern and Western anthropometric traits. We dissected its genomic structure at population level, individual level, and chromosome level by using 20,177 SNPs spanning nearly the entire chromosome 21. Our results showed that UIG was formed by two-way admixture, with 60% European ancestry and 40% East Asian ancestry. Overall linkage disequilibrium (LD) in UIG was similar to that in its parental populations represented in East Asia and Europe with regard to common alleles, and UIG manifested elevation of LD only within 500 kb and at a level of 0.1 < style="font-weight: bold;">we estimated that the admixture event of UIG occurred about 126 [107∼146] generations ago, or 2520 [2140∼2920] years ago assuming 20 years per generation. In spite of the long history and short LD of Uyghur compared with recent admixture populations such as the African-American population, we suggest that mapping by admixture LD (MALD) is still applicable in the Uyghur population but ∼10-fold AIMs are necessary for a whole-genome scan.

Link

AAPA 2008 abstracts

The 2008 meeting of the American Association of Physical Anthropologists will take place this April, and the book of abstracts for the conference is online in pdf format. As usual, there is a great variety of exciting research to be announced in the meeting; here is my sampling thereof:

A seemingly very important new piece of work on Central Anatolia:

O. Gokcumen et al., The Land of the Tired Ox: Ethnogenetic Insights into Rural Central Anatolian Population History

Excerpt: "For example, in one study area in the vicinity of Ankara, we have observed at least four distinct groups based on historical and ethnographic observations. Their self-claimed ancestries trace back to Afsar, Kurdish, Caucasian Cherkess, and Karaman groups. These groups came into the same area from different source regions and at different moments in history. Indeed, our data indicate that there were significant disparities between the paternal and maternal genetic diversity among these groups. These data also allow us to more accurately reconstruct the population history of the study area, as well as begin to provide new perspectives on the regional history of Central Anatolia in relation to historical Turkic invasions and perhaps the Neolithic transition. Finally, we discuss the utility of a more focal and detailed sampling approach for elucidating Anatolian population history."

I can only hope that more researchers will look into historical processes that have shaped modern populations. Too often I see research published which tries to infer human prehistory from modern populations, seemingly oblivious to the complex set of events in historical time that have shaped these populations. Anatolia, so often discussed in the context of the origin of the Neolithic is a prime example of this, as it contains multiple layers of population settlement and ethnic change.

M. C. Dulik et al. Y-chromosome variation in Altaian ethnic groups

Excerpt: "A large portion of all Altaian haplotypes belonged to haplogroup R. Differences in haplogroup frequency between the northern and southern Altaian populations were also observed, with more individuals from northern groups belonging to haplogroups N and Q, and haplogroup C being more prevalent in southern populations. In addition, there were village level patterns of NRY variation, while the overall diversity of NRY haplotypes suggested a significant cultural influence on the partitioning of genetic variation (i.e., patrilocality)."

The three elements involved in Siberian prehistory are indeed haplogroup R, in particular R1a1 which (in my opinion) represents the Western-derived Caucasoid element of likely Iranic affiliation, haplogroups N and Q which represent the Palaeo-Mongoloid element indigenous to Siberia and which has radiated from Siberia to the west (in the case of N) and to the east and into the Americas (in the case of Q), and the Mongoloid proper element which is associated with haplogroup C in this region, and which reflects the Eastern-derived movements of Mongoloid(-influenced) Altaic speakers such as the Mongols.

L. Pipes et al. Analysis of mtDNA in Mongolian Populations

J. Hawks. "Adaptive evolution of human hearing and the appearance of language"

Language requires not only a detailed anatomical and neurological system of language production, but also a highly adapted system of reception. Considering the frequency and amplitude range of human speech, the necessity of perceiving a large number of distinct speakers, the extended life history of humans, the need for children to learn phonemic distinctions at an early age, and the spatial distances covered by vocal communication in humans compared to other primates, it is likely that humans have distinctive auditory adaptations to language. This study tests the hypothesis of selection on the human auditory system, by interspecific genomic comparisons and genome-wide selection scans in living people. A set of hearing-related human genes shows clear signs of recurrent selected substitutions in humans compared to chimpanzees and macaques. These recurrent substitutions may have occurred at any time during human evolutionary history, but they were repeated with several selected variants for each gene. A smaller set of genes shows signs of significant population differentiation within the past 50,000 years, due to recent strong selection. Further, a relatively large set of hearing-related genes have segregating variants under recent strong selection in one or more human populations. These genes reflect continuing selection on hearing within the last 2000—3000 years. Together, these results suggest that human vocal communication exerted repeated selection pressures on the auditory system, that the system of human language continued to evolve during the Late Pleistocene, and that humans may still be adapting to language.

It seems that Hawks et al. paper on accelerated recent human evolution was just the beginning...

B.E. Hemphill. Are the inhabitants of Madaklasht an emigrant Persian population in northern Pakistan?: a dental morphometric investigation.

The answer: "Madaklasters share closest affinities to prehistoric Central Asians and more distant affinities to prehistoric inhabitants of the Iranian Plateau. Such results support the claim that the inhabitants of Madaklast are an intrusive population into Pakistan whose origins most likely may be found in northeastern Afghanistan and Tajikistan."

Someone should look at their genes. Human history is a giant jigsaw puzzle and it is populations that differ from their neighbors and came from somewhere else that allow us to catch a glimpse of the past (in this case prehistoric Central Asia).

N. Seguchi. "Re-analysis of the ainu-samurai hypothesis using population genetic analysis."

The conclusion: "The result shows that the Kamakura ties to the Ainu first, before it ties to the other ethnic Japanese. In addition, the Kamakura group shows more variability,indicating that the Kamakura group may have experienced significantly more gene flow. This indicates the Ainu-derived people who lived in East Japan at that time made a genetic contribution to the warrior class of Kamakura."

J. K. Rilling et al. "Abdominal depth as a principal determinant of human female attractiveness."

Excerpt: "Multiple linear regression analysis revealed that the depth of the lower torso at the umbilicus, or abdominal depth, was the strongest predictor of attractiveness, stronger than either BMI or WHR, and that its impact was significantly greater for video and side view stimuli in which it was clearly visible compared with front and back view stimuli. Women with shallow abdominal depth are more likely to be healthy, fertile and non-pregnant, suggesting that this may be an adaptive male preference that has been shaped by natural selection."

Huge paper on human genetic relationships based on 650K SNPs

If you thought that this week's Nature paper on human variation was nice, another new paper in Science will be another pleasant surprise. It seems that every time I turn my head geneticists are raising the number of SNPs they study. Lots of populations, 650K SNPs, and a treasure trove of new insight into where humans come from and how we differ from each other.

Before I get into the details of the paper, I want to reiterate my conviction that the problem of human origins is not really a hard one. It just requires a lot of data, a lot of populations, individuals sampled, a lot of genetic markers. Our history, our race, and now it seems even our ethnicity can be read off our genes. We just need to invest the money and effort to find out. With that said, it is sad that the same-old roster of populations from the CEPH panel makes yet another appearance.

There is really a lot on the paper that might interest you, but I will note a few points. First, look at the following PC plot from the paper.



No, your eyes aren't deceiving you. This paper is proof positive that European ethnicities can be distinguished from each other genetically. Even close-by populations (in this case the French and the Italians) are neatly separated. When geographic distance increases there isn't even a hint of confusion: e.g., Russians, Orcadians, and Basque are neatly and clearly separated from other groups. Doubtlessly there would be some more overlap if more individuals/population were used, but the thrust of the discovery is intact: it seems that several European ethnicities and local populations make sense not only culturally but also biologically.

Now, take a look at the standard STRUCTURE analysis which provides meaningful results up to K=7. The standard Sub-Saharan, Native American, East Asian, and Oceanian clusters are there, but now there is meaningful structure within the Caucasoids as well; they are broken into "Middle Eastern", "European", and "Central South Asian" groups.



I would guess that the "brown" Middle-Eastern cluster is largely an Arab/Semitic phenomenon, although the inclusion of the Berber Mozabites is interesting. If it reflected a pre-historic phenomenon, then it would be difficult to explain its apparent total lack of influence in Europe, except for a barely perceptible spillage into Tuscany, which once again reiterates the idiosyncratic "Middle Eastern" trace of that Italian population of likely Etruscan descendants.

The "Central South Asian" group is also extremely interesting, for several reasons. First, it reinforces the previous claim that the Kalash, rather than Greek descendants, as some romantics would have them, are simply a non-European native population, with no evidence of European ancestry. Second, it shows that there is minimal, yet evident European influence in Central Asia, which I would relate to the eastern Indo-Iranians. Third, Central Asian influence in Europe is non-evident, except for a trace among the Russians (and substantially more among the Adygei a people of the Caucasus). Fourth the minority Mongoloid and "Boreal" (Purple) influence in Russians is affirmed. Note that we are dealing with ethnic Russians from the north (Vologda oblast), and Russians are a heterogeneous people in terms of their origin.

We can only wish for inclusion of further populations in future studies of the kind. In particular, eastern and southeastern Europe and non-Arab West Asia, Siberia would be invaluable in further understanding Caucasoid origins, and perhaps uncovering additional structure.

Note that the CEPH panel has revealed that ethnic groups can be distinguished genetically, there is little more than it can offer in terms of understanding origins. The next milestone would be either to include previously unsampled populations, or to dig into ethnic groups themselves, and see if sub-ethnic entities are also discernible in our genomes. Genetic genealogists are in for a good time in the coming years...

Science 22 February 2008: Vol. 319. no. 5866, pp. 1100 - 1104

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

Jun Z. Li,1,2*{dagger} Devin M. Absher,1,2* Hua Tang,1 Audrey M. Southwick,1,2 Amanda M. Casto,1 Sohini Ramachandran,4 Howard M. Cann,5 Gregory S. Barsh,1,3 Marcus Feldman,4{ddagger} Luigi L. Cavalli-Sforza,1{ddagger} Richard M. Myers1,2{ddagger}

Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

Link

300K SNP paper on European genetic substructure

This is another recent paper using a large number of genetic markers to study genetic structure within a race. You can read the paper for yourselves, but some comments are in order.

First, this mirrors the results of another recent study on European-American population structure. Mediterranean populations are distinguished from Northern European populations and from Jews.

Doubtlessly, the discontinuities between the three groups evident in the Figure would be less clear if more populations were sampled, but nonetheless this is clear evidence that not only race, but ethnicity too has a genetic component.

If e.g., we were given the DNA of a German, a Greek, and a Jew, we would be able to tell them apart with very high probability. All it would take, would be to genotype them for the 300K SNPs, and subsequently score them for the first two principal components.

Another interesting feature of this study is the form of the Jewish cluster. The purple dots correspond to Jewsh with all four Jewish grandparents and they form a tight cluster. This is not the case when less stringent criteria (blue dots) are used.


This is a wonderful visual display of what happens to a partially inbred group (Ashkenazi Jews) as a result of intermixture. As long as within-group marriage patterns prevail, genetic similarity is maintained, but intermarriage leads to an attenuation of the group's genetic distinctiveness.

It is interesting to think of how this picture will change as genetic science moves forward:

If more populations are sampled, then the gaps between populations may "fill up". I would not be surprised, for example, if the French would occupy the gap between Spaniards and Germans.

If more SNPs were used, then populations that overlap greatly (say Greeks and Italians) might be separated.

Ethnic groups may differ both in culture and in genes, but these two dimensions of ethnicity are not independent. Differences in culture are barriers to gene flow; over time, such barriers differentiate gene pools. Conversely, genetic intermixture bring separate gene pools closer together, but also serves to homogenize cultures.

PLoS Genetics Vol. 4, No. 1, e4 doi:10.1371/journal.pgen.0040004

Analysis and Application of European Genetic Substructure Using 300 K SNP Information

Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, et al.

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans.

Link

Human eye color news

From the first paper, the frequency of HERC2 rs916977 superimposed on an iris color map (sadly taken from a 1965 reference):


The American Journal of Human Genetics,
doi:10.1016/j.ajhg.2007.10.003

Three Genome-wide Association Studies and a Linkage Analysis Identify HERC2 as a Human Iris Color Gene

Manfred Kayser et al.

Abstract

Human iris color was one of the first traits for which Mendelian segregation was established. To date, the genetics of iris color is still not fully understood and is of interest, particularly in view of forensic applications. In three independent genome-wide association (GWA) studies of a total of 1406 persons and a genome-wide linkage study of 1292 relatives, all from the Netherlands, we found that the 15q13.1 region is the predominant region involved in human iris color. There were no other regions showing consistent genome-wide evidence for association and linkage to iris color. Single nucleotide polymorphisms (SNPs) in the HERC2 gene and, to a lesser extent, in the neighboring OCA2 gene were independently associated to iris color variation. OCA2 has been implicated in iris color previously. A replication study within two populations confirmed that the HERC2 gene is a new and significant determinant of human iris color variation, in addition to OCA2. Furthermore, HERC2 rs916977 showed a clinal allele distribution across 23 European populations, which was significantly correlated to iris color variation. We suggest that genetic variants regulating expression of the OCA2 gene exist in the HERC2 gene or, alternatively, within the 11.7 kb of sequence between OCA2 and HERC2, and that most iris color variation in Europeans is explained by those two genes. Testing markers in the HERC2-OCA2 region may be useful in forensic applications to predict eye color phenotypes of unknown persons of European genetic origin.

Link

The American Journal of Human Genetics,
doi:10.1016/j.ajhg.2007.11.005

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color

Richard A. Sturm et al.

Abstract

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mapping of eye color SNPs in the intergenic region upstream of OCA2 and within the neighboring HERC2 (hect domain and RLD2) gene. We screened an additional 92 SNPs in 300–3000 European individuals and found that a single SNP in intron 86 of HERC2, rs12913832, predicted eye color significantly better (ordinal logistic regression R2 = 0.68, association LOD = 444) than our previous best OCA2 haplotype. Comparison of sequence alignments of multiple species showed that this SNP lies in the center of a short highly conserved sequence and that the blue-eye-associated allele (frequency 78%) breaks up this conserved sequence, part of which forms a consensus binding site for the helicase-like transcription factor (HLTF). We were also able to demonstrate the OCA2 R419Q, rs1800407, coding SNP acts as a penetrance modifier of this new HERC2 SNP for eye color, and somewhat independently, of melanoma risk. We conclude that the conserved region around rs12913832 represents a regulatory region controlling constitutive expression of OCA2 and that the C allele at rs12913832 leads to decreased expression of OCA2, particularly within iris melanocytes, which we postulate to be the ultimate cause of blue eye color.

Link

Genetic structure of European Americans

NOTE: I inadvertetdly posted a draft of this post. Here is the final post; I will leave the draft online since some people already commented on it, before I noticed it.

A previous study on Europeans discovered that Caucasoid Europeans, who form a genetic cluster on a global scale can be further distinguished into subclusters that are correlated with ancestry and geography. Now, a new study on European Americans (hat tip gnxp) appearing in the free online journal PLoS Genetics has carried out a similar analysis of the genetic structure of American "Caucasians".

What I find fascinating about this new study is that an ethnic subgroup within American Caucasoids, namely Ashkenazi Jewish Americans can be distinguished at this point from other Caucasoids. Here is the clustering based on the validated set of markers from the paper:

The distinctiveness of Jewish Americans is probably due to their having a portion of Middle Eastern ancestry. We can only say that Jewish Americans are clearly genetically distinct from the other ethnic groups presented in the study, although it is unclear whether they are distinct from other groups of Middle Eastern background.

As biologically-averse intellectuals continue to question the very existence of race, pragmatic scientists are moving into an era when not only race, but ethnicity may become genetically identifiable.

Unlike race which by definition refers to an identifiable biological cluster, ethnicity may (or may not) refer to such a cluster.

Ethnic distinctiveness is due to both culture and biology, and the relative proportions of the two factors are specific to a particular ethnic group.

When ethnic groups have split recently, co-inhabit a geographical space, frequently intermarry, etc., then it is likely that they will have small biological differences, whereas other ethnic groups may be biologically as well as culturally distinct.

We should be careful to note that there are two levels of ethnic biological distinctiveness: group distinctiveness and individual distinctiveness:

Group distinctiveness means: if you are given the photographs of ten Englishmen on one side and ten Russians on the other, you would be able to decide with a very high level of success which group represented the Russians and which one the Englishmen.

Individual distinctiveness means: if you are given the photographs of ten Englishmen and ten Russians in random order, you would still be able to sort out the Russians from the Englishmen; whether this is possible, and with what level of success is less obvious than in the previous case.

We must wait for more studies with larger samples and more markers to study the biological component of human ethnicity. At present, some groups do seem to have individual distinctiveness in a particular societal context and with a particular set of markers (e.g., Jewish vs. non-Jewish Americans), while others are less distinct (e.g., Greek vs. Italian Americans).

Greater genetic drift in East Asians than in Europeans

Nature Genetics 39, 1251 - 1255 (2007)
Published online: 9 September 2007 | doi:10.1038/ng2116

Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans

Alon Keinan et al.

Large data sets on human genetic variation have been collected recently, but their usefulness for learning about history and natural selection has been limited by biases in the ways polymorphisms were chosen. We report large subsets of SNPs from the International HapMap Project1, 2 that allow us to overcome these biases and to provide accurate measurement of a quantity of crucial importance for understanding genetic variation: the allele frequency spectrum. Our analysis shows that East Asian and northern European ancestors shared the same population bottleneck expanding out of Africa but that both also experienced more recent genetic drift, which was greater in East Asians.

Link

Caucasoid mtDNA in Iron Age Central China

More on the Yu Hong tomb. From the second link:

Yu Hong (d. 592) was a high-ranking member of a community of Sogdians who had settled on the northern border of China at the beginning of the fourth century. While barely in his teens, Yu Hong began his career in the service of the most powerful nomadic tribe at the time, known as the Ruru, and was posted as an emissary to several countries, including Iran.

From a book on the subject:

The highlight of the excavation was the superbly-carved white marble sarcophagus which bears detailed scenes of daily life, hunting, mythology, banqueting and entertainment that have a strong Central Asian influence, including Sogdian and Sassanian. Many of the figures depicted are Caucasian.

Proc Biol Sci. 2007 Apr 24;

Evidence of ancient DNA reveals the first European lineage in Iron Age Central China.

By Xie CZ, Li CX, Cui YQ, Zhang QC, Fu YQ, Zhu H, Zhou H on Proc Biol Sci

Various studies on ancient DNA have attempted to reconstruct population movement in Asia, with much interest focused on determining the arrival of European lineages in ancient East Asia. Here, we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China, and Taiyuan may be the easternmost location of the discovered remains of European lineage in ancient China.

Link

Y chromosomes of South Siberia

No abstract to this paper. An excerpt:

Archeological and paleontological evidence suggests that South Siberia is an area where the most ancient contacts occurred between the members of Caucasoid and Mongoloid peoples. These contacts have substantially affected the racial type of most populations of Eurasia. Analysis of mitochondrial DNA (mtDNA) inherited without recombination in the maternal line has shown that Southern Siberian populations have developed on a heterogeneous genetic basis. This is a result of not only the diversity of Mongoloid components that were either indigenous to the gene pools of Siberian populations since the Paleolithic Age or introduced in different periods of time from Central Europe and East Asia, but also the presence of the Caucasoid component expressed in different degrees in most populations that have contributed into this heterogeneity [1, 2]. The nonrecombining portion of the Y chromosome inherited in the paternal line is another genetic system widely used for studying the population genetic history. The Y chromosome polymorphism has been analyzed in a wide spectrum of Asian populations; nevertheless, the data on numerous aboriginal opulations of Southern Siberia are scanty with respect to both the number of populations and the set of loci studied. Therefore, there is no comprehensive idea as to how the gene pools of individual ethnic groups have been formed, taking into account the contributions of both paternal and maternal lineages [3, 4].

...

In general, our results suggest a significant genetic differentiation between the ethnic groups of Baikal and Altai–Sayan regions, which is mainly accounted for by
different contributions of the Central/East Asian and East European components into the gene pools of South Siberian ethnic groups.

Haplogroup distribution:

Doklady Biological Sciences, 2006, Vol. 411, pp. 466–470

The Diversity of Y-Chromosome Lineages in Indigenous Population of South Siberia

M. V. Derenko et al.

Convergent skin color evolution in Caucasoids and Mongoloids

MBE Advance Access published online on December 20, 2006

Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians

Heather L. Norton et al.

Human skin pigmentation shows a strong positive correlation with ultraviolet radiation (UVR) intensity, suggesting that variation in skin color is, at least partially, due to adaptation via natural selection. We investigated the evolution of pigmentation variation by testing for the presence of positive directional selection in six pigmentation genes using an empirical FST approach, through an examination of global diversity patterns of these genes in the CEPH-Diversity Panel, and by exploring signatures of selection in data from the International HapMap project. Additionally, we demonstrated a role for MATP in determining normal skin pigmentation variation using admixture mapping methods. Taken together (with the results of previous admixture mapping studies), these results point to the importance of several genes in shaping the pigmentation phenotype and a complex evolutionary history involving strong selection. Polymorphisms in two genes, ASIP and OCA2, may play a shared role in shaping light and dark pigmentation across the globe while SLC24A5, MATP, and TYR have a predominant role in the evolution of light skin in Europeans but not in East Asians. These findings support a case for the recent convergent evolution of a lighter pigmentation phenotype in Europeans and East Asians.

Link

Culture and ratings of attractiveness of different body shapes

Evolution and Human Behavior
Volume 27, Issue 6 , November 2006, Pages 443-456

Changing perceptions of attractiveness as observers are exposed to a different culture

Martin J. Tovée et al.

Abstract

It has been suggested that certain physical cues can be used to predict mate quality and that sensitivity to these cues would therefore be adaptive. From this, it follows that in environments where the optimal values for these features differ, the attractiveness preferences should also be different. In this study, we show that there are striking differences in attractiveness preferences for female bodies between United Kingdom (UK) Caucasian and South African Zulu observers. These differences can be explained by different local optima for survival and reproduction in the two environments. In the UK, a high body mass is correlated with low health and low fertility, and the converse is true in rural South Africa. We also report significant changes in the attractiveness preferences of Zulus who have moved to the UK. This suggests that these preferences are malleable and can change with exposure to different environments and conditions. Additionally, we show that Britons of African origin, who were born and who grew up in the UK, have exactly the same preferences as our UK Caucasian observers. These results suggest that humans have mechanisms for acquiring norms of attractiveness that are highly plastic, which allow them to track different ecological conditions through learning.

Link

Mongoloid components in Eastern Europe

Slavs and other eastern Europeans are typically Caucasoid although one does not seldom find among them individuals with certain attenuated Mongoloid influences. The extent of Mongoloid admixture in eastern Europe will eventually be determined by autosomal admixture studies which sample the relevant source populations of the Mongoloid component in Europe, namely the Uralic and Altaic speakers of Siberia and Central Asia.

At present, the only study which studied the genomic study of a Slavic sample of Russians (Science 20 December 2002: Vol. 298. no. 5602, pp. 2381 - 2385) determined a 93% membership coefficient in the main Caucasoid cluster, with a 3% membership in the main (East Asian) Mongoloid cluster. Unfortunately Central Asian Turkic and Finno-Ugrian populations from Europe and Asia were not sampled.

The presence of Mongoloid mtDNA types in East Europe is well established, but it should be remembered that movements from the east did not usually involve large numbers of women (*). Therefore, one expects that inference from mtDNA will underestimate the total number of immigrants.

Moreover, as I have pointed out before, Turkic speakers of Central Asia were likely to possess majority components of Caucasoid Y chromosomes associated with Mongoloid mtDNA components. Today, haplogroup C chromosomes make up a large component of Y-chromosome variation in Central Asia (including the famous "Genghis Khan" line), but these were probably added (from the east), late in history, since the Mongol expansion is at the end of the great period of Altaic migrations to the west (Huns, Seljuks, Ottomans, Bulgars, etc.)

As a result a proportion of the eastern immigrants into Europe would be undetectable with Y-chromosome markers, namely the substantial fraction with Caucasoid Y chromosomes and Mongoloid mtDNA. The male immigrants of this type would impart their Y chromosomes in the regions they invaded, but not their maternal mtDNA. In the Altai-Kizhi group, for example, 71% Caucasoid Y chromosomes are associated with 76% non-Caucasoid mtDNA.

Consider a population with 3/4 Caucasoid Y chromosomes and 3/4 Mongoloid mtDNA. Consider that the migrant group consists of 3/4 men and 1/4 women. Under such circumstances we would expect approximately the same rate of Mongoloid mtDNA and Y chromosomes in the recipient population. Moreover, the inferred admixture proportion from the frequencies of Mongoloid mtDNA and Y chromosomes would underestimate the true rate of Mongoloid admixture by a factor of 2.

Unfortunately, the presence of Mongoloid Y chromosomes has not been properly studied until now. In the recent Y chromosome study of the Czech Republic for example, the main Mongoloid Y-haplogroups (C, Q, O) likely to have accompanied the women bearing the 3% Mongoloid mtDNA were not examined and could be part of the Y*, P*, and K* paragroups. Similarly, none of these haplogroups were studied in a recent study on Poland and Germany.

In conclusion:

• The mtDNA evidence suggests a very low-level introgression of Mongoloid components into Eastern Europe.
• The extent of this admixture is likely to be underestimated by the genetic profile of the source population and the excess of male migrants.
• The best estimate of the admixture rate will be determined by autosomal studies that sample relevant Uralic-Altaic source populations, but is probably unlikely to amount to more than a few percentage points.
  

(*) Except in folk migrations such as those of the Kalmyks.

Caucasoid phenotypic variation

Racial Reality has a post displaying several facial composites of different Caucasoid populations and groups. See also my own composites of many European ethnic groups.