December 30, 2008

Craniofacial study of the Jomon of Japan

American Journal of Physical Anthropology doi:10.1002/ajpa.20985

Regional differences in craniofacial diversity and the population history of Jomon Japan

Tsunehiko Hanihara, Hajime Ishida


The people associated with the Jomon culture, the Neolithic inhabitants of Japan, are one of the key groups in the population history of East Asia, because they retain many archaic characters that may be traced back to Eurasian Upper Palaeolithic hunter-gatherers. In this study, the regional diversity of the Jomon skeletal series was estimated by applying the R-matrix method to 34 craniofacial measurements. The patterns of intraregional variation indicate little effect on the genetic structure of the Jomon from long-term gene flow stemming from an outside source. The regional diversities were further estimated by pooling all individuals into regional aggregates, and by computing the mean variance within local groups in each region. Although the pattern of phenotypic variation differs depending on the unit of analysis, the gradient of the diversity retains its identity. The Hokkaido region, the northernmost part of the Japanese archipelago, has the highest variance, followed by the regions of eastern Japan, while the southwestern regions have the lowest variance. These findings suggest that the Jomon ancestors of the northern part of Japan might have expanded southward to Honshu Island. Global analyses including samples from Eurasia, Africa, and Australia dating roughly to the same chronological periods as those of the Jomon samples, indicate that the Jomon cranial series share part of their ancestral gene pool with early northeastern Asians. The present findings support the archeologically suggested population growth and expansion in the northern half of the Eurasian continent during the late Pleistocene and early Holocene periods.


December 29, 2008

Anatomically modern humans outcompeted Neanderthals

There have been many Neanderthal stories this year. Here is a list:
  1. Did Cannibalism contribute to Neanderthal extinction?
  2. Archaeology magazine interview with John Hawks
  3. Divergence of modern humans and Neanderthals
  4. FOXP2 and Neanderthals revisited
  5. Complete Neanderthal mtDNA sequence
  6. Neanderthals grew fast, matured later (?)
  7. Reconstruction of female Neanderthal
  8. John Hawks stars in the "Neanderthal Code"!
  9. Neanderthals' trips to the sea in search of food
  10. Neanderthals and the Uluzzian
  11. Why did Neanderthals have broad noses?
  12. The Middle to Upper Paleolithic record of western Eurasia
  13. Belgian Spy Neanderthals 36,000 years BP old
Personally, I am in favor of explanations about Neanderthal demise that involve anatomically modern humans (AMHs), rather than "internal" processes such as #1 in the above list. After all, Neanderthals had been around for tens of thousands of years before they went extinct, and their extinction roughly coincided with the arrival of AMHs. That can't be a coincidence.

Did they die out due to competition? Or does their disappearance signal their genetic absorption by AMHs?

The fact of Neanderthals' extinction is highly significant. Europe could quite easily have supported both species if their population numbers were fairly low, approaching what John Hawks has described as "biblical models of human migration, like Noah-and-the-Flood level bottlenecks. " Competition increases as the ratio of resources/population increases. A live and let live attitude prevails if there is plenty for all.

It seems to me that for AMHs to either (i) absorb with almost no trace or (ii) displace/drive to extinction, the indigenous Neanderthal population of Europe, it would be necessary for a great number of AMHs to exist. Even if AMHs had a major technological/cognitive advantage -and the latest research suggests otherwise, e.g., #6, 8, 9- such a thorough dominance would be unlikely. At the very least, we might expect Neanderthals to have survived for a much longer period.

PLoS ONE doi:10.1371/journal.pone.0003972

Neanderthal Extinction by Competitive Exclusion

William E. Banks et al.



Despite a long history of investigation, considerable debate revolves around whether Neanderthals became extinct because of climate change or competition with anatomically modern humans (AMH).

Methodology/Principal Findings

We apply a new methodology integrating archaeological and chronological data with high-resolution paleoclimatic simulations to define eco-cultural niches associated with Neanderthal and AMH adaptive systems during alternating cold and mild phases of Marine Isotope Stage 3. Our results indicate that Neanderthals and AMH exploited similar niches, and may have continued to do so in the absence of contact.


The southerly contraction of Neanderthal range in southwestern Europe during Greenland Interstadial 8 was not due to climate change or a change in adaptation, but rather concurrent AMH geographic expansion appears to have produced competition that led to Neanderthal extinction.


December 27, 2008

2008 in review: Ethnicity Strikes Back

The major breakthrough of 2008 was the application of microarray technology to the problem of inferring ethnic ancestry.

At the beginning of this year, it may have been tenable to consider ethnic groups as mere cultural constructs, divorced from nature; at its conclusion, this opinion has been conclusively falsified.

It is now clear that ethnic groups are not only cultural-political formations, but also (at least in part) distinct biological entities, emerging naturally as clusters of similarity from the genetic continuum.

  1. 300K SNP paper on European genetic substructure
  2. New paper on genomic differences between Ashkenazi Jews and Europeans
  3. New study on global human variation based on SNPs and CNVs
  4. Huge paper on human genetic relationships based on 650K SNPs
  5. 500K SNP study of Oceanian populations
  6. 500K SNP Europe-wide study of genetic structure
  7. Population structure in Japan with 140k SNPs
  8. Genetic structure in Northern Europe with 250K SNPs
  9. Geography and Genetic structure in Europe (again)
  10. European population structure with 300K SNPs and 6,000 individuals
  11. Genomic substructure in Finns

Y chromosomes of the Gagauz

Am J Hum Biol. 2008 Dec 23. [Epub ahead of print]

Searching for the origin of Gagauzes: Inferences from Y-chromosome analysis.

Varzari A, Kharkov V, Stephan W, Dergachev V, Puzyrev V, Weiss EH, Stepanov V.

The Gagauzes are a small Turkish-speaking ethnic group living mostly in southern Moldova and northeastern Bulgaria. The origin of the Gagauzes is obscure. They may be descendants of the Turkic nomadic tribes from the Eurasian steppes, as suggested by the "Steppe" hypothesis, or have a complex Anatolian-steppe origin, as postulated by the "Seljuk" or "Anatolian" hypothesis. To distinguish these hypotheses, a sample of 89 Y-chromosomes representing two Gagauz populations from the Republic of Moldova was analyzed for 28 binary and seven STR polymorphisms. In the gene pool of the Gagauzes a total of 15 Y-haplogroups were identified, the most common being I-P37 (20.2%), R-M17 (19.1%), G-M201 (13.5%), R-M269 (12.4%), and E-M78 (11.1%). The present Gagauz populations were compared with other Balkan, Anatolian, and Central Asian populations by means of genetic distances, nonmetric multidimentional scaling and analyses of molecular variance. The analyses showed that Gagauzes belong to the Balkan populations, suggesting that the Gagauz language represents a case of language replacement in southeastern Europe. Interestingly, the detailed study of microsatellite haplotypes revealed some sharing between the Gagauz and Turkish lineages, providing some support of the hypothesis of the "Seljuk origin" of the Gagauzes. The faster evolving microsatellite loci showed that the two Gagauz samples investigated do not represent a homogeneous group. This finding matches the cultural and linguistic heterogeneity of the Gagauzes well, suggesting a crucial role of social factors in shaping the Gagauz Y-chromosome pool and possibly also of effects of genetic drift.


December 24, 2008

Math gender gap news

A couple of new papers have appeared recently, which paint two different pictures of the gender gap in science/math ability.

The New Scientist reports on the first one:
Why are there so few female Einsteins? Many people share a belief that while women can do science, there are far fewer women than men at the very top of the science hierarchy because women just aren't as innately good at science as men. Others feel this view is wrong but cannot easily put their finger on why.

They should be able to now. There are few women at the top of science because there are so few women in science. It's simple statistics.


To test this idea, Bilalic's team checked the records of the German chess federation – in which males outnumbered females 16 to one. They found that the statistical effect of this difference in numbers accounted for 96% of the observed difference in performance between the sexes. "There is little left for biological differences to explain," says Bilalic.

While statistics may explains the absence of females at the top, they don't explain why there are fewer females in the first place. If this is due to any innate differences in chess ability between the sexes it would have to influence whether children start to play the game at all, because the dropout rates for girls and boys once they do start are similar.

The sentence in bold, of course, undermines the whole argument. The pool of male chess players is much larger than the corresponding pool of female chess players. Hence, it cannot be assumed that male and female chess players represent random samples of the same portion of the ability curve.

To give a different example, there are probably far fewer female than male lumberjacks or miners. Those that exist may be every bit as good at their job as their male counterparts. But, the fact that there are so few of them isn't so much a question of preference, but of the physiological fact that men are on average much better at mining or cutting trees.

Women were, of course, denied access to certain occupations in the past. But, nowadays, and for several generations, women have had access to the professions and higher education, so it is becoming less tenable that their under-representation in science and math achievement is due to their lack of preference for these fields, rather than a small difference in ability, manifesting itself strongly at the high end of the ability curve.

The second paper undermines the thesis of the first, by demonstrating inherent differences between male and female non-verbal infants. From ScienceDaily:

"We've known for approximately 30 years that men and women can see an object from one perspective and then recognize that object after it has been rotated in space into a new position," said David S. Moore, professor of psychology at Pitzer College and Claremont Graduate University, both in Claremont, Calif., and an expert in the development of perception and cognition in infants. "In addition, while we have known that all people can do this, it turns out that men are quite a bit faster at it than women are. Previous studies have shown that this sex difference can be detected in children as young as 4 years of age, but our study is the first to have successfully found a way to assess the situation in young infants.

"Although we did not expect to find any sex differences in babies this young, our results suggest that the 5-month-old boys in our study used mental rotation to complete our task while the 5-month-old girls in our study did not," Moore said.

On the same subject, La Griffe du Lion has posted an analysis on the Math Sex Gap Revisited: a theory for everyone:
At the annual meeting of Women Against the Gap, Prodigy unveils a model of mathematical ability that brings together seemingly isolated facts. He demonstrates that there is a single math ability gap between the sexes, biological in origin, and independent of race, culture and geography. Prodigy introduces the theory of Everyone which accounts for all available data.

Expansion of E-V13 and I-M423 from the Balkans

The most interesting aspect of this paper is that it supports a European rather than Middle Eastern origin of E-V13 and I-M243 based on an analysis of relative Y-STR variance. However, the age estimates presented in this paper are based on the infamous "evolutionary mutation rate", and are thus suspect. What appears as "Mesolithic" using the wrong mutation rate is actually Bronze Age, although with hefty confidence intervals.

Furthermore, caution should be used when correlating TMRCA with archaeological events. As I have noted before, the founder of a haplogroup is not the same as the Most Recent Common Ancestor (MRCA) of the present-day population from that haplogroup. This study seems to argue against the Middle Eastern origin of E-V13 suggested by Cruciani et al..

When exactly E-V13 came to the Balkans remains to be seen, but its expansion is properly placed in a Bronze Age rather than Mesolithic time frame. Interestingly, the paper has turned up some additional evidence:
Only four E-M78*, which do not belong to any already described sub-clade, have been observed in the southern Balkans. Two of them (from Greece) turned out to be characterized by the mutation M521 and therefore represent a new M78 lineage.


The presence of E-M78* Y chromosomes in the Balkans (two Albanians), previously described virtually only in northeast Africa, upper Nile, gives rise to the question of what the original source of the E-M78 may have been.
This is suggestive that E-V13 expanded from the Balkans out of a pre-existing E-M78 ancestor, almost completely swamping that E-M78 population. When exactly E-M78 arrived in the Balkans, it is difficult to say, since Y-STR variance takes us only as far back as the MRCA who lived in the Bronze Age.

In any case, this paper adds important new data on Balkan Y-chromosomes, although it is unfortunately marred by facile Y-chromosome/archaeological correlations, and the use of the inappropriate evolutionary mutation rate.

At present, I see no reason to change my theory on the expansion of E-V13. The finding that E-V13 is less diverse in Anatolia and the Middle East further reinforces the idea of the Balkan origin of that expansion, while an estimated age in the 2nd millennium BC is consistent with the birth of the Greek world.

The authors write:
Interestingly, J-DYS445-6 and J-M92 (a sub-lineage of M67), both have expansion times between 7000 and 8000 years ago
Converted into non-"evolutionary" ages, these are again consistent with the expansion of the Greek world. J-M92 was correctly associated with the expansion of the Greek world by Di Giacomo et al. (2004) "Y chromosomal haplogroup J as a signature of the post-neolithic colonization of Europe", who did not fall into the evolutionary mutation rate trap.

Also of interest is the discovery of an extremely rare R1a*(xR1a1) in a single Macedonian Greek. Another instance of R1a*(xR1a1) was previously discovered in a Cretan Greek. R1a1 occurred in 16.3% of Greeks from Athens vs. 10.5% of Greeks from Macedonia, the opposite of what was observed by Semino et al. in 2000. R1a1 does not seem to have any clear geographical structure within Greece, which would be expected if it was of more recent introduction.

UPDATE: Having labeled E-V13 Mesolithic, the authors label haplogroups G and J2 as Neolithic. A most interesting observation (Table 1) is that haplogroup J2a-M410* and J2b-M12* have the maximum and second maximum Y-STR variance in the region, being much more diverse than other haplogroups supposedly representing pre-agricultural Europeans.

At least, such a finding should give pause to those who arrive at facile conclusions about ages of human migrations on the basis of Y-STR variance.

European Journal of Human Genetics doi:10.1038/ejhg.2008.249

Y-chromosomal evidence of the cultural diffusion of agriculture in southeast Europe

Vincenza Battaglia et al.


The debate concerning the mechanisms underlying the prehistoric spread of farming to Southeast Europe is framed around the opposing roles of population movement and cultural diffusion. To investigate the possible involvement of local people during the transition of agriculture in the Balkans, we analysed patterns of Y-chromosome diversity in 1206 subjects from 17 population samples, mainly from Southeast Europe. Evidence from three Y-chromosome lineages, I-M423, E-V13 and J-M241, make it possible to distinguish between Holocene Mesolithic forager and subsequent Neolithic range expansions from the eastern Sahara and the Near East, respectively. In particular, whereas the Balkan microsatellite variation associated to J-M241 correlates with the Neolithic period, those related to E-V13 and I-M423 Balkan Y chromosomes are consistent with a late Mesolithic time frame. In addition, the low frequency and variance associated to I-M423 and E-V13 in Anatolia and the Middle East, support an European Mesolithic origin of these two clades. Thus, these Balkan Mesolithic foragers with their own autochthonous genetic signatures, were destined to become the earliest to adopt farming, when it was subsequently introduced by a cadre of migrating farmers from the Near East. These initial local converted farmers became the principal agents spreading this economy using maritime leapfrog colonization strategies in the Adriatic and transmitting the Neolithic cultural package to other adjacent Mesolithic populations. The ensuing range expansions of E-V13 and I-M423 parallel in space and time the diffusion of Neolithic Impressed Ware, thereby supporting a case of cultural diffusion using genetic evidence.


December 23, 2008

Byzantine coins from the time of the sack of Jerusalem

Tourist discovers trove of 1,300-year-old coins in Jerusalem's City of David
A British tourist working in an archaeological dig in Jerusalem on Sunday unearthed a treasure of 264 gold coins from 1,300 ago. Archaeologists called the find "one of the most impressive deposits ever found in the capital."

The coins were found by Nadine Ross, who came to Israel for one month to volunteer at the archaeological site at the City of David. They all carry the portrait of the Roman emperor Heraclius, who ruled the empire between 610 and 641.

On one side of the coins, Heraclius is depicted wearing a uniform while clasping a cross in his right hand. The flipside of the coin also features the sign of the cross. According to archaeological records, these coins were made during the early years of Heraclius' rule, between 610 and 613 - one year before the 614 Persian conquest of Jerusalem.
Such a large cache of coins from one place is unusual, and is usually a sign that they were deliberately hidden away, their secret lost with the death of their owner.

In 630AD, the emperor Heraclius liberated Jerusalem from the Persians and Jews who sacked it it in 614AD. Thus, the owner of the coins, or his descendants, could quite easily have retrieved the hidden treasure, since only ~15 years had passed.

What seems likely is that the owner never lived to claim his property, being one of the ~90,000 victims of the slaughter of 614AD. By the time the Romans liberated Jerusalem the secret of the buried treasure was already lost.

December 22, 2008

X chromosome diversity in Africans and non-Africans

From the paper:
The ratio of the tMRCA between chromosome X and the autosomes in West Africans, 0.763 ± 0.026, is consistent with the expected 3/4, but it is lower than 3/4 in non-African populations: 0.635 ± 0.024 in North Europeans and 0.613 ± 0.026 in East Asians (Table 2, Supplementary Note and Supplementary Table 2 online).

I am fairly allergic to explanations invoking genetic drift, and I think that both selection and demography might play a role in the observed discrepancy.

Nature Genetics doi:10.1038/ng.303

Accelerated genetic drift on chromosome X during the human dispersal out of Africa

Alon Keinan et al.


Comparisons of chromosome X and the autosomes can illuminate differences in the histories of males and females as well as shed light on the forces of natural selection. We compared the patterns of variation in these parts of the genome using two datasets that we assembled for this study that are both genomic in scale. Three independent analyses show that around the time of the dispersal of modern humans out of Africa, chromosome X experienced much more genetic drift than is expected from the pattern on the autosomes. This is not predicted by known episodes of demographic history, and we found no similar patterns associated with the dispersals into East Asia and Europe. We conclude that a sex-biased process that reduced the female effective population size, or an episode of natural selection unusually affecting chromosome X, was associated with the founding of non-African populations.


December 19, 2008

mtDNA haplogroup L0 in elite Kenyan distance runners

Med Sci Sports Exerc. 2008 Dec 11.

Mitochondrial Haplogroups Associated with Elite Kenyan Athlete Status.

Scott RA, Fuku N, Onywera VO, Boit M, Wilson RH, Tanaka M, H Goodwin W, Pitsiladis YP.

The maternal inheritance of mitochondrial DNA (mtDNA) has enabled construction of detailed phylogenies. Analysis of key polymorphisms from these phylogenies allows mtDNA to be assigned to haplogroups, which have been associated with elite endurance performance. PURPOSE:: To compare the frequencies of mtDNA haplogroups found in elite Kenyan athletes with those in the general Kenyan population. METHODS:: DNA samples were obtained from 221 national level Kenyan athletes (N), 70 international Kenyan athletes (I), and 85 members of the general Kenyan population (C). mtDNA haplogroups were classified by sequencing 340 bases of hypervariable section (HVS I) and by genotyping known restriction sites. Frequency differences between groups were assessed using exact tests of population differentiation. RESULTS:: The haplogroup distribution of national (P = 0.023) and international athletes (P less than 0.001) differed significantly from controls, with international athletes showing a greater proportion of L0 haplogroups (C = 15%, N = 18%, I = 30%) and lower proportion of L3* haplogroups (C = 48%, N = 36%, I = 26%). Although a high number of international athletes originated from the Rift Valley province relative to controls (C = 20%, N = 65%, I = 81%), subjects from this province did not differ in haplogroup distribution from other regions (P = 0.23). Nor did Bantu subjects differ from Nilotic (P = 0.12) despite an overrepresentation of Nilotic languages among the athletes. CONCLUSIONS:: International athletes differed in their mtDNA haplogroup distribution relative to the general Kenyan population. They displayed an excess of L0 haplogroups and a dearth of L3* haplogroups. These findings suggest that mtDNA haplogroups are influential in elite Kenyan distance running, although population stratification cannot be ruled out.


Fallacies of Evolutionary Psychology @ Scientific American

Scientific American has an article on Evolution of the Mind: 4 Fallacies of Psychology. The Coda of the article:
Among Darwin’s lasting legacies is our knowledge that the human mind evolved by some adaptive process. After all, the human brain is even more costly to run than an internal-combustion engine these days, consuming 18 percent of the body’s energy intake while constituting merely 2 percent of its weight. We wouldn’t have such an organ if it hadn’t performed some important adaptive functions in our evolutionary past.

The challenge for evolutionary psychology is to move from this general fact to some evidentially well-supported specifics about the adaptive processes that shaped the mind. But, as we have seen, the evidence needed to substantiate accounts of adaptation in our lineage during the past couple of million years is scarce. And this isn’t the kind of evidence that is likely to materialize; such evidence is lost to us, probably forever. It may be a cold, hard fact that there are many things about the evolution of the human mind that we will never know and about which we can only idly speculate.

Of course, some speculations are worse than others. Those of Pop EP are deeply flawed. We are unlikely ever to learn much about our evolutionary past by slicing our Pleistocene history into discrete adaptive problems, supposing the mind to be partitioned into discrete solutions to those problems, and then supporting those suppositions with pencil-and-paper data. The field of evolutionary psychology will have to do better. Even its very best, however, may never provide us knowledge of why all our complex human psychological characteristics evolved.
I do have a distaste for popular evolutionary psychology, not because I don't think that a lot of human behavior is genetically defined and the result of adaptation (I do), but because the evidence for this adaptation is simply lacking.

We neither know how the brain works, nor how genes influence the way it works. Nor do we have a good quantitative handle on human behavior. Some aspects of it (general intelligence, for example) are better known than others, but a lot of psychology is more akin to opinion than to deep knowledge.

So, it seems that making a convincing case for adaptation in human behavior will remain a difficult problem for some time, and evolutionary psychology must find a way to go beyond hypothesizing towards hypothesis testing. The study of present day human genetic-behavioral variation will be invaluable to that end, although it will require us to overcome the idea of the human mind as more-or-less a finished product of the Paleolithic, and accept the idea of continuing and perhaps intensifying evolution.

El Greco, defender of Byzantine art

Hand-written Note Shows El Greco Defending Byzantine Style In Face Of Western Art
A new investigation could end many of the speculations about the works of El Greco and the man himself. A hand-written annotation to a book, similar to the glosses of Saint Emilianus, found in Spain in a copy of Lives of the most excellent architects, painters and sculptors by Giorgio Vasari, has led Nicos Hadjinicolau, a researcher from the Institute of Mediterranean Studies, to conclude that the artist – contrary to popular belief– was a defender of Byzantine art.


Hadjinicolau says there are no other records of the painter’s critical opinion on the art form aside from the hand-written annotation attributed to him. “The passage I have studied is the exception to the rule, the only time that he makes a comment – and a spirited one – against Vasari,” the expert tells SINC.
A literal translation of the note attributed to the painter reads: “If [Vasari] really knew the nature of the Greek style of which he speaks, he would deal with it differently in what he says. He compares it with Giotto, but what Giotto did is simple in comparison, because the Greek style is full of ingenious difficulties.”

December 18, 2008

Huge Greek necropolis from Himera, Sicily

The discovery of such a large number of burials is a rare opportunity for an ancient DNA study of the Greeks of Sicily. The age of the samples, and the fact that they are from freshly excavated graves will make it relatively easy to extract useful DNA from them. Let's hope that we see some results in the next few years.

Ancient Mass Graves of Soldiers, Babies, Found in Italy
More than 10,000 graves containing ancient amphorae, "baby bottles," and the bodies of soldiers who fought the Carthaginians were found near the ancient Greek colony of Himera, in Italy, archaeologists announced recently.

"It's probably the largest Greek necropolis in Sicily," said Stefano Vassallo, the lead archaeologist of the team that made the discoveries, in September.

The ancient burial ground was uncovered during the construction of a railway extension.

"The remains of Himera's buildings had been known and studied for a long time, and we knew there should be some graves. We didn't expect so many graves", said Vassallo, who works for the Italian province of Palermo's government.

"Each [mass grave] contains from 15 to 25 skeletons. They were all young healthy men and they all died a violent death. Some of the skeletons have broken skulls and in some cases we found the tips of the arrows that killed them," Vassallo said.

He thinks the human remains are from soldiers who died fighting the Carthaginians in a famous 480 B.C. battle described by Greek historian Herodotus of Halicarnassus.

Out of Iberia and into North Africa

American Journal of Physical Anthropology

Post-last glacial maximum expansion from Iberia to North Africa revealed by fine characterization of mtDNA H haplogroup in Tunisia

Lotfi Cherni et al.


The first large-scale fine characterization of Tunisian H lineages clarifies that the post-Last glacial maximum expansion originating in Iberia not only led to the resettlement of Europe but also of North Africa. We found that 46% of 81 Tunisian H lineages subscreened for 1,580 bp in mtDNA coding region were affiliated with H1 and H3 subhaplogroups, which are known to have originated in Iberia. Although no signs of local expansion were detected, which would allow a clear dating of their introduction, the younger and less diverse Tunisian H1 and H3 lineages indicate Iberia as the radiating centre. Major contributions from historical migrations to this Iberian genetic imprint in Tunisia were ruled out by the mtDNA gene pool similarity between Berber/Arab/cosmopolitan samples and some "Andalusian" communities, settled by the descendents of the "Moors" who once lived in Iberia for 10 centuries (between 8th and 17th centuries), before being expelled to Tunisia.


December 14, 2008

Genetic predisposition for fathering sons

A good explanation from BBC News:

Newcastle University researchers found men were more likely to have sons if they had more brothers and vice versa if they had more sisters.

They looked at 927 family trees, with details on 556,387 people from North America and Europe, going back to 1600.

The same link between sibling sex and offspring sex was not found for women.


In the years after World War I, there was an upsurge in boy births, and Dr Gellatly said that a genetic shift could explain this.

The odds, he said, would favour fathers with more sons - each carrying the "boy" gene - having a son return from war alive, compared with fathers who had more daughters, who might see their only son killed in action.

However, this would mean that more boys would be fathered in the following generation, he said.

Evolutionary Biology doi:10.1007/s11692-008-9046-3

Trends in Population Sex Ratios May be Explained by Changes in the Frequencies of Polymorphic Alleles of a Sex Ratio Gene

Corry Gellatly


A test for heritability of the sex ratio in human genealogical data is reported here, with the finding that there is significant heritability of the parental sex ratio by male, but not female offspring. A population genetic model was used to examine the hypothesis that this is the result of an autosomal gene with polymorphic alleles, which affects the sex ratio of offspring through the male reproductive system. The model simulations show that an equilibrium sex ratio may be maintained by frequency dependent selection acting on the heritable variation provided by the gene. It is also shown that increased mortality of pre-reproductive males causes an increase in male births in following generations, which explains why increases in the sex ratio have been seen after wars, also why higher infant and juvenile mortality of males may be the cause of the male-bias typically seen in the human primary sex ratio. It is concluded that various trends seen in population sex ratios are the result of changes in the relative frequencies of the polymorphic alleles of the proposed gene. It is argued that this occurs by common inheritance and that parental resource expenditure per sex of offspring is not a factor in the heritability of sex ratio variation.


December 13, 2008

Y chromosomes. mtDNA, and autosomal DNA from Tamil Nadu and Andhra Pradesh

This paper is a winner in my book, if only for this statement:
In addition, the Y-chromosome and mtDNA may both have been affected by natural selection, [46, 47] which can further complicate the interpretation of population history. Coalescence dates based on these systems must also be viewed with appropriate caution, in part because of their large confidence intervals. More importantly, a coalescence date is not necessarily a reliable indicator of the founding date of a population [45] because these dates are affected by the size of the founder population and by subsequent gene flow patterns.
BMC Genetics doi:10.1186/1471-2156-9-86

Genetic variation in South Indian castes: evidence from Y-chromosome, mitochondrial, and autosomal polymorphisms

W. S. Watkins et al.

Abstract (provisional)


Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.


We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.


Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions.


December 11, 2008

IQ and survival in war (Scottish soldiers of WWII)

Intelligence should be positively correlated with survival in war; on the other hand, intelligence may be correlated with the amount of risk shouldered, as more intelligent men may be preferred to carry out complex high-risk mission. So, it's not clear whether smarter-than-average or not tend to survive wars.

This study shows that among Scottish Army participants of WWII, survivors were less intelligent than non-survivors, but also that non-participants in the Army were more intelligent than participants. Of course, this latter finding may be due to non-Army men being e.g. in the Navy, for which no data exist.

Certainly this data shows some relationship between IQ and military participation/survival, although the effect does not seem to be very pronounced.

The WWII experience was probably one of near-universal participation by the combat-age male population of the countries involved, and it would be interesting to see comparable data from volunteer Armies, such as the current US Army, where IQ data probably exist.

Intelligence doi:10.1016/j.intell.2008.11.003

Childhood IQ and in-service mortality in Scottish Army personnel during World War II

Janie Corley et al.


The Scottish Mental Survey of 1932 (SMS1932) provides a record of intelligence test scores for almost a complete year-of-birth group of children born in 1921. By linking UK Army personnel records, the Scottish National War Memorial data, and the SMS1932 dataset it was possible to examine the effect of childhood intelligence scores on wartime military service mortality in males. There were 491 matches between World War II (WWII) Scottish Army fatalities and the SMS1932 database; 470 (96%) had an age 11 mental ability score recorded. The mean (S.D.) age 11 IQ score of those who died on active service in WWII was 100.78 (15.56), compared with 97.42 (14.87) for male Army survivors (p less than 0.0001; Cohen's d = 0.22). Men who took part in the SMS1932 and who were not found in the Army database had a higher mean score (100.45, S.D. =14.97) than those men who had been in the Army, regardless of whether they died or survived (mean IQ = 97.66, S.D. = 14.94; p less than 0.0001; Cohen's d = 0.19). Male soldiers with a higher childhood IQ had a slightly increased risk of dying during active service in WWII. Men who did not join the Army had a higher IQ than men who did. Further research in this area should consider naval and air force personnel records in order to examine more fully the complex relationship between IQ and survival expectancy during active service in WWII.


Inbreeding depression and IQ

Intelligence doi:10.1016/j.intell.2008.10.007

Inbreeding depression and IQ in a study of 72 countries

Michael A. Woodley


In this ecological study, a robust negative correlation of r = − .62 (P less than .01) is reported between national IQs and consanguinity as measured by the log10 transformed percentage of consanguineous marriages for 72 countries. This correlation is reduced in magnitude, when IQ is controlled for GDP per capita (r = − .41, P less than .01); education index (r = − .40, P less than .01); and democracy index (r = − .42, P less than .01). Multiple regression analysis revealed that in the absence of the democracy index; percentage consanguineous marriages, education index and GDP per capita all exhibited stable final standardized β coefficients, however consanguinity had the least impact (β = 0, P greater than .05) whereas GDP per capita had the highest (β = .35, P greater than .01). This result is interpreted in light of cultural feedback theory, whereby it is suggested that consanguinity could subtly influence IQ at larger scales as a result of small IQ handicaps bought about through inbreeding being amplified into much larger differences through their effect on factors that maximize IQ such as access to education and adequate nutrition. Finally, consideration is given to future potential research directions.


December 10, 2008

Looking good is more important than smelling good

J Soc Psychol. 2008 Dec;148(6):765-73.

Beauty is mostly in the eye of the beholder: olfactory versus visual cues of attractiveness.

Foster JD.

Olfaction is an important determinant of attractiveness, possibly even more so than vision when judgments are made by women. However, research that directly compares these cues using actual stimuli (e.g., t-shirt odors) is lacking. In this study, 44 women rated the attractiveness of t-shirt odors and facial photographs of 21 men either independently (i.e., first rated t-shirts, then rated photographs) or together (i.e., made overall ratings on the basis of t-shirts and photographs presented simultaneously). Photograph ratings were far more predictive of overall attractiveness than were t-shirt ratings. This was true for female participants who were fertile or infertile (i.e., using hormonal birth control). Body odor only predicted overall attractiveness when fertile women made the ratings.


December 09, 2008

Reduction of human cranial diversity and distance from Africa

It is important to note what this paper has actually discovered, which is not clear from the abstract, and is only briefly discovered in the paper itself.

The paper does not prove that climate has not played an important role in the shaping of human cranial variation. Rather it shows that it does not play an important role in the level of diversity found in different populations. But, I really can't think why anyone would propose that.

Let's take a particular trait, say nose breadth or cranial breadth. It has been demonstrated that the former tends to be narrower and the latter broader in more northerly compared to more equatorial regions. But, this is a difference in the means and not a difference in the variance of the traits in question.

The authors write:
All the most informative traits were distributed in the anterior region of the cranium (yet not all anterior traits were highly informative). This came as a surprise as the anterior regions of the cranium are generally assumed to be more affected by natural selection (i.e. facial area and cranial breadth), while the temporal bone and some traits of the neurocranium are considered to reflect population history (Beals et al. 1984; Franciscus & Long 1991; Roseman 2004; Harvati & Weaver 2006).

Diversity is reduced in either of two ways:
  • Serial bottlenecks, when a subset of the variation present in the ancestral population migrates to new regions
  • Selection, which reduces diversity in the traits under selection
Under the scenario of bottlenecks, it is expected that all traits should be equally affected by the reduction of diversity.

Under the scenario of selection, however, it is expected that traits under selection will be more affected by the new ecological conditions that occur away from the cradle.

The finding that the anterior region of the cranium is more informative in terms of reduced diversity is actually consistent with selection and not with bottlenecks, since it is in this part, in nasal features, facial flatness, prognathism, etc. that populations have developed strongly differentiated types under selection.

Furthermore, in this paper the study is limited to skulls from the last 2,000 years. But, if bottlenecks are indeed responsible for the reduction of diversity, then this reduction of diversity would be visible in the earliest Homo sapiens skulls from the various regions, as these would be descended from the few bottlenecked migrants. Are Upper Paleolithic Europeans, for example, more or less diverse than Africans of equivalent age, or even modern Africans?

On the contrary, recent skulls may be less diverse than the earliest ones, due to a longer period of selection, i.e., the tens of thousands of years between the earliest Homo sapiens in Europe or Asia and the ones of the last 2,000 years. Moreover, this selection ought to have been strongest in regions further from Africa, as this is correlated with different environments (although not necessarily the 3 climate variables considered here).

In conclusion:
  • Within-population variance decreases with distance from Africa, but this does not measure between-population difference in mean trait values
  • Both bottlenecks and selection result in reduced variance
  • A stronger variance-reduction signal in the anterior cranium is more consistent with selection than with bottlenecks
  • The bottlenecks theory should be more visible in early, not recent skulls as those studied in this paper. Recent skulls should have reduced variance compared to their more ancient counterparts due to a long period of selection.

Proceedings of the Royal Society B doi:10.1098/rspb.2008.1563

Distance from Africa, not climate, explains within-population phenotypic diversity in humans

Lia Betti et al.


The relative importance of ancient demography and climate in determining worldwide patterns of human within-population phenotypic diversity is still open to debate. Several morphometric traits have been argued to be under selection by climatic factors, but it is unclear whether climate affects the global decline in morphological diversity with increasing geographical distance from sub-Saharan Africa. Using a large database of male and female skull measurements, we apply an explicit framework to quantify the relative role of climate and distance from Africa. We show that distance from sub-Saharan Africa is the sole determinant of human within-population phenotypic diversity, while climate plays no role. By selecting the most informative set of traits, it was possible to explain over half of the worldwide variation in phenotypic diversity. These results mirror those previously obtained for genetic markers and show that ‘bones and molecules’ are in perfect agreement for humans.


Genomic substructure in Finns

American Journal of Human Genetics doi: 10.1016/j.ajhg.2008.11.005

The Genome-wide Patterns of Variation Expose Significant Substructure in a Founder Population

Eveliina Jakkula et al.


Although high-density SNP genotyping platforms generate a momentum for detailed genome-wide association (GWA) studies, an offshoot is a new insight into population genetics. Here, we present an example in one of the best-known founder populations by scrutinizing ten distinct Finnish early- and late-settlement subpopulations. By determining genetic distances, homozygosity, and patterns of linkage disequilibrium, we demonstrate that population substructure, and even individual ancestry, is detectable at a very high resolution and supports the concept of multiple historical bottlenecks resulting from consecutive founder effects. Given that genetic studies are currently aiming at identifying smaller and smaller genetic effects, recognizing and controlling for population substructure even at this fine level becomes imperative to avoid confounding and spurious associations. This study provides an example of the power of GWA data sets to demonstrate stratification caused by population history even within a seemingly homogeneous population, like the Finns. Further, the results provide interesting lessons concerning the impact of population history on the genome landscape of humans, as well as approaches to identify rare variants enriched in these subpopulations.


December 08, 2008

A visual display of biological and social race

This is as clear display of the difference between biological and social race.

Populations from the three major human biological races (European Americans from Caucasoids, Yoruba from Negroids, Japanese/Chinese from Mongoloids) are clearly separable, with no overlap.

The "black race" to which African Americans are said to belong is seen as an almost perfect linear combination of Caucasoids and Negroids. It is not a biological race, but rather the result of admixture between the two races.

The same can be seen in other admixed groups such as the Uyghur, who are a combination of Caucasoids and Mongoloids. In that case, however, the admixture is more ancient, and the opportunity to further mix with representatives of the unadmixed groups is more limited. Therefore, the blend has been completed, and most individuals have similar admixture proportions from the ancestral groups. African Americans, on the other hand are much more variable in their individual ancestry components, from ~100% Negroid, to more Caucasoid than Negroid.

PLoS Genetics doi: 10.1371/journal.pgen.1000294

Effects of cis and trans Genetic Ancestry on Gene Expression in African Americans

Alkes L. Price et al.


Variation in gene expression is a fundamental aspect of human phenotypic variation. Several recent studies have analyzed gene expression levels in populations of different continental ancestry and reported population differences at a large number of genes. However, these differences could largely be due to non-genetic (e.g., environmental) effects. Here, we analyze gene expression levels in African American cell lines, which differ from previously analyzed cell lines in that individuals from this population inherit variable proportions of two continental ancestries. We first relate gene expression levels in individual African Americans to their genome-wide proportion of European ancestry. The results provide strong evidence of a genetic contribution to expression differences between European and African populations, validating previous findings. Second, we infer local ancestry (0, 1, or 2 European chromosomes) at each location in the genome and investigate the effects of ancestry proximal to the expressed gene (cis) versus ancestry elsewhere in the genome (trans). Both effects are highly significant, and we estimate that 12±3% of all heritable variation in human gene expression is due to cis variants.


December 07, 2008

Y chromosomes of Uttar Pradesh (North India)

The main objection I have to these conclusions is with respect to J2:
Haplogroup J2* was observed 77 times. Its frequency was higher in the Shia (19.5%) and Sunni (15.4%) sample set than in the other three upper caste populations (6.3% in Bhargavas, 12.5% in Chaturvedis, and 11.9% in Brahmins).


Kivisild et al. (2003) also Figure 3. Migratory routes of paternal lineages of Indian upper caste and Muslim populations. reported the presence of a J2 clade and postulated that the origin of the J2 clade in India was probably Central Asia. Their hypothesis is based on eight populations taken from different parts of India. They observed the J2 clade in ~13% of the sample. The major Middle Eastern lineage present in our study was J2* with an average frequency of 13.8% and its frequency among Shias was the highest (19.5%). We suggest that the J2* lineage of the studied populations might be derived from the Middle East.We suggest that the J2* lineage of the studied populations might be derived from the Middle East. This might have been due to two different episodes of migrations, one concomitant with the development and spread of agriculture ~8000-10 000 years ago (Renfrew 1989; Cavalli-Sforza 2005), and the other more recent migration being the arrival of Muslim rulers 1000 years ago.

I think there are two reasons why J2 may have arrived in Indian caste populations from Central Asia, probably with R1a1:
  • Hindu J2 generally lacks any downstream mutations (e.g., M67) which are frequent in Middle East; this argues against its recent introduction, associated with the Muslims. Moreover, if the Hindu population had undergone recent admixture, then other Middle Eastern haplogroups (J1, E1b1b1, G, R1b) would be found in them at more than zero or trace frequency. So, it seems that J2 is not the result of recent admixture.
  • On the other hand, if J2, and especially J2a had been introduced by Neolithic agriculturalists in India during the Neolithic, then we would not expect that it be correlated with social caste today.
Therefore I am in agreement with Kivisild, that J2 arrived into the Hindu population from Central Asia. In the Muslim population, however, it may be of two sources: religious conversion of Hindu castes, or recent Near Eastern origin.

With respect to R2, I would not place its origin far from India, although it's not clear where exactly it originated.

As I wrote in the Origin of Hindu Brahmins:
The three most populous haplogroups (R1a1, R2, J2a) are the best candidates for lineages of exogenous origin, and have Bronze Age coalescence time, in accordance with the traditional theory. However, indigenous lineages (H1 and L1) and others with fewer numbers did enter into the Brahmin gene pool. The majority (64%) does appear to trace its ancestry to the early Indo-Aryans.
In this study, the combined frequency of these haplogroups (including J2 rather than J2a, since no downstream markers were typed) are in these upper-caste groups: 61.5% in Bhargavas, 68.2% in Chaturvedis, and 60.2% in Brahmins.

Related posts:

Annals of Human Biology doi: 10.1080/03014460802558522

Presence of three different paternal lineages among North Indians: A study of 560 Y chromosomes

Zhongming Zhao et al.


Background: The genetic structure, affinities, and diversity of the 1 billion Indians hold important keys to numerous unanswered questions regarding the evolution of human populations and the forces shaping contemporary patterns of genetic variation. Although there have been several recent studies of South Indian caste groups, North Indian caste groups, and South Indian Muslims using Y-chromosomal markers, overall, the Indian population has still not been well studied compared to other geographical populations. In particular, no genetic study has been conducted on Shias and Sunnis from North India.

Aim: This study aims to investigate genetic variation and the gene pool in North Indians.

Subjects and methods: A total of 32 Y-chromosomal markers in 560 North Indian males collected from three higher caste groups (Brahmins, Chaturvedis and Bhargavas) and two Muslims groups (Shia and Sunni) were genotyped.

Results: Three distinct lineages were revealed based upon 13 haplogroups. The first was a Central Asian lineage harbouring haplogroups R1 and R2. The second lineage was of Middle-Eastern origin represented by haplogroups J2*, Shia-specific E1b1b1, and to some extent G* and L*. The third was the indigenous Indian Y-lineage represented by haplogroups H1*, F*, C* and O*. Haplogroup E1b1b1 was observed in Shias only.

Conclusion: The results revealed that a substantial part of today's North Indian paternal gene pool was contributed by Central Asian lineages who are Indo-European speakers, suggesting that extant Indian caste groups are primarily the descendants of Indo-European migrants. The presence of haplogroup E in Shias, first reported in this study, suggests a genetic distinction between the two Indo Muslim sects. The findings of the present study provide insights into prehistoric and early historic patterns of migration into India and the evolution of Indian populations in recent history.


December 06, 2008

Genetic structure in East Asia using 200K SNPs

The table of paired Fst values for East Asian populations is here. The PCA plots are seen on the left.

PLoS ONE 3(12): e3862. doi:10.1371/journal.pone.0003862

Analysis of East Asia Genetic Substructure Using Genome-Wide SNP Arrays

Chao Tian et al.


Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's less than 0.0025 with CHB). For PCA, the first two PC's showed a pattern of relationships that closely followed the geographic distribution of the different East Asian populations. PCA showed substructure both between different East Asian groups and within the Han Chinese population. These studies have also identified a subset of East Asian substructure ancestry informative markers (EASTASAIMS) that may be useful for future complex genetic disease association studies in reducing type 1 errors and in identifying homogeneous groups that may increase the power of such studies.


Smart people have better sperm

Intelligence doi:10.1016/j.intell.2008.11.001

Intelligence and semen quality are positively correlated

Rosalind Arden et al.


Human cognitive abilities inter-correlate to form a positive matrix, from which a large first factor, called ‘Spearman's g’ or general intelligence, can be extracted. General intelligence itself is correlated with many important health outcomes including cardio-vascular function and longevity. However, the important evolutionary question of whether intelligence is a fitness-related trait has not been tested directly, let alone answered. If the correlations among cognitive abilities are part of a larger matrix of positive associations among fitness-related traits, then intelligence ought to correlate with seemingly unrelated traits that affect fitness—such as semen quality. We found significant positive correlations between intelligence and 3 key indices of semen quality: log sperm concentration (r = .15, p = .002), log sperm count (r = .19, p less than .001), and sperm motility (r = .14, p = .002) in a large sample of US Army Veterans. None was mediated by age, body mass index, days of sexual abstinence, service in Vietnam, or use of alcohol, tobacco, marijuana, or hard drugs. These results suggest that a phenotype-wide fitness factor may contribute to the association between intelligence and health. Clarifying whether a fitness factor exists is important theoretically for understanding the genomic architecture of fitness-related traits, and practically for understanding patterns of human physical and psychological health.


Fat people are slow to react

HOMO - Journal of Comparative Human Biology doi:10.1016/j.jchb.2008.06.006

Relationship between simple reaction time and body mass index
Purchase the full-text article

A. Skurvydas et al.


The aim was to establish the relationship between simple reaction time in motor response in young adults in relation to their body physique, as represented by body mass index. Forty-five young male participants were allocated to one of three anthropometric groups, based on their body mass index. Participants performed 100 reaction-time trials with instructions to move a joystick, as quickly as possible, as soon as they detected a single star appearing in the centre of a monitor. All data were statistically selected into seven intervals and data from the mode frequency interval were precisely analysed. Participants from the group with greater body mass index reacted significantly slower than others. We did not record group lateral differences based on simple reaction time in each selected group. We recommend for future researchers the importance of identification of the level of body mass index of participants prior to testing them for effectiveness of simple sensori-motor reactions.


December 05, 2008

Brain volume and IQ in children

Intelligence doi:10.1016/j.intell.2008.10.005

A genetic analysis of brain volumes and IQ in children

Marieke van Leeuwen et al.


In a population-based sample of 112 nine-year old twin pairs, we investigated the association among total brain volume, gray matter and white matter volume, intelligence as assessed by the Raven IQ test, verbal comprehension, perceptual organization and perceptual speed as assessed by the Wechsler Intelligence Scale for Children-III. Phenotypic correlations between the brain volumes and intelligence traits ranged between .20 and .33. Processing speed and brain volume did not correlate. The relation between brain volume and intelligence was entirely explained by a common set of genes influencing both sets of phenotypes.


December 04, 2008

Major study of Iberian Y-chromosomes (Adams et al.)

with 2 Updates (latest: 9 Dec 08)

This article will be an invaluable resource for students of Iberian Y-chromosome diversity, due to the numerous 18-marker haplotypes from all regions contained in the supplement.

The authors modeled the Iberian population as a 3-way mix with "Basque", "Sephardic", and "North African". The main thesis is that the fairly substantial "Sephardic" and "North African" components identified are evidence of substantial religious conversion of Jews and Muslims.

The North African component may be roughly correct; it is similar to the 6% reported for Sicily, which was also occupied by Muslims. The Sephardic component is however suspect, as it may be of either Arabic or Italian origin, or indeed even earlier population movements from the Eastern Mediterranean.

Another point of contention is with the use of Basques as pre-Sephardic/Muslim Iberians. The Christian population of Iberia prior to the arrival of the Jews and Muslims, included non-Basque Celtiberians, Romance speakers, as well as a Visigoth/Germanic layer.

Nor is it clear that the North African component in Iberians stems from Muslim converts, since bidirectional movement of populations across Gibraltar may predate the occupation of Iberia.


To see the reliability of this type of study, consider that what this study terms "Sephardic", is what another recent study termed "Phoenician". In the previous study Ibiza was considered Phoenician-influenced and compared with Mallorca and Minorca. In this one, Ibiza is assigned a hefty 33% "Sephardic Jewish" influence, while Minorca only -7.5%. At least, one would think they'd pick an admixture method that didn't result in negative contributions...

Choose your parental populations carefully, mix, shake, and get whatever result you please: Neolithic, Phoenician, Jewish, there's something for every taste.


Figure of frequencies added at the top of the post.

From the paper:
To formally assess the impact of North African and Sephardic Jewish contributions on the indigenous population, we carried out admixture analysis, employing the mY estimator and treating the study populations as hybrids of three parental populations. We chose the Basques as the Iberian parental sample. This is justified on the basis of a relative absence of Muslim occupation of the Basque region and supported by the genetic distinctiveness of the Basque and neighboring Gascon samples (Figure 3).

In plain English, the authors could just as well have written: "Basques are distinct from other Iberians. This may be due to either (i) the fact that there were indeed differences between Basques and other Iberians even before the Muslim occupation/Jewish settlement: after all they occupy their own region, not Iberia-at-large, and speak a different language. Or, (ii) it could be that the rest of the Iberians have undergone substantial admixture with Muslims and Jews. We arbitrarily choose hypothesis (ii) as our premise, and ¡qué sorpresa! our data backs up our pre-supposed idea."

More from the paper:
An additional factor that could lead to overestimation of Sephardic Jewish ancestry proportions is the effect of other influences on the Iberian Peninsula from eastern Mediterranean populations that might have imported lineages such as G, K*, and J. These influences fall into two different time periods: the Neolithic era, beginning in 10 KYA, the demographic effects of which are a matter for heated debate;1 and the last three millennia, the time period of Greek and Phoenician colonization.65 Effects in the second case are expected to be most marked in the eastern part of our sample area, but despite this, the apparent Sephardic Jewish ancestry proportions remain substantial in the west (Figure 4). The confounding effects of earlier population movement are likely to be particularly strong for Ibiza, Majorca, and Minorca, whose island natures make them more susceptible to influence by immigration and subsequent drift than inland sites. For example, history records that Ibiza, found to have a high apparent Sephardic Jewish ancestry proportion in our study, had an insignificant Jewish population compared to its neighbors66 yet had previously been an important Phoenician colony. Likewise, Minorca is recorded as having a substantial Jewish population,66 yet here, it shows no Sephardic Jewish ancestry.

It is true that Greek or Phoenician influence would be concentrated in particular regions. Whether Y-chromosomes "stay put" for a period of 2.5 thousand years is a different question. But, Neolithic Y-chromosomes certainly would have had ample time to be fairly uniformly distributed across the peninsula. And, the most important single aspect of Iberian history, i.e., the Roman conquest, which would have introduced not only the dominant language, but also a fair amount of genes is totally ignored.

In fact this is the single reference to the Roman period in this paper:
The Jewish presence was very long-established, with some evidence that it predated the Christian era; many Jews, however, are thought to have arrived during the Roman period
But, seriously, in the Roman period, not only Jews, but most importantly Romans settled in Iberia. And, by the way, they must have been numerous enough to change the language. But, let's ignore these pesky Romans and pretend that Iberians are a simple mix of Basques/Moroccan/Jews.

Bottom line: great data, subpar interpretation.

American Journal of Human Genetics doi:

The Genetic Legacy of Religious Diversity and Intolerance: Paternal Lineages of Christians, Jews, and Muslims in the Iberian Peninsula

Susan M. Adams et al.


Most studies of European genetic diversity have focused on large-scale variation and interpretations based on events in prehistory, but migrations and invasions in historical times could also have had profound effects on the genetic landscape. The Iberian Peninsula provides a suitable region for examination of the demographic impact of such recent events, because its complex recent history has involved the long-term residence of two very different populations with distinct geographical origins and their own particular cultural and religious characteristics--North African Muslims and Sephardic Jews. To address this issue, we analyzed Y chromosome haplotypes, which provide the necessary phylogeographic resolution, in 1140 males from the Iberian Peninsula and Balearic Islands. Admixture analysis based on binary and Y-STR haplotypes indicates a high mean proportion of ancestry from North African (10.6%) and Sephardic Jewish (19.8%) sources. Despite alternative possible sources for lineages ascribed a Sephardic Jewish origin, these proportions attest to a high level of religious conversion (whether voluntary or enforced), driven by historical episodes of social and religious intolerance, that ultimately led to the integration of descendants. In agreement with the historical record, analysis of haplotype sharing and diversity within specific haplogroups suggests that the Sephardic Jewish component is the more ancient. The geographical distribution of North African ancestry in the peninsula does not reflect the initial colonization and subsequent withdrawal and is likely to result from later enforced population movement--more marked in some regions than in others--plus the effects of genetic drift.


Middle Stone age started 276,000 years ago

It is interesting that fairly modern tools were found so much earlier than previously thought. Whether anatomically modern humans existed back then is yet to be determined. This result shows that different levels of technological sophistication were to be found at the same point in time: mankind back then was not one species with one level of culture. And, indeed the earliest Homo sapiens, Omo I and II, were followed tens of thousands years later by Herto who was more "archaic" anatomically. Culture and anatomy do not go hand in hand.

Geology doi:10.1130/G25213A.1

Diachronous dawn of Africa's Middle Stone Age: New 40Ar/39Ar ages from the Ethiopian Rift

Leah E. Morgan1 and Paul R. Renne


The Middle Stone Age (MSA) of Africa, like the Middle Paleolithic of Europe, is thought to represent a time period wherein toolmakers acquired significant increases in cognitive abilities and physical dexterity. Existing data fail to resolve whether the MSA emerged gradually, abruptly, or discontinuously, and whether this industry reflects the activity of Homo sapiens. Here we present new 40Ar/39Ar geochronological data revealing that advanced MSA archaeology at two sites in the main Ethiopian Rift is older than 276 ka, much older than technologically comparable MSA archaeology from elsewhere. An age of 183 ka for a unit farther upsection, along with the technological stasis observed throughout the section, indicates that similar technology was used here for ~93 ka. These results suggest that MSA technology evolved asynchronously in different places, and challenge the notion of a distinct time line for either the appearance of the MSA or the disappearance of the earlier Acheulean. These and other recent results indicate that the oldest known MSA consistently predates fossil evidence for the earliest Homo sapiens.


Evolutionary genetics of lactase persistence

Related: Lactase persistence in Africans and non-Africans.

Human Genetics doi: 10.1007/s00439-008-0593-6

Lactose digestion and the evolutionary genetics of lactase persistence

Catherine J. E. Ingram et al.


It has been known for some 40 years that lactase production persists into adult life in some people but not in others. However, the mechanism and evolutionary significance of this variation have proved more elusive, and continue to excite the interest of investigators from different disciplines. This genetically determined trait differs in frequency worldwide and is due to cis-acting polymorphism of regulation of lactase gene expression. A single nucleotide polymorphism located 13.9 kb upstream from the lactase gene (C-13910 > T) was proposed to be the cause, and the −13910*T allele, which is widespread in Europe was found to be located on a very extended haplotype of 500 kb or more. The long region of haplotype conservation reflects a recent origin, and this, together with high frequencies, is evidence of positive selection, but also means that −13910*T might be an associated marker, rather than being causal of lactase persistence itself. Doubt about function was increased when it was shown that the original SNP did not account for lactase persistence in most African populations. However, the recent discovery that there are several other SNPs associated with lactase persistence in close proximity (within 100 bp), and that they all reside in a piece of sequence that has enhancer function in vitro, does suggest that they may each be functional, and their occurrence on different haplotype backgrounds shows that several independent mutations led to lactase persistence. Here we provide access to a database of worldwide distributions of lactase persistence and of the C-13910*T allele, as well as reviewing lactase molecular and population genetics and the role of selection in determining present day distributions of the lactase persistence phenotype.


Cranial robusticity in Australians

From the paper:
Instead, cranial robusticity among the Australians and other modern humans can reasonably be explained on the basis of current knowledge of cranial development-function, as well as a phylogenetic scenario consistent with genetic studies of the population history of Aboriginal Australians (e.g. Hudjashov et al., 2006). Thus, the earliest Australians might be thought of as having evolved from the earliest modern humans who migrated from Africa into East/Southeast Asia around 60-70 kyr. The Australian Pleistocene/Early Holocene human record indicates the presence of marked variability in cranial form. However, it is not possible with present genetic data to determine whether the continent was colonised during a single migration by a population with a highly variable cranial form or in two major events by people with different cranial morphologies.
From Hudjashov et al. (2007) mentioned in the text:
The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.

Journal of Archaeological Science doi:10.1016/j.jas.2008.11.021

Possible Causes and Significance of Cranial Robusticity Among Pleistocene-Early Holocene Australians

Darren Cunroe


An analysis of possible developmental-functional causes of cranial form suggests that the unusual morphology of ‘robust’ Pleistocene/Early Holocene Australians such as Willandra Lakes Human 50 might best be explained by four underlying factors: possession of a 1) large neurocranium, 2) narrow cranial base, 3) viscerocranium with considerable midfacial projection, and 4) large dentition, especially the cheek teeth, with their associated large jaws and high volume masticatory muscles. Some of these features are likely to be highly heritable, while others are caused/exaggerated by influences from ageing processes, diet, and a hunter-gatherer lifestyle in an arid environment. These underlying ‘causes’ are either apomorphies of H. sapiens (1 & 2) and thus absent from pre-modern specimens such as from Ngandong, or represent plesiomorphic features of latter Homo (3 & 4). It is concluded that combining current knowledge of cranial development-function with genetic studies of the population history of Aboriginal Australians provides the most parsimonious solution to understanding their evolutionary origins.


Age of Italian R1b Y-chromosomes (amended Jan. 5, 2009)


Capelli et al. Mol Phylogenet Evol. 2007 Jul;44(1):228-39 have provided ASD values for R1*(xR1a1) in several Italian locations. In the Italian context, this most likely represents haplogroup R1b and indeed R-M269.

The authors write:
Microsatellite variation was investigated by the analysis of the following 10 microsatellites: DYS 388, 393, 392, 19, 390, 391, 389 I and II and 385—which is a double allele locus.


Y-STRs were used to estimate intra-haplogroup diversity. Locus DYS385 has a duplicated allele pattern that can not be resolved assigning each allele to the corresponding locus. We thus decided to exclude DYS385 from STR variance estimation. Similarly, to avoid double estimation of locus variation, repeat number at locus DYS389 II was calculated by subtracting the number of repeats at DSY389 I.
The average mutation rate over these loci is:

(0.00057+0.00075+0.00061+0.00168+0.00227+0.00351+0.00188+0.00226)/8 = 0.00169 using the Chandler (pdf) rates, or

(0.00057+0.00079+0.00045+0.00245+0.00237+0.00283+0.00237+0.00343)/8 = 0.00191 using the YHRD rates, and the Chandler rate for DYS 388.

In the following table, I list the estimated age using the above germline mutation rate. Note that both variance and ASD accumulate at near the germline mutation rate, and are associated with substantial confidence intervals.

Thus, I list age estimates both with a "standard" model (25 years/generation, germline rate), and my own preferred model (31.5 years/generation, 0.87*germline rate *). All ages are in thousands of years.

[begin amend] These authors use an average squared distance between all pairs of alleles as implemented in Microsat, rather than between alleles and a putative ancestral allele. Therefore the ages given below have been divided by 2, compared to the initial version of this post.

Chandler rates
YHRD rates

Standard Dienekes
Standard Dienekes
0.467 3.5 5
3.1 4.4
0.486 3.6 5.2
3.2 4.6
0.298 2.2 3.2
2 2.8
0.544 4 5.8
3.6 5.2
0.623 4.6 6.7
4.1 5.9
0.701 5.2 7.5
4.6 6.6
0.529 3.9 5.7
3.5 5
0.414 3.1 4.4
2.7 3.9
0.297 2.2 3.2
1.9 2.8
0.527 3.9 5.6
3.4 5
0.533 3.9 5.7
3.5 5.1
0.5 3.7 5.4
3.3 4.7

(Sample codes: AMA,
Apennine Marche; CMA, Central Marche; CTU, Central Tuscany; ELB, Elba Island (Tuscany); NEL, North–East Latium; NWA, North–West Apulia;
SAP, South Apulia; SLA, South Latium; TLB, Tuscany–Latium border; VLB, Val Badia (Alto Adige); WCL, West Calabria; WCP, West Campania.)

[end amend]

Furthermore, I calculated ASD from an ancestral haplotype (either modal or median: they coincide) for Anatolian data from Cinnioglu et al. Hum Genet (2004) 114 : 127–148. The ASD value over the same set of markers is 0.408 corresponding to an age estimate of 5.3-9.1kya using any set of assumptions.

Notice further that the value of 0.408 is inflated by the inclusion of R1*(xR1a1) chromosomes that may not be native to Anatolia, such as several R-M73 examples that are often found in Central Asia (Underhill et al. Nature Genetics 26 (2000)). Removal of only examples #442-443 which are conspicuous for having a rare DYS390=19 allele, 5 repeat units away from the modal, reduces the ASD even further to 0.327, and a corresponding age estimate to 4.3-7.3ky.

UPDATE (Dec 5)

[In the following, ASD is calculated from an ancestral haplotype]

The Cinnioglu et al. data for R1b1b2-M269 chromosomes give an ASD of 0.31, corresponding to an age of 4.1-6.6ky.

The data published in Bosch et al. (Annals of Human Genetics (2005) 69,1–30) for haplogroup R1b-P25 from the Balkans, give an ASD of 0.35 or an age of 4.6-7.7ky.


The data from Di Gaetano et al. European Journal of Human Genetics (2008) for Sicily have a variance of 0.36 using a set of markers that does not include DYS 388, but includes DYS439, which has a Chandler rate of 0.00530 and a YHRD rate of 0.00635, leading to an average rate of 0.00228 (according to Chandler) or 0.00264 (according to YHRD) or an age range of 3.4-4.9ky

Update (Jan 5, 2009)

[In the following, ASD is calculated from an ancestral haplotype]

Zalloua et al. have a sample of R1b Cypriot males with an ASD of 0.4 over the same markers as Capelli et al. This is virtually identical to the R1*(xR1a1) data for Anatolia. The age corresponds to 5.2-8.6ky.


These results suggest that R-M269 diversity in Italy, the Balkans, Anatolia, and Cyprus is similar, making it difficult to trace the origin of this haplogroup on this basis; clearly more data is needed.

Tentatively, there are several reasons why a European rather than West Asian origin seems reasonable:

  1. R-M269 is more frequent in Europe than in Asia
  2. Both forms of R-M269, haplotypes Ht15 and Ht35 are present in Europe; the little Ht15 found in West Asia can be easily explained historically.
  3. The sister clade R1a is found at high frequency in Europe, and may have spread from here to the Eurasiatic steppes.
  4. Small-scale introduction of R1b in West Asia is more parsimonious than large-scale replacement of European Y-chromosomes by R1b chromosoomes, unaccompanied by other typically West Asian haplogroups such as J2, and presenting a cline with its maximum in the Atlantic

(*) As explained here