December 29, 2005

The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form (?)

C. Loring Brace and colleagues have published a new paper in PNAS which examines several populations from West Eurasia and Africa based on 24 cranial measurements.

The first canonical variate (horizontal) clearly separates the Niger-Congo group from the other populations:

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According to Brace et al:
When the samples used in Fig. 1 are compared by the use of canonical variate plots as in Fig. 2, the separateness of the Niger-Congo speakers is again quite clear. Interestingly enough, however, the small Natufian sample falls between the Niger-Congo group and the other samples used. Fig. 2 shows the plot produced by the first two canonical variates, but the same thing happens when canonical variates 1 and 3 (not shown here) are used. This placement suggests that there may have been a Sub-Saharan African element in the make-up of the Natufians (the putative ancestors of the subsequent Neolithic), although in this particular test there is no such evident presence in the North African or Egyptian samples. As shown in Fig. 1, the Somalis and the Egyptian Bronze Age sample from Naqada may also have a hint of a Sub-Saharan African component. That was not borne out in the canonical variate plot (Fig. 2), and there was no evidence of such an involvement in the Algerian Neolithic (Gambetta) sample.

Brace et al. also combined samples into regional groups. The canonical variate plot again shows the separate of the Niger-Congo group, and the intermediacy of the Natufians between West Eurasians and North/East Africans and Eurasians.

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The raw Mahalanobis distances are quite informative.

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It can be easily seen that the Niger-Congo have high distances from all other populations, except Northeast Africans. Northeast Africans are however closer to Late Prehistoric Eurasians and Modern Europeans than to the Niger-Congo group. This, once more, establishes the intermediacy of Northeast Africans between Caucasoids and Sub-Saharan Africans.

All populations except the Niger-Congo and the Natufians are close to each other. The Natufians have very high distances from other samples. Their closest neighbors are first, Late Prehistoric Eurasia, and second, Niger-Congo.

According to Brace:
The generally high D2 values for the Natufian sample in Table 3 are almost certainly a reflection of the very small sample size.
The Natufian sample consisted of only 4 individuals. Thus, it appears that the high distances of the Niger-Congo group are indicative of its biological distinctiveness, whereas the high distances of the Natufians are due to the small sample size.

Brace's conclusion is stated in conditional form:
If the Late Pleistocene Natufian sample from Israel is the source from which that Neolithic spread was derived, then there was clearly a Sub-Saharan African element present of almost equal importance as the Late Prehistoric Eurasian element. At the same time, the failure of the Neolithic and Bronze Age samples in central and northern Europe to tie to the modern inhabitants supports the suggestion that, while a farming mode of subsistence was spread westward and also north to Crimea and east to Mongolia by actual movement of communities of farmers, the indigenous foragers in each of those areas ultimately absorbed both the agricultural subsistence strategy and also the people who had brought it.
The "if" portion of the statement is problematic. While Natufians are widely acknowledged as a culture anticipating the arrival of the Neolithic, they were not the first Neolithic agriculturalists, nor where they the immediate source of the transmission of agriculture. According to Pinhasi and Pluciennik (CURRENT ANTHROPOLOGY Volume 45, Number S4, August-October 2004):
Analysis of the material suggests that there was considerable morphological heterogeneity among the earliest farmers of the Levant belonging to the Pre-Pottery Neolithic but that similar variability is generally not seen among the earliest mainland agriculturalists of south-eastern Europe. We propose that this may be explained by the existence of a genetic "bottleneck" among Anatolian populations and that it supports models of the largely exogenous origin of many early Neolithic populations in this region.
Thus, the sample of 4 Natufian individuals does not represent the first pre-pottery Neolithic populations, and moreover, it does not represent the immediate source of the Neolithic in Europe, which was that of the Neolithic agriculturalists of Anatolia. As Pinhasi and Pluciennik state:
Analysis of morphological variability in the Near East and Europe (here and in Pinhasi 2003) suggests that the Epipalaeolithic populations from the Natufian Levant were noticeably different to the Mesolithic populations described from the Danube Gorge, the western Mediterranean, and central Europe. No close similarities were observed between Early Neolithic and Mesolithic European groups in any of the regions studied, with the possible exception of Mediterranean Europe. However, neither were clear affinities observed between Epipalaeolithic Near Eastern groups and any other Neolithic or Mesolithic groups.
The last statement is important, because it establishes that the Natufians did not have clear associations with the first Neolithic groups. So, while they are believed to be pre-agricultural culturally they are not related to any Neolithic groups biologically.

Brace finds similarities between the ancient Neolithic culture-bearers and modern Mediterranean populations, which is no doubt accurate. On the other hand, in continental Europe, the "signal" of the Neolithic populations has been absorbed by the indigenous inhabitants. This is all fine, and agrees nicely with the picture presented sixty five years ago by Carleton Coon, whereby the invasion of Europe by gracile dolichomorphs (skeletally Mediterranean) populations was followed by a period of absorption and "re-emergence" of the Upper Paleolithic types and their mixtures with the Mediterraneans.

Indeed, the early inhabitants of Northern Europe were robust broad-faced Cro-Magnoids, unlike the gracile narrow-faced Mediterraneans which diffused through Central Europe from a proximate Southeastern European source. Brace studies Cro-Magnon to propose that:
If this analysis shows nothing else, it demonstrates that the oft-repeated European feeling that the Cro-Magnons are ‘‘us’’ (47) is more a product of anthropological folklore than the result of the metric data available from the skeletal remains.
Yes, this bizarre statement is not supported by his own data, which shows that Cro-Magnon shows that the Modern European sample is the only one to which Cro-Magnon is aligned to, however distantly:

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The retention of the "Upper Paleolithic" signal in modern Europeans is quite impressive, since Europe's colonization did not cease with Cro-Magnon in the first Upper Paleolithic.

Cro-Magnon was a coarse-featured and robust skull atypical of modern Europeans, but one may still find individuals in Europe which resemble him: Brace et al. did not test for his resemblance to individuals. Moreover, he did not test Cro-Magnon against individual European populations. For example, Jantz and Owsley concluded that:
Using raw measurements, 6 of 8 express an affinity to Norse, and with the shape variables of Darroch and Mosimann ([1985]), 5 of 8 express a similarity to Norse. Using shape variables reduces the Mahalanobis distance, substantially in some cases. Typicality probabilities (Wilson, [1981]), particularly for the shape variables, show the crania to be fairly typical of recent populations. The results presented in Table 1 are consistent with the idea that Upper Paleolithic crania are, for the most part, larger and more generalized versions of recent Europeans. Howells ([1995]) reached a similar conclusion with respect to European Mesolithic crania.

I have sent the following questions to Dr. Brace regarding his study. If and when he responds, and if I am granted permission to publish his response, I will do so in these entry:
You state that Modern Europeans are not very closely linked to
Neolithic/Bronze Age Europeans, yet in Table 3, the distance between
"Modern Europe" and "Late Prehistoric Eurasia" is 1.87 which is the
lowest among all population pairs. "Late Prehistoric Eurasia" is
defined as:

"Then Neolithic samples from Denmark, England, France, Germany, and
Portugal were combined with Bronze Age samples from England, Jericho,
and Mongolia to make a ''Late Prehistoric Eurasia'' sample."

This would seem to indicate a strong affinity between Neolithic/Bronze
Age Europeans and modern Europeans.

Moreover, you state that "the oft-repeated European feeling that the
Cro-Magnons are ''us'' (47) is more a product of anthropological
folklore than the result of the metric data available from the
skeletal remains."

But, in Table 4, Cro-Magnon I shows mixed affiliations between Modern
Europe and Late Prehistoric Eurasia. The inability to fall completely
in either Modern Europe or LP Eurasia is not surprising, since Modern
Europe and Late Prehistoric Eurasia are extremely close to each other
(Table 3). So, the data in Table 4 seem to suggest that Cro-Magnon I
did in fact resemble modern Europeans and Late Prehistoric Eurasians.

I would be very interested in hearing your comments.

Proc. Natl. Acad. Sci. USA, 10.1073/pnas.0509801102

The questionable contribution of the Neolithic and the Bronze Age to European craniofacial form

C. Loring Brace et al.

Many human craniofacial dimensions are largely of neutral adaptive significance, and an analysis of their variation can serve as an indication of the extent to which any given population is genetically related to or differs from any other. When 24 craniofacial measurements of a series of human populations are used to generate neighbor-joining dendrograms, it is no surprise that all modern European groups, ranging all of the way from Scandinavia to eastern Europe and throughout the Mediterranean to the Middle East, show that they are closely related to each other. The surprise is that the Neolithic peoples of Europe and their Bronze Age successors are not closely related to the modern inhabitants, although the prehistoric/modern ties are somewhat more apparent in southern Europe. It is a further surprise that the Epipalaeolithic Natufian of Israel from whom the Neolithic realm was assumed to arise has a clear link to Sub-Saharan Africa. Basques and Canary Islanders are clearly associated with modern Europeans. When canonical variates are plotted, neither sample ties in with Cro-Magnon as was once suggested. The data treated here support the idea that the Neolithic moved out of the Near East into the circum-Mediterranean areas and Europe by a process of demic diffusion but that subsequently the in situ residents of those areas, derived from the Late Pleistocene inhabitants, absorbed both the agricultural life way and the people who had brought it.


December 28, 2005

2005 in Review

Some memorable posts/studies from the year that is coming to an end; one per month, most recent first.
  1. Clusters Strike Back (II)
  2. mtDNA of early central European farmers
  3. The Genetic Legacy of the Manchu
  4. Stop the presses... huge papers on brain evolution in recent humans
  5. Haplogroup frequency correlations in Southeastern Europe
  6. Early Modern Humans
  7. Thomas Jefferson's patrilineal origin
  8. The mitochondrial time depth of humanity
  9. Human generation length. Male: 31-32, Autosomal: 28-30, Female: 25-28
  10. Prehistoric Basques were closer to modern Near Easterners
  11. Older dates for Omo
  12. Y-STRs in Europe

Reproductive isolates in Jerba Island

Am J Hum Biol. 2005 Dec 25;18(1):149-153 [Epub ahead of print]

Islands Inside an Island: Reproductive Isolates on Jerba Island.

Loueslati BY, Cherni L, Khodjet-Elkhil H, Ennafaa H, Pereira L, Amorim A, Ben Ayed F, Ben Ammar Elgaaied A.

Jerba Island, located in South Eastern Tunisia, is inhabited by four ethnic groups: Berbers, Arabs, sub-Saharans, and Jews. All live in distinct areas, although the Arabs are also distributed all over the island. The first Arab settlement was founded in the 7th century A.D., so co-existence with Berbers has lasted for more than a millennium. Religious and cultural differences have represented an obstacle to the intermixing of these groups, and among both Arabs and Berbers marriages usually occur between members from the same extended family. Using new mtDNA data and previously described Y-chromosome STR-defined haplotypes, we tested whether this reported inbreeding would be reflected in the differentiation between Berber and Arab communities. Concerning mtDNA, the Berber group presented a greater Eurasian contribution (87%), and, surprisingly, no U6 haplotypes were found; in contrast, the Arabs showed a larger contribution of sub-Saharan lineages (24%) and the U6 haplogroup amounted to 10%. Another source of evidence for the reproductive isolation of the two groups was revealed through the analysis of haplotype matching (both mtDNA and Y-chromosome), showing that matching probabilities between them is of the same order of magnitude of that observed when contrasting samples from different European countries.


Back mutation in mtDNA haplogroup C

Am J Hum Biol. 2005 Dec 25;18(1):59-65 [Epub ahead of print]

A revertant of the major founder Native American haplogroup C common in populations from northern South America.

Torres MM, Bravi CM, Bortolini MC, Duque C, Callegari-Jacques S, Ortiz D, Bedoya G, Groot de Restrepo H, Ruiz-Linares A.

We examined the mtDNA RFLP diversity of 17 Native American populations from Colombia. Five of the populations studied were found to have variable frequencies of a mtDNA type lacking the characteristic changes of haplogroups A-D. Sequencing of mtDNA HVS-I and II showed that this "null" RFLP type carries all the substitutions characteristic of Native American founder lineage C. A back mutation has therefore recreated the +13,259 HincII/-13,262 AluI restriction sites that tipify RFLP haplogroup C. This revertant C lineage is further characterized by three changes in HVS-II sequence: C/T transitions at positions 115 and 152, and the deletion of an A residue at position 116. This lineage is observed at high frequency mostly in populations from Greenberg's Equatorial-Tucano linguistic family. Genetic structure analyses are consistent with the reversion mutation occurring at an early stage during the tribalization process.


Y-chromosome diversity in the Solomon Islands

Am J Hum Biol. 2005 Dec 25;18(1):35-50 [Epub ahead of print]

Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands.

Cox MP, Mirazon Lahr M.

The Solomon Islands lie in the center of Island Melanesia, bordered to the north by the Bismarck Archipelago and to the south by Vanuatu. The nation's half-million inhabitants speak around 70 languages from two unrelated language groups: Austronesian, a language family widespread in the Pacific and closely related to languages spoken in Island Southeast Asia, and "East Papuan", generally defined as non-Austronesian and distantly related to the extremely diverse Papuan languages of New Guinea. Despite the archipelago's presumed role as a staging post for the settlement of Remote Oceania, genetic research on Solomon Island populations is sparse. We collected paired samples from two regions that have populations speaking Austronesian and Papuan languages, respectively. Here we present Y-chromosome data from these samples, the first from Solomon Islands. We detected five Y-chromosome lineages: M-M106, O-M175, K-M9*, K-M230, and the extremely rare clade, K1-M177. Y-chromosome lineages from Solomon Islands fall within the range of other Island Melanesian populations but display markedly lower haplogroup diversity. From a broad Indo-Pacific perspective, Y-chromosome lineages show partial association with the distribution of language groups: O-M175 is associated spatially with Austronesian-speaking areas, whereas M-M106 broadly correlates with the distribution of Papuan languages. However, no relationship between Y-chromosome lineages and language affiliation was observed on a small scale within Solomon Islands. This pattern may result from a sampling strategy that targeted small communities, where individual Y-chromosome lineages can be fixed or swept to extinction by genetic drift or favored paternal exogamy.


December 23, 2005

Y-chromosomes and mtDNA from the Balkans

An important new study on the Balkans, which includes a Greek sample from Thrace, as well as samples from Aromun (Vlach) populations.


It is unfortunate that this study did not study the distribution of deep clades of the Y-chromosomal phylogeny, e.g., in haplogroups J, I, and K*(xP). Nonetheless, the study furthers our understanding of the Y-chromosomal population of Balkan populations, by sampling populations from Albania, the FYRO Macedonia, Romania, and Northeastern Greece, including Vlach (Aromun) speakers.

The shallow depth of the typed markers did not allow the detection of structure. Most haplogroup frequencies occurred in similar frequencies with few significant differences between populations.

Aromuns appear to have a higher frequency overall of haplogroup R1b, which would definitely suggest "Roman" connections, which the authors discount on the basis of searches which they conducted in yhrd. Ultimately, their arguments are not very convincing, since yhrd only allows for exact matches, and any "Roman" contribution to the Aromuns is two thousand years old.

The inclusion of almost all E3b1-M78 chromosomes in the alpha-cluster which is typical of the Balkans was confirmed once again.

R1a1 chromosomes did not exhibit a star-like phylogeny; this may indicate heterogeneity in the origin of R1a1 chromosomes.

Also of interest is the detection of foreign elements in the Balkan population. Such elements were not found in Greeks, but were found occasionally in the form of haplogroups E1 and H in some of the others.

This study seems to agree broadly with my previous observations about the co-occurrence of haplogroups J2 and R1b in the Balkans; these two haplogroups are frequent in most populations, contrasting with most of the Slavs from the western Balkans that have low frequencies.

Annals of Human Genetics (Online Early)

Paternal and maternal lineages in the Balkans show a homogeneous landscape over linguistic barriers, except for the isolated Aromuns

E. Bosch et al.


The Balkan Peninsula is a complex cultural mosaic comprising populations speaking languages from several branches of the Indo-European family and Altaic, as well as culturally-defined minorities such as the Aromuns who speak a Romance language. The current cultural and linguistic landscape is a palimpsest in which different peoples have contributed their cultures in a historical succession. We have sought to find any evidence of genetic stratification related to those cultural layers by typing both mtDNA and Y chromosomes, in Albanians, Romanians, Macedonians, Greeks, and five Aromun populations. We have paid special attention to the Aromuns, and sought to test genetically various hypotheses on their origins.

MtDNA and Y-chromosome haplogroup frequencies in the Balkans were found to be similar to those elsewhere in Europe. MtDNA sequences and Y-chromosome STR haplotypes revealed decreased variation in some Aromun populations. Variation within Aromun populations was the primary source of genetic differentiation. Y-chromosome haplotypes tended to be shared across Aromuns, but not across non-Aromun populations. These results point to a possible common origin of the Aromuns, with drift acting to differentiate the separate Aromun communities. The homogeneity of Balkan populations prevented testing for the origin of the Aromuns, although a significant Roman contribution can be ruled out.


December 22, 2005

Positive selection in NAT2 gene

An interesting new preprint from the AJHG deals with two genes involved in acetylation. The most important finding is that an allele of the NAT2 locus has been under positive selection in Western/Central Eurasians in the last ~6,500 years. According to the researchers' provisional hypothesis:
In this context, given the geographic distribution of the slow acetylator phenotype and the estimated expansion time of the slowest-encoding 341T>C mutation (5,797-7,005 years ago in West/Central Eurasians), it is tempting to hypothesize that the emergence of agriculture in West Eurasia could be at the basis of such environmental changes. Indeed, there is accumulating evidence that this major transition resulted in a profound modification of human diets and lifestyles (Cordain et al. 2005) and consequently, in the exposure to human chemical environment (Ferguson et al. 2002). Moreover, the highest frequencies of slow acetylators are observed in the Middle East (fig. 5), one of the first regions where agriculture originated ~10,000 years ago, and these frequencies decrease towards Western Europe, North Africa and India, three regions where agriculture was subsequently diffused from the Fertile Crescent (Harris 1996).
American Journal of Human Genetics (in press)

Deciphering the ancient and complex evolutionary history of human arylamine N-acetyltransferase genes

Etienne Patin et al.

The human N-acetyltransferase genes NAT1 and NAT2 encode two phase II enzymes that metabolize various drugs and carcinogens. Functional variability at these genes has been associated with adverse drug reactions and cancer susceptibility. Mutations in NAT2 leading to the so-called "slow" acetylation phenotype reach high frequencies worldwide, questioning the significance of altered acetylation in human adaptation. To investigate the role of population history and natural selection in shaping NATs variation, we characterized genetic diversity through re-sequencing and genotyping of NAT1, NAT2 and the pseudogene NATP in a collection of 13 different populations with distinct ethnic background and demographic pasts. This combined study-design allowed us to define a detailed map of linkage disequilibrium of the NATs region as well as to perform a number of sequence-based neutrality tests and the Long Range Haplotype (LRH) test. Our data revealed distinctive patterns of variability for the two genes: the reduced diversity observed at NAT1 is consistent with the action of purifying selection while NAT2 functional variation contributes to high levels of diversity. In addition, the LRH test identified a particular NAT2 haplotype (NAT2*5B) under recent positive selection in Western/Central Eurasians. This haplotype harbors the mutation 341T>C and encodes the "slowest" acetylator NAT2 enzyme, suggesting a general selective advantage for the slow acetylator phenotype. Interestingly, the NAT2*5B haplotype, which seems to have conferred a selective advantage during the past ~6,500 years, exhibits today the strongest association with susceptibility to bladder cancer and adverse-drug reactions. On the whole, the patterns observed for NAT2 illustrate well how geographically and temporally-fluctuating xenobiotic environments may have influenced not only our genome variability but also our present-day susceptibility to disease.

Natural selection in the last 50,000 years

Gene Expression alerts me to a new paper on natural selection in Homo sapiens. Researchers have identified almost 2,000 genes which have been targeted by natural selection in modern humans of the last 50,000 years, i.e., since the emergence of behaviorally modern humanity and its spread around the world.

I will post more from the paper once it becomes "live". For the moment, from ScienceNow:
The genes belong to several biologically important categories, including genes important in defense against disease, controlling the cell cycle, protein metabolism, and nervous system functioning, the researchers report online this week in Proceedings of the National Academy of Sciences.
The New Scientist also covers this paper:
One way to look for genes that have recently been changed by natural selection is to study mutations called single-nucleotide polymorphisms (SNPs) – single-letter differences in the genetic code. The trick is to look for pairs of SNPs that occur together more often than would be expected from the chance genetic reshuffling that inevitably happens down the generations.

Such correlations are known as linkage disequilibrium, and can occur when natural selection favours a particular variant of a gene, causing the SNPs nearby to be selected as well.


Moyzis speculates that we may have similarly “domesticated” ourselves with the emergence of modern civilisation.

“One of the major things that has happened in the last 50,000 years is the development of culture,” he says. “By so radically and rapidly changing our environment through our culture, we’ve put new kinds of selection [pressures] on ourselves.”

Genes that aid protein metabolism – perhaps related to a change in diet with the dawn of agriculture – turn up unusually often in Moyzis’s list of recently selected genes. So do genes involved in resisting infections, which would be important in a species settling into more densely populated villages where diseases would spread more easily. Other selected genes include those involved in brain function, which could be important in the development of culture.
You might also want to read my older post on Human domestication reconsidered, which reports on anthropological changes which are also evidence of human domestication:
Helen Leach is proposing that the Late Pleistocene and early Holocene (archaeologically Neolithic) humans underwent changes similar to those of animals that underwent the domestication process. So, she argues that if we apply terminology consistently, we must also entertain the possibility that humans themselves are a domesticated species.


Here is the abstract and link to the open-access article. With "Darwinian" in the title and "Darwin's fingerprint" in one of the figures, I think that someone is having fun sticking it in to the creationism/ID crowd.

Proc. Natl. Acad. Sci. USA. (published online)

Global landscape of recent inferred Darwinian selection for Homo sapiens

Eric T. Wang et al.

By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The {approx}1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.

Link (open access)

Ancient balanced polymorphism preserved in Chinese ethnic minorities

Interesting preprint from AJHG which reports the discovery of a balanced polymorphism at high frequency in some Chinese ethnic minorities, at a smaller frequency in the Han, and its absence in Europeans and a limited sample of Africans. The great age of this polymorphism makes it a likely candidate for being of local East Asian origin before the emergence of anatomically modern humans.

American Journal of Human Genetics (preprint)

An ancient, balanced polymorphism in a regulatory region of human MHC is retained in Chinese minorities but lost worldwide

Xiaoyi Liu et al.


The coding regions of many MHC (HLA in human) molecules are believed to be subjected to balancing selection. But it is less certain whether the regulatory regions of such coding sequences are also subjected to the same type of selection. Here we studied the polymorphism of the regulatory regions of the HLA-DPA1 and -DPB1 genes among ethnic minorities in southwestern China. Phylogenetic analysis revealed two deep clades over 10 million years old. Linkage disequilibrium between the regulatory and coding regions of DPA1 is almost complete, hinting at coadaptive balancing selection on the entire region. Thus, the molecular mechanism of balancing selection in MHC may involve expression modulation, in addition to coding region polymorphisms. While the frequency of this polymorphism is greater than 30% in some ethnic minorities, it decreases to less than 5% among southern Han Chinese and vanishes among Europeans. As suspected, some ancient balanced polymorphisms, lost in major populations, still exist in isolated ethnicities. These isolated populations could thus contribute disproportionately to the total diversity of modern humans.

December 21, 2005

Did haplogroup J2a1 originate in Greece?

In A multistep process for the dispersal of a Y chromosomal lineage in the Mediterranean area, Patrizia Malaspina and colleagues identified "Network 1.2", a group of chromosomes identified by a deletion in the DYS413 locus:
Chromosomes grouped into network 1.2 are identified by short CA repeats (<=18) in both PCR fragments at DYS413. All chromosomes within this group can be linked to each other in a network by assuming insertion or deletion of a single CA unit in one of the fragments. By the same criterion, they could not be linked to any other chromosome in a sample of 1801 chromosomes (Malaspina et al. 2000) from Western Eurasia and North Africa.
These chromosomes all belonged to the J2-M172 clade of the Y-chromosome phylogeny, and in the latest phylogenetic revisions, they are now termed as J2a1.

Intriguingly, Malaspina et al. carried out a microsatellite diversity analysis within Network 1.2, which I have not seen repeated on a regional basis since. The results of this analysis:
The largest variances, after averaging across the four loci, are found in Continental Greece, Crete and Romania (>0.40),followed by Continental Turkey (0.36) and Italy (0.32). A super-pool consisting of all typed network 1.2 chromosomes from West Asia, except Turkey, produced the low value of 0.31. Considering that the area from which a population spread is generally characterized by a comparatively higher genetic variance than the areas colonized later (Wooding & Ward, 1997; Barbujani, 2000), these data identify the Balkans, Aegean and Anatolia as the possible homeland harbouring the largest variation within network 1.2, with decreasing values both east/south-east and west of it.
Actually, the microsatellite variance is higher in Greece 0.487, Crete 0.457, the entire Balkans (incl. Greece) 0.478, and Romania 0.4075, all of which are higher than in Anatolia.

This certainly does not seem to be the signature of colonization of the Balkans by pioneer groups of farmers from the east. Moreover, there have been numerous historical attested movements of Balkan peoples into Anatolia, incl. the Phrygians, Thracians, and Greeks. Indeed, by the time that the first Turkic speakers arrived in Anatolia, the peninsula was dominated by Greek and Armenian speakers, both of which had ultimate Balkan origins (the Armenians being Phrygian colonists with ultimate Thraco-Macedonian origins). Obviously these movements affected the genetic composition of the Anatolian population, increasing the diversity of J2a1 lineages there. Hence, the original differential between the Balkans and Anatolia may have been even higher.

However, it could be argued that mobility within the Byzantine and Ottoman Empires may have introduced J2a1 from Anatolia to the Balkans. However, this does not explain the high diversity of J2a1 in Romania and Italy which were little if at all affected by Anatolian populations.

Moreover the idea that J2a1 originated in Greece also explains the coastal distribution of J2 in the Mediterranean, observed by Di Giacomo et al.. It is well-known that Greek colonization was especially maritime.

It also explains why in the Balkans, the western Dinaric regions show little J2: Greeks had few colonies in the Adriatic, whereas colonization of present-day Bulgaria and its Black Sea coast was extensive.

Moreover, Balkan J2 belongs primarily and near-exclusively to clade J2b (old J2e), contrasting greatly with Greeks where both J2b and J2a (mainly J2a1) are present. This, again signifies the differentiation of Greek J2 from Balkan J2, with the former belonging more to the J2a clade.

Furthermore, unlike Slavs of the Balkans that have only a little J2b and almost no J2a, Ukrainians have more J2a than J2b, and more J2 altogether. Unlike the West Balkans, the Ukraine was home to both ancient and more recent Greek colonies and settlements.

The higher frequency of J2 in southern Italy and Sicily compared to northern Italy, is also explained by this theory, as these regions were colonized by Greeks, whereas northern Italy was not.

J2a is also present in Egypt which was conquered by Macedonian Greeks, as well as Iran, but drops to a small frequency in India, and is there limited to the upper castes. This may reflect its presence in the ancient Indo-Aryans and its survival in the Brahmin caste, or alternatively may be the result of intermarriage between the Bactrian Greek aristocracy and high-class Hindus. In any case, if one accepts that the Indo-Aryans of India originated from an ultimate steppe group which was an outgrowth of the Tripolye-Cucuteni culture of the Balkans, the presence of J2a1 among Brahmins ceases to be a mystery.

In all likelihood, J2a1 originated before the ethnogenesis of the Greeks, and may be associated with multiple population movements from the Greek-Balkan region. However, I believe that it makes better sense to view it as a Balkan-Greek clade than a West-Asian one.

Clusters strike back (II)

Rosenberg's 2002 study which proved that individuals could be assigned to a genetic cluster which matched exactly their race sparked a lot of debate, since it demonstrated -even though those terms were not used- that "continental geographical origin" maps directly to genetic identity.

Serre and Paabo subsequently disputed the claims of Rosenberg, by claiming that clusters become less distinct if a continuous geographical sampling scheme is chosen, as opposed to sampling from distinct populations, and also if an "uncorrelated alleles" models was used.

But, as I have explained before, the results obtained by S&P are an artefact of greatly reducing their sample size (to obtain a geographically uniform sample, as opposed to little "chunks" of individuals from different populations). Moreover, the assumption of uncorrelated alleles is no better than the assumption of linked alleles used by Rosenberg. In human populations alleles tend to co-occur, and are thus correlated to some degree.

Clusters emerge when one uses a sufficiently intelligent clustering technique, has a sufficient sample size, and a large number of informative markers. Absence of clusters does not prove absence of structure. [1]


Now, Rosenberg et al. have published a new article in PLoS Genetics with almost 1,000 loci, which systematically addresses the whole "clines vs. clusters" controversy. This is the knockout punch to the criticism of Serre and Paabo:

Other factors besides sample size and number of markers, however, may influence clustering patterns. Serre and Pääbo [10] argued that the geographic dispersion of the sample and the assumption made about whether or not allele frequencies are correlated across populations had substantial influences on genetic clustering. They suggested that individuals are less strongly placed into clusters when the sample is more geographically uniform, and when allele frequencies are assumed to be uncorrelated. Consequently, they claimed that the geographic clusters obtained by Rosenberg et al. [3] were artifacts of the sampling design and of the use of a model of correlation among allele frequencies across populations. However, much of the geographic dispersion analysis of [10] was based on two datasets with 89 and 90 individuals and 20 loci, in general too little data for clustering to be apparent [3,4,9]. The remainder of their geographic analysis, as well as the source of their comments about uncorrelated frequencies, was a comparison to the Rosenberg et al. [3] results of several analyses of 261 individuals chosen to be equally distributed across the 52 populations studied. Serre and Pääbo's analyses assumed allele frequencies to be uncorrelated across populations, whereas Rosenberg et al. had assumed that they were correlated. Thus, although a difference in results was seen between the analyses in [10] and those in [3], the attribution of this difference specifically to a difference in geographic dispersion or to a difference in assumptions about allele frequency correlations is problematic, because both of these variables differed between studies, as did the number of individuals.
In agreement with the suggestion of [10], the assumption made about allele frequency correlations is also seen to have a substantial impact. Because large allele frequency correlations exist across populations, however, the basis for the supposition by [10] that allele frequencies are uncorrelated is questionable.
Rosenberg et al. studied "clusteredness", which is 1 if individuals are assigned completely to a single cluster, and 0 if they are equally assigned to all clusters, varied:
Holding the number of clusters, sample size, and allele frequency correlation model fixed, the general trend was that clusteredness was noticeably smaller for ten and 20 loci, and was larger for 50 or more loci (Figure 3). [DP: Better clustering with more loci]


When the number of loci, sample size, and correlation model were held constant, K = 2 (that is, two clusters) generally produced smaller clusteredness than did the larger values of K (Figures 3 and 4; Table 1). For the correlated allele frequencies model, K = 5 and K = 6 tended to have higher clusteredness than did K = 3 and K = 4, whereas the reverse was true for the uncorrelated model (Figure 4). [DP: K=3 and K=4 represents human genetic structure less clearly than a model with 5 continental clusters, or 6 ones, splitting Northern from Southern Amerindians. In other words, the number of clusters or races is not arbitrary, but some numbers of K fit the data better than others]

Holding the number of loci, number of clusters, and correlation model fixed, clusteredness was generally higher for the samples of size 250 and 500 than it was for the samples of size 100 (Figures 3 and 4; Table 1). [DP: Clusters emerge more clearly, when larger sample sizes are used, because larger sample sizes enable better estimation of model parameters]
and why do such robust clustering results emerge?
Loosely speaking, it is these small discontinuous jumps in genetic distance—across oceans, the Himalayas, and the Sahara—that provide the basis for the ability of STRUCTURE to identify clusters that correspond to geographic regions.
and the obligatory (PC-mandated) statement on race, which however does not deny its existence, but claims that the existence of clusters is true, irrespective of one's definition of race:
Our evidence for clustering should not be taken as evidence of our support of any particular concept of “biological race.” In general, representations of human genetic diversity are evaluated based on their ability to facilitate further research into such topics as human evolutionary history and the identification of medically important genotypes that vary in frequency across populations. Both clines and clusters are among the constructs that meet this standard of usefulness: for example, clines of allele frequency variation have proven important for inference about the genetic history of Europe [15], and clusters have been shown to be valuable for avoidance of the false positive associations that result from population structure in genetic association studies [16]. The arguments about the existence or nonexistence of “biological races” in the absence of a specific context are largely orthogonal to the question of scientific utility, and they should not obscure the fact that, ultimately, the primary goals for studies of genetic variation in humans are to make inferences about human evolutionary history, human biology, and the genetic causes of disease.

PLoS Genetics Volume 1 | Issue 6 | DECEMBER 2005

Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure

Noah A. Rosenberg et al.

Previously, we observed that without using prior information about individual sampling locations, a clustering algorithm applied to multilocus genotypes from worldwide human populations produced genetic clusters largely coincident with major geographic regions. It has been argued, however, that the degree of clustering is diminished by use of samples with greater uniformity in geographic distribution, and that the clusters we identified were a consequence of uneven sampling along genetic clines. Expanding our earlier dataset from 377 to 993 markers, we systematically examine the influence of several study design variables—sample size, number of loci, number of clusters, assumptions about correlations in allele frequencies across populations, and the geographic dispersion of the sample—on the “clusteredness” of individuals. With all other variables held constant, geographic dispersion is seen to have comparatively little effect on the degree of clustering. Examination of the relationship between genetic and geographic distance supports a view in which the clusters arise not as an artifact of the sampling scheme, but from small discontinuous jumps in genetic distance for most population pairs on opposite sides of geographic barriers, in comparison with genetic distance for pairs on the same side. Thus, analysis of the 993-locus dataset corroborates our earlier results: if enough markers are used with a sufficiently large worldwide sample, individuals can be partitioned into genetic clusters that match major geographic subdivisions of the globe, with some individuals from intermediate geographic locations having mixed membership in the clusters that correspond to neighboring regions.


[1] For example, some researchers in physical anthropology disputed the existence of races, due to the discordance between different traits, such as the cephalic index, or facial index. W.W. Howells, convincingly proved that once you used dozens of variables you could recreate the racial groups of traditional physical anthropology. However, since the clustering method he used was a simple Euclidean-distance one, he could not assign individuals successfully to major clusters (races). Thus, he accepted the validity of individual populations, but not of geographical aggregates of populations (races).

Now that computing power is cheap, we can easily apply a sophisticated model-based approach- similar to the program structure used by geneticists- and assign individuals to their races, and even to smaller-order clusters.
[2] See also, the first Clusters strike back post about a different study which supports the validity of clusters as descriptors of human genetic variation.

December 20, 2005

The Mediterranean Face (IX)

Picking up where we left off a long time ago, another good example of the Mediterranean racial type, Greek model Evi Adam.

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Pre-Columbian syphilis in the Old World

International Journal of Osteoarchaeology (Early View)

A pre-Columbian case of congenital syphilis from Anatolia (Nicaea, 13th century AD)

Y. S. Erdal


In this study, the skeleton of an approximately 15-year-old child, dating back to the Late Byzantine period (13th century AD) is examined with the aim of determining where this specimen fits in the continuing arguments on the origins of syphilis. It was unearthed during an excavation at an amphitheatre in Nicaea dating to the Roman period. The Nicaea specimen displays common symptoms found in the majority of people with congenital syphilis such as Hutchinson's incisor, mulberry molar, darkened enamel, radial scar on frontal bone, sabre tibia, syphilitic dactylitis, and gummatous and non-gummatous osteomyelitis on almost every post-cranial bone. Because of the sub-periosteal new bone formation, the medullary spaces in some long bones are narrowed or completely obliterated. These lesions, which were observed via macroscopic and radiological examination, reflect the late stages of congenital syphilis. The specimen, when examined together with increasing numbers of other finds from the Old World, contributes to the argument that venereal syphilis did exist in the Old World before 1493, and brings forward the need to revise the Columbian hypothesis, which maintains that syphilis is a new disease carried to the Old World from the New World by Columbus' crew.


December 19, 2005

mtDNA haplogroup H and sepsis survival

mtDNA haplogroup H is very common in Caucasoids, reaching frequencies of ~50%. This certainly suggested that it may confer some advantage. It would be interesting to do a study on its frequency in several archeo-DNA samples that are now available compared to that in modern populations.

A new study in the Lancet provides the first evidence of a survival advantage for mtDNA haplogroup H. From the BBC news story:
It has long been thought that there may be a connection between the workings of the mitochondria and how the body reacts to fight infections, such as MRSA and pneumonia.

Researchers identified 10 major variants of mtDNA.

Patients from each variant group were monitored and researchers found people with a particular variant - called haplogroup H - were more than twice as likely as those from any of the other groups to survive for six months.

There was no evidence to suggest that people from haplogroup H were any less likely to contract a severe infection in the first instance.


Haplogroup H is the most recent genetic variation to evolve, but is also the most common - 40% of people have it.
The Lancet 2005; 366:2118-2121

Mitochondrial DNA and survival after sepsis: a prospective study

Simon V Baudouin et al.


Human genome evolution has been shaped by infectious disease. Although most genetic studies have focused on the immune system, recovery after sepsis is directly related to physiological reserve that is critically dependent on mitochondrial function. We investigated whether haplogroup H, the most common type of mitochondrial DNA (mtDNA) in Europe, contributes
to the subtle genetic variation in survival after sepsis.

In a prospective study, we included 150 individuals who were sequentially admitted to the intensive care unit in a hospital in Newcastle upon Tyne, UK. After clinical data were obtained, patients underwent mtDNA haplotyping by analysis with PCR and restriction fragment length polymorphism. As endpoints, we used death during the 6-month period or survival at 6 months.

Follow-up was complete for all study participants, although the haplotype of two patients could not be reliably determined. On admission to the intensive care unit, the frequency of mtDNA haplogroup H in study patients did not differ between study patients admitted with severe sepsis and 542 age-matched controls from the northeast of England. MtDNA haplogroup H was a strong independent predictor of outcome during severe sepsis, conferring a 2·12-fold (95% CI
1·02-4·43) increased chance of survival at 180 days compared with individuals without the haplogroup H.

Although haplogroup H is the most recent addition to the group of European mtDNA, paradoxically it is also the most common. Increased survival after sepsis provides one explanation for this observation. MtDNA haplotyping offers a new means of risk stratification of patients with severe infections, which suggests new avenues for therapeutic intervention.

December 18, 2005

Y-chromosome haplogroups in US populations

A new comprehensive study of US Y-chromosomal haplogroups is published in Forensic Science International. US populations, with the exception of Native Americans, are usually neglected by researchers, because they have very little to offer in the reconstruction of ancient population movements which are the focus of many papers.

For the US population as a whole:
The most common haplogroup is R-M269 (37.8%), which is found in all of the ethnic groups. This haplogroup predominates in Western European populations [23]. E-P1, the second most frequent haplogroup in the U.S. (17.7%), is the most common haplogroup in West African populations [24]. It is found at high frequencies in our AA samples, and at lower frequencies in HA samples from the Eastern U.S. (Fig. 1). Three haplogroups that originate in Northern and Western European populations include I-P30 (6.1%), the third most common haplogroup in our U.S. sample, I-P19 (2.8%) and I-P37 (1.6%). Haplogroups that likely originate in Eastern and Southern European populations are also present in our U.S. database, including R-M17 (3.4%), E-M78 (2.4%), G-P15 (2.4%), and J-M172 (1.5%). The fourth and fifth most frequent haplogroups in our database, Q-P36 (5.9%) and Q-M3 (5.8%), along with C-P39 (1.5%), are founding Native-American Y chromosomes [30]. These haplogroups are frequent in our NA and HA samples, and are found at low frequency in our AA, EA, and SA samples. Asian-derived chromosomes, primarily in haplogroups O and N, are extremely rare in all but our SA sample.

MDS plot showing some of the differences between states:

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Forensic Science International (advance access)

Population structure of Y chromosome SNP haplogroups in the United States and forensic implications for constructing Y chromosome STR databases

Michael F. Hammer et al.


A set of 61 Y chromosome single-nucleotide-polymorphisms (Y-SNPs) is typed in a sample of 2517 individuals from 38 populations to infer the geographic origins of Y chromosomes in the United States and to test for paternal admixture among African-, European-, Hispanic-, Asian-, and Native-Americans. All of the samples were previously typed with the 11 core U.S. Y chromosome short tandem repeats (Y-STRs) recommended by SWGDAM, which revealed high levels of among ethnic group variation and low levels of among-population-within-ethnic-group variation. Admixture estimates vary greatly among populations and ethnic groups. The frequencies of non-European (3.4%) and non-Asian (4.5%) Y chromosomes are generally low in European–American and Asian–American populations, respectively. The frequencies of European Y chromosomes in Native-American populations range widely (i.e., 7–89%) and follow a West to East gradient, whereas they are relatively consistent in African–American populations (26.4 ± 8.9%) from different locations. The European (77.8 ± 9.3%) and Native-American (13.7 ± 7.4%) components of the Hispanic paternal gene pool are also relatively constant among geographic regions; however, the African contribution is much higher in the Northeast (10.5 ± 6.4%) than in the Southwest (1.5 ± 0.9%) or Midwest (0%). To test for the effects of inter-ethnic admixture on the structure of Y-STR diversity in the U.S., we perform subtraction analyses in which Y chromosomes inferred to be admixed by Y-SNP analysis are removed from the database and pairwise population differentiation tests are implemented on the remaining Y-STR haplotypes. Results show that low levels of heterogeneity previously observed between pairs of Hispanic-American populations disappear when African-derived chromosomes are removed from the analysis. This is not the case for an unusual sample of European–Americans from New York City when its African-derived chromosomes are removed, or for Native-American populations when European-derived chromosomes are removed. We infer that both inter-ethnic admixture and population structure in ancestral source populations may contribute to fine scale Y-STR heterogeneity within U.S. ethnic groups.


Dazzling Indian mtDNA haplogroup M

Mmm, I don't think I've seen the word "dazzling" on a paper title yet. Of interest from the paper:
A particular case in question is the origin of haplogroup M1, which is mainly found in Northeast Africa and the Near East (Quintana-Murci et al. 1999). Due to the fact that M1 bears variant nucleotides, for example, at site 16311 in common with haplogroup M4, at 16129 with M5, and at 16249 with haplogroup M34, it has been proposed that M1 might have some affinity with Indian M haplogroups (Roychoudhury et al. 2001). This inference, however, could not receive support from our complete sequencing information. Indeed, the reconstructed ancestral motifs of all Indian M haplogroups turned out to be devoid of those variations that characterized M1, i.e., 6446, 6680, 12403, and 14110 (Maca-Meyer et al. 2001; Herrnstadt et al. 2002). Therefore, those common mutations in the control region rather reflect random parallel mutations. There is no evidence whatsoever that M1 originated in India.
It was pointed out that macrohaplogroups M, N, and R are universally distributed in Eurasia but differentiated into distinct haplogroups in East Asia, Oceania, Southeast Asia, and theAndaman Islands in particular (Macaulay et al. 2005; Thangaraj et al. 2005). This finding is further strengthened by our newly obtained Indian M data since the mutations that characterize the basal M lineages in India are virtually unique and not shared by those of East Asian, Oceanian, and Southeast 16 Asian M lineages (Ingman et al. 2000; Ingman and Gyllensten 2003; Kong et al. 2003; Tanaka et al. 2004; Friedlaender et al. 2005; Macaulay et al. 2005). This star-like and non-overlapping pattern of the mtDNA phylogeny is in good agreement with the proposed scenario that the initial dispersal of modern human into Eurasia some 60 thousand years ago was rather rapid along the Asian coastline (Macaulay et al. 2005; Thangaraj et al. 2005; Forster and Matsumura 2005).
Molecular Biology and Evolution (advance access)

The Dazzling Array of Basal Branches in the mtDNA Macrohaplogroup M from India as Inferred from Complete Genomes

Chang Sun et al.


Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in our recent analysis of Indian mtDNA macrohaplogroup N and selected 56 mtDNAs from over 1,200 samples across India for complete sequencing, with the intention to cover all Indian autochthonous M lineages. As a result, the phylogenetic status of previously identified haplogroups based on control-region and/or partial coding-region information, such as M2, M3, M4, M5, M6, M30, and M33, was solidified or redefined here. Moreover, seven novel basal M haplogroups (viz. M34-M40) were identified and yet another five singular branches of the M phylogeny were discovered in the present study. The comparison of matrilineal components among India, East Asia, Southeast Asia, and Oceania at the deepest level yielded a star-like and non-overlapping pattern, reflecting a rapid mode of modern human dispersal along the Asian coast after the initial "Out-of-Africa" event.


December 17, 2005

Sengupta et al. (2006) online

The Indian Y-chromosome paper that I blogged about earlier is available online in its final early view version, including all the supplementary materials. I have to say that the researchers give to the term "supplementary materials" a whole new meaning. Let's hope that other researchers emulate the good example of these authors.


Several items of interest:

Frequency of haplogroup J2a in several Greek populations, incl. some previously unpublished ones:

Crete: 32.1% (Di Giacomo et al. 2004)
Greece: 14.4% (Di Giacomo et al. 2004)
Greece: 11.9% (Semino et al. 2004)
Macedonia (Greece): 7.2% (Semino et al. 2004)
Nea Nikomedeia: 3.4% (Roy King, unpublished data)
Sesklo: 8.8% (Roy King, unpublished data)
Peloponnese: 14.0% (Roy King, unpublished data)
New phylogeny of haplogroup J2:

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Frequency distribution of haplogroup J2a (Crete, which has the world maximum is not shown for some reason).

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Microsatellite variance within R1a1 and R2:

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December 16, 2005

Skin color gene in humans and fish

New Science paper on allele which explains much of the difference in pigmentation between Europeans and Sub-Saharan Africans. Interestingly, Sub-Saharan Africans and East Asians both share the same ancestral allele, which means that the light pigmentation of East Asians is not caused by this gene. From an accompanying news story in the magazine:

People come in many different hues, from black to brown to white and shades in between. The chief determinant of skin color is the pigment melanin, which protects against ultraviolet rays and is found in cellular organelles called melanosomes. But the genetics behind this spectrum of skin colors have remained enigmatic. Now, on page 1782 of this week's issue of Science, an international team reports the identification of a zebrafish pigmentation gene and its human counterpart, which apparently accounts for a significant part of the difference between African and European skin tones. One variant of the gene seems to have undergone strong natural selection for lighter skin in Europeans.


The new work is raising goose bumps among skin-color researchers. "Entirely original and groundbreaking," says molecular biologist Richard Sturm of the University of Queensland in Brisbane, Australia. Anthropologist Nina Jablonski of the California Academy of Sciences in San Francisco, California, notes that the paper "provides very strong support for positive selection" of light skin in Europeans. Researchers have not been sure whether European pale skin is the result of some selective advantage or due to a relaxation of selection for dark skin, after the ancestors of modern Europeans migrated out of Africa into less sunny climes.

Yet the authors agree that the new gene, SLC24A5, is far from the whole story: Although at least 93% of Africans and East Asians share the same allele, East Asians are usually light skinned too. This means that variation in other genes, a handful of which have been previously identified, also affects skin color.


The team concludes that between 25% and 38% of the skin-color difference between Europeans and Africans can be attributed to SLC24A5 variants.
And from the actual paper paper:
The allele frequency for the Thr111 variant ranged from 98.7 to 100% among several European-American population samples, whereas the ancestral alanine allele (Ala111) had a frequency of 93 to 100% in African, Indigenous American, and East Asian population samples (fig. S6) (29, 30). The difference in allele frequencies between the European and African populations at rs1426654 ranks within the top 0.01% of SNP markers in the HapMap database (29), consistent with the possibility that this SNP has been a target of natural or sexual selection.
Science 16 December 2005:
Vol. 310. no. 5755, pp. 1782 - 1786

SLC24A5, a Putative Cation Exchanger, Affects Pigmentation in Zebrafish and Humans

Rebecca L. Lamason et al.

Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.

mtDNA of the Inuit

Am J Phys Anthropol. 2005 Dec 13; [Epub ahead of print]

mtDNA variation in Inuit populations of Greenland and Canada: Migration history and population structure.

Helgason A, Palsson G, Pedersen HS, Angulalik E, Gunnarsdottir ED, Yngvadottir B, Stefansson K.

We examined 395 mtDNA control-region sequences from Greenlandic Inuit and Canadian Kitikmeot Inuit with the aim of shedding light on the migration history that underlies the present geographic patterns of genetic variation at this locus in the Arctic. In line with previous studies, we found that Inuit populations carry only sequences belonging to haplotype clusters A2 and D3. However, a comparison of Arctic populations from Siberia, Canada, and Greenland revealed considerable differences in the frequencies of these haplotypes. Moreover, large sample sizes and regional information about birthplaces of maternal grandmothers permitted the detection of notable differences in the distribution of haplotypes among subpopulations within Greenland. Our results cast doubt on the prevailing hypothesis that contemporary Inuit trace their all of their ancestry to so-called Thule groups that expanded from Alaska about 800-1,000 years ago. In particular, discrepancies in mutational divergence between the Inuit populations and their putative source mtDNA pool in Siberia/Alaska for the two predominant haplotype clusters, A2a and A2b, are more consistent with the possibility that expanding Thule groups encountered and interbred with existing Dorset populations in Canada and Greenland.


December 14, 2005

Teeth before and after the advent of agriculture

American Journal of Physical Anthropology (Early View)

Tooth wear and dental pathology at the advent of agriculture: New evidence from the Levant

Vered Eshed, Avi Gopher , Israel Hershkovitz


Differences in patterns of diet and subsistence through the analysis of dental pathology and tooth wear were studied in skeletal populations of Natufian hunter-gatherers (10,500-8300 BC) and Neolithic populations (8300-5500 BC, noncalibrated) from the southern Levant. 1,160 Natufians and 804 Neolithic teeth were examined for rate of attrition, caries, antemortem tooth loss, calculus, periapical lesions, and periodontal processes. While the Natufian people manifest a higher rate of dental attrition and periodontal disease (36.4% vs. 19%), Neolithic people show a higher rate of calculus. Both populations manifested low and similar rates of caries (6.4% in the Natufian vs. 6.7% in the Neolithic), periapical lesions (not over 1.5%), and antemortem tooth loss (3.7% vs. 4.5%, respectively). Molar wear pattern in the Neolithic is different than in the Natufian. The current study shows that the dental picture obtained from the two populations is multifactorial in nature, and not exclusively of dietary origin, i.e., the higher rate and unique pattern of attrition seen in the Natufian could result from a greater consumption of fibrous plants, the use of pestles and mortars (which introduce large quantities of stone-dust to the food), and/or the use of teeth as a third hand. The two major conclusions of this study are: 1) The transition from hunting and gathering to a food-producing economy in the Levant did not promote changes in dental health, as previously believed. This generally indicates that the Natufians and Neolithic people of the Levant may have differed in their ecosystem management (i.e., gathering vs. growing grains), but not in the type of food consumed. 2) Changes in food-preparation techniques and nondietary usage of the teeth explain much of the variation in tooth condition in populations before and after the agricultural revolution.


The Americas before the Mongoloids: the Paleoindians of Brazil

Proc. Natl. Acad. Sci. USA (Early view)

Cranial morphology of early Americans from Lagoa Santa, Brazil: Implications for the settlement of the New World

Walter A. Neves and Mark Hubbe

Comparative morphological studies of the earliest human skeletons of the New World have shown that, whereas late prehistoric, recent, and present Native Americans tend to exhibit a cranial morphology similar to late and modern Northern Asians (short and wide neurocrania; high, orthognatic and broad faces; and relatively high and narrow orbits and noses), the earliest South Americans tend to be more similar to present Australians, Melanesians, and Sub-Saharan Africans (narrow and long neurocrania; prognatic, low faces; and relatively low and broad orbits and noses). However, most of the previous studies of early American human remains were based on small cranial samples. Herein we compare the largest sample of early American skulls ever studied (81 skulls of the Lagoa Santa region) with worldwide data sets representing global morphological variation in humans, through three different multivariate analyses. The results obtained from all multivariate analyses confirm a close morphological affinity between South-American Paleoindians and extant Australo-Melanesians groups, supporting the hypothesis that two distinct biological populations could have colonized the New World in the Pleistocene/Holocene transition.


Asian domesticated species in the Americas

Proc. Natl. Acad. Sci. USA (Early view)

An Asian origin for a 10,000-year-old domesticated plant in the Americas

David L. Erickson et al.

New genetic and archaeological approaches have substantially improved our understanding of the transition to agriculture, a major turning point in human history that began 10,000-5,000 years ago with the independent domestication of plants and animals in eight world regions. In the Americas, however, understanding the initial domestication of New World species has long been complicated by the early presence of an African enigma, the bottle gourd (Lagenaria siceraria). Indigenous to Africa, it reached East Asia by 9,000-8,000 before present (B.P.) and had a broad New World distribution by 8,000 B.P. Here we integrate genetic and archaeological approaches to address a set of long-standing core questions regarding the introduction of the bottle gourd into the Americas. Did it reach the New World directly from Africa or through Asia? Was it transported by humans or ocean currents? Was it wild or domesticated upon arrival? Fruit rind thickness values and accelerator mass spectrometer radiocarbon dating of archaeological specimens indicate that the bottle gourd was present in the Americas as a domesticated plant by 10,000 B.P., placing it among the earliest domesticates in the New World. Ancient DNA sequence analysis of archaeological bottle gourd specimens and comparison with modern Asian and African landraces identify Asia as the source of its introduction. We suggest that the bottle gourd and the dog, two "utility" species, were domesticated long before any food crops or livestock species, and that both were brought to the Americas by Paleoindian populations as they colonized the New World.


December 13, 2005

Y chromosomes of Norway

This should be of interest to Norwegians and those suspecting "Viking" ancestry.

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From the paper:
Haplogroup frequency distributions in the different Norwegian regions are presented (Fig. 1). The frequency of P*(xR1a) varied from 26% in the east to 45% in the south, BR*(xDE, J, N3, P) from 30% in the west to 42% in the south and R1a from 13% in the south to 32% in the middle. N3 was most frequent in the north (11%; 18.6% in the northernmost county Finnmark) and totally absent in the south. Haplogroup DE and J were rare in all regions. We observe a relatively high frequency of P*(xR1a) and R1a in the population sample from south-west and east, respectively.

Frequency of haplotypes:
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Uralic admixture in the non-Saami Norwegian population:
Haplogroup N3 has been interpreted as a signature of Uralic Finno-Ugric speaking males migrating to northern Scandinavia about 4000–5000 years ago [9], [17], [35] and [60]. In the present study, N3 is observed at 4% in the overall population and at 11% in the northern region corresponding to 150,000 and 50,000 inhabitants, respectively. These numbers exceed the total number of Saami inhabitants, which is officially recognized as about 50,000 ( In northern Norway, the N3 percentage is 18.6% in Finnmark, 8.6% in Troms and 8.4% in Nordland (which are the three northernmost counties—Nordland being located to the south of the other two (Supplementary Data Online, Fig. 2)). There is thus a considerable pool of Saami and/or Finnish Y-chromosomes in the Norwegian population and particularly in the north.

Also of interest is the discovery of a new haplogroup:
A new haplogroup, not described earlier, was found in a single sample. Deduced from its biallelic type, it might represent a new 12f2 deletion within haplogroup P*(xR1a). The haplogroup it defines has been given the temporary name P*(xR1a)/12f2c (M. Jobling personal communication). Its haplotype composition is 15-10-17-24-10-13-14-11,14-12. There are already two known 12f2 deletions within hgJ and hgD2.

Forensic Sci Int. 2005 Dec 6; [Epub ahead of print] Links

Geographical heterogeneity of Y-chromosomal lineages in Norway.

Dupuy BM, Stenersen M, Lu TT, Olaisen B.

Y-chromosomal variation at five biallelic markers (Tat, YAP, 12f2, SRY(10831) and 92R7) and nine multiallelic short tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II and DYS388) in a Norwegian population sample are presented. The material consists of 1766 unrelated males of Norwegian origin. The geographical distribution of the population sample reflects fairly well the population distribution around the year 1942, which is the median birth year of the index persons. Seven hundred and twenty-one different Y-STR haplotypes but 726 different lineages (Y-STRs plus biallelic markers) were encountered. We observed six known (P*(xR1a), BR(xDE, J, N3, P), R1a, N3, DE, J), and one previously undescribed haplogroup (probably a subgroup within haplogroup P*(xR1a)). Four of the haplogroups (P*(xR1a), BR(xDE, J, N3, P), R1a and N3) represented about 98% of the population sample. The analysis of population pairwise differences indicates that the Norwegian Y-chromosome distribution most closely resembles those observed in Iceland, Germany, the Netherlands and Denmark. Within Norway, geographical substructuring was observed between regions and counties. The substructuring reflects to some extent the European Y-chromosome gradients, with higher frequency of P*(xR1a) in the south-west and of R1a in the east. Heterogeneity in major founder groups, geographical isolation, severe epidemics, historical trading links and population movements may have led to population stratification and have most probably contributed to the observed regional differences in distribution of haplotypes within two of the major haplogroups.


DNA from pre-Columbian mummy

The mummy belonged in mtDNA haplogroup B.

Am J Phys Anthropol. 2005 Dec 9; [Epub ahead of print]

Molecular characterization of a pre-Columbian mummy and in situ coprolite.

Luciani S, Fornaciari G, Rickards O, Labarga CM, Rollo F.

The history of Homo sapiens dispersal around the world and inherent interpopulation contacts and conflicts has given rise to several transitions in his relationships with the natural world, with the final result of changes in the patterns of infectious disease (McMichael [2001] Ecosystem Health 7:107-115). Of particular interest, in this context, is the contact between Amerindians and Europeans that started at the end of the 15th century, and the resulting exchange of microbes. We successfully recovered ancient DNA from a pre-Columbian mummy from Cuzco (Peru), radiocarbon-dated to 980-1170 AD, for which consistent mtDNA amplifications and sequences were obtained. The analysis of mtDNA revealed that the mummy's haplogroup was characteristic of Native American populations. We also investigated a sample of feces directly isolated from the intestines of the mummy, using a polymerase chain reaction system designed to detect the broadest spectrum of bacterial DNAs. The analysis of results, following a criterion of "paleoecological consistency" (Rollo and Marota [1998] Philos. Trans. R. Soc. Lond. [Biol.] 354: 111-119), demonstrated that some vestiges of the original microbial flora of the feces were preserved. In particular, we were able to identify the DNA of Haemophylus parainfluenzae, thus suggesting that this recently recognized pathogen was present in precontact Native Americans.


December 10, 2005

Y-DNA testing comparison chart

The International Society of Genetic Genealogy (ISOGG) has posted a very useful chart comparing several Y-chromosome testing options on the market. This will be useful to anyone starting out to uncover the secrets of their patrilineal ancestor.

The Irish Modal Haplotype

A new paper reports a 17-microsatellite haplotype (14-12-25-11-14-13-9-11-12-15-12-12-13-16-11-10-11 defined over: DYS19, DYS388, DYS390, DYS391, DYS392, DYS393, DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, DYS389I, DYS389B (calculated by subtracting the DYS389I repeat score from that of DYS389II), DYS460, DYS461, and DYS462) which occurs at a frequency of 8.2% in Ireland, 16.9% in NW Ireland, and is significantly associated with surnames descended from a medieval Irish dynasty.

Am. J. Hum. Genet. (online early)

A Y-Chromosome Signature of Hegemony in Gaelic Ireland

Laoise T. Moore et al.

Seventeen-marker simple tandem repeat genetic analysis of Irish Y chromosomes reveals a previously unnoted modal haplotype that peaks in frequency in the northwestern part of the island. It shows a significant association with surnames purported to have descended from the most important and enduring dynasty of early medieval Ireland, the Uí Néill. This suggests that such phylogenetic predominance is a biological record of past hegemony and supports the veracity of semimythological early genealogies. The fact that about one in five males sampled in northwestern Ireland is likely a patrilineal descendent of a single early medieval ancestor is a powerful illustration of the potential link between prolificacy and power and of how Y-chromosome phylogeography can be influenced by social selection.


December 07, 2005

Ancient Egyptian dental pattern

Ancient Egyptians had simple, mass-reduced teeth. This contrasts with the dental pattern of Sub-Saharan Africans who had (Irish, 2000) massive complex teeth:
Dentitions of Late Pleistocene Jebel Sahaba Nubians have extremely high frequencies of complex, mass-additive (and other) traits, including UI1 labial curvature, UI1 shoveling, Bushman Canine, UC distal accessory ridge, midline diastema, sixcusped LM1, LM2 Y-5, and LP1 Tome’s root. Furthermore, they exhibit low frequencies of typical North African features. This trait combination is ubiquitous in sub-Saharan Africans (Irish & Turner, 1990; Irish, 1993, 1997, 1998a,b, for details).
From the new article:
However, all 15 samples exhibit morphologically simple, mass reduced dentitions that are similar to those in populations from greater North Africa (Irish, 1993, 1998a–c, 2000) and, to a lesser extent, western Asia and Europe (Turner, 1985a; Turner and Markowitz, 1990; Roler, 1992; Lipschultz, 1996; Irish, 1998a). Similar craniofacial measurements among samples from these regions were reported as well (Brace et al., 1993).

And from Hanihara et al. a different study which shows the same Caucasoid affiliations of the Egyptian dental pattern. Thanks to the reader who pointed this out.

Free Image Hosting at

Am J Phys Anthropol. 2005 Dec 5; [Epub ahead of print]

Who were the ancient Egyptians? Dental affinities among Neolithic through postdynastic peoples.

Irish JD.

Qualitative and quantitative methods are employed to describe and compare up to 36 dental morphological variants in 15 Neolithic through Roman-period Egyptian samples. Trait frequencies are determined, and phenetic affinities are calculated using the mean measure of divergence and Mahalanobis D(2) statistics for discrete traits; the most important traits in generating this intersample variation are identified with correspondence analysis. Assuming that the samples are representative of the populations from which they derive, and that phenetic similarity provides an estimate of genetic relatedness, these affinities are suggestive of overall population continuity. That is, other than a few outliers exhibiting extreme frequencies of nine influential traits, the dental samples appear to be largely homogenous and can be characterized as having morphologically simple, mass-reduced teeth. These findings are contrasted with those resulting from previous skeletal and other studies, and are used to appraise the viability of five Egyptian peopling scenarios. Specifically, affinities among the 15 time-successive samples suggest that: 1) there may be a connection between Neolithic and subsequent predynastic Egyptians, 2) predynastic Badarian and Naqada peoples may be closely related, 3) the dynastic period is likely an indigenous continuation of the Naqada culture, 4) there is support for overall biological uniformity through the dynastic period, and 5) this uniformity may continue into postdynastic times.


JC virus genotype and modern human origins

This paper provides yet more evidence for my observation about the ancient split of humanity between Paleoafricans (having Af1 genotype and found in western/central Africa) and Afrasians (having Af2 genotype and found throughout Africa and Eurasia). The situation is similar in mtDNA, with Afrasians belonging exclusively to the L3 clade, and in Y chromosomes where they belong exclusively to the CR-M168 clade.

In other words, the Out-of-Africa population was not part of a single panmictic African population, but of a specific east African population (Afrasians) which dispersed both into Eurasia and into the rest of the African continent. In Eurasia, the Afrasians encountered Neandertals and other older humans, replacing them almost completely with little (and contested) intermixture. In Africa, which is the cradle of mankind, the Afrasians met with older populations of archaic sapiens (Paleoafricans) leading to a dual (Afrasian+Paleoafrican) structure of most Sub-Saharan populations which is not seen outside the African continent.

The new contribution of this particular paper is that the "Afrasian" Af2 clade is also split into a major clade encompassing most genotypes, and a minor one which represents an early movement of humans into southern Africa.

Am J Phys Anthropol. 2005 Dec 5; [Epub ahead of print]

Phylogenetic analysis of major African genotype (Af2) of JC virus: Implications for origin and dispersals of modern Africans.

Takasaka T, Kitamura T, Sugimoto C, Guo J, Zheng HY, Yogo Y.

Both mtDNA and the Y chromosome have been used to investigate how modern humans dispersed within and out of Africa. This issue can also be studied using the JC virus (JCV) genotype, a novel marker with which to trace human migrations. Africa is mainly occupied by two genotypes of JCV, designated Af1 and Af2. Af1 is localized to central/western Africa, while Af2 is spread throughout Africa and in neighboring areas of Asia and Europe. It was recently suggested that Af1 represents the ancestral type of JCV, which agrees with the African origin of modern humans. To better understand the origin of modern Africans, we examined the phylogenetic relationships among Af2 isolates worldwide. A neighbor-joining phylogenetic tree was constructed based on the complete JCV DNA sequences of 51 Af2 isolates from Africa and neighboring areas. According to the resultant tree, Af2 isolates diverged into two major clusters, designated Af2-a and -b, with high bootstrap probabilities. Af2-a contained isolates mainly from South Africa, while Af2-b contained those from the other parts of Africa and neighboring regions of Asia and Europe. These findings suggest that Af2-carrying Africans diverged into two groups, one carrying Af2-a and the other carrying Af2-b; and that the former moved to southern Africa, while the latter dispersed throughout Africa and to neighboring regions of Asia and Europe. The present findings are discussed with reference to relevant findings in genetic and linguistic studies.