Ancient Greek theater discovered

Ancient Greek Theater Discovered

Feb. 16, 2007 — Sections of an ancient Greek theater were discovered on Thursday during construction work in an Athens suburb, archaeologists said.

Until now, only two such buildings were known in the ancient city where western theater originated more than 2,500 years ago.

Fifteen rows of concentric stone seats have been located so far in the northwestern suburb of Menidi, according to Vivi Vassilopoulou, Greece's general director of antiquities.

"Another section appears to lie under a nearby road," she told The Associated Press.

"(The remains) were discovered during excavation work, supervised by archaeologists, for a new building," Vassilopoulou said. "But it is still very early to offer any conclusions."

The structure has not yet been dated, and further details are expected to emerge following a full excavation.

Menidi is thought to be built over the ancient village of Acharnae, the largest of a string of rural settlements outside ancient Athens. Ancient writers mention a theater at Acharnae, but no traces of it had been found until now.

The village was linked with Dionysos, the ancient god of theater and wine, as the Athenians believed that ivy — his sacred plant — first grew there.

Built in semicircular tiers on hillsides, ancient theaters were monumental, open-air structures that could seat thousands of spectators.

Theater first emerged as an art form in late 6th century B.C. Athens, where ancient playwrights competed for a prize during the annual festival of Dionysos — in whose cult the art originated.

The works of Sophocles, Aeschylus, Euripides and Aristophanes were performed in the theater of Dionysos under the Acropolis.

Originally a terrace where spectators sat on the bare earth above a circular stage, it was rebuilt in stone during the 4th century B.C. and could sit up to 14,000 people.

Another smaller theater has been discovered in southern Athens.

Sub-Saharan African mtDNA admixture in several West Eurasian (Caucasoid) populations

The recent article on Etruscan mtDNA contains a useful overview table of mtDNA haplogroups in several West Eurasian (Caucasoid) populations, collected from both this study as well as the literature. Extracted from this table is the following table of mtDNA L (Sub-Saharan African) sequences in the listed populations. Scroll down because blogger added a lot of vertical space above the table.

POPULATION	Sample Size	% L sequences
Palestinians	117	13.68
Jordan	494	12.55
Portugal-South	203	10.84
Iraq	116	9.48
Syria	328	9.15
Portugal-Center	203	6.4
Spain-North-West	216	3.7
Portugal-North	188	3.19
Latium	138	2.9
Non-Europeans	4739	2.85
Lebanon	176	2.84
Volterra	114	2.63
Kurds	82	2.44
Sicily	105	1.9
Turks	340	1.76
Andalusia	114	1.75
Spain-North-East	179	1.68
Casentino	122	1.64
Murlo	86	1.16
Crete	202	0.99
Marche	813	0.98
Tuscans	322	0.93
Finland	121	0.83
Europe (w/o Tuscans)	10589	0.79
Bulgaria	141	0.71
Bosnia	144	0.69
Spain-Center	148	0.68
Basque	156	0.64
England	335	0.6
Sardinia	370	0.54
Switzerland	228	0.44
Campania	313	0.32
France	332	0.3
Germany	335	0.3
Iran	436	0.23
Poland	542	0.18
Caucasus-North-West	1179	0.17
Apulia-Calabria	226	0
Armenia	191	0
Austria	99	0
Azerbaijan	48	0
Bavaria	249	0
Caucasus-North-East	820	0
Czech-Republic	83	0
Estonia	558	0
Georgia	412	0
Greece	155	0
Ireland	300	0
Latvia	299	0
Lemnos	60	0
Lombardy	177	0
Norway	556	0
Piedmont	169	0
Rhodes	42	0
Romania	94	0
Russia	397	0
Scotland	1199	0
Slovakia	129	0
Slovenia	104	0
Sweden-Denmark	75	0
Wales	92	0

An overview of child well-being in rich countries

The full report is here.

Rosenberg et al. on Indian population structure

A reader alerted me to a new paper by Noah Rosenberg et al. which studied the genomic ancestry of Indian populations. The paper is in PLoS Genetics, and is thus free to read. I just reproduce the results of the STRUCTURE analysis for ease of reference.


Of particular interest is the fact that Indian populations have little influence by the pink (main Mongoloid) cluster. As I have stated before on numerous occasions, whatever similarity between Indians and East Asians is due to ancient common ancestry (evidenced e.g., in their common possession of mtDNA macrohaplogroup M), rather than any significant "East Asian" ancestry. From the paper:

We found that allele frequencies in India showed detectably greater similarity to populations in Europe and the Middle East than to those in East Asia (Figure 4). This result is consistent with the fact that the cluster corresponding to India in Figure 2A subdivides a previously obtained cluster corresponding to Europe, the Middle East, and Central/South Asia [19].

The genetic homogeneity of Indians may be resolved with more markers:

This observation, together with the reasonably strong support in the neighbor-joining tree for particular groupings within India, suggests that a detectable amount of population structure does exist in the Indian data and that the addition of more loci might cause clusters corresponding to specific subsets of the Indian sample to become distinguishable. It is noteworthy, however, that in previous analyses of other geographic regions [19,28] using smaller numbers of markers, subclusters have been more easily identifiable elsewhere than was seen here for India with 1,200 markers.

PLoS Genetics

Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India

Noah A. Rosenberg et al.

Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population.

Link

Ancient Basque DNA

This is quite exciting, since it appears to be the first large-scale study of ancient Y chromosomes in the literature that I am aware of, with 33 male individuals studied, in addition to the mtDNA work. Here are the Y chromosome haplogroup assignments.



Current Anthropology Volume 48, Number 1

Influences of the European Kingdoms of Late Antiquity on the Basque Country
An Ancient-DNA Study

A. Alzualde

The Aldaieta cemetery (6th–7th century AD, Basque Country) provides an excellent opportunity for analysing the relationships between biology and culture. Culturally it presents material features whose origins lie in the Northern Pyrenean Frankish kingdom, while genetically it reveals greater affinity to the present-day populations of the northern Iberian Peninsula. This raises the question of the degree of influence exerted by the large European kingdoms that emerged after the fall of the Roman Empire over the populations located on the fringes of their expansion. An analysis of the genetic constitution, both patrilineal (Y-chromosome) and matrilineal (mitochondrial DNA), of the individuals buried in the cemetery, together with demographic and cultural data, points to a stratified or hierarchical society in which certain lineages were linked to family groups of higher social and/or economic status. This higher status, which seems to have been transmitted through family members, may have been attained by individuals who were involved in military activities with the Frankish army. It may be suggested that the major European kingdoms of Late Antiquity had not only a cultural influence but also some influence on the biosocial behaviour of the populations located on their peripheries.

Link

Asian Origins of Etruscan cattle

From the New Scientist:

The team found that almost 60% of the mitochondrial DNA in cows in the central Tuscan region of the country - where the Etruscan civilisation is thought to have arisen - was the same as that in cows from Anatolia and the Middle East. There was little or no genetic convergence between cows from the north and south of Italy and those from Turkey and the Middle East, the researchers say.

Proceedings of the Royal Society B: Biological Sciences (online early)

The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA

Marco Pellecchia et al.

The Etruscan culture developed in Central Italy (Etruria) in the first millennium BC and for centuries dominated part of the Italian Peninsula, including Rome. The history of the Etruscans is at the roots of Mediterranean culture and civilization, but their origin is still debated: local or Eastern provenance? To shed light on this mystery, bovine and human mitochondrial DNAs (mtDNAs) have been investigated, based on the well-recognized strict legacy which links human and livestock populations.

In the region corresponding to ancient Etruria (Tuscany, Central Italy), several Bos taurus breeds have been reared since historical times. These breeds have a strikingly high level of mtDNA variation, which is found neither in the rest of Italy nor in Europe. The Tuscan bovines are genetically closer to Near Eastern than to European gene pools and this Eastern genetic signature is paralleled in modern human populations from Tuscany, which are genetically close to Anatolian and Middle Eastern ones.

The evidence collected corroborates the hypothesis of a common past migration: both humans and cattle reached Etruria from the Eastern Mediterranean area by sea. Hence, the Eastern origin of Etruscans, first claimed by the classic historians Herodotus and Thucydides, receives strong independent support. As the Latin philosopher Seneca wrote: Asia Etruscos sibi vindicat (Asia claims the Etruscans back).

Link

Mismatch: Why Our World No Longer Fits Our Bodies

A new book which proposes that human health and lifespan will deteriorate because our bodies are no longer adapted in the increasingly foreign environment in which we find ourselves. I think that there is a three-way race between evolution, cultural change, and medical science. We may very well have sub-optimal genes for our modern environments, and evolution may not be able to catch up with the rates of cultural change, but medical science -by default- allows human beings to counterbalance our natural shortcomings. Until today, it has seemed to won the race, as increasing human lifespans indicate, but perhaps not into the future.

Here is a Guardian article on the book. An excerpt from the publisher:

We have built a world that no longer fits our bodies. Our genes - selected through our evolution - and the many processes by which our development is tuned within the womb, limit our capacity to adapt to the modern urban lifestyle. There is a mismatch. We are seeing the impact of this mismatch in the explosion of diabetes, heart disease and obesity. But it also has consequences in earlier puberty and old age.

Bringing together the latest scientific research in evolutionary biology, development, medicine, anthropology and ecology, Peter Gluckman and Mark Hanson, both leading medical scientists, argue that many of our problems as modern-day humans can be understood in terms of this fundamental and growing mismatch. It is an insight that we ignore at our peril.

African origin of Helicobacter pylori

Nature (advance online publication)

An African origin for the intimate association between humans and Helicobacter pylori

Bodo Linz et al.

Infection of the stomach by Helicobacter pylori is ubiquitous among humans. However, although H. pylori strains from different geographic areas are associated with clear phylogeographic differentiation1, 2, 3, 4, the age of an association between these bacteria with humans remains highly controversial5, 6. Here we show, using sequences from a large data set of bacterial strains that, as in humans, genetic diversity in H. pylori decreases with geographic distance from east Africa, the cradle of modern humans. We also observe similar clines of genetic isolation by distance (IBD) for both H. pylori and its human host at a worldwide scale. Like humans, simulations indicate that H. pylori seems to have spread from east Africa around 58,000 yr ago. Even at more restricted geographic scales, where IBD tends to become blurred, principal component clines in H. pylori from Europe strongly resemble the classical clines for Europeans described by Cavalli-Sforza and colleagues7. Taken together, our results establish that anatomically modern humans were already infected by H. pylori before their migrations from Africa and demonstrate that H. pylori has remained intimately associated with their human host populations ever since.

Link

European population stratification based on 10,000 markers

This is a very important preprint from the AJHG. The following statement from the paper confirms my previous observations:

Furthermore, PC3 and PC4, respectively, emphasize the separation of the Basques and Finns from other Europeans (Figure 5). The Basques are known to have unusual allele frequencies for several marker systems24 and speak a unique non-Indo-European language. In line with their non-Indo-European Uralic language and previous Y-chromosome work,25 the Finns show evidence of an increased affinity to the Central Asian populations when placed in an inter-continental context (Figure 1A and 1B).

For the Asiatic origins of the main Finnish Y-chromosome haplogroup N, mentioned in the paragraph, see here.

The results of the STRUCTURE analysis are fairly informative:


Note that for K=2, the main separation is between Sub-Saharans and the rest. Observe also that the east African Burunge -unlike the Mende- exhibit participation in the Eurasian cluster. As I have argued before, east Africa is a transitional zone between Sub-Saharan Africa and Eurasia.

For K=3 the Negroids are separated from the Caucasoids, and the blue cluster encompasses Mongoloids, Brahmins, and the Indian Mala caste. This is again expected, since Mongoloids (from the Altai) and South Asians share deep ancestry, evidenced e.g., by the mtDNA superhaplogroup M. Note also that Finns participate in this Asian cluster.

For K=4 the distinction between Mongoloids and South Asians becomes apparent. The Finns are now aligned partly with the Altaians, a relationship which persists for higher K.

For K=6 an interesting cluster encompassing mainly populations from the Mediterranean (plus Armenians) emerges.

As for the Greeks, they exhibit no substantial participation in the non-Caucasoid clusters. Note however, small Sub-Saharan contributions in the North African, Middle Eastern populations, in accordance with the previous evidence for elevated Sub-Saharan mtDNA in Arabic speaking populations.

Also from the paper:

Within the two broad Northern (Polish, Irish, English, Germans and some Italians) and Southeastern (Greeks, Armenians, Jews and some Italians) clusters further reliable structure is less obvious as individuals from different population samples are often interspersed with each other. Thus in some cases, geographic distance or physical barriers are not well reflected. For instance, despite their insular origin, Irish and English individuals cluster with the continental Germans and Poles. Similarly large geographical gaps, such as between Greece and Armenia, are much less obvious at the genetic level. Conversely, Italy appears to be a zone of sharp
differentiation over small distances. Some Italians cluster with the Northern Europeans while others fall into the Southeastern grouping (Figure 2A).

The similarity between Greece and Armenia is interesting in light of the historical evidence of the Balkan origins of the Phrygo-Armenians that I have blogged about before. The differentiation of Italians is probably due both to the Hellenic-Anatolian origins of some Italians from antiquity, as well as the Northern European origins of others, especially since the fall of the Western Roman Empire.

Update (Feb 9). It escaped my notice that a light blue cluster centered on the Burunge emerges at K=5. This element in their ancestry, differentiating them from the Mende seems to be specific to them among studied populations, and is assigned to the yellow (Caucasoid) cluster for lower K. This confirms my suggestions for an indigenous (non-Negroid) east African element which is related to the Caucasoids.

American Journal of Human Genetics (in press)

Measuring European Population Stratification using Microarray Genotype Data

Marc Bauchet et al.

A proper understanding of population genetic stratification—differences in individual ancestry within a population—is crucial in attempts to find genes for complex traits through association mapping. We report on genome-wide typing of ca. 10,000 single nucleotide polymorphisms (SNPs) in 297 individuals to explore population structure in Europeans of known and unknown ancestry. The results reveal the presence of several significant axes of stratification, most
prominently in a North-Southeastern trend, but also along an East-West axis. We also demonstrate the selection and application of EuroAIMs (European Ancestry Informative Markers) for ancestry estimation and correction. The Coriell “Caucasian” and CEPH Utah sample panels, often used as proxies for European populations, are found to reflect different subsets of the continent’s ancestry.

Link

Mexican American admixture mapping

American Journal of Human Genetics (in press)

A Genome-Wide SNP panel for Mexican American Admixture Mapping

Chao Tian et al.

For admixture mapping studies in Mexican Americans (MAM) we define a genome-wide SNP panel that can distinguish between chromosomal segments of Amerindian (AMI) or European (EUR) ancestry. These studies used genotypes for > 400K SNPs defined in EUR and both Pima and Mayan AMI to define a set of ancestry informative markers (AIMs). The use of two AMI populations was necessary to remove a subset of SNPs that distinguished genotypes of only one AMI subgroup from EUR genotypes. The AIMs set contained 8144 SNPs separated by a minimum of 50 kb with only three intermarker intervals >1 Mb and had EUR/AMI Fst values > 0.30 (mean Fst = 0.48), and Mayan/Pima Fst values < 0.05 (mean Fst < 0.01). Analysis of a subset of these SNP AIMs suggested that this panel may also distinguish ancestry between EUR and other disparate AMI groups including Quechuan from South America. We show, using realistic simulation parameters which are based on our analyses of MAM genotyping results, that this panel of SNP AIMs provides good power for detecting disease-associated chromosomal segments for genes with modest ethnicity risk ratios. A reduced set of 5287 SNP AIMs captured almost the same admixture mapping information but smaller SNP sets show substantial drop-off in admixture mapping information and power. The results will enable studies of type 2 diabetes, rheumatoid arthritis and other diseases where epidemiological studies suggest differences in the distribution of ancestry associated susceptibility.

Link

British pagans demand prehistoric human remains for reburial

Let's hope that scientists and politicians around the world stand firm against this kind of muddle-headedness.

Give us back our bones, pagans tell museums

British pagan groups are increasingly asking for human remains and grave goods from pre-Christian burials to be returned to them as well. The presence of what they see as their ancestors in dusty drawers or under harsh display lights is an affront to their religion. To them, the bones are living beings, whose existence is bound up with their religious descendants and the sacred land.

...

Other pagans are less impressed with what science has to offer. "Any story that is reconstructed from that data will be an imagined past, which usually turns out to be a blueprint of the present imposed upon the past," said Mr Davies. The druid council is not against studying human remains per se, he said, but does object to their retention in museums. "They are not samples, they are bits of body, they are bits of people, bits of spirit."

...

His view is far from universal. Some in the museum community say it is unfair for scientists to impose their world view on pagans. "We think that there is actually an intellectual argument for pagan claims to be taken seriously," said Prof Bienkowski, "It is a different world view which, actually, like the scientific world view can be neither proved nor disproved. It is actually our responsibility to take those views into account." What right, he asks, do scientists have to speak for the bones either?

Clinal Y chromosome variation in Italy

Warning bells always go off in my head when I read that modern populations, especially in "central" world areas such as Italy are the result of prehistoric events and untouched by modern events. In particular, this seems to be the result of phylogenetic resolution within haplogroups, as well as the indiscriminate use of relevant "source" populations for proposed historical movements. A recent article on Indian Y chromosomes was a prime example of this tendency, rejecting the contribution of Central Asian Indo-Aryan speakers on the basis of modern Central Asians, who as I pointed out, possess Y chromosome types that were added in recent historical times by Altaic speakers who inundated the area.

I will restate my thesis that modern gene pools, especially for Y chromosome ones, were shaped to a much greater extent by historical events than is currently accepted. So far, the mtDNA evidence is accumulating about sharp differences between modern and ancient inhabitants in various localities, making the idea of continuity since the Neolithic or even the Paleolithic more doubtful. The caricature of genetic history as a Paleolithic substratum with limited Neolithic adstrata and negligible historical influences will no doubt be revealed in the years to come.

Mol Phylogenet Evol. 2006 Dec 13; [Epub ahead of print]

Y chromosome genetic variation in the Italian peninsula is clinal and supports an admixture model for the Mesolithic-Neolithic encounter.

Capelli C, Brisighelli F, Scarnicci F, Arredi B, Caglia' A, Vetrugno G, Tofanelli S, Onofri V, Tagliabracci A, Paoli G, Pascali VL.

The Italian peninsula, given its geographical location in the middle of the Mediterranean basin, was involved in the process of the peopling of Europe since the very beginning, with first settlements dating to the Upper Paleolithic. Later on, the Neolithic revolution left clear evidence in the archeological record, with findings going back to 7000 B.C. We have investigated the demographic consequences of the agriculture revolution in this area by genotyping Y chromosome markers for almost 700 individuals from 12 different regions. Data analysis showed a non-random distribution of the observed genetic variation, with more than 70% of the Y chromosome diversity distributed along a North-South axis. While the Greek colonisation during classical time appears to have left no significant contribution, the results support a male demic diffusion model, even if population replacement was not complete and the degree of Neolithic admixture with Mesolithic inhabitants was different in different areas of Italy.

Link

Near Eastern origins of Etruscans

It seems that the ancient authors who recorded the eastern origin of the Etruscans are vindicated. This is from a preprint in AJHG.

Mitochondrial DNA Variation of Modern Tuscans Supports the Near Eastern Origin of Etruscans

Alessandro Achilli et al.

The origin of the Etruscan people has been a source of major controversy for the past 2,500 years and several hypotheses have been proposed to explain their language and sophisticated culture, including an Aegean / Anatolian origin. To address this issue, we analyzed the mitochondrial DNA (mtDNA) of 322 subjects from three well-defined areas of Tuscany and compared their sequence variation with that of 55 Western Eurasian populations. Interpopulation comparisons reveal that the modern population of Murlo – a small town of Etruscan origin – is characterized by an unusually high frequency (17.5%) of Near Eastern mtDNA haplogroups. Each of these haplogroups is represented by different haplotypes, thus dismissing the possibility that the genetic allocation of the Murlo people is due to drift. Other Tuscan populations do not show the same striking feature; however, overall ~5% of mtDNA haplotypes in Tuscany are shared exclusively between Tuscans and Near Easterners and occupy terminal positions in the phylogeny. These findings support a direct and rather recent genetic input from the Near East – a scenario in agreement with the Lydian origin of Etruscans. Such a genetic contribution has been extensively diluted by admixture, but it appears that there are still locations in Tuscany, such as Murlo, where traces of its arrival are readily detectable.

Link (pdf)

Y chromosomes of Japan

A nice new study combining Y-haplogroups and STR polymorphisms has appeared.

Annals of Human Genetics (online early)

Y-chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y-STR Polymorphisms

I. Nonaka et al.

We investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611*, O3/-LINE1 del, and O3/-021354*) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.

Link

Thomas Jefferson's Y chromosome

I had previously posted that Thomas Jefferson belonged to haplogroup K2, a relatively rare haplogroup. Now, a study has appeared which places his Y chromosome in a global context.

American Journal of Physical Anthropology (early view)

Thomas Jefferson's Y chromosome belongs to a rare European lineage

Turi E. King et al.

We have characterized the Y chromosome carried by President Thomas Jefferson, the general rarity of which supported the idea that he, or a patrilineal relative, fathered the last son of his slave Sally Hemings. It belongs to haplogroup K2, a lineage representing only 1% of chromosomes worldwide, and most common in East Africa and the Middle East. Phylogenetic network analysis of its Y-STR (short tandem repeat) haplotype shows that it is most closely related to an Egyptian K2 haplotype, but the presence of scattered and diverse European haplotypes within the network is nonetheless consistent with Jefferson's patrilineage belonging to an ancient and rare indigenous European type. This is supported by the observation that two of 85 unrelated British men sharing the surname Jefferson also share the President's Y-STR haplotype within haplogroup K2. Our findings represent a cautionary tale in showing the difficulty of assigning individual ancestry based on a Y-chromosome haplotype, particularly for rare lineages where population data are scarce.

Link

Rogers et al. contra "Out of Africa"

I had blogged about this research when it appeared in a conference, but now the article has been published in a journal. This is definitely a paper that will spark interest although it is quite "heretical" in the sense that it defies the consensus interpretation of recent genetic studies. I expect that there will be responses from the "Out of Africa" camp in the next year. I will comment further on the paper if I have time to read it.

MBE Advance Access published online on January 30, 2007

Ancestral Alleles and Population Origins: Inferences Depend on Mutation Rate

Alan R. Rogers et al.

Previous studies have found that at most human loci, ancestral alleles are "African," in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans.

This paper challenges that view, first by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in insertion polymorphisms, and an even smaller bias in non-coding loci. Thus, the strong bias that was originally observed must reflect some factor that varies among data sets—something other than population history. This factor may be the per-locus mutation rate: the African bias is most pronounced in loci where this rate is high.

The distribution of ancestral alleles among populations has been studied using two methods. One of these involves comparing the fractions of loci that reach maximal frequency in each population. The other compares the average frequencies of ancestral alleles. The first of these methods reflects history in a manner that depends on the mutation rate. When that rate is high, ancestral alleles at most loci reach their highest frequency in the ancestral population. When that rate is low, the reverse is true. The other method—comparing averages—is unresponsive. Average ancestral allele frequencies are affected neither by mutation rate nor by the history of population size and migration. In the absence of selection and ascertainment bias, they should be the same everywhere. This is true of one data set, but not of two others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies between data sets.

Link