September 30, 2005

Geographical distance and ethnicity as predictors of genetic diversity

This paper proposes that geography is a better determinant of human genetic variation than ethnicity (read: race). There are two problems with the paper.

One, they use the proportion of shared alleles as a measure of similarity. Under this measure, three populations A, B, C that share the same alleles will be grouped as similar, even if the alleles occur in very similar frequencies in A and B and different frequencies in C. Sharing of alleles is expected to be influenced by geography: most alleles are pan-human, and few are population specific; racial differentiation consists both in different frequency of pan-human alleles and possession of population specific variants.

Two, their claim that geography is a better predictor than ethnicity is due to the fact that their geographical determinant is complex, consisting of pairwise geographical distances between the 51 populations, whereas their ethnicity determinant is simple, consisting of population placement in one of four clusters. It is not surprising that a complex predictor explains more variance than a simpler alternative, but this has little to do with the superiority of geography over ethnicity as a predictor.

Human Genetics (Online first)

Geography is a better determinant of human genetic differentiation than ethnicity

Andrea Manica et al.


Individuals differ genetically in their susceptibility to particular diseases and their response to drugs. However, personalized treatments are difficult to develop, because disease susceptibility and drug response generally have poorly characterized genetic architecture. It is thus tempting to use the ethnicity of patients to capture some of the variation in allele frequencies at the genes underlying a clinical trait. The success of such a strategy depends on whether human populations can be accurately classified into discrete genetic ethnic groups. Despite the heated discussions and controversies surrounding this issue, there has been essentially no attempt so far to quantify the relative power of ethnic groups and geography at predicting the proportion of shared alleles between human populations. Here, we present the first such quantification using a dataset of 51 populations typed at 377 autosomal microsatellite markers, and show that pair-wise geographic distances across landmasses constitute a far better predictor than ethnicity. Allele-sharing between human populations worldwide decays smoothly with increasing physical distance. We discuss the relevance of these patterns for the expected distribution of variants of medical interest. The distribution patterns of gene coding for simple traits are expected to be highly heterogeneous, as most such genes experienced strong natural selection. However, variants involved in complex traits are expected to behave essentially neutrally, and we expect them to fit closely our predictions based on microsatellites. We conclude that the use of ethnicity alone will often be inadequate as a basis for medical treatment.


Physical Attractiveness and Health

Psychol Bull. 2005 Sep;131(5):635-53.

Physical attractiveness and health in Western societies: a review.

Weeden J, Sabini J.

Evidence from developed Western societies is reviewed for the claims that (a) physical attractiveness judgments are substantially based on body size and shape, symmetry, sex-typical hormonal markers, and other specific cues and (b) physical attractiveness and these cues substantially predict health. Among the cues that the authors review, only female waist-to-hip ratio and weight appear to predict both attractiveness and health in the claimed manner. Other posited cues--symmetry and sex-typical hormonal markers among them--failed to predict either attractiveness or health (or both) in either sex. The authors find that there is some indication that attractiveness has an overall relationship with health among women, but little indication that male attractiveness relates to male health.


September 29, 2005

Thrombosis-causing polymorphism in Caucasoids

Mol Genet Metab. 2005 Sep 23; [Epub ahead of print]

Factor V Leiden, prothrombin 20210A, methylenetetrahydrofolate reductase 677T, and population genetics.

Bauduer F, Lacombe D.

Thrombosis results from the interaction between predisposing genetic polymorphisms and acquired risk factors. Two of the main prothrombotic alleles, Factor V (FV) Leiden and prothrombin 20210A, are only encountered among European populations. They are estimated to have arisen about 21,000-34,000 years ago as founding mutations after the evolutionary divergence of Caucasians from Asians, and have been subsequently dispersed by the Neolithic migrations. These polymorphisms may have developed by means of genetic drift or natural selection by possibly conferring a reduced risk of bleeding. Of note, FV Leiden is nearly absent in the Basques, a European population of pre-Neolithic individualization. The C677T mutation of the methylenetetrahydrofolate reductase gene may induce hyperhomocysteinemia and could slightly increase the risk of arterial or venous thrombosis and pregnancy loss in individuals with folic acid deficiency. Through a selective phenomenon, the frequency of the mutation may parallel the intake of this vitamin within populations. Hence, this allele is underrepresented in Sub-Saharan Africa, Indonesia, and in the Inuits and a positive North to South gradient has been described in Europe. Thus, these three inherited prothrombotic polymorphisms represent interesting tools for population genetics studies.


September 28, 2005

Peter Frost on the evolution of blondness

This is an interesting hypothesis, but one which suffers from a lack of genetic documentation. If indeed there was an imbalance in the operational sex ratio of early northern and eastern Europeans, then one could discover its signal in patterns of diversity of Y-chromosomal and mitochondrial polymorphisms in depigmented vs. non-depigmented Caucasoids.

My own theory explains the evolution of blondness as a paedomorphic trait that was differentially selected in Caucasoid populations due to its interaction with other phenotypic traits.

Briefly, I propose that hair acts as a frame, drawing attention to an individual's features. The prehistoric northern Caucasoids were broad-faced and coarse-featured (Cro-Magnoid) with a robust type of appearance. Dark hair would act to emphasize these robust features in women, while light hair would act to de-emphasize them, giving a more "feminine" appearance.

After Neolithic times, in the south appeared the narrow-faced and gracile types (Mediterranean), who had a more refined appearance, and these types gradually spread, replacing the coarse types. Coarse-featured women needed an extra boost to compete against the more feminine narrow-faced ones, and light hair provided that boost.

Thus in the long-term there was a trend for selection of narrow-faced women over broad-faced ones, but also a trend for selection of blonde women because of the advantage of robust-blondes over robust-brunettes. This explains the joint survival of blondism and robust types (named Brunn, Faelisch, East Baltic, Borreby, etc.) in northern latitudes.

We can definitely observe the first trend in the palaeoanthropological record, as the skeletally Cro-Magnoid population was gradually replaced by Nordoid types in northern Europe. The second trend cannot be directly observed, but the clinal gradation of hair blondism from a peri-Baltic nexus strongly suggests a more recent spread. This may also be sugggested by some ancient DNA analyses and the possibly late Paleolithic origin of an allele for light pigmentation recently discovered.

Evolution and Human Behavior (in press)

European hair and eye color
A case of frequency-dependent sexual selection?

Peter Frost


Human hair and eye color is unusually diverse in northern and eastern Europe. The many alleles involved (at least seven for hair color) and their independent origin over a short span of evolutionary time indicate some kind of selection. Sexual selection is particularly indicated because it is known to favor color traits and color polymorphisms. In addition, hair and eye color is most diverse in what used to be, when first peopled by hunter-gatherers, a unique ecozone of low-latitude continental tundra. This type of environment skews the operational sex ratio (OSR) of hunter-gatherers toward a male shortage in two ways: (1) men have to hunt highly mobile and spatially concentrated herbivores over longer distances, with no alternate food sources in case of failure, the result being more deaths among young men; (2) women have fewer opportunities for food gathering and thus require more male provisioning, the result being less polygyny. These two factors combine to leave more women than men unmated at any one time. Such an OSR imbalance would have increased the pressures of sexual selection on early European women, one possible outcome being an unusual complex of color traits: hair- and eye-color diversity and, possibly, extreme skin depigmentation.


September 27, 2005

DNA preserved in crystals of ancient bones

Extracting DNA from ancient bones currently consists of turning a piece of bone, usually a tooth, into powder, and carrying out an amplification process that multiplies the number of DNA fragments that may be preserved.

Unfortunately, this procedure has two problems: first, DNA is often damaged post mortem and thus may not reflect the genetic structure of the organism under study; second, contamination from anyone in contact with the specimen is a risk. In particular, any modern sequences extracted from it are automatically suspect.

Now, a new method has been devised to address these problems. Scientists have observed that within certain crystal-like regions of partially fossilized bones there may exist DNA in well-preserved state. It is not as good as living-tissue DNA, and in some cases no DNA is preserved in those regions, but it is a lot better than DNA from the entire specimen.

The way this works is counterintuitive: the crystal structures preserve about 2 orders of magnitude less DNA than the entire sample. So, why throw away so much genetic material? Because the amplification process can start with very small numbers of sequences, it doesn't really matter how much DNA you begin with; it's much more important that this DNA be "pure". So, a few good DNA sequences are preferrable to many times more, but mixed with bad ones.

How does one get to the DNA within those crystal aggregates. The researchers have devised a technique which applies a type of acid to the specimen. This acid eats through most of it, but is unable to penetrate the crystals. So, the crystals are all that remain after oxidization. As an added bonus, this process also eats up any contaminant sequences which may have polluted the sample, but such contaminant sequences are unable to penetrate into the crystals.

More research needs to be done to see whether or not this technique can be widely applied, but it certainly seems that scientists are working hard to maximize the extraction of genetic material from ancient remains.

PNAS (Early edition)

Michal Salamon et al.

Relatively well preserved DNA is present in the crystal aggregates of fossil bones

DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones.


Origins of haplogroups NO, N, N2, and N3

Source Human Y-chromosomal variation in European populations (pdf):

The spread of tuberculosis

Genghis Khan's previous claim to genetic fame was linked to the presence in about 0.5% of the population of the entire world and in a substantial portion of the population of Central Asia, of a unique Y-chromosome haplotype.

Now, a team of geneticists led by Igor Mokrusov are uncovering the darker aspects of the Great Khan's conquests. From their press release.
Mokrousov's team hypothesized that, given the strong gender bias of TB infectivity and the likely family-based mode of TB transmission during pre-industrialized times, M. tuberculosis dissemination has reflected the unidirectional inheritance of the paternally transmitted human Y chromosome. To test this hypothesis, the authors compared the genetic profiles of a common form of M. tuberculosis, called the Beijing genotype, with known patterns of prehistoric and recent human migrations, as well as with global patterns of Y-chromosome variation. Strikingly, they observed that over the past 60,000-100,000 years, the dispersal and evolution of M. tuberculosis appears to have precisely ebbed and flowed according to human migration patterns.

The authors describe how the Beijing genotype of M. tuberculosis originated in a specific human population called the K-M9 in central Asia approximately 30,000-40,000 years ago following a second "out of Africa" migration event. The bacteria and its human host then disseminated northeast into Siberia between 20,000-30,000 years ago and throughout eastern Asia between 4,000-10,000 years ago. More recently, the Beijing genotype of M. tuberculosis was introduced into northern Eurasia, perhaps by Genghis Khan himself during the 1200's, and into South Africa, possibly through sea trade contacts with Indonesia or China during the last 300 years.

Please note that while most news will doubtlessly focus on the Genghis Khan angle, the spread of haplogroup K-M9 occurred in deep prehistory. Only much later did a a particular genotype of M. tuberculosis spread, perhaps by the actions of Genghis Khan, although there have been multiple incursions of Mongoloid peoples which may account for the current distribution, and as the authors note, its introduction into South Africa was an independent event.


I have finished reading the paper, and the argument that the authors make for the introduction of the variant in Europe by the armies of Genghis Khan is quite ingenuous:
Since the Beijing genotype is not a European endemic variant, the published PC analysis of European human populations allows us to rule out those migrations that equally concerned both Russia and Europe as sources of the Beijing strains. These are defined by Finno-Ugric (PC2) (Cavalli-Sforza 2001), Scythe (PC3) (Cavalli-Sforza 2001), and Hun (Christian 1998) expansions. We may further speculate that trade contacts as such, even long-lasting ones, are not sufficient for an effective dissemination of the M. tuberculosis strains if they are not supported by a kind of demic diffusion of the strains’ carriers, manifested as population growth and migration. The Silk Road connected China with Europe for almost two millennia, 2 BC–1600 AD (Christian 1998), and this route may have been opened much earlier, based on the transfer of the first ceramics technology from Japan to the Middle East and Europe at the beginning of agricultural practice (Cavalli-Sforza 2001). However, it is appropriate to reiterate that Beijing strains are not identified as a European endemic variant.

Finally, we suggest the TB spread related to the Genghis (or Chinggiz) Khan invasion to be more plausible. The Mongol empire of the 13th century brought the different parts of Eurasia closer than they had ever been before and created an economic and cultural system embracing much of the Eurasian land mass (Christian 1998). It was also a period of remarkable ethnic mixing since the Mongol army grew by incorporating the armies of many different nations that it had defeated, including Han Chinese (Christian 1998). McNeill (1976) suggested that Mongol invasions also unified Eurasia epidemiologically, allowing the exchange of the disease vectors throughout Eurasia. Genghis Khan did eventually come in the center of Europe, but for a short time. This was sufficient for the dissemination of Yersinia pestis to occur, but not for that of the far less contagious M. tuberculosis. Even if some M. tuberculosis Beijing genotype strains had been brought to Europe in this way, this may not have manifested rapidly. Subsequently, the Black Death that decimated European human populations could have efficiently eliminated rare carriers of the M. tuberculosis Beijing genotype. By contrast, further close interaction between Rus’ and Orda was prolonged for three centuries, and it may be possible that the Mongol invasion and the subsequent yoke/cohabitation were indeed the vehicle that brought M. tuberculosis Beijing genotype strains to Russia
The authors are noting that there have been multiple movements of peoples from Asia to Europe. So, how do they conclude that the Mongols of Genghis Khan are implicated? If the genotype was brought e.g., by the Huns, or the Scythians, or the Finno-Ugrians, then we would expect to find it commonly in Europe, because these movements affected large parts of the continent. But, the Beijing haplotype is not a European variant, so by a process of elimination these movements are probably not responsible for its dissemination.

Rather, it is the Mongols who held Russia -but not Europe- captive for three centuries, and Russia is the country in Europe where the Beijing genotype is found. Moreover, since the Mongols recruited soldiers from China, they could have acquired the genotype, and then brought it to Russia. It is then during the centuries of Mongol domination, at the western edge of Mongol expansion that the Beijing genotype was brought to Russia.

Genome Research

Origin and primary dispersal of the Mycobacterium tuberculosis Beijing genotype: Clues from human phylogeography

Igor Mokrousov et al.


We suggest that the evolution of the population structure of microbial pathogens is influenced by that of modern humans. Consequently, the timing of hallmark changes in bacterial genomes within the last 100,000 yr may be attempted by comparison with relevant human migrations. Here, we used a lineage within Mycobacterium tuberculosis, a Beijing genotype, as a model and compared its phylogeography with human demography and Y chromosome-based phylogeography. We hypothesize that two key events shaped the early history of the Beijing genotype: (1) its Upper Palaeolithic origin in the Homo sapiens sapiens K-M9 cluster in Central Asia, and (2) primary Neolithic dispersal of the secondary Beijing NTF::IS6110 lineage by Proto-Sino-Tibetan farmers within east Asia (human O-M214/M122 haplogroup). The independent introductions of the Beijing strains from east Asia to northern Eurasia and South Africa were likely historically recent, whereas their differential dissemination within these areas has been influenced by demographic and climatic factors.


September 26, 2005

Babies and foreign music

A recent article in PNAS has studied the responses of babies to music. 6-month old babies show general patterns of response to music regardless of whether or not it is foreign to their culture or not. 12-month old babies on the other hand, show a different pattern of response to their own culture's music compared to that of other cultures. However, babies had the ability to detect changes in foreign music, whereas adults lacked this ability. Previous research on non-native speech patterns and foreign faces also indicated that adults have difficulty differentiating between them.

PNAS vol. 102 no. 35 12639-12643

Tuning in to musical rhythms: Infants learn more readily than adults

Erin E. Hannon and Sandra E. Trehub

Domain-general tuning processes may guide the acquisition of perceptual knowledge in infancy. Here, we demonstrate that 12-month-old infants show an adult-like, culture-specific pattern of responding to musical rhythms, in contrast to the culture-general responding that is evident at 6 months of age. Nevertheless, brief exposure to foreign music enables 12-month-olds, but not adults, to perceive rhythmic distinctions in foreign musical contexts. These findings may indicate a sensitive period early in life for acquiring rhythm in particular or socially and biologically important structures more generally.


Bottleneck in European population

Human Genetics (online first)

Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population

Claudia Schmegner et al.

Abstract The inference of the demographic history of populations from genetic variability data is not only of academic interest. It also provides background information for the identification of genes which may have played a role in human evolution or in the aetiology of human disease. To obtain a clear picture of this background, it is necessary to compare data obtained from a number of genomic loci. Due to its very low recombination rate, the NF1 gene region can be regarded as a further suitable locus. A combined resequencing and SNP typing project in a European population disclosed the presence of only two well separated subgroups of NF1 sequences. Statistical analysis revealed a bimodal distribution of the pairwise differences, a positive value of Tajima’s D and a TMRCA of 700,000 years for the whole sample, and pairwise differences indicative for a growing population and TMRCAs of 130,000 to 150,000 years for the subgroups. Together, the data lead to a model that the recent European population went through a bottleneck during the last 150,000 years of its history. Regarding the given timeframe, this bottleneck could either reflect a speciation event which led to the anatomically modern human (AMH), or a severe reduction of the population size during the emigration of AMHs out of Africa or the immigration into Europe.


mtDNA haplogroups in Koreans

Here are the frequencies of mtDNA haplogroups in Koreans:

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International Journal of Legal Medicine (Online first)

Mitochondrial DNA control region sequences in Koreans: identification of useful variable sites and phylogenetic analysis for mtDNA data quality control

Hwan Young Lee et al.

Abstract We have established a high-quality mtDNA control region sequence database for Koreans. To identify polymorphic sites and to determine their frequencies and haplotype frequencies, the complete mtDNA control region was sequenced in 593 Koreans, and major length variants of poly-cytosine tracts in HV2 and HV3 were determined in length heteroplasmic individuals by PCR analysis using fluorescence-labeled primers. Sequence comparison showed that 494 haplotypes defined by 285 variable sites were found when the major poly-cytosine tract genotypes were considered in distinguishing haplotypes, whereas 441 haplotypes were found when the poly-cytosine tracts were ignored. Statistical parameters indicated that analysis of partial mtDNA control region which encompasses the extended regions of HV1 and HV2, CA dinucleotide repeats in HV3 and nucleotide position 16497, 16519, 456, 489 and 499 (HV1ex+HV2ex+HV3CA+5SNPs) and the analysis of another partial mtDNA control region including extended regions of HV1 and HV2, HV3 region and nucleotide position 16497 and 16519 (HV1ex+HV2ex+HV3+2SNPs) can be used as efficient alternatives for the analysis of the entire mtDNA control region in Koreans. Also, we collated the basic informative SNPs, suggested the important mutation motifs for the assignment of East Asian haplogroups, and classified 592 Korean mtDNAs (99.8%) into various East Asian haplogroups or sub-haplogroups. Haplogroup-directed database comparisons confirmed the absence of any major systematic errors in our data, e.g., a mix-up of site designations, base shifts or mistypings.


Left-handedness and breast cancer

Breast cancer risk double for left-handed women

Women who are left-handed are at increased risk of developing breast cancer at an early age, research has suggested.

Scientists believe that women who are born left-handed may have been exposed to higher levels of sex hormones in the womb.

They are more than twice as likely to be diagnosed with pre-menopausal breast cancer, according to a study published in the online version of the British Medical Journal. Researchers from the University Medical Centre in Utrecht followed more than 12,000 women born between 1932 and 1941.

They took into account other risk factors for breast cancer, such as body weight, smoking habits, family history and socio-economic status. Even when all these were adjusted for, women who were left-handed were 2.41 times more likely to develop breast cancer before the menopause.

Link (Independent)

Homosexual women tend to be more left-handed as well.

Fellow nationals make the best lovers

When it comes to sex, patriotism is the order of the day among men and women. 34 per cent of Europeans and 25 per cent of Americans are convinced that the best lovers can be found in their own country. Bringing up the rear are the Dutch (13 per cent), the Belgians (14 per cent) and the Germans (15 per cent). In these three countries, Italians are considered as the best lovers and this is hardly surprising, because the respondents in another 13 out of the 20 countries surveyed rated the Italians second best. 69 per cent of Italians are convinced that the best sexual partners can be found in their own country. This is topped only by the Greeks, where 77 per cent believe this.


European champions

After defeating Germany in the finals, France in the semi-finals, Russia in the quarter-finals, and Israel in the elimination round, Greece is the new European Basketball champion.

Greece 78 - Germany 62

Greece 67 - France 66

Russia 61 - Greece 66

Greece 67 - Israel 61

September 25, 2005

Neanderthal teeth growth rate comparable to that of modern humans

Proc. Natl. Acad. Sci. (Published online)

Anterior tooth growth periods in Neandertals were comparable to those of modern humans

Debbie Guatelli-Steinberg et al.


A longstanding controversy in paleoanthropology surrounds the question of whether Neandertals shared the prolonged growth periods of modern humans. To address this question, this investigation compares the duration of enamel formation in Neandertals with that of three comparative modern human groups. Because dental and somatic growth are correlated with each other, dental growth periods are indicative of overall periods of growth. Growth increments on the anterior teeth of Neandertals, modern Inuit, and modern people from Newcastle and southern Africa were counted and their means compared. In addition, potential variation in the time spans represented by growth increments was considered and incorporated into the analysis of enamel formation times. These analyses show that Neandertal imbricational enamel formation times, although likely to have been faster than those of the Inuit, are not likely to have been faster than those of the Newcastle sample and for some teeth are clearly slower than those of the southern African sample. Thus, Neandertal tooth growth and, by extension, somatic growth, appears to be encompassed within the modern human range of interpopulation variation.


John Hawks has more on this topic.

September 24, 2005

Out of Africa vs. Multiregionalism, the debate that will not end

I was recently glancing through the excellent Human Evolutionary Genetics, and one of the opinion boxes in the book was titled "Modern Human origins - why it's time to move on". In it, Robert Foley and Marta Mirazon Lahr pronounce the victory of the out of Africa model and the death of multiregionalism:
The 'out of Africa' model of human evolution has basically proved to be empirically sound, and the field is now (at last!) moving on.
On the other hand, Erik Trinkaus, on a recent article on modern human emergence seems to reject the pure Out of Africa model as well as the regional continuity model:
Versions of the assimilation model have remained contenders for the interpretation of modern human phylogenetic emergence, if frequently overshadowed by the more polarized regional continuity (with gene flow) and (out of Africa with) replacement scenarios. The last two interpretations are finally intellectually dead. Both are contradicted by available evidence, and it is time for the discussion to move on. Yet, despite the general acceptance of some form of the assimilation model, issues remain.
So, perhaps we should move on, but where? Most anthropologists and geneticists today may reject the multiregional model, and accept that most recent human ancestry is derived from Africa, yet the existence and extent of non-African ancestry in modern humans is a matter of great controversy.

For example Michael Hammer and colleagues have recently published a paper which explicitly rejects the African-ness of a particular haplotype on the X chromosome. A paper on the non-admixture between moderns and Neanderthals, but also a paper on a 3-million year old polymorphism in Europeans which may have been introduced into the European gene pool by Neanderthals. Not to mention of lice speaking of modern human-erectus hybridization in Asia, a 2 million year old non-African polymorphism in Asians, 1.1 million year polymorphism in North Africa and the Middle East, and research which suggests that the fact that Africans have more ancestral alleles than non-Africans should not be interpreted as evidence of an African origin of humanity (all of them here).

Henry Harpending and Vinayak Eswaran have written a letter in the latest issue of Science, in which he takes issue with another article on ancient Out-of-Africa migrations and their Orang Asli descendants:
For example, nuclear loci rarely, if ever, show the low coalescence times (~200,000 years) seen in mtDNA, nor do they show strictly African roots. Indeed, there is now growing evidence of strictly non-African polymorphisms that date to before the birth of modern humans (1-5).
Vincent Macaulay and the other authors of the paper reply:
In cases where autosomal loci do have the necessary resolution, they suggest the replacement model (6-8). The discordant population-size estimates referred to by Harpending and Eswaran are likely more apparent than real, since these long-term values are usually obtained with the multiregional stipulation of random mating and constant population size. The analysis of overly simplistic models with methods that throw away what little information there is in most of these loci throws up straw men, such as the apparent lack of "strong signals of expansion" in some autosomal loci (9).
It is becoming awfully hard to keep up with the debate, especially since the experts themselves interpret the evidence in completely different ways. Should we despair of the ability of genetics to throw any light on our species' origin, and go back on discovering and measuring skulls? The African mitochondrial Eve discovery seemed to tilt the balance towards the Out of Africa hypothesis (first proposed forcefully by W.W. Howells), but our optimism that genetics would succeed where palaeoanthropology had failed may have been premature. Almost twenty years later, the discussion seems to have barely just begun!

What do you think?

Which model of human origins do you accept?
Out-of-Africa with Assimilation
Multiregional evolution

Free polls from
Read also, the Multiregional Stipulation Society by John Hawks.

Phylogenetic methods and Melanesian languages

Traditional linguistic methods compare languages by noting the similarities in vocabulary between them. However, vocabulary changes at a relatively high rate, so beyond a few thousand years in the past, the shared vocabulary of two related languages will be about the same as that between two randomly chosen languages.

Language, however, is not limited to vocabulary, but extends to grammatical rules, syntax, phonology, etc. So, two related languages will be similar to each other in these respects as well. Perhaps by using the knowledge which they provide we might be able to reconstruct the relationships between languages beyond the time barrier posed by vocabulary, and into a Paleolithic time frame.

Michael Dunn and colleagues have applied phylogenetic methods inspired by biology to this problem. Biological populations are quite similar to languages, because they also change over time, becoming dissimilar when they are separated, while retaining some of the structure of their common ancestors. So, by applying biological thinking we might be able to reconstruct a linguistic phylogeny.

Dunn et al. first applied this approach to Oceanic Austronesian languages, confirming that their method is able to reproduce the branching pattern of a well-understood language family. Next, they applied their method to Papuan languages of Melanesia, which are considered isolates without any clear relationships to each other. The resulting phylogeny shows a remarkable correspondence with geography. Thus, phylogenetic methods applied to non-vocabulary elements of language were able to trace the differentiation of Melanesian languages during the Paleolithic settlement of that region of the world.

Science, Vol 309, Issue 5743, 2072-2075

Structural Phylogenetics and the Reconstruction of Ancient Language History

Michael Dunn et al.

The contribution of language history to the study of the early dispersals of modern humans throughout the Old World has been limited by the shallow time depth (about 8000 ± 2000 years) of current linguistic methods. Here it is shown that the application of biological cladistic methods, not to vocabulary (as has been previously tried) but to language structure (sound systems and grammar), may extend the time depths at which language data can be used. The method was tested against well-understood families of Oceanic Austronesian languages, then applied to the Papuan languages of Island Melanesia, a group of hitherto unrelatable isolates. Papuan languages show an archipelago-based phylogenetic signal that is consistent with the current geographical distribution of languages. The most plausible hypothesis to explain this result is the divergence of the Papuan languages from a common ancestral stock, as part of late Pleistocene dispersals.


September 22, 2005

Affinities of Early Upper Paleolithic Europeans (II)

W.W. Howells, 1997, Getting Here: the story of Human Evolution, p. 188.
If Upper Paleolithic people were "European" from about 35,000 B.P., then such population distinctions are at least that old. And the Cro-Magnons were already racially European, i.e., Caucasoid. This has always been accepted because of the general appearance of the skulls: straight faces, narrow noses, and so forth. It is also possible to test this arithmetically ... Except for Predmosti 4, which is distant from every present and past population population, all of these skulls show themselves to be closer to "Europeans" than to other peoples - Mladec and Abri Pataud comfortably so, the other two much more remotely.
See also Affinities of Early Upper Paleolithic Europeans.

Selection in human mtDNA

The issue of selection on human mtDNA is quite controversial, because mtDNA has been used to infer patterns of human history and prehistory. In particular, the identification of the coalescence of human mitochondria types to a recent "African Eve" ancestor has been one of the arguments in favor of the recent Out of Africa replacement hypothesis.

A new study in Genetics examines the role that selection has played in the evolution of human mtDNA.
The coalescent date of the human mitochondrial DNA tree using this rate is 160,000 (S.D. 22,000) years. This coalescent date is broadly consistent with the dates of the Homo sapiens fossils recognized so far from Ethiopia (CLARK et al. 2003; MCDOUGALL et al. 2005; WHITE et al. 2003). The most recent common ancestor of all the Eurasian, American, Australian, Papua New Guinean and African lineages in clade L3 dates to 65,000 ± 8,000 years while the average coalescent time of the three basic non-African founding haplogroups M, N, and R is 45,000 years.
This confirms my previous observation that mtDNA variation in humans points to increased diversity among African populations who are descended partially from ancient "Paleoafrican" populations, while Africans and non-Africans are descended from "Afrasians", a group probably living in Africa in the last few tens of thousands of years and containing a subset of the diversity of the widely dispersed anatomically modern population of Africa. The date of the "Afrasian" group L3 is roughly compatible with the ~40kBP date for the wide appearance of modern humans in Eurasia and the emergence of modern behavior. The coalescence times of Eurasian mtDNA are also comparable with that of the Microcephalin variants, which (like M, N, and R) also show a primary non-African distribution.

Getting back to the paper:
The direction of threonine and valine substitution with other amino acids was significantly different between populations with neutral and significantly negative Tajima’s D values, respectively (Table 3), and between haplogroups: in H1 sequences sampled broadly from Europe and Near East, 7 of 11 non-synonymous mutations resulted in the replacement of threonine and valine with alanine and isoleucine, while only three mutations resulted in a change towards threonine or valine (Figure 1). In contrast to this pattern, in haplogroup V sequences from Finland (FINNILÄ et al. 2001), where populations continued to rely largely on hunting and fishing for subsistence even after the first contacts with farmers, 6 of 7 replacement polymorphisms resulted in a change to threonine and valine, and none in the replacement of the latter two amino acids (p<0.01). style="font-weight: bold;">The potential role of selection in affecting fixation probabilities at different non-silent positions undermines the appropriateness of using the average mitochondrial clock over all sites in dating events in human population history. Despite the evidence of departures from neutrality and high levels of homoplasy at the interspecies level, the phylogenetic approach for analyzing mtDNA sequence data at the intraspecies level remains viable because the reconstruction of the basic branches is robust and the excess of non-synonymous substitutions affects mainly the terminal branches of the tree.
What the authors are basically saying is that the basic branches of the tree don't show a substantial evidence of selection. This is not surprising, since these are old lineages that have withstood the test of time. It is the younger "unproven" terminal branches, i.e., the more recent lineages within the major branches that show evidence of selection.

One has to wonder whether the basic branches may also have been the remnant of selection from a wider pool of mtDNA variants. That is, they may be the variants that have survived in competition with their cousins when they too were young, tens of thousands of years ago.

Genetics (online early)

The role of selection in the evolution of human mitochondrial genomes

Toomas Kivisild et al.


High mutation rate in mammalian mitochondrial DNA generates a highly divergent pool of alleles even within species that have dispersed and expanded in size recently. Phylogenetic analysis of 277 human mitochondrial genomes revealed a significant (p<0.01) excess of rRNA and non-synonymous base substitutions among hotspots of recurrent mutation. Most hotspots involved transitions from guanine to adenine that, together with thymine to cytosine transitions, illustrate the asymmetric bias in codon usage at synonymous sites on the heavy-strand DNA. The mitochondrion-encoded tRNAThr varied significantly more than any other tRNA gene. Threonine and valine codons were involved in 259 of the 414 amino acid replacements observed. The ratio of non-synonymous changes from and to threonine and valine differed significantly (P=0.003) between populations with neutral (22/58) and those with significantly negative Tajima's D values (70/76), independent of their geographic location. In contrast to a recent suggestion that the excess of non-silent mutations is characteristic to Arctic populations implying their role in cold adaptation, we demonstrate that the surplus of non-synonymous mutations is a general feature of the young branches of the phylogenetic tree, affecting also those that are found only in Africa. We introduce a new calibration method of the mutation rate of synonymous transitions to estimate the coalescent times of mtDNA haplogroups.


September 21, 2005

Human population genetic structure

I was re-reading a classic paper [1] by Wilson et al. which first used the model-based software STRUCTURE program to cluster human populations. This approach was later used by Rosenberg et al. [2] with many more populations and markers. The following two tables from the paper are quite useful. The first table shows (right column) the probability of the number of clusters K given the data.

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As you can see, this probability is ~1 for K=4. Contrary to often repeated claims, the number of subdivisions ("races") of a group of individuals is not arbitrary, but for a set of individuals some numbers (in this case 4) are much better than others. Of course with more markers or larger samples, some of these clusters may be further refined, but the basic structure would not change. An alternative clustering with say 2 or 3 clusters would not emerge.

The second table shows that human populations usually fall within the clusters that correspond to the classical anthropological racial categories.

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It is also interesting that the Ethiopians belong in the Caucasoid cluster A and also in the Negroid cluster C. The Ethiopians don't "fit well" in the 4-race scheme, but this is a fact that was also appreciated by traditional anthropology. In all likelihood, both ancient links between Proto-Eurasians and East Africans and recent migrations of Caucasoids into East Africa are responsible for Ethiopian intermediacy.

Admixture analysis using K clusters summarizes the genetic structure of populations and individuals with K numbers adding up to 1, i.e., with K-1 degrees of freedom. But, they cannot distinguish between similarity deriving from common descent, or from recent admixture.

For example, Kazakhs and South Asians both score highly for European and Asian ancestry in Ancestry By DNA type tests. But, in the case of the former, this is due to admixture between Caucasoids and Mongoloids in Central Asia, whereas in the latter it is due to admixture between Caucasoids and Proto-Asians, i.e., non-Mongoloid people sharing common descent with East Asians.

This is why autosomal markers are useful for determining overall (genomic) similarity, but we have to turn to haploid markers such as mtDNA and the Y chromosome to interpret this similarity. Such markers can be tied to regions and times of origin and can thus be used to determine the actual processes of expansion and admixture that have led to the observable genetic variation.

[1] J.F. Wilson et al. Nature Genetics 29, 265 - 269 (2001)
[2] N.A. Rosenberg et al. Science, Vol 298, Issue 5602, 2381-2385

September 20, 2005

BARCODE and the dating of sub-haplogroups

A new paper introduces BARCODE, a new software program that can be used to infer the age of different sub-haplogroups. The age is presented as a fraction of the time for the entire haplogroup, thus allowing for the comparative dating of the antiquity of lineages. Below is the dating of several sub-haplogroups within Y-haplogroups E, J, and I.

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Human Genetics (Online first)

Independent methods for evolutionary genetic dating provide insights into Y-chromosomal STR mutation rates confirming data from direct father–son transmissions

Francesca Luca et al.

Abstract Five datasets consisting of samples jointly typed for Y-chromosomal Unique Event Polymorphism (UEP) and simple tandem repeat (STR) markers were re-examined with independent methods for dating the different UEP-defined lineages. We report on the results obtained with an original program which performs comparative dating (BARCODE) in comparison with coalescent analyses performed with BATWING under various prior conditions. For the first time these are equalized across datasets. We also report on the results concerning STR mutability as obtained with both methods. The dating results for the entire series of sub-haplogroups are highly correlated. Within coalescent analyses, dating-estimates under a wide range of priors tend to converge. As to STR mutation rates the main findings are: (1) large variations among loci within the same dataset with both methods, also when the same prior was used for all loci; (2) figures in most cases above 1×10−3 and often above 2×10−3; (3) a few loci that mutate differently across studies. These results closely match those obtained from direct observation of father–son transmissions. Overall, this work supports the use of genetic dating procedures that take into account the complexity of the phenomenon, with a repertoire of priors tailored on the particular dataset.


Blind test of DNA BioScience

DNA Bioscience is a British firm which offers (among other things) the Ancestry By DNA test. Recently, the company was featured in a Guardian story, in which four journalists from the paper submitted their DNA samples and the company predicted their skin color and ethnic origin. Person A was an Eastern European Jew who was predicted as being European with East Asian admixture, a reasonable finding, since both Ashkenazi Jews and eastern Slavs have some degree of Asian admixture. Person B was a Sub-Saharan African who was classified as such, again a reasonable result. Person C was a native Briton who was however given minor Native American ancestry, again underscoring the tendency of the test to wrongly predict such ancestry in persons without any possible Native American connection. Person D was a native Indian. The company shrewdly inferred his origin, even though a European-East Asian-Sub-Saharan-Native American mix does not reflect the origin of Indians. The suggestions that the individual had East Asian grandparents or his ancestors reached Britain through Africa (to explain the Sub-Saharan component) are of course rationalizations, and a good example of a case where this type of test is not useful.

All in all, this small test establishes once again the strength of admixture testing in predicting majority ancestry, its overreporting of minority ancestry that does not exist, and its difficulty in dealing with populations that fall outside the group of a priori chosen populations.

Stability of British height in England since the Neolithic

Medieval ancestors measured up to our height standards

OUR ANCESTORS were as tall as we are, contrary to popular belief. Over the past five millennia the average height of men in Britain has remained stable at about 170cm (5ft 7in), and that of women at 160cm (5ft 3in).


Botai and horse domestication

See also the updated entry on the redating of the Dereivka stallion, including some comments from Dr. David Anthony. Now that Dereivka has been redated as belonging to the Scythian Iron Age, the Botai (east of the Urals) represents the earliest evidence of possible horse riding. Levine writes:

Another example of this commitment to an earliest date is Anthony’s argument that the domesticated horse was present in the Ukraine earlier than in Kazakhstan. His evidence for this comes from bitwear studies of two samples of lower second premolars from two Eneolithic sites, Botai in northern Kazakhstan (5 from a total of 19 teeth) and Dereivka in the Ukraine (2 from a total of 6 teeth). He implies from this that horse domestication spread from west to east (Anthony 1995).

The redating of the Dereivka stallion casts doubt on the idea that horse domestication spread from west to east. Certainly it might have, but there is no direct evidence for the prior existence of domesticated horses in Ukraine than in Kazakhstan (Botai). But is the pattern of tooth wear interpreted as bit wear unambiguous evidence of horse riding? Levine writes:

The question of whether the wear pattern described by Anthony and Brown could have had other causes has not been adequately addressed. Their unbitted sample of feral horses consisted of 20 individuals from two North American populations (mustangs from the mountains of Nevada and barrier island ponies from the Atlantic Coast). They have generalized from this small sample that unbitted horses could not manifest the wear pattern they describe as unique to bitwear. On the other hand, Angela von den Driesch (personal communication) has observed
that similar, if not identical, wear on the lower second premolar can result from abnormal occlusion with the upper second premolar.

As far as we know, then, beveling on the anterior part of the lower P2 masticatory surface could be caused by bitwear or abnormal occlusion. Either a domesticated horse or a wild one that had been tamed could be bitted. The absence of bitwear could indicate that a horse had not been ridden recently or regularly before its death, that it was ridden unbitted, or that it never was ridden. We must conclude from this that bitwear should not be used without corroboration as proof of domestication. This is not to say that bitwear studies should not be carried out. On the contrary, their use should be much more widespread, but in conjunction with other methods of analysis.

From the conclusions:

The results of the analyses carried out on the data from Dereivka and Botai suggest that the vast majority of the horses from those sites were killed in the hunt. Different hunting techniques were employed at each of them: stalking or chasing at Dereivka and driving or surrounding at Botai. The possibility that some of the horses might have been tamed or domesticated, as suggested by Anthony and Brown’s bitwear studies, is certainly not excluded. However, the possibility that the wear pattern they define as bitwear could have other causes has not been disproved.
See also Domestication, Breed Diversification and Early History of the Horse.

Journal of Anthropological Archaeology
Volume 18, Issue 1 , March 1999, Pages 29-78

Botai and the Origins of Horse Domestication

Marsha A. Levine


This paper explores some issues related to the origins of horse domestication. First, it focuses on methodological problems relevant to existing work. Then, ethnoarchaeological and archaeozoological methods are used to provide an alternative approach to the subject. Ethnological, ethological, and archaeological data are used to construct a series of population structure models illustrating a range of human–horse relationships. Analysis of assemblages from the Eneolithic sites of Botai (northern Kazakhstan) and Dereivka (Ukraine) suggests that horses at these sites were obtained largely by hunting.



Dr. Anthony writes in the comments section. I have placed his comments in the blog entry because haloscan comments get deleted after a few months.
1. I have argued that horse domestication spread from west to east because the cultures of Ukraine and the the Volga-Ural region certainly had domesticated animals (cattle and sheep) before 5000 calBC, while the cultures of northern Kazakhstan remained foragers until at least 3500 calBC (when they probably adopted horse-herding), and perhaps until 2500 calBC (when they finally began to adopt domesticated cattle and sheep, 2500 years after the cultures of the western steppes). Horses were included with cattle and sheep in funeral sacrifices in the western steppes between 5000-4500 calBC and were portrayed there in mobile art, while in the eastern (Kazakh) steppes horses played no special role in ritual or in art until the Botai culture appeared, about 3500 BCE. Botai was a radically new kind of culture in the Kazakh steppes, with large settlements and dense deposits of animal bone consisting of 70-90% horse bones. This specialized horse hunting economy appeared with bit wear and stabling soils full of horse dung in the settlement of Botai. Bit wear also appeared at the related settlement of Kozhai 1. The Botai people were foragers who rode domesticated horses to hunt wild horses, a peculiar adaptation that existed only in Kazakhstan and only between 3500-3000 calBC.

2. Levine is incorrect in stating that what we have defined as bit wear can appear on the teeth of wild horses; her description of our sample size is incorrect; and her statement that bit wear could have other causes is an unsupported speculation. In a forthcoming paper in a BAR volume edited by Sandra Olsen we describe a new sample of 74 never-bitted Pleistocene equid teeth, studied with our methods. None of them shows a bevel measurement of 3mm, our threshold for bit wear. No one, including von den Dreisch and Levine, has described a population of wild horses that exhibits this kind of wear facet as the result of natural wear. Bit wear clearly distinguishes bitted from never-bitted populations at better than the .001 level of confidence. Levine's criticism of our bit wear statistics in the Journal of Anthropological Anthropology confused the issue by comparing our median measurement for bitted horses to our maximum measurement for never-bitted horses, implying that only .5mm separated them. This was a basic error. Comparing median to median and maximum to maximum, the statistical separation is very good.

3. Levine distinguishes between horses that are merely 'tamed' and those that are 'domesticated'. Tamed horses might have been ridden regularly in the hunt and in war, but this is unimportant in her scheme if they do not show the measurements she expects for a 'domesticated' horse. Culturally, this turns anthropological zoology upside down. When people began to ride horses regularly the world was changed. Whether leg bone measurements changed at the same time is an interesting question, but not nearly as interesting as identifying ridden horses.

September 17, 2005

Y chromosome haplogroups in Byelorussians

Genetika. 2005 Aug;41(8):1132-6.

[Frequencies of Y chromosome binary haplogroups in Belarussians]

[Article in Russian]

[No authors listed]

The compositions and frequencies of Y-chromosome haplogroups identified by genotyping 23 biallelic loci of its nonrecombining region (YAP, 92R7, DYF155S2, 12f2, Tat, M9, M17, M25, M89, M124, M130, M170, M172, M174, M173, M178, M201, M207, M242, M269, P21, P25, and P37) have been determined in a sample of 68 Belarussians. Eleven haplogroups have been found in the Belarussian gene pool (E, F*, G, I, I1b, J2, N3a*, Q*, R1*, R1a1, and R1b3). Haplogroup R1a1 is the most frequent; it includes 46% of all Y chromosomes in this sample. The frequencies of haplogroups I1b and I are 17.6 and 7.3%, respectively. Haplogroup N3a* is the next in frequency. The frequencies of haplogroups E, J2, and R1b3 are 4.4% each; that of R1* is 3%; and those of F*, G, and Q* are 1.5% each.


September 16, 2005

Haplogroup frequency correlations in Southeastern Europe (part II)

I've added five new populations to my previous dataset (SIT: Southern Italians, ESC: East Sicilians, SWS: Southwest Sicilians, NWS: Northwest Sicilians, CYP: Cyprus), taken from this recent paper. The resulting principal components plot again shows the J2/R1b/E3b "coastal" vs. I/R1a1 "continental" groupings along the first principal component (right vs. left respectively).

Viruses, mitochondria, cells, etc.

Carl Zimmer posts a fascinating description on new research about the ever-more-fascinating stuff that is found in our cells. It was first thought that cells are nice containers, designed to keep our DNA safely shielded in their nuclei, but it turns out that our cells contain DNA fragments of quite diverse origins, which have managed to strike up an alliance for their joint proliferation:
Here’s the history as they now see it: the free-living, oxygen-breathing ancestors of mitochondria were infected with some nasty T3/T7 viruses. Most of the time the viruses were fatal. But some mutant tried to replicate itself inside a proto-mitochondrion and failed. Its genes were trapped in the genome of its host. Its host was able to reproduce, and one of its descendants took up residence inside the cell of a eukaryote. At some point after this merger, a mutation caused the virus’s DNA and RNA copying genes to come back online. They took over the job of making these molecules, and the mitochondria’s own genes for this job were later stripped out of its genome.

It’s a plausible hypothesis for a number of reasons. Filee and Forterre didn’t just pull the notion that viral genes can become active again out of a hat; this sort of viral resurrection has been documented in other species. Not only is the hypothesis plausible, but it’s a tantalizing as well. It suggests that we are chimeras built from the DNA of eukaryotes, bacteria, and viruses, all mixed together through a natural version of genetic engineering. Forterre even argues that these sorts of results are going to turn out to be the tip of the iceberg. Like many scientists, he believes that before life was based on DNA, the Earth was inhabited by RNA-based life. He argues that DNA was an invention of viruses of these RNA-based organisms, which the RNA-based organisms then seized for their own use. All this may not make you any fonder of the chickenpox you may have had as a kid, but it may at least give you a feeling of kinship.

September 15, 2005

Y chromosome perspective on Mediterranean populations

Capelli et al. have written an important new article on Y-chromosomal variation in the Mediterranean basin. This is the most comprehensive study yet on the region, using a combination of biallelic polymorphisms defining haplogroups and microsatellites over several Mediterranean populations, including many population samples taken from the literature. Moreover, mtDNA and autosomal data are also included, and these tend to support the authors' broad findings.

The key finding is that Mediterranean populations can be grouped into four main clusters: North Africa, Arab, Central-East, and West Mediterranean. The North African cluster exhibits high frequencies of North African specific haplotypes within haplogroup E3b. The Arab cluster exhibits high frequencies of J*(xJ2), which is rarer elsewhere.

According to the authors, there has been very little gene flow from North Africa into Europe. Moreover, Near Eastern populations should not be considered a unity, but are differentiated depending on the extent of Arab admixture exemplified by J*(xJ2) chromosomes. Modern Near Easterners are thus not representative of the early Neolithic people who migrated into Europe. J*(xJ2) chromosomes associated with Arabs are also present in North Africans, but North Africans have maintained their own Y-chromosomal peculiarities, typified by haplogroup E3b haplotypes.

It is unfortunate that a mainland Greek sample was not included, but to make up for it, there is a Cypriot sample, in addition to three Sicilian samples. These populations which are largely of Greek origin are very similar to Greeks in general, and belong to the Central-East cluster. Their inclusion also allow us to test my previously expressed hypothesis that haplogroup R1a1 was rare in ancient Greek populations. Indeed, this haplogroup is found at a frequency of 1.8-3.1% in Sicilians, Cypriots and Southern Italians, thus essentially confirming my idea. On the other hand, haplogroup I*(xI1b2) is found at frequencies from 3.4-15.7%, and is thus (as I have said before), much more likely to have been present in the ancient Greek population.

The study also examines briefly the origins of the Jews. Sephardic Jews are shown to resemble Mediterraneans more, while Ashkenazi resemble Arabs more.

The table of frequencies also allows us to ascertain the prevalence of Negroid admixture in Sicily, a popular subject in certain circles, and one which is shown to be without any basis in fact. In 212 Sicilians in total, no haplogroup A, E3a, or E*(xE3a,E3b) chromosomes were detected. Two haplogroup A chromosomes were detected in Cyprus, one in Sardinia, and two E3a, E*(xE3b, E3a) chromosomes in Malta. This is about the extent of male Sub-Saharan African introgression in the Mediterranean: 5 out of 656.

From the conclusions:
The significant genetic structuring of populations facing the Mediterranean basin into three groupings, Near Eastern Arab, Mediterranean and North African, is related to the demographic processes that have occurred since first populating the area. The distribution of Neolithic technologies was probably paralleled by demographic expansion in the Mediterranean basin, and subsequent westward migration by Phoenicians and Greeks contributed to the distribution of Y chromosome types of most likely Near East origin. The Arab conquest in particular appears to have had a dramatic influence on the East and South Mediterranean coasts, with differential sex-related gene flow playing a major role in the distribution of genetic variation. The presence of Arab Y chromosome lineages in the Middle East suggests that most have experienced substantial gene flow from the Arabian peninsula. This result raises the issue of the correctness of identifying all Near Eastern populations as reliable representations of the original Neolithic groups that expanded from the Middle East towards the European peninsula.

Annals of Human Genetics (online early)

Population Structure in the Mediterranean Basin: A Y Chromosome Perspective

C. Capelli et al.


The Mediterranean region has been characterised by a number of pre-historical and historical demographic events whose legacy on the current genetic landscape is still a matter of debate. In order to investigate the degree of population structure across the Mediterranean, we have investigated Y chromosome variation in a large dataset of Mediterranean populations, 11 of which are first described here. Our analyses identify four main clusters in the Mediterranean that can be labelled as North Africa, Arab, Central-East and West Mediterranean. In particular, Near Eastern samples tend to separate according to the presence of Arab Y chromosome lineages, suggesting that the Arab expansion played a major role in shaping the current genetic structuring within the Fertile Crescent.


Allele for light pigmentation has been positively selected in Europeans

A new paper shows that a polymorphism on the AIM1 locus which is associated with human pigmentation has been under strong positive selection in Europeans, reaching almost fixation in tested European populations (0.89 in South Africans and 0.96 in Germans), while being rare elsewhere. The derived allele is associated with lighter overall pigmentation. This contrasts to the situation with the MC1R locus in which the ancestral variant is maintained by selection in Negroids, but multiple unrelated mutations outside Africa have resulted in lighter-skinned phenotypes. Unlike the MC1R where relaxation of selection constraints were observed in non-Africans, the new AIM1 polymorphism has been positively selected.

The time of the common ancestor of alleles bearing the haplotype is estimated to be 10,965 years, although the 95% confidence interval is wide from 1,328 to 39,609 years. We should probably not speculate on what triggered the selection based on this very uncertain dating, but the repopulation of Europe after the last glaciation may be a candidate. As humans spread to higher latitudes, they may have been subjected to higher selective pressures for light pigmentation. It would be interesting to determine the frequency of the polymorphism in different Caucasoid populations and determine the most likely ancestral populations.

Molecular Biology and Evolution
(published online)

Evidence for Recent Positive Selection at the Human AIM1 Locus in a European Population

Mikiko Soejima et al.


Two missense polymorphisms (E272K and L374F) of the AIM1 locus, encoding a melanocyte differentiation antigen, were shown to have a clear association with human ethnicities. These two nonpathogenic SNPs may be associated with human pigmentation variation. In this study, we investigated sequence variation in the coding region and exon-flanking sequence and found low genetic variation only in subjects of European descent. All four statistical tests applied to the 7.55-kb region surrounding the L374F polymorphism detected statistically significant deviations from selective neutrality in Europeans. In addition, haplotype analysis revealed that one haplotype carrying 374F was overrepresented in this population, and the low rate of variation, with some features of selective sweeps, was shown to be statistically significant. These results suggest that positive selection recently has been acting or has acted on at least this region of the melanogenic gene and that an advantageous haplotype spread rapidly in Europe.


Horses were not ridden in the fifth millennium BC

The first domesticated horses were used for meat and for drawing wheeled vehicles. The idea that horses were ridden before the 1st millennium BC is one of the arguments of the adherents of the Pontic steppe thesis of Indo-European origins, because ridden horses would give a significant military advantage, and thus allow the steppe people to overwhelm the settled agricultural populations of Old Europe.

There are however no depictions of horse riding in art before the 1st millennium BC, or in the earliest texts of Indo-European speakers. So, some archaeologists have sought alternative ways of establishing that horses were ridden. To ride a horse, one needs a bit which is put in the horse's mouth and reins by which the horse is controlled. The teeth of a horse that have a hard bit will show evidence of wear in a distinctive pattern, and this will allow us to infer that it was ridden.

The following excerpt from a recent review of Robert Drews' Early riders: the beginning of mounted warfare in Asia and Europe by Karlene Jones-Bley in Journal of Indo-European Studies vol 33, no. 1/2 shows how this ingenuous hypothesis has not survived radiocarbon dating.
Nevertheless, the entire bit wear thesis collapsed once the skull of the "cult stallion" was subjected to radiocarbon dating and was found to have died before 700 and 200BC. Thus, even if the evidence for bit wear were valid (and there are those who still question even this), it didn't happen at Dereivka until the Iron Age when no one doubts the existence of horse riding and hard bits.


Dr. David Anthony, who proposed the bit wear hypothesis has sent me an e-mail in which he gives some additional information.

The date of the domestication of the horse is still poorly understood, but horses certainly were domesticated and used for riding in the northern Eurasian steppes by the middle of the fourth millennium BCE, and they were grouped with cattle, sheep, and humans in funeral rituals that excluded obviously wild animals during the fifth millennium BCE. The 3500BCE date for riding is supported at Khvalynsk in northern Kazakhstan, dated 3500-3000 BCE, where in addition to bit wear on horse premolars, stabling soils full of horse dung were found, and whole horse carcasses were regularly brought into the settlement for butchering as a regular practice over the course of hundreds of years. The occupants had no cattle or sheep, no draft animals other than horses, so if the horses at Botai were wild it is difficult to understand how they were brought into the settlement. The inclusion of horses in human graves dated 4500 BCE is documented at Khvalynsk on the middle Volga, a cemetery where the sacrificed animals included parts of 52 sheep/goat, 23 cattle, and 11 horses, and no obviously wild animals. Khvalynsk sites also have yielded stone maceheads shaped like horseheads and bone plaques carved in the shape of horses. The bit-worn horse teeth at Dereivka were re-dated to 700-200 BCE by me, the same person who identified the bit wear, but the article in which I announced the re-dating of the Dereivka teeth also described the evidence from Botai and Khvalynsk. Dereivka was not the only site with early bit wear in the steppes. No credible or accurate criticisms of bit wear analysis have yet been published, so the detection of bit wear remains a valid way to identify bitted horses in the archaeological record. Please see Anthony, David W. and Dorcas Brown, 2000, "Eneolithic horse exploitation in the Eurasian steppes: diet, ritual and riding," Antiquity 74: 75-86.


John Hawks reports on Bones, a new TV drama series about forensic anthropologists. Inspired be real-life forensic anthropologist and writer Kathy Reichs.

September 14, 2005

The Myths of the 20th century

The first half of the 20th century was dominated by the myth of human inequality. According to this myth, human beings could be ordered in a scale of worth, with some individuals and groups being deemed superior and others inferior.

The second half of the 20th century was dominated by the myth of human identity. According to this myth, human beings were inherently the same, except for cosmetic external differences and the sexual differences necessary for procreation. Any observable differences in health, intelligence, personality, or beauty were deemed to stem from prejudices of the observer or the effects of environmental influences.

The first myth was a consequence of widespread means of transportation, which enabled the meeting of races and cultures. It was also a consequence of quantitative anthropology which enabled the measurement of human beings, and their classification according to measurable quantities such as the cephalic index or the facial angle.

The second myth was a result of the great emancipation movements. Previously marginalized groups, such as women and minorities found themselves in possession of the same rights as white males. It was believed that their previously socially inferior position would soon be changed, and that once people became unprejudiced and educated, then all genders and races would exhibit similar outcomes in life.

The myth of human inequality was the common-sense reaction to the previous Christian worldview of equality of men. People could no longer hold that view once faced with the dramatic differences in appearance, culture, and behavior between different groups. It was common-sense, but wrong, because human beings are not single-dimensional entities and cannot be ordered on a unique scale.

The myth of human identity was the moral reaction to the old society which subjugated a good portion of its population. It was wrong, because the power structures of society are not only the result of prejudice, oppression, and opportunity, but also a manifestation of innate differences between human individuals and groups.

Today, neither human inequality, nor human identity are any longer tenable positions. So, what will be our new myths for the 21st century?


Για τη διευκόλυνση της επικοινωνίας στα Ελληνικά όσων ενδιαφέρονται για θέματα ανθρωπολογίας, γενετικής, ιστορίας, κτλ. μπορείτε να συμμετάσχετε στις συζητήσεις στη διαδικτυακή κοινότητα ΑΝΘΡΩΠΟΣ. Προφανώς αρχικά δεν υπάρχουν αρκετά μέλη, αλλά ελπίζω πως με τον καιρό θα μαζευτούνε εκεί όσοι και όσες ενδιαφέρονται για φιλική συζήτηση πάνω σε αυτά τα αντικείμενα στην Ελληνική γλώσσα.

September 13, 2005

Were modern humans neighbors to Neanderthals?

A pretty good article on the controversy of modern human-Neanderthal interactions. The conventional orthodoxy that moderns and Neanderthals co-existed in Europe has been shaken by the fact that none of the Aurignacian archaeological assemblages, which were once believed to have been created by modern humans, are actually associated with modern human bones. So, the only way to associate them with modern humans is to claim that their sophistication makes it unlikely that they were created by Neanderthals, i.e., to presuppose that Neanderthals were dumber than modern humans and could not have created those artifacts. But, some of the Neanderthals' genes may persist in modern Europeans, so we shouldn't assume that Neanderthals were genetic dead-ends that had nothing (cultural or genetic) to offer to the first anatomically modern humans during their arrival in Europe.

On a somewhat related note, John Hawks writes about a recent conference on Rethinking the Human Revolution.

September 10, 2005

Ancient British mtDNA

One more paper added to the growing list of studies of ancient DNA. This time around, scientists have studied the mtDNA of Britons from the 4th to 11th century AD. The scope of the study is one of the largest I've seen so far, with 319 dental samples and 156 individuals in total. The haplogroup frequencies are shown below; the ancient sample is also split into Early and Late Saxon periods.

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The comparative modern mtDNA were taken from the following regions. It is a bit peculiar that more continental European samples are missing, while Armenians and Palestinians are listed.
The comparative data set from modern populations of Europe for the founder and genetic distance analyses consisted of mtDNA HVS-I sequences from the following populations: Armenia (N=191), England (N=258), Estonia (N=149), northern France (N=101), Finland (N=176), Iceland (N=467), Norway (N=565), northern Germany (N=107), Palestine (N=117), Saami (N=176), Scotland (N=981), Spain (N=181) and Western Isles (N=181).
Molecular Biology and Evolution (advance access)

Tracing the Phylogeography of Human Populations in Britain Based on 4th-11th Century mtDNA Genotypes

A. Töpf et al.


Some of the transitional periods of Britain during the first millennium AD are traditionally associated with the movement of people from continental Europe, composed largely of invading armies (e.g. the Roman, Saxon and Viking invasions). However, the extent to which these were migrations (as opposed to cultural exchange) remains controversial. We investigated the history of migration by women by amplifying mtDNA from ancient Britons who lived between approximately 300-1,000 AD, and compared these with 3,549 modern mtDNA database genotypes from England, Europe and the Middle East. The objective was to assess the dynamics of the historical population composition by comparing genotypes in a temporal context. Towards this objective we test and calibrate the use of rho-statistics to identify relationships between founder and source populations. We find evidence for shared ancestry between the earliest sites (predating Viking invasions) with modern populations across the north of Europe from Norway to Estonia, possibly reflecting common ancestors dating back to the last glacial epoch. This is in contrast with a late Saxon site in Norwich, where the genetic signature is consistent with more recent immigrations from the south, possibly as part of the Saxon invasions.


September 09, 2005

Stop the presses... huge papers on brain evolution in recent humans

I am very sure that a set of new papers (one two) in Science will generate a huge amount of buzz. I will blog in more detail about them later, but for now, this Red Nova story covers the findings pretty well. The interesting part:
The team also observed geographic differences. For haplogroup D of ASPM, they found that it occurs more frequently in Europeans and surrounding populations including, North Africans, Middle Easterners, and South Asians, and at a lower incidence in East Asians, New World Indians and sub-Saharan Africans. For microcephalin, the researchers found that haplogroup D is more abundant in populations outside of sub-Saharan Africa.
For now, from the papers:

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Fig. 3. Global frequencies of Microcephalin haplogroup D chromosomes (defined as having the derived C allele at the G37995C diagnostic SNP) in a panel of 1184 individuals.

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Fig. 1. Worldwide frequencies of ASPM haplogroup D chromosomes (defined as having the derived G allele at the A44871G diagnostic polymorphism), based on a panel of 1186 individuals.


Here is what these studies mean:
  • Microcephalin and ASPM are genes involved in regulating brain size
  • A variant of Microcephalin has reached very high frequencies in non-Sub-Saharan Africans in the last 37,000 years.
  • A variant of ASPM has reached very high frequencies especially in Caucasoids but also in some southern Mongoloids and Australoids in the last 5,800 years.
  • It is almost inconceivable that these two factors were caused by random factors (drift). Therefore selection has acted on these two genes, favoring the new Microcephalin variant in non-Sub-Saharan Africans and the ASPM especially in Caucasoids, but also to a lesser extent in some southern Mongoloid and Australoid groups.
  • We know absolutely nothing about what the new Microcephalin and ASPM variants actually do. What we do know is that they confer some substantial advantage that has caused them to grow in numbers. Perhaps, they confer some cognitive or behavioral ability.
These are the facts. The interpretation of the facts must wait until we have more information. However, the dates for the expansion of the two variants are extremely suggestive.

In a recent article, Erik Trinkaus has surveyed the human paleoanthropological record, and wrote that:
The earliest candidates for human anatomical modernity, those between ca. 150,000 and 195,000 years B.P. in Africa, are best considered as bridging a morphological gap between late archaic and early modern humans.


The spread of modern humans thoughout Africa and into Eurasia occurred after 50,000 years B.P. and probably after 40,000 years B.P., 100,000 years after their appearance.
Now, it may be a coincidence that the spread of humans throughout Africa and into Eurasia happened at around the same time that the new Microcephalin variant appeared, but the timing is certainly suggestive.

The question is: why did the new variant not get selected in Sub-Saharan Africans? There are only two possible explanations:
  • There is something in the Sub-Saharan African environment which did not allow the variant to be selected; in other words: the variant did not confer an advantage in Africa itself.
  • The gene pool of most Sub-Saharan Africans did not possess the new Microcephalin variant. Hence the variant did not get selected because it was lacking in the Sub-Saharan African gene pool.

Now, it is well known that the greatest difference in modern human genetic variation is between Sub-Saharan Africans and non-Sub-Saharan Africans. This is the result of the fact that humans originated in Africa, and possess only a subset of the variation that exists there.

As I have written before, there is good reason to believe that a human group originated in eastern Africa ("Afrasians") and came to colonize the rest of the world in relatively recent times. But, the rest of the African continent was already inhabited by pre-existing anatomically modern humans ("Paleoafricans") since at least 150,000 years in the past. These "Paleoafricans" were separated from the "Afrasians", as evidenced by the fact that typical "Paleoafrican" markers, originating long before the 40,000BP cutoff date, such as Y-haplogroups A and B and mtDNA haplogroups L0-L2 are not found in Eurasia.

If my theory is correct, then we don't need to propose some unquantifiable peculiarity of the African environment. Rather, the new Microcephalin variant has a low frequency in Sub-Saharan Africans precisely because it emerged in the Afrasians of eastern Africa that started colonizing the world around 40,000BP and was later added to the Paleoafrican populations of Sub-Saharan Africa. It simply has not had enough time to spread in most of Africa!

The second variant (of ASPM) is even more impressive, because it started to spread only 5,800 years ago, although the confidence margins are wide. The only movement which could have affected so many populations of Eurasia, regardless of language, in the last few millennia is the Neolithic expansion, followed by population growth in the first civilizations of the Near East and China.

It seems all by certain that the variant first appeared in Western Eurasia. It could have been carried easily to the east by the Near Eastern Neolithic people who reached India. It would only take a small step to make the jump to the Mongoloid world; once introduced into the population, it would also undergo the same selection process that made it so frequent among Caucasoids. However, agriculture begins much later among Mongoloids and even later among Australoids. So, the low frequency of the new variant in these populations is a consequence of the fact that it has had less time to spread among these populations.

The new ASPM variant is lacking in Sub-Saharan Africans and Native Americans. These results can be easily explained:
  • Sub-Saharan African agriculture is late, and moreover there has been almost no gene flow from Eurasia into Sub-Saharan Africa, with a few occasional exceptions. So, the ASPM variant did not exist in the Sub-Saharan African gene pool, and could thus have not been selected.
  • Native Americans migrated into the New World in Paleolithic times. Naturally, the ASPM variant was not present in their ancestral gene pool yet, so it could not have been selected.
The importance of these new papers is that cognitive evolution in Homo sapiens did not stop after our lineage became anatomically modern, and it did not stop when a subet of anatomically modern humans set out to colonize the world 40,000 years ago from eastern Africa, and it did not stop when Neolithic man appeared 10,000 years ago. Evolution has continued, and the proof for it is in the genetic variation of living human populations.

Science, Vol. 309 No. 5741

Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans

Patrick D. Evans et al.

The gene Microcephalin (MCPH1) regulates brain size and has evolved under strong positive selection in the human evolutionary lineage. We show that one genetic variant of Microcephalin in modern humans, which arose ~37,000 years ago, increased in frequency too rapidly to be compatible with neutral drift. This indicates that it has spread under strong positive selection, although the exact nature of the selection is unknown. The finding that an important brain gene has continued to evolve adaptively in anatomically modern humans suggests the ongoing evolutionary plasticity of the human brain. It also makes Microcephalin an attractive candidate locus for studying the genetics of human variation in brain-related phenotypes.


Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens

Nitzan Mekel-Bobrov et al.

The gene ASPM (abnormal spindle-like microcephaly associated) is a specific regulator of brain size, and its evolution in the lineage leading to Homo sapiens was driven by strong positive selection. Here, we show that one genetic variant of ASPM in humans arose merely about 5800 years ago and has since swept to high frequency under strong positive selection. These findings, especially the remarkably young age of the positively selected variant, suggest that the human brain is still undergoing rapid adaptive evolution.