Rushton and genital size: one more time

J. Philippe Rushton asserts [1]:
Orientals are the most K, Blacks are the most r, and Whites fall in between. Being more r means: [. . .] more developed primary sexual characteristics (size of penis, vagina, testes, ovaries)
Rushton apparently has many convinced the above assertions are ironclad facts. They are not. Despite Rushton's sometimes selective presentation of evidence, what data exist (on "size of penis, vagina, testes") fail to consistently align with Rushton's Asian < White < African framework.

Penis size

Rushton claims [2]:

We averaged the ethnographic data on erect penis and found the means to approximate:
Orientals, 4 to 5.5 in. in length and 1.25 in. in diameter;
Caucasians, 5.5 to 6 in. in length and 1.5 in. in diameter;
blacks, 6.25 to 8 in. in length and 2 in. in diameter.
The numbers above are apparently lifted directly (or indirectly via Coon's Racial Adaptations) from a book by "A French Army Surgeon" ("Jacobus X" / Jacobus Sutor) published in 1898 (so much for "averages" of "the ethnographic data"; Rushton cites "A French Army Surgeon" as merely an "e.g." of "the ethnographic record", but Rushton's "ethnographic record" is apparently limited to the supposed observations of a single 19th-century individual).

The numbers given for blacks (ranging up to "8 in. in length" for population means) are implausible on their face, and no modern study of blacks comes close to supporting anything but the very low end of that suggested range.

A study of Nigerians (n=115) finds "mean [stretched] penile length was 13.37 cm [5.26 inches] with a median of 13 cm" [3]. Another study, on 320 Nigerians, finds "average [presumably flaccid] length of the penis (81.6 +/- 0.94 mm); circumference of the penis (88.3 +/- 0.02 mm)" [4].

The Kinsey data, which may be less than ideal but which are cited by Rushton both directly and indirectly, suggest any difference in mean penile dimensions between black and white men in America is measurable in fractions of an inch:
White males had an average flaccid penis length of 4.0 inches, whereas the average black male's detumescent member measured 4.3 inches. But when erect, the average white penis was 6.2 inches long, whereas the average black's was 6.3 inches--still longer, but not by much. (Average circumference for whites was 3.7 inches; for blacks, 3.8.)

When Rushton cites WHO condom standards in support of his theory, he is merely indirectly referencing the Kinsey data (plus a sample from Thailand, and one from Australia). WHO did no original research. Their sole "African" sample is the American black sample from Kinsey [7].

[Update: Rushton claims the WHO specify three condom sizes [1]:
The World Health Organization Guidelines specify a 49-mm-width condom for Asia, a 52-mm-width for North America and Europe, and a 53-mm-width for Africa.
I'd taken Rushton at his word here and had not bothered to check his WHO claim beyond determining that WHO did no original research on the subject (as stated above). In reality, it's clear from the guidelines that WHO specify exactly two widths [7]:
WHO specifies a width of 49 mm or 53 mm with a tolerance of ±2 for individual condoms and ±1 for the average of the lot.
The WHO don't make distinctions among Europe, Africa, and Asia, but between Asia and everyone else [7]:
Condoms are made in various widths. Based on studies in Australia, Thailand and the USA, and the experience of major agencies, the wider condoms (flat width 52-55 mm) will be preferred in Australia, Africa, Europe, Latin America, the Middle East and North America, and the narrower condoms (47-51 mm) will be preferred in several Asian countries (see Appendix III). Other widths are also made for small specialized markets.
Note: the ranges encompass tolerances in the specification; only two distinct widths are specified.]

Testes size

Rushton reviews most of the evidence of which I'm aware in his 1987 paper [2]:
Measurements taken from living subjects as well as those at autopsy, show the size of testes is twofold lower in Asian men than Europeans (9 g vs 21 g), a difference too large to be accounted for entirely in terms of body size (Diamond, 1986; Short, 1984). [. . .] Contrary to the general trend, Freeman (1934) observed that, at autopsy, American blacks had less heavy testes than American whites (13g vs 15g). [. . .] Subsequently Daniel, Fienstein, Howard-Peebles, and Baxley (1982) found no black-white difference in testicular volume among American adolescents, while Ajmani, Jain, and Saxena (1985) found larger scrotal circumference in Nigerians than Europeans (212.6 mm vs 195.1 mm or 8.37 in. vs 7.68 in.)
Strangely, by 2000, Rushton seems to have grown somewhat amnesiac [1]:
Race differences in testicle size have also been measured (Asians = 9 grams, Europeans = 21 g). This is not just because Europeans have a slightly larger body size. The difference is too large. A 1989 article in Nature, the leading British science magazine, said that the difference in testicle size could mean that Whites make two times as many sperm per day as do Orientals. So far, we have no information on the relative size of Blacks.
Rushton also conveniently ignores "A French Army Surgeon" where the latter's claim fails to line up with the former's theory:
In no branch of the human race are the male organs more developed than in the African Negro. I am speaking of the penis only and not of the testicles, which are often smaller than those of the majority of Europeans.

Vaginal size

Rushton claims (apparently again relying on "A French Army Surgeon"):
Women were proportionate to men, with Orientals having smaller vaginas and blacks larger ones, relative to Caucasians.
Modern studies fail to bear out this claim, which tends to further reduce the credibility of Rushton's 19th-century source. One study using MRI finds "[r]ace was not associated with any differences in measurements of vaginal dimensions" [5]. A different study finds [6]:
posterior cast length is significantly longer, anterior cast length is significantly shorter and cast width is significantly larger in Hispanics than in the other two groups and (2) the Caucasian introitus is significantly greater than that of the Afro-American subject.
Nor do the "Afro-American" subjects have deeper vaginas: "[a]verage rod lengths for Caucasians and Afro-Americans were 11.51 and 11.18 cm [. . .] significantly different as measured by t test" [6].

References

[1] Race, Evolution, and Behavior 2nd Special Abridged Edition (pdf)

[2] Rushton, J.P. & Bogaert, A.F. (1987) Race differences in sexual behavior: Testing an evolutionary hypothesis. Journal of Research in Personality 21(4): pp. 536-7 (link)

[3] Orakwe JC et al. Can physique and gluteal size predict penile length in adult Nigerian men? West Afr J Med. 2006 Jul-Sep;25(3):223-5. (link)

[4] Ajmani ML et al. Anthropometric study of male external genitalia of 320 healthy Nigerian adults. Anthropol Anz. 1985 Jun;43(2):179-86. (link)

[5] Barnhart KT et al. Baseline dimensions of the human vagina. Hum Reprod. 2006 Jun;21(6):1618-22. Epub 2006 Feb 14. (link)

[6] Pendergrass PB et al. Comparison of vaginal shapes in Afro-American, caucasian and hispanic women as seen with vinyl polysiloxane casting. Gynecol Obstet Invest. 2000;50(1):54-9. (link)

[7] WHO Global Programme on AIDS. Specification and Guidelines for Condom Procurement. Appendix VII, Regional or Ethnic Differences in Erect Penis Size. Geneva: WHO, 1995. (pdf)

Ancient Mongolian mtDNA

I'd be more interested in Y-DNA results from the same time and place, which might help support or refute the "Genghis Khan" Y signature claim. The unsurprising presence of European morphological features in some skeletons is perhaps attributable to admixture by Iranian speakers, which would also likely be detected in a Y-DNA analysis.
American Journal of Physical Anthropology; Published Online: 25 Jul 2008

Ancient DNA analysis of human remains from the upper capital city of Kublai Khan

Yuqin Fu et al.

Keywords
ancient DNA • mitochondrial DNA • human origins • China

Abstract
Analysis of DNA from human archaeological remains is a powerful tool for reconstructing ancient events in human history. To help understand the origin of the inhabitants of Kublai Khan's Upper Capital in Inner Mongolia, we analyzed mitochondrial DNA (mtDNA) polymorphisms in 21 ancient individuals buried in the Zhenzishan cemetery of the Upper Capital. MtDNA coding and noncoding region polymorphisms identified in the ancient individuals were characteristic of the Asian mtDNA haplogroups A, B, N9a, C, D, Z, M7b, and M. Phylogenetic analysis of the ancient mtDNA sequences, and comparison with extant reference populations, revealed that the maternal lineages of the population buried in the Zhenzishan cemetery are of Asian origin and typical of present-day Han Chinese, despite the presence of typical European morphological features in several of the skeletons. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc.

[link]

Genetics of criminality

Press release:
In one of the first studies to link molecular genetic variants to adolescent delinquency, sociological research published in the August issue of the American Sociological Review identifies three genetic predictors--of serious and violent delinquency--that gain predictive precision when considered together with social influences, such as family, friends and school processes.

[. . .]

The three genetic polymorphisms that predict delinquency include:

1. the 30-base pair (bp) promoter-region with a variable number tandem repeat (VNTR) in the monoamine oxidase A (MAOA) gene,

2. the 40-bp VNTR in the dopamine transporter 1 (DAT1) gene and

3. the Taq1 polymorphism in the dopamine D2 receptor (DRD2) gene. MAOA regulates several brain neurotransmitters important in behavioral motivation, aggression, emotion and cognition (e.g., serotonin, dopamine, norepinephrine).
The paper:
The Integration of Genetic Propensities into Social-Control Models of Delinquency and Violence among Male Youths

Authors: Guo, Guang; Roettger, Michael E.; Cai, Tianji

Source: American Sociological Review, Volume 73, Number 4, August 2008 , pp. 543-568(26)

Abstract:
This study, drawing on approximately 1,100 males from the National Longitudinal Study of Adolescent Health, demonstrates the importance of genetics, and genetic-environmental interactions, for understanding adolescent delinquency and violence. Our analyses show that three genetic polymorphisms—specifically, the 30-bp promoter-region variable number tandem repeat (VNTR) in MAOA, the 40-bp VNTR in DAT1, and the Taq1 polymorphism in DRD2—are significant predictors of serious and violent delinquency when added to a social-control model of delinquency. Importantly, findings also show that the genetic effects of DRD2 and MAOA are conditional and interact with family processes, school processes, and friendship networks. These results, which are among the first that link molecular genetic variants to delinquency, significantly expand our understanding of delinquent and violent behavior, and they highlight the need to simultaneously consider their social and genetic origins.
My guess is genetic differences such as these (along with IQ) will ultimately be shown to account for a much larger fraction of cross-racial variation in crime than racial differences in circulating testosterone levels (which seem far from fixed). I don't have population frequency data for the specific polymorphisms mentioned above, but the SNP rs979606 in MAOA, for example, varies in the familiar Asian <> European <> African pattern. Update: Racial differences are also apparent in DRD2 Taq1 genotypes and the DAT1 40 bp VNTR, though their meaning is not clear to me yet.

Another relevant paper:
Neuropsychopharmacology (2008) 33, 425–430; doi:10.1038/sj.npp.1301417; published online 11 April 2007

A Non-Additive Interaction of a Functional MAO-A VNTR and Testosterone Predicts Antisocial Behavior

Rickard L Sjöberg et al.

Abstract

A functional VNTR polymorphism in the promoter of the monoamine oxidase A gene (MAOA-LPR) has previously been shown to be an important predictor of antisocial behavior in men. Testosterone analogues are known to interact with the MAOA promoter in vitro to influence gene transcription as well as in vivo to influence CSF levels of the MAO metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) in human males. We examined the possible joint effects of testosterone (measured in CSF) and MAOA-LPR genotype on antisocial personality disorder and scores on the Brown–Goodwin Aggression scale in 95 unrelated male criminal alcoholics and 45 controls. The results confirm that MAOA genotype and CSF testosterone interact to predict antisocial behaviors. The MAOA/testosterone interaction also predicted low levels of CSF MHPG, which tentatively suggests the possibility that the interaction may be mediated by a direct effect on gene transcription. If replicated these findings offer plausible explanations for previous inconsistencies in studies of the relationship between testosterone and male human aggression, as well as for how MAOA genotype may influence aggressive behavior in human males.
Keywords:

antisocial personality disorder, antisocial behavior, MAO-A gene, testosterone, gene by hormone interaction, MHPG

Confounding factors in 2D:4D studies

This tends to reinforce my doubts about the meaningfulness of direct comparisons of digit ratio across groups.

American Journal of Physical Anthropology; Published Online: 9 Jul 2008

Brief Communication: Latent toxoplasmosis and salivary testosterone concentration - Important confounding factors in second to fourth digit ratio studies

Jaroslav Flegr et al.

Keywords
infection • postnatal changes • Toxoplasma • androgens • 2D:4D

Abstract
A sexually dimorphic characteristic, the second to fourth digit ratio (2D:4D ratio), has been shown to reflect the prenatal concentration of sex steroid hormones and to correlate with many personality, physiological, and life history traits. The correlations are usually stronger for the right than the left hand. Most studies have shown that the 2D:4D ratio does not vary with age or postnatal concentration of sex steroid hormones. Recently, a strong association between left hand 2D:4D ratio and infection with a common human parasite Toxoplasma has been reported. We hypothesized that the confounding effect of Toxoplasma infection on left hand 2D:4D ratio could be responsible for the stronger association between different traits and right hand rather than left hand 2D:4D ratio. This confounding effect of toxoplasmosis could also be responsible for the difficulty in finding an association between 2D:4D ratio and age or postnatal steroid hormone concentration. To test this hypothesis, we analyzed the association between sex and age and 2D:4D ratio in a population of 194 female and 106 male students with and without controlling for the confounding variables of Toxoplasma infection and testosterone concentration. Our results showed that the relationship between age and sex and 2D:4D ratio increased sharply when Toxoplasma infection and testosterone concentration were controlled. These results suggest that left hand 2D:4D ratio is more susceptible to postnatal influences and that the confounding factors of Toxoplasma infection, testosterone concentration and possibly also age, should be controlled in future 2D:4D ratio studies. Because of a stronger 2D:4D dimorphism in Toxoplasma-infected than Toxoplasma-free subjects, we predict that 2D:4D ratio dimorphism as well as right hand/left hand 2D:4D ratio dimorphism will be higher in countries with a high prevalence of Toxoplasma infection than in those with a low prevalence. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc.

[link]

Does not follow

Rienzi asserts, based on this study [1], that 'Personal "self-identification" is not enough. Genetic analyses of ancestry are required.' Rienzi clearly implies this study of "African Americans" indicates a need for individual genetic ancestry analysis of white Americans--an absurd conclusion.

Studies have repeatedly shown American blacks average ~20% European admixture, while white Americans show minimal if any non-European admixture. Gene flow was overwhelmingly one way.

It is no surprise that among American blacks "self-report of a high degree of African ancestry in a three-generation family tree did not accurately predict degree of African ancestry". The overwhelming majority of American blacks have "African" (black) parents and grandparents. No doubt most of Aframs' European genes entered the Afram gene pool more than 3 generation ago. Aframs without recent white ancestors may range from light-skinned to coal-black. We see no such variations in the phenotypes of white Americans.

Additionally, most white Americans who care to can construct pedigrees for themselves much deeper than three generations.

While I personally find genetic ancestry analysis interesting, and look forward to further developments in the field, as of now I see nothing of benefit for the overwhelming majority of white Americans in any commercially available test of individual admixture.


[1] Comparing genetic ancestry and self-described race in african americans born in the United States and in Africa. Yaeger R, Avila-Bront A, Abdul K, Nolan PC, Grann VR, Birchette MG, Choudhry S, Burchard EG, Beckman KB, Gorroochurn P, Ziv E, Consedine NS, Joe AK. Cancer Epidemiol Biomarkers Prev 2008;17(6):1329-38

More ancient DNA results from Xinjiang

I'm unfamiliar with the site and I haven't read the paper, but based on the dates mentioned (~500 BC to 1 AD) these results again most likely have little or no bearing on the question or the origins of the older, Northern European-looking mummies (which date to as early as ~1800 BC).

Sci China C Life Sci. 2008 Mar;51(3):205-13.

Mitochondrial DNA analysis of human remains from the Yuansha site in Xinjiang, China.

Gao S, Cui Y, Yang Y, Duan R, Abuduresule I, Mair VH, Zhu H, Zhou H.

Laboratory of Ancient DNA, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130012, China.

The Yuansha site is located in the center of the Taklimakan Desert of Xinjiang, in the southern Silk Road region. MtDNA was extracted from fifteen human remains excavated from the Yuansha site, dating back 2,000-2,500 years. Analysis of the phylogenetic tree and the multidimensional scaling (MDS) reveals that the Yuansha population has relatively close relationships with the modern populations of South Central Asia and Indus Valley, as well as with the ancient population of Chawuhu.

PMID: 18246308 [PubMed - indexed for MEDLINE]

Some ancient DNA results from the Tarim Basin

Note: some clown references this paper on Wikipedia in the following context:
The cemetery at Yanbulaq contained 29 mummies which date from 1800–500 BC, 21 of which are Caucasoid—the earliest Caucasoid mummies found in the Tarim Basin—and eight of which are of the same Caucasoid physical type found at Qäwrighul.[1]:237 . However, more recent genetic studies painted a more complex picture (Xie et al., 2007). It showed both european and asian characteristics.

In fact, this study has no bearing on the origins of the Northern Europoid "Tarim mummies". Sampul is a much later site, which according to physical anthropologists was populated primarily by Central Asian "Eastern Mediterranean" types. Mallory and Mair discuss the findings of Han Kangxin:
The Qäwrighul remains are relatively homogeneous and they exhibit features associated with a type known as Proto-Europoid, a rather robust Caucasoid, especially well represented in Northern Europe and the steppelands and forest-steppe of Russia and the Ukraine. Similar remains occur in the Bronze Age cemeteries of southern Siberia, Kazakhstan, Central Asia and the Lower Volga. [. . .]

The next oldest remains derive from the Yanbulaq cemetery near Humul (Hami), situated to the northeast of Qäwrighul and the easternmost cemetery investigated. Here Han Kangxin identified 21 of the 29 complete skulls as Mongoloids and these are the earliest definite evidence of Mongoloids in East Central Asia. The remaining skulls, however, belonged to Caucasoids who are closest to those from Qäwrighul and point to the same general direction for their origins, i.e. the steppelands to the north and west.

The single skull recovered from among the inhumation burials at Shambalay near Tahkurgan in the far west of the Tarim Basin has been compared with the type that spanned the Mediterranean across Central Asia; this type also includes the Saka tribes of the southern Pamirs.

A much larger sample of 58 skulls was recovered from one of the mass graves at Alwighul in the Tangri Tagh (Tian Shan). Here Han distinguishes two Caucasoids types: the Eastern Mediterranean or Indo-Afghan type with their long and high skulls and the broader and rounder skulls of the Pamir-Ferghana type; Han also identified hybrids of these two subtypes as well as some evidence of Mongoloid admixture. By now, the attentive reader will know we owe another caveat; the three physical types employed by Han Kangxin -- Proto-Europoids, Indo-Afghans and Pamir-Ferghanans -- are largely relabelled Nordics, Mediterraneans, and Alpines, terms that send shivers of apprehension down the spines of Western biological anthropologists.

[. . .]

The Sampul cemetery provides us with our only physical anthropological evidence of the southern Silk Road in the vicinity of Khotan. Although the cemetery contained various individual graves employing some form of log coffin, all the burials examined derive from the group graves which date to the first centuries BC. Han Kangxin has identified the remains as belonging to the same Indo-Afghan type that one encounters among the Saka of the southern Pamirs.

[pp. 236-239; The Tarim Mummies]



Progress in Natural Science, Volume 17, Number 8, pp. 927-933(7)

Mitochondrial DNA analysis of ancient Sampula population in Xinjiang

Xie Chengzhi Li Chunxiang Cui Yinqiu Cai Dawei Wang Haijing Zhu Hong Zhou Hui

Abstract: The archaeological site of 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 analyzed by 364 bp of the mitochondrial DNA hypervariable region I (mtDNA HVR-I), 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.

Keywords: ancient DNA mitochondrial DNA Sampula ancient populations

[link]

The authors detect the following haplogroups: U3 (in four individuals), N (x2), C (x2), B, F1a, G, M, and T2.

Oceania: tracing population history and adaptation with genome-wide SNP data

MBE Advance Access published online on June 3, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn128

Gene Flow and Natural Selection in Oceanic Human Populations, Inferred from Genome-wide SNP Typing

Ryosuke Kimura1,*, Jun Ohashi2, Yasuhiro Matsumura3, Minato Nakazawa4, Tsukasa Inaoka5, Ryutaro Ohtsuka6, Motoki Osawa1 and Katsushi Tokunaga2

It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide SNP typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called "Slow train" model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation, and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.

Key Words: adaptive evolution • gene flow • human genome • SNP • Oceania

http://mbe.oxfordjournals.org/cgi/content/short/msn128v1?rss=1

Isotopic analysis of an LBK mass grave

The Telegraph reports the study as follows:
Neolithic men were prepared to fight for their women

[. . .]

Many archaeologists have argued that women have long motivated cycles of violence and blood feuds throughout history but there has really been no solid archaeological evidence to support this view.

Now a relatively new method has been used to work out the origins of the victims tossed into a mass grave of skeletons, and so distinguish one tribe from another, revealing that neighbouring tribes were prepared to kill their male rivals to secure their women some 7000 years ago.

The Durham University research, described in the academic journal Antiquity, focused on 34 skeletons found buried in the village of Talheim in the south-west of Germany.

[. . .]

Lead author Dr Alex Bentley says the simplest explanation is that the women of one tribe were captured.

"It seems this community was specifically targeted, as could happen in a cycle of revenge between rival groups. Although resources and population were undoubtedly factors in central Europe around that time, women appear to be the immediate reason for the attack.

"Our analysis points to the local women being regarded as somehow special and were therefore kept alive."

Antiquity

Volume: 82 Number: 316 Page: 290–304

Isotopic signatures and hereditary traits: snapshot of a Neolithic community in Germany

R. Alexander Bentley1, Joachim Wahl2, T. Douglas Price3 and Tim C. Atkinson4

1Department of Anthropology, Durham University, 43 Old Elvet, Durham DH1 3HN, UK (Email: r.a.bentley@durham.ac.uk) 2RP Stuttgart, Landesamt für Denkmalpflege, Osteologie, Stromeyersdorfstraße 3, D-78467, Konstanz, Germany (Email: Joachim.Wahl@rps.bwl.de) 3Department. of Anthropology, University of Wisconsin, 1180 Observatory Dr., Madison, WI 53706-1393, USA (Email: tdprice@wisc.edu) 4Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, UK (Email: t.atkinson@ucl.ac.uk)

A group of Linearbandkeramik people at Talheim, Germany were previously found to have died at the same time, probably in a massacre, and the authors were able to ask some searching questions of their skeletons. The isotope signatures of strontium, oxygen and carbon, which gave information on diet and childhood region, showed up three groups which correlated with hereditary traits (derived previously from the analysis of the teeth). In the local group, there were many local children but no adult women, suggesting they had been selectively taken alive at the time of the massacre. Another group, with isotope signatures derived from upland areas, includes two men who may have been closely related. A third group has a composition suggestive of a nuclear family. The variations of one type of isotope signature with another suggested subtle interpretations, such as transhumance, and a probable labour division in the community between stockholders and cultivators. Here we see the ever-growing potential of these new methods for writing the ‘biographies’ of prehistoric skeletons.

Keywords: Neolithic, Germany, LBK, Talheim, isotope analysis, hereditary traits, trans-humance

http://www.antiquity.ac.uk/ant/082/ant0820290.htm

Hydraulic cement: Thank the English, not the Romans

[re: hysterical Medocentrist outburst elsewhere]

Portland cement as widely used today was originally formulated by Englishman William Aspdin, building on the work of other Englishmen, including his father Joseph Aspdin and, ultimately, John Smeaton:
Smeaton investigated the cementing properties of various mortars, made from lime obtained from various locations, and discovered that the best mortars were made from the calcination of limes that contained considerable proportions of clay minerals (argillaceous lime). This was the first occasion that the importance of clay mixed with the lime had been recognized in the formation of a hydraulic setting cement. It was found that limes that did not dissolve completely in nitric acid (clay being insoluble in the acid) possessed good hydraulic properties (Kohlhaas, 1983). The cementitious agent Smeaton finally used was made from such a clay containing lime which was mixed with an equal quantity of pozzolana (Lea, 1970). The lighthouse that he constructed stood for 123 years until 1879 and only failed when its foundations were undermined by the sea. Smeaton's conclusions about the importance of the presence of clay were not published until after his death in 1792. Smeaton was the first to call himself a civil engineer (as distinct from a military engineer). In the preface to his book, Hydraulischen Moertel, W Michaelis stated in 1869 (in translation):
A century has elapsed since the famous Smeaton completed the building of the Eddystone Lighthouse. Not only the seafaring but for all humanity stands as a true signal of blessed work, a light in the dark night. From the scientific point of view it illuminated the darkness of nearly 2000 years.

The errors which came to us from the Romans and which were shared even by the excellent Belidor, were dispersed.

The Eddystone Lighthouse is the foundation upon which our knowledge of hydraulic mortars has been built and is the chief pillar of modern construction. Smeaton freed us from the shackles of tradition by showing us that the purest and hardest limestone is not the best, at least for hydraulic purposes, and that the source of the hydraulicity of lime mortar must be sought in the argillacrious admixtures (Draffin, 1976).
The cement was called 'Roman cement' although it in no way resembled the true Roman cement, except for its hydraulic setting reactions.

[Mary S. J. Gani; Cement and Concrete; p. 5]


The Romans ceased building with high-quality concrete by around A.D. 300. Our modern knowledge of cement owes nothing to them.
Cement was used from the decline of the Empire and through the Middle Ages, but none of it was any good until comparatively recent times (Davey, 1961). [. . .]

In this case, it was not that a Roman secret was lost, rather that the Romans, who did no testing, never learned what they had. The very idea of testing is comparatively recent, and the engineer John Smeaton, who tested samples for the construction of the Eddystone Light in the years 1756– 1759 (Davey, 1961) is, I suspect, the first man on the planet deliberately to test cements of differing compositions.

[Thomas Nelson Winter. Roman Concrete: The Ascent, Summit, and Decline of an Art. Transactions of the Nebraska Academy of Sciences 7 (1979), pp. 137-143.]

Europeans more highly evolved, not "genetically weaker"

This part of John Hawks' most recent post is worth pointing out:
What is amazing to me is that these same geneticists embrace hypotheses of population history that cannot possibly have happened. The other geneticists quoted in the article, Carlos Bustamante and his graduate student Kirk Lohmueller, wrote a paper earlier this spring arguing that deleterious mutations have reached high frequency in Europeans (moreso than Africans) because of a bottleneck during European history. The press reported this work as "Whites genetically weaker than blacks, study finds." The hypothesis in the paper is that protein-coding sites otherwise conserved in most mammals may differ among humans because of relaxed selection in a bottleneck.

Here's why they're wrong: their bottleneck is impossible. They propose that the European population was a small, isolated population of 5,700 effective individuals from 214,000 years ago up to the Last Glacial Maximum. I suppose I should take some encouragement that they believe Neandertals were European ancestors (because otherwise, where exactly would this small, isolated population of Europeans have lived). But it's still quite impossible -- it implies no gene flow between Africans and Europeans across that entire span. You see, that is the only way that genetic drift can lead to this kind of result -- large differences in frequencies between continents for hundreds of deleterious alleles. It takes a bottleneck of exceptional length, along with complete isolation.

In what has become a troubling trend, these details were hidden away in the online supplementary information of the paper. It is no surprise that most people read only the paper's conclusions, without critically evaluating the methods. But when the assumptions are hidden so that it takes an effort to look at them, you can understand that the paper does not receive the kind of scrutiny that it deserves. These are not obscure laboratory techniques; they are the basic evidence on which the conclusions were based.

Now, Bustamante knows that positive selection has been very important in recent human evolution, because he wrote an important paper on the subject in 2005. I wrote about the paper at the time -- it was one of the works that really got us thinking about acceleration in the first place. So why in the world did their more recent paper adopt such a ridiculous model of population history?

In any event, I don't think that either of these studies from earlier this year are relevant to our acceleration results. They address different aspects of genetic variation. However, acceleration may help to explain the high frequencies of some gene variants conserved in other mammals -- the results explained by Lohmueller and colleagues as relaxed selection under a bottleneck.

The acceleration of recent positive selection would predict that many otherwise conserved gene variants may be segregating in humans, because they are the targets of positive selection. These conserved sites are among those most likely to show a strong sign of recent selection, because adaptive changes on them are necessarily rare (we know they're rare, because they haven't happened very often among other species). Most such sites are still conserved in humans -- it's just not possible to change their function in adaptive ways. But the massive ecological changes of recent human history have created the opportunity for adaptive responses that are not present in other mammalian lineages. We shouldn't be surprised to see that some such changes are currently underway.

Kin selection and the evolution of virulence

Heredity (2008) 100, 484–488; doi:10.1038/sj.hdy.6801093; published online 23 January 2008

Kin selection and the evolution of virulence (pdf)

A Buckling and M A Brockhurst

Social interactions between conspecific parasites are partly dependent on the relatedness of interacting parasites (kin selection), which, in turn, is predicted to affect the extent of damage they cause their hosts (virulence). High relatedness is generally assumed to favour less competitive interactions, but the relationship between relatedness and virulence is crucially dependent on the social behaviour in question. Here, we discuss the rather limited body of experimental work that addresses how kin-selected social behaviours affect virulence. First, if prudent use of host resources (a form of cooperation) maximizes the transmission success of the parasite population, decreased relatedness is predicted to result in increased host exploitation and virulence. Experimental support for this well-established theoretical result is surprisingly limited. Second, if parasite within-host growth rate is a positive function of cooperation (that is, when individuals need to donate public goods, such as extracellular enzymes), virulence is predicted to increase with increasing relatedness. The limited studies testing this hypothesis are broadly consistent with this prediction. Finally, there is some empirical evidence supporting theory that suggests that spiteful behaviours are maximized at intermediate degrees of relatedness, which, in turn, leads to minimal virulence because of the reduced growth rate of the infecting population. We highlight the need for further thorough experimentation on the role of kin selection in the evolution of virulence and identify additional biological complexities to these simple frameworks.

Keywords: experimental evolution, parasite, cooperation, spite, microbe, public goods

Ancient Japan: Jomon vs. Yayoi limb proportions

American Journal of Physical Anthropology; 10.1002/ajpa.20853; Published Online: 16 May 2008

Variation in limb proportions between Jomon foragers and Yayoi agriculturalists from prehistoric Japan

Daniel H. Temple et al.

Keywords: ecogeography, canalization, phenotypic plasticity, Allen's rule, migration

Variation in limb proportions between prehistoric Jomon and Yayoi people of Japan are explored by this study. Jomon people were the descendents of Pleistocene nomads who migrated to the Japanese Islands around 30,000 yBP. Phenotypic and genotypic evidence indicates that Yayoi people were recent migrants to Japan from continental Northeast Asia who likely interbred with Jomon foragers. Limb proportions of Jomon and Yayoi people were compared using RMA regression and Quick-Test calculations to investigate relative variability between these two groups. Cluster and principal components analyses were performed on size-standardized limb lengths and used to compare Jomon and Yayoi people with other groups from various climatic zones. Elongated distal relative to proximal limb lengths were observed among Jomon compared to Yayoi people. Jomon limb proportions were similar to human groups from temperate/tropical climates at lower latitudes, while Yayoi limb proportions more closely resemble groups from colder climates at higher latitudes. Limb proportional similarities with groups from warmer environments among Jomon foragers likely reflect morphological changes following Pleistocene colonization of the Japanese Islands. Cold-derived limb proportions among the Yayoi people likely indicate retention of these traits following comparatively recent migrations to the Japanese Islands. Changes in limb proportions experienced by Jomon foragers and retention of cold-derived limb proportions among Yayoi people conform to previous findings that report changes in these proportions following long-standing evolution in a specific environment. Am J Phys Anthropol, 2008. © 2008 Wiley-Liss, Inc.

Ancient Britons "had geometry skills to rival Pythagoras"

The Independent reports:
Stone Age Britons had a sophisticated knowledge of geometry to rival Pythagoras – 2,000 years before the Greek "father of numbers" was born, according to a new study of Stonehenge.

Five years of detailed research, carried out by the Oxford University landscape archaeologist Anthony Johnson, claims that Stonehenge was designed and built using advanced geometry.

The discovery has immense implications for understanding the monument – and the people who built it. It also suggests it is more rooted in the study of geometry than early astronomy – as is often speculated.

Mr Johnson believes the geometrical knowledge eventually used to plan, pre-fabricate and erect Stonehenge was learnt empirically hundreds of years earlier through the construction of much simpler monuments.

[. . .]

The experimental archaeology demonstrates that most of the monument was pre-planned and that the great stones were pre-fabricated off-site and then installed by surveyor-engineers.

"For years people have speculated that Stonehenge was built as a complex astronomical observatory. My research suggests that, apart from mid-summer and mid-winter solar alignments, this was not the case," said Mr Johnson. "It strongly suggests that it was the knowledge of geometry and symmetry which was an important component of the Neolithic belief system."

"It shows the builders of Stonehenge had a sophisticated yet empirically derived knowledge of Pythagorean geometry 2000 years before Pythagoras," he said.

(via rogueclassicism)

Human population history: a reconstruction based on HGDP genome-wide SNP data

From the press release:
'Our technique enables us to identify more subtle details about genetic contributions than other methods,' said Dr Garrett Hellenthal from the Department of Statistics at Oxford, a co-author on the paper. 'By incorporating the inheritance of 'blocks' of DNA between generations, rather than just individual genes, it captures a panoramic view of the sharing of patterns of DNA across the entire human genome. This allows us to consider a vast number of possible colonisation scenarios - not just the ones people have already thought of - and use an algorithm to determine the most likely migration routes.'

The new technique was used to analyse 2540 genetic markers using Single Nucleotide Polymorphism data from 927 individuals of diverse ethnicity whose DNA was collected by the Human Diversity Project.

'Humans like to tell stories and amongst the most captivating is the story of the global spread of modern humans from their original homeland in Africa,' said Dr Daniel Falush of University College Cork, a co-author on the paper. 'Traditionally this has been the preserve of anthropologists but geneticists are now starting to make an important contribution. However, genetic evidence is still typically analysed in the light of anthropological preconceptions; statistical techniques help us to see things more objectively.'

The researchers believe their method can cope with much larger datasets with over 500,000 genetic markers. Further developments of the technique should allow human ancestry to be reconstructed in unprecedented detail and give a perspective independent of anthropological theory and interpretation.

Sounds interesting, but no doubt far from definitive looking at only 2540 SNPs and a limited number of populations.
PLoS Genet 4(5): e1000078. doi:10.1371/journal.pgen.1000078

Inferring Human Colonization History Using a Copying Model

Garrett Hellenthal et al.

Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single “Out-of-Africa” bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

[. . .]

Gene Flow from Europe to East Asia around the Arctic Circle

In our inferred scenario there is little gene flow between East Asian and Europeans and the Yakut is the only East Asian population to have two European donors; the Russians and the Orcadians. The Russian contribution is not surprising because the Yakut live in North East Russia. The Orcadian contribution is particularly noteworthy because removing these donors reduces the log-likelihood of generating the Yakut chromosomes by 2.5 times more than removing donors from any other population (Table S2). The Orcadians are also the only other European population to donate to other East Asians, namely the Han from Northern China and the Hezhen, who are also amongst the most Northerly East Asian populations in the sample. On this basis we hypothesize that there has been an episode of gene flow from Europe to East Asia. We tested the robustness of this inference by putting Orcadians last in the ordering. The Yakut replaced the Orcadians with Sardinians, who are a major donor to the Orcadians. The Hezhen and the Han from Northern China did not acquire new European donors, consistent with the gene flow from Europe being less quantitatively important to these two populations than to the more Northerly Yakut. Orcadians did not gain any East Asian donors by being placed last in the ordering, strengthening the inference that the direction of the gene flow was from Europe to East Asia.

Finns were not included in the analysis, but this independent evidence of west-east gene flow in northern Eurasia is in line with the theory that N3 (Tat C) Y chromosomes diffused from Northeastern Europeans to Siberians rather than the reverse:
The peculiar Y chromosomal DNA variant, known as Tat C, is also dominant in almost all the indigenous peoples of Siberia, from the nomadic Yakuts right across to the Chukchis and Siberian Inuits living on the shores of the Bering Strait - regardless of what language they may communicate in.

According to Prof. Villems, the "point" in all this is that among the Finno-Ugric races of Europe this genetic inheritance is much more diverse, more multibranched, and hence apparently older than among any of the Siberian peoples.

Height (ESHG 2008 abstracts)

European Human Genetics Conference (abstract database)


PPARG and PPARGC1A gene variants are associated with height in athletes

I. A. Mozhayskaya, I. I. Ahmetov, V. A. Rogozkin;
St Petersburg Research Institute of Physical Culture, St Petersburg, Russian Federation.
Presentation Number: P06.238
PPARgamma nuclear receptor positively promotes adipogenesis and negatively regulates osteoblast differentiation, indicating that PPARgamma is a negative regulator of bone mass. The Ala12 variant of PPARG gene Pro12Ala polymorphism is associated with lower transcriptional activity, increased body mass index and height in humans. PPARGC1A has been identified as a transcriptional coactivator of PPARgamma. Carriers of the Ser482 allele have been reported to have lower levels of PPARGC1A by comparison with Gly482 allele homozygotes. Therefore, one could expect that the Gly482Ser polymorphism might affect height too. The aim of the study was to investigate an association of PPARG Pro12Ala and PPARG1CA Gly482Ser polymorphisms with height in Russian male rowers and speed skaters. The study involved 99 rowers (height - 191.1 (5.4) cm, weight - 86 (9.7) kg; aged 20-27) and 64 speed skaters (height - 179.6 (6) cm, weight - 74.9 (8.8) kg; aged 20-25). Rowers were divided into three groups: the highest group (195-204 cm), the middle group (189-194 cm) and the lowest group (182-188 cm). Gene polymorphisms were determined by PCR-RLFP. We found that the presence of the PPARG 12Ala allele was significantly associated with higher body height (Ala/Ala+Pro/Ala- 182.7 (4.9) cm vs. Pro/Pro - 178.7 (6.1) cm; P=0.023) in speed skaters. The frequency of the PPARG1CA 482Ser allele was significantly higher in the highest group of rowers (33.3%), than in the middle (22.5%) and the lowest (18.8%) groups (P=0.032). In conclusion, functional polymorphisms in PPARG and PPARG1CA genes may influence the growth of the skeleton in male athletes.


Genome-wide association analysis identifies multiple loci associated with normal variation in height
M. N. Weedon1, H. Lango1, G. Lettre2, .. The GIANT Consortium1,2;
1Peninsula Medical School, Exeter, United Kingdom, 2Broad Institute, Boston, MA, United States.
Presentation Number: P07.060
There are many single gene disorders that affect stature, but little is known about the genetic variants that explain normal variation of adult height. The availability of genome-wide association data offers new opportunities to identify the genes involved in normal growth.
Recent meta-analyses of genome-wide association studies (GWAS), using up to 16,000 individuals, have identified 22 independent loci associated with height (p<5x10-8). The GIANT consortium has now extended these analyses, using imputation methods, to combine association results from 13 GWAS, with a total sample size of >32,000 individuals.
Initial meta-analysis identified 111 independent loci with p<1x10-5 and 50 with p<5x10-7. Confirmed loci implicate a wide range of molecular processes involved in normal growth. These include Hedgehog signaling (PTCH1, HHIP, IHH), chromatin remodeling (SCMH1, HMGA2), and basic cell cycling (CDK6, ANAPC13). Some of the variants and genes have been connected to other diseases, including cancer, suggesting that variants associated with height may also influence disease susceptibility. Many of the associated loci include genes known to be involved in growth based on monogenic human studies. Other loci implicate genes previously unsuspected to have a role in growth, and represent excellent candidate genes for, as yet unexplained, growth-related single gene disorders.
Combining data from many genome-wide association studies is likely to result in the identification of hundreds of loci that influence adult height. These data should result in an unprecedented increase in our knowledge of the genetics of growth and development.


A genome-wide scan of adult human stature and skeletal size

Presentation Time: Tuesday, 10:45 a.m. - 11:00 a.m.
N. Soranzo1, F. Rivadeneira2, U. Chinappen3, M. Inouye1, B. J. Richards3, S. Potter1, R. Gwilliam1, K. Papadakis4, E. Wheeler1, I. Barroso1, D. Hart5, G. Livshits6, R. J. F. Loos7, D. Strachan4, N. J. Wareham7, T. D. Spector3, A. Uitterlinden2, P. Deloukas1;
1The Wellcome Trust Sanger Institute, Hinxton, United Kingdom, 2Erasmus MC, Rotterdam, The Netherlands, 3School of Medicine, King’s College London, London, United Kingdom, 4St George's, University of London, London, United Kingdom, 5St. Thomas' Hospital, London, United Kingdom, 6Tel Aviv University, Tel Aviv, Israel, 7Institute of Metabolic Science, Cambridge, United Kingdom.
Presentation Number: C13.1
Human adult stature is a classical quantitative trait and a paradigm for genetic association studies of quantitative trait variation. We have carried out a meta-analysis of four genome-wide association scans of stature produced using the Illumina HumanHap300 SNP panel in 10,050 adults from four population-based cohorts (TwinsUK, EPIC Norfolk and 1958 Birth Cohort from the UK and the Rotterdam Study from the Netherlands). We have identified eighteen loci showing association with height with P-values of less than 10-5, which we have brought forward for replication in an independent sample of 9,000 individuals.
The signals identified provide strong evidence for replication in genomic regions previously implicated in height, including HMGA2 (rs8756, P-value = 5x10-13) and GDF5-UQCC (rs4911494, P-value = 1.5x10-10). In addition, we have identified novel candidate genetic loci for human height, some of which are in or near genes implicated in cellular growth and development (HHIP, ADAMTSL3 and DLEU7). In an attempt to dissect the mechanisms underlying human growth, we have tested the association of these novel candidate height loci with different measurements of skeletal growth. Our results provide both novel and confirmatory evidence for the implication of genes and pathways in human growth, thus contributing to the understanding of the biological processes underlying many common and severe human diseases.


Genome wide association analysis in human height of European-originated monozygotic female twins
J. A. Kettunen1,2, I. Lindqvist2, S. Ripatti2,3, T. D. Spector4, N. G. Martin5, L. Peltonen1,2, M. Perola2;
1Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 2National Public Health Institute, Helsinki, Finland, 3Karolinska Institutet, Stockholm, Sweden, 4Twin Research and Genetic Epidemiology Unit, King's College, London, United Kingdom, 5Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Austria.
Presentation Number: P06.126
Stature (i.e. adult height) is a quantitative trait with high heritability. Various interesting regions in the human genome have been linked to adult stature but only few have been confirmed by later studies. Two genome wide association (GWA) studies have been published recently and they identified two loci (HMGA2 and GDF5-UQCC) to be strongly associated to stature after extensive replication studies. In this study we report a genome wide association analysis performed on 1631 European monozygotic female twin pairs from the GenomEUtwin consortium. One of each pair was genotyped with the Illumina HumanHap300-duo chip. Whole genome association analysis was performed with the PLINK-program. Area of residence and age were used as covariates in all of the analyses. Our study had two goals: We wanted to reduce the environmental variance by using the mean of each pair as a phenotype. We observed an association (p = 3.14*10-6) on 8q24 locus underlying the linkage peak identified previously in our linkage scan on European dizygotic twins (LOD 3.28). The replication study is underway for the most significant findings in this GWA scan. Second, we analyzed whether we could pinpoint any regions in genome which would be associated to the difference within each pair. This approach was aiming to find genes responsible for increasing variance in human height, thus potentially indicating for example GxE interaction or imprinting/gene silencing. The most significant finding for variance in stature (p = 1.22 * 10-5) was identified on 6q14 region.


Genetic analysis of adult stature in Dutch isolated population

I. V. Zorkoltseva1, T. I. Axenovich1, C. M. van Duijn2;
1Institute of Cytology and Genetics, Novosibirsk, Russian Federation, 2Department of Epidemiology & Biostatistics, Erasmus MC, Rotterdam, Netherlands.
Presentation Number: P06.008
We analysed a large complex pedigree from a Dutch genetically isolated population. About 2600 of 19700 pedigree members were phenotyped and genotyped for autosomal 5208 SNPs (Illumina 6K linkage panel). Complex segregation analysis of adult height was performed under mixed model including effects of biallelic major gene, polygene, age and sex. We used likelihood approximation based on breaking pedigree loops. The results confirmed large contribution of genes in the trait variance (h2 = 0.85 ) and significance of major gene effect in accordance with Elston-Stewart test. Three genotypic means were estimated as 183.5, 178.3 and 174.6 cm in males at 40 years with average difference of male and female genotypic means about 13 cm. The putative major gene explained 18% of trait variance.
A genome-wide scan was performed by variance-components method using Merlin program. Prior to analysis, the pedigree was split into smaller non-overlapping fragments, with maximum bit-size of 18. No loci demonstrated significant linkage, however for 6 loci linkage was suggestive:
SNP Chr Position(cM) LodScore
rs1993104 19 56.9 2.71
rs1873191 18 44.7 2.60
rs1019845 2 195.8 2.27
rs958883 5 123.3 2.15
rs936347 16 17.2 2.11
rs216223 17 2.1 2.11

Of these six loci, five were identified in previous linkage analyses, while locus at chromosome 16 (rs936347) was new.

2008-05-26 links

Statistical Modeling, Causal Inference, and Social Science: Voting patterns of Jews and other religious groups; Quarterbacks and psychometrics

Studium generale: Die Hausmaus in der Weltgeschichte

Mathilda's Anthropology Blog: The domestication and ancient pedigree of the housecat

Plomin et al.: Testing replication of a 5-SNP set for general cognitive ability in six population samples

mtDNA and disease: no association between the common [mitochondrial DNA haplogroups] and prostate cancer in the Korean population

AJPA: Middle Eastern and European mtDNA lineages characterize populations from eastern Crete

Positive selection at MC1R in Europeans?

BMC Genetics 2008, 9:31doi:10.1186/1471-2156-9-31

Nucleotide diversity and population differentiation of the Melanocortin 1 Receptor gene, MC1R

Sharon A Savage et al.

Background
The melanocortin 1 receptor gene (MC1R) is responsible for normal pigment variation in humans and is highly polymorphic with numerous population-specific alleles. Some MC1R variants have been associated with skin cancer risk.

Results
Allele frequency data were compiled on 55 single nucleotide polymorphisms from seven geographically distinct human populations (n = 2306 individuals). MC1R nucleotide diversity, ?, was much higher (10.1 × 10-4) than in other genes for all subjects. A large degree of population differentiation, determined by FST, was also present, particularly between Asia and all other populations, due to the p.R163Q (c.488 G>A) polymorphism. The least amount of differentiation was between the United States, Northern Europe, and Southern Europe. Tajima's D statistic suggested the presence of positive selection in individuals from Europe.

Conclusion
This study further quantifies the degree of population-specific genetic variation and suggests that positive selection may be present in European populations in MC1R.

[. . .]

Numerous studies have demonstrated associations between specific MC1R variants and red hair, light skin, poor tanning ability and heavy freckling [4-9]. A recent genome-wide association scan confirmed the role of MC1R SNPs in hair, eye, and skin pigmentation[3]. The functional role of many of these variants has been described [10-13]. Several MC1R variants are also associated with increased risk of malignant melanoma in a variety of populations [14-22] The effect of MC1R polymorphisms in melanoma risk appears to extend beyond its effect on pigmentation in most of these investigations, and to be linked to melanomas harboring mutations in the BRAF oncogene[23].

Several hypotheses have been generated in an effort to understand the evolutionary history of skin pigmentation in humans. It has been suggested that as humans migrated out of Africa to climates with more limited exposure to sunlight, relaxation of functional constraints in pigmentation genes, including MC1R, or selection for functionally relevant variants that led to lighter skin pigmentation occurred[24]. This could result in an improved ability to synthesize vitamin D in the presence of limited sunlight exposures [25-27]. It has also been suggested that darker skin is favored in regions closer to the equator for protection against ultraviolet radiation[24]. In addition, differences in skin pigmentation could protect against pathogens and cold injury, and may have also been important in sexual selection[28].

[. . . ]

Several studies have evaluated genetic adaptation of the MC1R gene for evidence of positive selection with conflicting results. Some studies suggested that purifying selection is present in Africa and that relaxation of functional constraint in non-African populations, instead of positive selection, is present[25,27,40]. On the other hand, most recent studies have found evidence of positive selection at other pigmentation genes. For example, Myles et al [2] found evidence for positive selection in the DCT gene among individuals of Chinese ancestry. In their study, MC1R interpretations were limited because of the different SNPs genotyped between the Perlegen and HapMap data sets studied. In a study of 118 putative skin pigmentation genes, data were consistent with positive selection in subjects from Europe (OCA2, TYRP1, and KITLG) and in Asians (DCT, EGFR, and DRD2)[38]. Unfortunately, MC1R could not be evaluated in that study due to ascertainment criteria. It was also suggested that at least weak, recent positive selection may be present in MC1R, based on the AF variability between CEPH Utah and East Asian HapMap samples[3]. Our data suggest that MC1R may be under positive selection in some populations, although additional studies are needed to further evaluate this finding.

Longevity (ESHG 2008 abstracts)

European Human Genetics Conference (abstract database)


The relation of common diseases SNPs and life span: no evidence for shared genetic component
O. Y. Byichkova1, O. A. Makeeva1, I. V. Tsimbal'uk2, K. V. Puzyrev3, V. N. Maksimov4, V. P. Puzyrev1,2;
1Research Institute of Medical Genetics, Tomsk, Russian Federation, 2Siberian State Medical University, Tomsk, Russian Federation, 3Research Institute of Cardiology, Tomsk, Russian Federation, 4Research Institute of Therapy, Novosibirsk, Russian Federation.
Presentation Number: P07.028
Life span is a multifactorial trait with a strong genetic component. Besides the number of genes has been directly implicated into the processes of ageing and longevity, the genes responsible for common diseases such as cardiovascular (CVD) or immunity disorders are also had to be under intent consideration. The persistence and both elimination from human populations ‘predisposing’ common genetic variants is forced by a complex interplay of different evolutionary processes; some variants being unfavorable during particular periods of life can offer their owners advantages on the others. Latter should be taken into account e.g. while developing genetic test and interpreting frequently discrepant genetic data on disease association. Testing the hypothesis that CVD predisposing alleles can be related to the life span, we investigate several cohorts: healthy controls of childbearing age (aged from 20 to 45, n=282), nonagenarians (aged 90 and over, n=235) and patients with cardiovascular disease (arterial hypertension with different complications) (n=231) from the same geographic region and ethnicity (East Siberia, Russians) and genotyped for several well-known CVD candidate genes polymorphisms (G-308A TNF, C894T NOS3, and A1166C AGTR1). While all the three SNPs under study affected several important cardiovascular endophenotypes (arterial blood pressure measurements, cardiac parameters, left ventricular hypertrophy development est.) no significant differences had been revealed among nonagenarians and middle aged group. In this study we never found actual proof for the stated hypothesis, though a huge amount of other genetic variants and the larger samples are needed to be tested before its decline.


Age-dependent genetic polymorphism frequencies and Gene - Pass

V. S. Baranov1, H. V. Baranova2, O. S. Glotov1;
1Ott’s Institute of Obstetrics & Gynecology, St.Petersburg, Russian Federation, 2European Institute of Personalized Prevention, Nice, France.
Presentation Number: P07.058
The report highlights the results of collaborative studies of personalized anti-aging medicine and its impact into longevity and aging. Special attention is paid to the gene nets of cardiovascular diseases, renin-angiotensin system, diabetus mellitus, osteoporosis etc. Polymorphic variants of at least some particular genes such as ACE, AGT, PAII, MTHFR, APOE, also as metabolic genes, like GSTs and other oxidative stress markers (NOS) are considered as the most plausible candidates of the genes crucial for aging. Molecular analysis of these particular genes supplemented with relevant metabolic genes testing, responsible for efficiency of detoxification system might have substantial contribution into personalyzed anti - aging medicine. The data on allele frequencies distribution for 10 differenet genes in newborns (106), 119 middle age and 148 old people over 69 are presented Relevant gene testing supplemented with its adequate sophisticated interpretation and constructive recommendations might have substantial contribution to human health and should be considered as a new highly promising tool in anti-aging medicine “Gene - pass ” term is suggested for the individual DNA data bank reflecting increased personal susceptibility to these common disorders. Tremendous impact to its practical application could be achieved through wide scale application of biochip technology. The latter are already available or are in progress for a number of multifactorial diseases. Special attention is paid to Genetic Pass of Reproductive Health - a version of Genetic Pass adjusted to the needs of pregnant woman. Life in harmony with personal gene makeup remains indispensable prerequisite of longevity and good health..


Study on a possible effect of four longevity candidate genes (ACE, PON1, PPAR-gamma, APOE) on human fertility

R. M. Corbo1,2, L. Ulizzi1, L. Piombo1, R. Scacchi2;
1La Sapienza University, Rome, Italy, 2CNR Institute of Molecular Biology and Pathology, Rome, Italy.
Presentation Number: P07.080
A possible effect on fertility of four genes [angiotensin 1-converting enzyme (ACE), paraoxonase (PON1), peroxisome proliferator-activated receptor gamma (PPAR-g), and apolipoprotein E(APOE)] previously found associated with longevity was sought in order to determine whether they have a pleiotropic action at different life ages. The study population was 151 Italian subjects whose reproductive life took place at the beginning of the demographic transition (declining fertility and longer life expectancy) and who had produced a mean number of children (3.6±2.3) such as to be still useful to detect a differential reproductive efficiency associated with different genotypes.
Of these four longevity candidate genes, only PPAR-g and APOE appeared to have an effect on fertility, indicating their possible influence on reproductive efficiency. The PPAR-g Pro/Ala genotype, which in a previous study (Barbieri et el. 2004) showed a positive association with longevity only in men, was found associated with a higher number of children (6.1 ± 3.3) than Pro/Pro genotype (3.3 ± 1.9, p=0.001) only in men. Compared with the other APOE alleles, the APOE*2 allele, considered as an allele favouring a longer life-span, was confirmed to be associated with the lowest fertility (p=0.03). The logistic regression analysis indicated that APOE and PPAR-g polymorphisms act as independent determinants of reproductive efficiency. These data suggest that the APOE*2 allele may follow the model of antagonist pleiotropy, whereas the PPAR-g Pro/Ala genotype seems to exert beneficial effects both early in life and in advanced age in a gender-specific way.

A Saami admixture estimate

As always, I tend to be skeptical about the utility of HLA for accurately determining population affinities.
European Journal of Human Genetics advance online publication 14 May 2008; doi: 10.1038/ejhg.2008.88

Genetic origin of the Swedish Sami inferred from HLA class I and class II allele frequencies

Åsa Johansson et al.

Sami of northern Scandinavia are genetic outliers among European populations and their origin has been difficult to determine. In order to study the genetic origin of the Swedish Sami, we have performed high-resolution typing of the class I HLA-A and -B loci and the class II DRB1, DQB1 and DQA1 loci in the northern and southern Swedish Sami. Several of the common class I alleles in Sami (B*0702, B*1501, B*4002 and A*0301) are found at high frequency in other European populations. However, a number of class I and class II alleles (B*4001, A*2402, DRB1*0901 and DRB1*1101) in the Swedish Sami are characteristic of Asian populations. Admixture analyses indicate that 87% of the Sami gene pool is of European origin and that the Asian contribution is 13%. Our HLA analyses indicate a higher proportion of Asian ancestry in the Sami than shown by previous genetic studies.

Keywords: Sami, HLA, genetic origin, admixture