The face of Johann Sebastian Bach

A reader alerts me to a new forensic reconstruction of J. S. Bach. You can read about it (in English) in Deutsche Welle:

He only posed for one portrait, by Leipzig painter Elias Gottlob Haussmann, which has been reproduced in countless books.

But can anyone be sure that's really what Bach looked like?

Working with a cast of the composer's skull on loan from the Bach Museum in Eisenach, Scottish anthropologist Caroline Wilkinson has created a 3-D representation of the face of a man who died in 1750 at the age of 65.

Northern dogs, ancient and modern

This is an interesting study because it highlights once again a very important point: conclusions about prehistoric events based on modern populations should always be taken with a grain of salt. In this case, modern Scandinavian dogs harbor an mtDNA haplogroup at high frequency (HgD) not found in other dog breeds. This led previous research into the erroneous conclusion that there was an ancient dog domestication event in prehistoric Scandinavia. However, when one looks at actual ancient Scandinavian dogs, one fails to find HgD. Thus the suggestion that modern northern European dogs are similar to ancient northern European dogs is not supported.

BMC Evol Biol. 2008 Feb 28;8(1):71 [Epub ahead of print]

Barking up the wrong tree: Modern northern European dogs fail to explain their origin.

Malmstrom H, Vila C, Gilbert MT, Stora J, Willerslev E, Holmlund G, Gotherstrom A.

ABSTRACT: BACKGROUND: Geographic distribution of the genetic diversity in domestic animals, particularly mitochondrial DNA, has often been used to infer centers of domestication. The underlying presumption is that phylogeographic patterns among domesticates were established during, or shortly after the domestication. Human activities are assumed not to have altered the haplogroup frequencies to any great extent. We studied this hypothesis by analyzing 24 mtDNA sequences in ancient Scandinavian dogs. Breeds originating in northern Europe are characterized by having a high frequency of mtDNA sequences belonging to a haplogroup rare in other populations (HgD). This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe. RESULTS: The sequences observed in the ancient samples do not include the haplogroup indicative for northern European breeds (HgD). Instead, several of them correspond to haplogroups that are uncommon in the region today and that are supposed to have an Asian origin. CONCLUSION: Thus, we find no evidence for local domestication. We conclude that interpretation of the processes responsible for current domestic haplogroup frequencies should be carried out with caution if based only on contemporary data. They do not only tell their own story, but also that of humans.

Link

mtDNA of Karkar Islanders

Info on Karkar Island in Wikipedia.

Ann Hum Genet. 2008 Feb 28 [Epub ahead of print]

Mitochondrial DNA Variation in Karkar Islanders.

Ricaut FX, Thomas T, Arganini C, Staughton J, Leavesley M, Bellatti M, Foley R, Mirazon Lahr M.

We analyzed 375 base pairs (bp) of the first hypervariable region (HVS-I) of the mitochondrial DNA (mtDNA) control region and intergenic COII/tRNA(Lys) 9-bp deletion from 47 Karkar Islanders (north coast of Papua New Guinea) belonging to the Waskia Papuan language group. To address questions concerning the origin and evolution of this population we compared the Karkar mtDNA haplotypes and haplogroups to those of neighbouring East Asians and Oceanic populations. The results of the phylogeographic analysis show grouping in three different clusters of the Karkar Islander mtDNA lineages: one group of lineages derives from the first Pleistocene settlers of New Guinea-Island Melanesia, a second set derives from more recent arrivals of Austronesian speaking populations, and the third contains lineages specific to the Karkar Islanders, but still rooted to Austronesian and New Guinea-Island Melanesia populations. Our results suggest (i) the absence of a strong association between language and mtDNA variation and, (ii) reveal that the mtDNA haplogroups F1a1, M7b1 and E1a, which probably originated in Island Southeast Asia and may be considered signatures of Austronesian population movements, are preserved in the Karkar Islanders but absent in other New Guinea-Island Melanesian populations. These findings indicate that the Karkar Papuan speakers retained a certain degree of their own genetic uniqueness and a high genetic diversity. We present a hypothesis based on archaeological, linguistic and environmental datasets to argue for a succession of (partial) depopulation and repopulation and expansion events, under conditions of structured interaction, which may explain the variability expressed in the Karkar mtDNA.

Link

Who's a Jew?

Steve Sailer points me to this article in the New York Times regarding the strict criteria adopted by the Chief Rabbinate in Israel:

One day last fall, a young Israeli woman named Sharon went with her fiancé to the Tel Aviv Rabbinate to register to marry. They are not religious, but there is no civil marriage in Israel. The rabbinate, a government bureaucracy, has a monopoly on tying the knot between Jews. The last thing Sharon expected to be told that morning was that she would have to prove — before a rabbinic court, no less — that she was Jewish. It made as much sense as someone doubting she was Sharon, telling her that the name written in her blue government-issue ID card was irrelevant, asking her to prove that she was she.

...

In recent years, the state’s Chief Rabbinate and its branches in each Israeli city have adopted an institutional attitude of skepticism toward the Jewish identity of those who enter its doors. And the type of proof that the rabbinate prefers is peculiarly unsuited to Jewish life in the United States. The Israeli government seeks the political and financial support of American Jewry. It welcomes American Jewish immigrants. Yet the rabbinate, one arm of the state, increasingly treats American Jews as doubtful cases: not Jewish until proved so.

...

Seth Farber is an American-born Orthodox rabbi whose organization — Itim, the Jewish Life Information Center — helps Israelis navigate the rabbinic bureaucracy. He explained to me recently that the rabbinate’s standards of proof are now stricter than ever, and stricter than most American Jews realize. Referring to the Jewish federations, the central communal and philanthropic organizations of American Jewry, he said, “Eighty percent of federation leaders probably wouldn’t be able to reach the bar.” To assist people like Sharon, Farber has become a genealogical sleuth. He is the first to warn, though, that solving individual cases cannot solve a deeper crisis.

If you want to find out the end of Sharon's story, read the article. This story highlights the deep divide between those with a more subjectivistic idea of religious identity or ethnicity, emphasizing self-image, and those seeking a set of more objective criteria.

How to switch your comments from Blogger to Haloscan or backwards and not lose your existing comments

Not really anthropological-related, but I was looking for a way to switch the comments on the blog from Haloscan to Blogger and not lose all the existing past comments. As far as I could tell there is no "clean" way to achieve this, so this is my work-around.

First of all, if you just replaced the haloscan code in your template with the blogger code, this would result in all your previous posts having new blogger comments. So, that solution is out.

I simply created a new user account for posting in my blog, whose blogger profile name is "dienekesp" rather than "Dienekes". Now, when I post as "dienekesp", the <$BlogItemAuthor$> tag takes the value "dienekesp".

Next, you place both the haloscan comment-generating code, and the blogger comment-generating code in your template, and you "comment out" the code you don't want to use by two simple JavaScripts:

<script type="text/javascript"><!--
if ("<$BlogItemAuthor$>"!="Dienekes")
document.write("\< !--"); //-->
</script>

BLOGGER COMMENT CODE

<script type="text/javascript"><!--
if ("<$BlogItemAuthor$>"!="Dienekes")
document.write("--\>");
//-->;
</script>

The same code as above should also be repeated for the Haloscan comments code, but with "dienekesp" instead of "Dienekes". So, from now on whenever I post as "dienekesp", Blogger comments will be used; when I post as "Dienekes", Haloscan comments will be used. All the older posts which had been posted as "Dienekes" will retain their existing comments.

PS: It goes without saying that this trick is provided as-is with no guarantee that it will work or acceptance of responsibility if it doesn't or you wreck your blog in your process. Make sure you back up your template in advance.

Did Cannibalism contribute to Neanderthal extinction?

See the earlier post on Cannibalistic Neanderthals.

Medical Hypotheses doi:10.1016/j.mehy.2007.12.014

A potential role for Transmissible Spongiform Encephalopathies in Neanderthal extinction

Simon Underdown

The Neanderthals were a Eurasian human species of the genus Homo that disappeared approximately 30,000 years ago. The cause or causes of their extinction continues to intrigue specialists and non-specialists alike. Here a contributory role for Transmissible Spongiform Encephalopathies (TSEs) is suggested. TSEs could have infected Neanderthal groups as a result of general cannibalistic activity and brain tissue consumption in particular. Further infection could then have taken place through continued cannibalistic activity or via shared used of infected stone tools. A modern human hunter-gatherer proxy has been developed and applied as a hypothetical model to the Neanderthals. This hypothesis suggests that the impact of TSEs on the Neanderthals could have been dramatic and have played a large part in contributing to the processes of Neanderthal extinction.

Link

East-West cranial differentiation in Central and Northern America

A very related previous blog entry on East-west cranial differences of South Americans. Also read a major study on Native American genetic variation. Also of interest, the Peopling of the Americas, and New synthesis on the first arrivals into the New World. Directly related to the issue of East-West differentiation in the Americas is the post on South American mtDNA, re-interpretation of its prehistory.

Journal of Human Evolution Volume 54, Issue 3, March 2008, Pages 296-308

East-West cranial differentiation in pre-Columbian populations from Central and North America

Héctor M. Pucciarelli

Abstract

In a recent study we found that crania from South Amerindian populations on each side of the Andes differ significantly in terms of craniofacial shape. Western populations formed one morphological group, distributed continuously over 14,000 km from the Fuegian archipelago (southern Chile) to the Zulia region (northwestern Venezuela). Easterners formed another group, distributed from the Atlantic Coast up to the eastern foothills of the Andes. This differentiation is further supported by several genetic studies, and indirectly by ecological and archaeological studies. Some authors suggest that this dual biological pattern is consistent with differential rates of gene flow and genetic drift operating on both sides of the Cordillera due to historical reasons. Here we show that such East-West patterning is also observable in North America. We suggest that the “ecological zones model” proposed by Dixon, explaining the spread of the early Americans along a Pacific dispersal corridor, combined with the evolution of different population dynamics in both regions, is the most parsimonious mechanism to explain the observed patterns of within- and between-group craniofacial variability.

Link

Domesticated cattle of predominantly Neolithic origin but with some aurochs mtDNA

See also The origin of European cattle, and Neolithic Near Eastern Origin of domesticated cattle. Some introductory information about the aurochs via the BBC and Wikipedia and the Extinction Website.

Curr Biol. 2008 Feb 26;18(4):R157-8.

Mitochondrial genomes of extinct aurochs survive in domestic cattle.

Achilli A, Olivieri A, Pellecchia M, Uboldi C, Colli L, Al-Zahery N, Accetturo M, Pala M, Kashani BH, Perego UA, Battaglia V, Fornarino S, Kalamati J, Houshmand M, Negrini R, Semino O, Richards M, Macaulay V, Ferretti L, Bandelt HJ, Ajmone-Marsan P, Torroni A.

Archaeological and genetic evidence suggest that modern cattle might result from two domestication events of aurochs (Bos primigenius) in southwest Asia, which gave rise to taurine (Bos taurus) and zebuine (Bos indicus) cattle, respectively [1-3]. However, independent domestication in Africa [4,5] and East Asia [6] has also been postulated and ancient DNA data raise the possibility of local introgression from wild aurochs [7-9]. Here, we show by sequencing entire mitochondrial genomes from modern cattle that extinct wild aurochsen from Europe occasionally transmitted their mitochondrial DNA (mtDNA) to domesticated taurine breeds. However, the vast majority of mtDNAs belong either to haplogroup I (B. indicus) or T (B. taurus). The sequence divergence within haplogroup T is extremely low (eight-fold less than in the human mtDNA phylogeny [10]), indicating a narrow bottleneck in the recent evolutionary history of B. taurus. MtDNAs of haplotype T fall into subclades whose ages support a single Neolithic domestication event for B. taurus in the Near East, 9-11 thousand years ago (kya).

Link (pdf)

Migrations in the Baltic region inferred from Y chromosomes and mtDNA

From the paper on Y-haplogroup I1a:

Haplogroup I1a is suggested to have its origins in the Iberian refugium, from where it spread northward and now has its highest frequencies in Northern Europe (Rootsi et al. 2004). The haplotype matches to Germany and Poland imply that I1a has arrived to the Nordic countries from the Southern Baltic Sea region, which is historically plausible. The coalescense age of the haplogroup is about 5000 years lower than the age of the earliest archaeological findings from the Northern Baltic Sea region, which suggests a Neolithic arrival. There are two possible migration routes from Central Europe to the Northern Baltic Sea region: an exclusive western route via Sweden, an eastern route via the Baltic states, or via both to Eastern Finland and Karelia (Fig. 5). The surprisingly high diversities of I1a among the eastern Finnish and Baltic populations, and the lack of association between the Western Finns and the Swedes in SAMOVA analysis suggest that I1a has been involved in bifurcating migrations both via Sweden and the Baltic states, and that the presence of the haplogroup in Finland and Karelia is not merely due to Swedish influence. The low frequency of I1a among the Baltic populations may be due to later effects of genetic drift or replacement.

I am personally doubtful of the Iberian origin of Y-haplogroup I1a. Its presence in Iberia and France, as well as its high diversity there may be the result of migration from northern Europe, a genetic trace of the Germanic Volkerwanderung. One certainly needs to consider this effect. There are probably a couple of papers just waiting to be written by looking at Y-chromosomes of Germanic descendants in Southwestern Europe by looking at either surnames or early cemetaries.

With regard to Y-haplogroup N3:

The frequency distribution and age of haplogroup N3 in our study sample was consistent with the earlier studies (Lahermo et al. 1999, Zerjal et al. 2001, Tambets et al. 2004, Karlsson et al. 2006, Rootsi et al. 2007). According to the YHRD database, the haplotypes most common in Finland and Karelia were relatively unique, which is not unexpected, since data from most Eurasian populations where N3 is common is not publicly available. It seems evident that the Finns and Karelians share a history regarding haplogroup N3. In the database comparisons, we also observed that N3 may mark a westward diffusion in the north from Finland to Sweden and in the south from the Baltic countries to Poland and Germany.

The researchers also reiterated the previous idea of a dual origin of N3, as shown in the figure, with different clades being represented in Finland and the Baltic states, with Estonia being intermediate between the two.

With regard to Y-haplogroup R1a1:

It is plausible that both R1a1 and I1a were carried to the Baltic Sea region via the same Neolithic migrations from Germany/Poland. The higher coalescence age and the starlike network structure of R1a1 are consistent with the probable higher diversity and frequency of R1a1 in the original source population(s), a consequence of the wider geographical distribution of the haplogroup. It is an important observation that in the Baltic Sea region R1a1 is mainly associated to Central European rather than eastern or Russian influence. However, haplotype frequency comparisons (Derenko et al. 2006, Willuweit & Roewer 2007) give some indication of Russian gene flow as a partial source of R1a1 in Karelia, which would be plausible given the long period of admixture with Slavs (Fig. 5). However, the Y-chromosomal diversity in Karelia has been heavily affected by drift and founder effects. Another haplogroup with eastern affinity is I1b (Rootsi et al. 2004), whose presence in Karelia and the Baltic states is probably a sign of Russian gene flow.

This is an important discovery, and a great first step in uncovering the structure within this widespread haplogroup. Even though R1a1 Y-chromosomes were studied in a lot of populations, including e.g., the Balkans, India, the Altai, unfortunately we know next to nothing about its phylogenetic substructure. Without such knowledge, R1a1 spread has been variously interpreted as a signal of postglacial colonization, Kurgan expansions, or the spread of Slavic languages.

Finally, the genetic legacy of the Saami is visible in mtDNA:

The eastern elements in the mtDNA variation of the Baltic Sea region are intertwined with the Saami influence. Recent studies of the mtDNA variation among the Saami show a link to the Volga-Ural region (Tambets et al. 2004, Ingman & Gyllensten 2006), which is now shown to exist also among the Karelians and, to a lesser degree, among the other populations from the Baltic Sea region as well. Additionally, the presence of U4 in the Eastern Baltic Sea populations may represent eastern influence, since it is typical for the Volga-Ural region (Bermisheva et al. 2002). The high diversity of this haplogroup in the Baltic region, observable in the haplotype network, suggests a complex history, and rules genetic drift out as a cause of the high frequency. All in all, these mtDNA haplogroups may be maternal reflections of the eastern influence that can be most clearly observed in the Y-chromosomal haplogroup N3.

Annals of Human Genetics doi:10.1111/j.1469-1809.2007.00429.x

Migration Waves to the Baltic Sea Region

T. Lappalainen et al.

In this study, the population history of the Baltic Sea region, known to be affected by a variety of migrations and genetic barriers, was analyzed using both mitochondrial DNA and Y-chromosomal data. Over 1200 samples from Finland, Sweden, Karelia, Estonia, Setoland, Latvia and Lithuania were genotyped for 18 Y-chromosomal biallelic polymorphisms and 9 STRs, in addition to analyzing 17 coding region polymorphisms and the HVS1 region from the mtDNA. It was shown that the populations surrounding the Baltic Sea are genetically similar, which suggests that it has been an important route not only for cultural transmission but also for population migration. However, many of the migrations affecting the area from Central Europe, the Volga-Ural region and from Slavic populations have had a quantitatively different impact on the populations, and, furthermore, the effects of genetic drift have increased the differences between populations especially in the north. The possible explanations for the high frequencies of several haplogroups with an origin in the Iberian refugia (H1, U5b, I1a) are also discussed.

Link

The Macedonian Issue

The issue of the naming dispute between Greece and the Former Yugoslav Republic of Macedonia (FYROM) is currently in the news, so this is a good time to address some facts pertaining to it.

The dispute centers around the issue of the use of the adjective "Macedonian". This adjective has a geographical sense, describing someone who is from the geographical region of Macedonia. However, for the inhabitants of FYROM, it also has an ethnic sense, since many (or most) Slavic-speaking inhabitants of FYROM consider themselves to be Macedonian in an ethnic sense. I will distinguish between these two uses as Geo-Macedonians and Slavo-Macedonians henceforth.

Three types of criteria are used with regard to ethnic identification: language, self-definition, descent.

Descent is the easier one to address: according to most reputable genetic studies, Geo-Macedonians tend to be more of indigenous Balkan origins. In short, Geo-Macedonians, whether they speak Greek, Vlach, Albanian, or Slavic, and whether they live in Greece or the FYROM are characterized by genetic characteristics attesting to a substantial amount of distinctive southern Balkan ancestry, having, in particular substantial frequencies of Y-haplogroups E and J.

Genetically-speaking Geo-Macedonians are Balkan Europeans, and are differentiated both from Northern-Balkan/Central/Eastern Europeans as well as from West Asians.

Language is also easy to address. Within Geo-Macedonia, several languages and dialects are spoken, including Greek, Slavic, Vlach, and Albanian. These languages were established at different times, with the oldest attested one being the Greek. A Slavic language spoken in the FYROM is named "Macedonian" by the Slavo-Macedonians.

Sometimes, it is asserted by scholars from FYROM that Ancient Macedonian was not a Greek dialect, but a separate Indo-European language. While these claims are not very serious, they are actually irrelevant to the modern issues at hand, since the "Macedonian" of the Slavo-Macedonians has no relationship to the ancient language: it is a Slavic idiom dating at most from the 6th c. AD.

Self-Identity is more complex. It is true that Slavic speakers from FYROM have a Macedonian ethnic identity, but Geo-Macedonians in Greece have a Greek ethnic identity. Thus, Greek Macedonians assert the name "Macedonian" in a geographical sense, i.e., "Greeks from the region of Macedonia", whereas Slavo-Macedonians assert it in an ethnic sense, i.e., "Members of the Macedonian ethnic group".

To summarize, we must make these points:

• Slavo-Macedonians from FYROM assert a Macedonian ethnicity, as well as (in some cases) continuity with ancient Macedonia
• Such continuity with ancient Macedonia can be based either on language, or on descent.
• Linguistic continuity between Slavic Macedonian and the ancient Macedonian dialect/language does not exist.
  
• Continuity of descent from the ancient Macedonians to the modern ones is not limited to the Slavic-speaking Slavo-Macedonians. Slav Macedonians have no monopoly on Macedonian "blood".
  

Thus, in what sense is the name Republic of Macedonia a reasonable choice for the FYROM?

• It does not encompass the entirety of Macedonia (as a geographical region).
  
• The Macedonian dialect/language of Slavic is not related to the ancient Macedonian language/dialect.
• The people of FYROM have a Macedonian ethnic self-identity, but the Greeks of Macedonia have a Greek ethnic self-identity. One's "right" to the name of Macedonian infringes on the other's right to use it in a different sense; the name "Macedonian" is thus ambiguous.

There are only two reasonable choices for the name of the FYROM.

Republic of Upper Macedonia describes the state geographically, since FYROM includes the northern part of historical Macedonia, as well as other historically non-Macedonian regions.

Republic of Slav Macedonia describes the state linguistically, since FYROM includes the mainly Slav-speaking portion of historical Macedonia.

The name New Macedonia might also be considered, but does not really describe the identity of FYROM as clearly as the above two.

My personal preference would be for Upper Macedonia, a clear, unambiguous geographical description that has certain advantages over Slav Macedonia:

• There are Slav speakers also in Bulgarian and Greek Macedonia.
• FYROM includes also Albanian, Vlach, and Greek speakers who might not be as open to the name "Slav Macedonia".
  

This is the time for cool-headed reflection on the part of both Greeks and the Slavo-Macedonians:

• The people of Greece are justified in wanting to deny exclusive rights to the Macedonian name to FYROM, because FYROM encompasses only part of Macedonia: geographically, the northern part; genetically, a subset of the Macedonian blood; linguistically, a Slavic dialect of the Macedonian region.
• The people of FYROM are justified in wanting to have some rights to the name Macedonian: they inhabit parts of Macedonia, they speak a Macedonian dialect of the Slavic group, and they have come to think of themselves as a separate nation from other Balkan Slavs.
  

Acceptance of a single name for all uses such as Republic of Upper Macedonia is the reasonable thing to do.

Huge paper on human genetic relationships based on 650K SNPs

If you thought that this week's Nature paper on human variation was nice, another new paper in Science will be another pleasant surprise. It seems that every time I turn my head geneticists are raising the number of SNPs they study. Lots of populations, 650K SNPs, and a treasure trove of new insight into where humans come from and how we differ from each other.

Before I get into the details of the paper, I want to reiterate my conviction that the problem of human origins is not really a hard one. It just requires a lot of data, a lot of populations, individuals sampled, a lot of genetic markers. Our history, our race, and now it seems even our ethnicity can be read off our genes. We just need to invest the money and effort to find out. With that said, it is sad that the same-old roster of populations from the CEPH panel makes yet another appearance.

There is really a lot on the paper that might interest you, but I will note a few points. First, look at the following PC plot from the paper.



No, your eyes aren't deceiving you. This paper is proof positive that European ethnicities can be distinguished from each other genetically. Even close-by populations (in this case the French and the Italians) are neatly separated. When geographic distance increases there isn't even a hint of confusion: e.g., Russians, Orcadians, and Basque are neatly and clearly separated from other groups. Doubtlessly there would be some more overlap if more individuals/population were used, but the thrust of the discovery is intact: it seems that several European ethnicities and local populations make sense not only culturally but also biologically.

Now, take a look at the standard STRUCTURE analysis which provides meaningful results up to K=7. The standard Sub-Saharan, Native American, East Asian, and Oceanian clusters are there, but now there is meaningful structure within the Caucasoids as well; they are broken into "Middle Eastern", "European", and "Central South Asian" groups.



I would guess that the "brown" Middle-Eastern cluster is largely an Arab/Semitic phenomenon, although the inclusion of the Berber Mozabites is interesting. If it reflected a pre-historic phenomenon, then it would be difficult to explain its apparent total lack of influence in Europe, except for a barely perceptible spillage into Tuscany, which once again reiterates the idiosyncratic "Middle Eastern" trace of that Italian population of likely Etruscan descendants.

The "Central South Asian" group is also extremely interesting, for several reasons. First, it reinforces the previous claim that the Kalash, rather than Greek descendants, as some romantics would have them, are simply a non-European native population, with no evidence of European ancestry. Second, it shows that there is minimal, yet evident European influence in Central Asia, which I would relate to the eastern Indo-Iranians. Third, Central Asian influence in Europe is non-evident, except for a trace among the Russians (and substantially more among the Adygei a people of the Caucasus). Fourth the minority Mongoloid and "Boreal" (Purple) influence in Russians is affirmed. Note that we are dealing with ethnic Russians from the north (Vologda oblast), and Russians are a heterogeneous people in terms of their origin.

We can only wish for inclusion of further populations in future studies of the kind. In particular, eastern and southeastern Europe and non-Arab West Asia, Siberia would be invaluable in further understanding Caucasoid origins, and perhaps uncovering additional structure.

Note that the CEPH panel has revealed that ethnic groups can be distinguished genetically, there is little more than it can offer in terms of understanding origins. The next milestone would be either to include previously unsampled populations, or to dig into ethnic groups themselves, and see if sub-ethnic entities are also discernible in our genomes. Genetic genealogists are in for a good time in the coming years...

Science 22 February 2008: Vol. 319. no. 5866, pp. 1100 - 1104

Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation

Jun Z. Li,1,2*{dagger} Devin M. Absher,1,2* Hua Tang,1 Audrey M. Southwick,1,2 Amanda M. Casto,1 Sohini Ramachandran,4 Howard M. Cann,5 Gregory S. Barsh,1,3 Marcus Feldman,4{ddagger} Luigi L. Cavalli-Sforza,1{ddagger} Richard M. Myers1,2{ddagger}

Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.

Link

New study on global human variation based on SNPs and CNVs

A new letter in Nature combines data from single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) across 29 human populations. STRUCTURE results from the paper are below based on SNPs, haplotypes, and CNVs. Note in particular the Green cluster, which was not seen in some previous studies that did not include Oceanian populations, the differentiation between African farmers and hunter-gatherers, and the differentiation between northern and southern Mongoloids evident in the bottom row.



Nature 451, 998-1003 (21 February 2008) | doi:10.1038/nature06742; Received 2 December 2007; Accepted 29 January 2008

Genotype, haplotype and copy-number variation in worldwide human populations

Mattias Jakobsson1,2,14, Sonja W. Scholz4,5,14, Paul Scheet1,3,14, J. Raphael Gibbs4,5, Jenna M. VanLiere1, Hon-Chung Fung4,6, Zachary A. Szpiech1, James H. Degnan1,2, Kai Wang7, Rita Guerreiro4,8, Jose M. Bras4,8, Jennifer C. Schymick4,9, Dena G. Hernandez4, Bryan J. Traynor4,10, Javier Simon-Sanchez4,11, Mar Matarin4, Angela Britton4, Joyce van de Leemput4,5, Ian Rafferty4, Maja Bucan7, Howard M. Cann12, John A. Hardy5, Noah A. Rosenberg1,2,3 & Andrew B. Singleton4,13


Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups1, 2, 3. Here we report the analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected—including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas—the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.

Link

Pinghua Han Chinese are not of Han origin

An interesting study which demonstrates how a small subgroup of the Han Chinese, the Pinghua have a different origin than the rest of the Han. As in the case of some Finnish origin Russians, this illustrates that despite the general genetic coherence of ethnic groups, they can nonetheless include segments that were grafted onto their body. It is indeed the fact that ethnic groups constitute in a sense in many cases their own mini-races that allows us to identify outlier populations of different origins.

J Hum Genet. 2008 Feb 13 [Epub ahead of print]

Pinghua population as an exception of Han Chinese's coherent genetic structure.

Gan RJ et al.

The Han Chinese is the largest single ethnic group in the world, consisting of ten Chinese branches. With the exception of the Pinghua branch, the genetic structure of this group has been studied extensively, and Y chromosome and mitochondrial (mt)DNA data have demonstrated a coherent genetic structure of all Han Chinese. It is therefore believed that the Pinghua branch, being members of an old branch of the Han Chinese, despite being scattered in and around Guangxi Province where members of the Daic and Hmong-Mien are more prevalent than Han Chinese, is no exception. We have studied 470 individual samples (including 195 males) from Pinghua populations and other ethnic groups (Zhuang, Kam, Mulam, Laka, and Mien) from six areas (Hezhou, Fuchuan, Luocheng, Jinxiu, Sanjiang, and Wuxuan) in the north of the Guangxi Zhuang Autonomous Region of China. Both mtDNA and the Y chromosomes were typed in these samples. High frequencies of the Y chromosome haplogroups O2a* and O*, which always present at a high frequency among the populations of the southern minorities, were found in Pinghua populations. Only Pinghua populations in Luocheng and Jinxiu maintain the Han frequent haplogroup O3a5a. mtDNA lineages B4a, B5a, M*, F1a, M7b1, and N* were found in Pinghua populations, exhibiting a pattern similar to the neighboring indigenous populations, especially the Daic populations. Cluster analyses (dendrograms, principal component analyses, and networks) of Pinghua populations, the other Han branches, and other ethnic groups in East Asia indicated that Pinghua populations are much closer to the southern minorities than to the other Han branches. Admixture analyses confirmed this result. In conclusion, we argue that Pinghua populations did not descend from Han Chinese, but from southern minorities. The ancestral populations of Pinghua people were assimilated by the Han Chinese in terms of language, culture, and self-identification and, consequently, the Pinghua people became an exceptional branch of Han Chinese's coherent genetic structure.

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News on Arabian mtDNA

Not one but two recent paper on Arabian mtDNA, giving us a better idea of its geographical structure. I am not sure what to make of the assertion in the first paper that the Arabian peninsula has been the recipient of genetic input from Australia; well, it's in an open access journal so you can form your own opinions.

BMC Evol Biol. 2008 Feb 12;8(1):45 [Epub ahead of print]

Mitochondrial DNA structure in the Arabian Peninsula.

Abu-Amero KK, Larruga JM, Cabrera VM, Gonzalez AM.

ABSTRACT: BACKGROUND: Two potential migratory routes followed by modern humans to colonize Eurasia from Africa have been proposed. These are the two natural passageways that connect both continents: the northern route through the Sinai Peninsula and the southern route across the Bab al Mandab strait. Recent archaeological and genetic evidence have favored a unique southern coastal route. Under this scenario, the study of the population genetic structure of the Arabian Peninsula, the first step out of Africa, to search for primary genetic links between Africa and Eurasia, is crucial. The haploid and maternally inherited mitochondrial DNA (mtDNA) molecule has been the most used genetic marker to identify and to relate lineages with clear geographic origins, as the African Ls and the Eurasian M and N that have a common root with the Africans L3. RESULTS: To assess the role of the Arabian Peninsula in the southern route, we genetically analyzed 553 Saudi Arabs using partial (546) and complete mtDNA (7) sequencing, and compared the lineages obtained with those present in Africa, the Near East, central, east and southeast Asia and Australasia. The results showed that the Arabian Peninsula has received substantial gene flow from Africa (20%), detected by the presence of L, M1 and U6 lineages; that an 18% of the Arabian Peninsula lineages have a clear eastern provenance, mainly represented by U lineages; but also by Indian M lineages and rare M links with Central Asia, Indonesia and even Australia. However, the bulk (62%) of the Arabian lineages has a Northern source. CONCLUSIONS: Although there is evidence of Neolithic and more recent expansions in the Arabian Peninsula, mainly detected by (preHV)1 and J1b lineages, the lack of primitive autochthonous M and N sequences, suggests that this area has been more a receptor of human migrations, including historic ones, from Africa, India, Indonesia and even Australia, than a demographic expansion center along the proposed southern coastal route.

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Am J Phys Anthropol. 2008 Feb 6 [Epub ahead of print]

Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen.

Cerný V et al.

Despite its key location for population movements out of and back into Africa, Yemen has not yet been sampled on a regional level for an investigation of sub-Saharan, West Eurasian, and South Asian genetic contributions. In this study, we present mitochondrial DNA (mtDNA) data for regionally distinct Yemeni populations that reveal different distributions of mtDNA lineages. An extensive database of mtDNA sequences from North and East African, Middle Eastern and Indian populations was analyzed to provide a context for the regional Yemeni mtDNA datasets. The groups of western Yemen appear to be most closely related to Middle Eastern and North African populations, while the eastern Yemeni population from Hadramawt is most closely related to East Africa. Furthermore, haplotype matches with Africa are almost exclusively confined to West Eurasian R0a haplogroup in southwestern Yemen, although more sub-Saharan L-type matches appear in more northern Yemeni populations. In fact, Yemeni populations have the highest frequency of R0a haplotypes detected to date, thus Yemen or southern Arabia may be the site of the initial expansion of this haplogroup. Whereas two variants of the sub-Saharan haplogroup M1 were detected only in southwestern Yemen close to the Bab el-Mandeb Strait, different non-African M haplotypes were detected at low frequencies ( approximately 2%) in western parts of the country and at a higher frequency (7.5%) in the Hadramawt. We conclude that the Yemeni gene pool is highly stratified both regionally and temporally and that it has received West Eurasian, Northeast African, and South Asian gene flow.

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New synthesis on the first arrivals into the New World

In the open access journal PLoS One.

A Three-Stage Colonization Model for the Peopling of the Americas

Andrew Kitchen et al.

Abstract

Background

We evaluate the process by which the Americas were originally colonized and propose a three-stage model that integrates current genetic, archaeological, geological, and paleoecological data. Specifically, we analyze mitochondrial and nuclear genetic data by using complementary coalescent models of demographic history and incorporating non-genetic data to enhance the anthropological relevance of the analysis.

Methodology/Findings

Bayesian skyline plots, which provide dynamic representations of population size changes over time, indicate that Amerinds went through two stages of growth ≈40,000 and ≈15,000 years ago separated by a long period of population stability. Isolation-with-migration coalescent analyses, which utilize data from sister populations to estimate a divergence date and founder population sizes, suggest an Amerind population expansion starting ≈15,000 years ago.

Conclusions/Significance

These results support a model for the peopling of the New World in which Amerind ancestors diverged from the Asian gene pool prior to 40,000 years ago and experienced a gradual population expansion as they moved into Beringia. After a long period of little change in population size in greater Beringia, Amerinds rapidly expanded into the Americas ≈15,000 years ago either through an interior ice-free corridor or along the coast. This rapid colonization of the New World was achieved by a founder group with an effective population size of ≈1,000–5,400 individuals. Our model presents a detailed scenario for the timing and scale of the initial migration to the Americas, substantially refines the estimate of New World founders, and provides a unified theory for testing with future datasets and analytic methods.

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Maternal common ancestry between pygmies and farmers in Central Africa

This is an Open Access article in PNAS.

PNAS 10.1073/pnas.0711467105

Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter–gatherers and Bantu-speaking farmers

Lluís Quintana-Murci et al.

Abstract

Two groups of populations with completely different lifestyles—the Pygmy hunter–gatherers and the Bantu-speaking farmers—coexist in Central Africa. We investigated the origins of these two groups and the interactions between them, by analyzing mtDNA variation in 1,404 individuals from 20 farming populations and 9 Pygmy populations from Central Africa, with the aim of shedding light on one of the most fascinating cultural transitions in human evolution (the transition from hunting and gathering to agriculture). Our data indicate that this region was colonized gradually, with an initial L1c-rich ancestral population ultimately giving rise to current-day farmers, who display various L1c clades, and to Pygmies, in whom L1c1a is the only surviving clade. Detailed phylogenetic analysis of complete mtDNA sequences for L1c1a showed this clade to be autochthonous to Central Africa, with its most recent branches shared between farmers and Pygmies. Coalescence analyses revealed that these two groups arose through a complex evolutionary process characterized by (i) initial divergence of the ancestors of contemporary Pygmies from an ancestral Central African population no more than {approx}70,000 years ago, (ii) a period of isolation between the two groups, accounting for their phenotypic differences, (iii) long-standing asymmetric maternal gene flow from Pygmies to the ancestors of the farming populations, beginning no more than {approx}40,000 years ago and persisting until a few thousand years ago, and (iv) enrichment of the maternal gene pool of the ancestors of the farming populations by the arrival and/or subsequent demographic expansion of L0a, L2, and L3 carriers.

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