March 31, 2012

Iceman's sheep belonged to mtDNA haplogroup B




Abstract Top

Methodology/Principal Findings




From the paper:





Serikbai Abilev et al.



March 28, 2012

A rare look at the Y chromosomes of Afghanistan

I often bemoan the fact that some of the regions of the world that are most interesting to the student of prehistory (e.g., Mesopotamia and the Iranian Plateau) seem to also be the ones with more than their fair share of political trouble, hindering efforts to study them with the newest set of tools. Afghanistan is certainly one case that hasn't been quite the most welcoming of places in recent decades.

The country is transitional between the Iranic speaking world of Iran and the Indo-Aryan speaking world of South Asia, as well as between the Indo-Iranian world and the (mostly) Turkic-speaking world of Central Asia. Hence, the absence of data for that country has been acutely felt for all those who are trying to understand "what happened" in Eurasia.

The appearance of a new paper by the Genographic Project is a welcome sight, and a good example of what is best about this Project. I haven't been exactly a fan of the Genographic's interpretation of their own data, but kudos to them for getting them in the first place.

From the paper:
Pashtuns are the largest ethnic group in Afghanistan, accounting for about 42 percent of the population, with Tajiks (27%), Hazaras (9%), Uzbeks (9%), Aimaqs (4%), Turkmen people (3%), Baluch (2%), and other groups (4%) making up the remainder [6]. In the present study, eight ethnic groups were examined, with a focus on the largest four groups: - The Pashtuns, traditionally lived a seminomadic lifestyle, they reside mainly in southern and eastern Afghanistan and in western Pakistan. They speak Pashto which is a member of the Eastern Iranian languages. - The Tajiks are a Persian-speaking ethnic group which are closely related to the Persians of Iran. In Afghanistan, they are the largest Tajik population outside their homeland to the north in Tajikistan. - The Hazara population speaks Persian with some Mongolian words. They believe they are descendants of Genghis Khan's army that invaded during the twelfth century. - The Uzbeks are a Turkic speaking group that have been living a sedentary farming lifestyle in Northern Afghanistan.
The main features of the Y-chromosome gene pool:
Genotyping revealed 32 halpogroups present in Afghanistan's ethnic groups among our samples. Haplogroups R1a1a-M17, C3-M217, J2-M172, and L-M20 were the most frequent when Afghan ethnic groups were pooled, together comprising >66% of the chromosomes. Absolute and relative haplogroup frequencies are tabulated in Table S4.
-The PCA analysis (left) showcases wonderfully the correspondence between different haplogroups and the three main regions of the Near East (green), South Asia (yellow), and Central Asia (purple).

It is a real shame that the newer markers available within the most prominent R-M17 haplogroup were not tested:
The prevailing Y-chromosome lineage in Pashtun and Tajik (R1a1a-M17), has the highest observed diversity among populations of the Indus Valley [46]. R1a1a-M17 diversity declines toward the Pontic-Caspian steppe where the mid-Holocene R1a1a7-M458 sublineage is dominant [46]. R1a1a7-M458 was absent in Afghanistan, suggesting that R1a1a-M17 does not support, as previously thought [47], expansions from the Pontic Steppe [3], bringing the Indo-European languages to Central Asia and India.
Nonetheless, I can't really disagree with the dismissal of the R-M17/Indo-European theory. R-M17 is simply too populous in South Asia to be the genetic legacy of "Indo-Europeans": (i) under an elite-dominance model, its frequency is way too high (compared to well-attested examples of elite dominance, e.g., Hungary or Turkey where the genetic legacy of the elite element is in the minority), (ii) under a folk migration model, it is difficult to understand why a hypothetical migrating Indo-European people would have such an overwhelming influence in the region while at the same time hardly influencing at all other densely occupied agricultural landscapes of the Eurasian steppe periphery; moreover, no autosomal signal corresponding to a migration from eastern Europe to South Asia really exists -the main cline of variation links South with West Asia, not Europe- and the small signal that does exist does not really correspond to observed levels of R-M17.

From the paper:
The E1b1b1-M35 lineages in some Pakistani Pashtun were previously traced to a Greek origin brought by Alexander's invasions [48]. However, RM network of E1b1b1-M35 found that Afghanistan's lineages are correlated with Middle Easterners and Iranians but not with populations from the Balkans.
Greek populations are not homogeneous in their haplogroup E frequencies, so it would be useful to consider the possibility that the lack of this frequent Southeastern European haplogroup in South Asia may not reflect a complete lack of Greek influence in this region, but rather, an influence from a structured ancient Greek population.

Looking at the Y-haplogroup composition:

A few points of interest:

  • The clear link between C/N/O with Central Asia
  • A clear difference between Persian and Pashto speakers in terms of inverse J2a/R1a frequences
  • The paucity of J1 chromosomes (only 1 Tajik) testifies to the absence of relatively recent Middle Eastern influences associated with the spread of Islam; consistent with the absence of the autosomal "Southwest Asian" component in South/Central Asia.
  • Paucity of R1b, except in a couple Uzbeks and a Tajik; I have argued before that R1a had an early distribution in the arc of flatlands north and east of the Caspian, while R1b a complementary distribution in the smaller arc of the highlands west and south of it, out of which the Tocharians may have originated.
  • The small Nurestani sample comprises of J2a, R1a, and R2; these are linguistic relatives of the Kalash of Pakistan who -unlike the latter- were converted to Islam in the 19th century.
I would say that the evidence is pretty clear that the earliest Iranians may have included haplogroups R1a and J2, although I would not wager on their relative proportions and overall contribution to modern Iranian-speaking populations. For whatever reason, it seems that Kurds and Persians ended up with a J2-over-R1a advantage, while Pathans and (plausibly) Turkified Central Asian former Iranian speakers with the reverse. Nonetheless, the occurrence of both haplogroups in most Iranian groups, as well as in most Indo-Aryan ones is quite telling. It is unfortunate that the relationships between these Y chromosomes (still J2a*! six years after Sengupta et al.) and their West Eurasian brethren was not further pursued.

Hopefully, the data can be re-used down the road once the phylogeny of different haplogroups (and R1a in particular) is better understood. As I've stated before on this blog, I take Y-STR based age estimates with a huge grain of salt, so I would not put much faith in any of the ones presented in this paper.

Related: Firasat et al. (2006), Y-chromosomes of Afghanistan, Lashgary et al. (2011), Regueiro et al. (2006).

PLoS ONE doi:10.1371/journal.pone.0034288


Marc Haber et al.




High mtDNA mutation rate from deep-rooted Costa Rican pedigrees

American Journal of Physical Anthropology DOI: 10.1002/ajpa.22052

High mitochondrial mutation rates estimated from deep-rooting costa rican pedigrees

Lorena Madrigal et al.




Improved eigenanalysis with Minimum Average Partial test (Shriner 2012)




Human Heredity Vol. 73, No. 2, 2012


Daniel Shriner



mtDNA links between Africa and Europe, old and new (Cerezo et al. 2012)

Link to open access supplementary material.

Genome Research DOI: 10.1002/ajpa.22052

Reconstructing ancient mitochondrial DNA links between Africa and Europe

María Cerezo et al.




March 27, 2012

Cranial variation and the transition to agriculture in Europe

Students of physical anthropology won't be surprised that Pinhasi and von Cramon-Taubadel find that the Neolithic and pre-Neolithic populations in Europe were differentiated cranially as they were apparently genetically.

It has long been recognized that the ancient European population was different than the Upper Paleolithic population of the continent. Carleton Coon ascribed this differentiation to migration of narrow-faced Mediterraneans into the territory of the robust broad-faced Upper Paleolithics. Ilse Schwidetzky also viewed migration from the Southeast of gracile Mediterraneans who gradually replaced broad-faced Cro-Magnoids.

So, it is nice to read that the re-analysis of a wide assortment of skulls on 15 cranial variables has revealed that:
The major shape differences separating hunter-gatherer Mesolithic populations and farming Neolithic populations are coded by PC1 with Neolithic specimens having longer and taller vaults, and Mesolithic specimens having larger, and broader faces.
There are two (or three) puzzles in European prehistory:
  • How the latter became brachycephalized until early modern times
  • Why they have become partially debrachycephalized in the most recent of times
Anthropologists have tended to favor either migration or adaptation to explain these trends, with some even suggesting simple phenotypic plasticity without any major genetic change. It is now clear that -whatever the role of adaptation or plasticity- the Upper Paleolithic population of Europe did not simply change to become more gracile on its own, but was affected by an already gracile population of foreign origin who set the ball rolling. There is already work on the genetic basis of facial structure, so, it is quite possible that eventually we'll be able to track directly the genetic changes underlying the phenotypic transformation of Europeans.

From the paper:

Human Biology vol. 84

Cranial variation and the transition to agriculture in Europe

Ron Pinhasi, Noreen Von Cramon-Taubadel




March 26, 2012

Similarity matrices and clustering (Lawson and Falush)




Similarity matrices and clustering algorithms for population identification using genetic data

Daniel John Lawson and Daniel Falush


A large number of algorithms have been developed to identify population
structure from genetic data. Recent results show that the information used
by both model-based clustering methods and Principal Components Analysis
can be summarised by a matrix of pairwise similarity measures between
usually treating markers as independent but differing in the weighting given
to polymorphisms of different frequencies. Additionally, methods are now being
developed that better exploit the power of genome data by taking linkage
of common clustering algorithms, and evaluate their performance through a
after using a dimension reduction technique such as Principal Components
Based on these results, we describe the population structure signal
contained in each similarity matrix, finding that accounting for linkage leads
to significant improvements for sequence data. We also perform a comparison
on real data, where we find that population genetics models outperform
generic clustering approaches, particularly in regards to robustness against
features such as relatedness between individuals.


March 24, 2012

Report on the symposium on Modern Human Genetic Variation

Joshua Akey summarizes the talks of a recent symposium at the Swedish Royal Academy of Sciences. Two bits of information stand out from his report. The first:

In another talk focused on demography, Mattias Jakobsson (Uppsala University, Sweden) presented novel data on the impact of the agricultural revolution on the genetics of contemporary European populations. Specifically, Jakobsson and colleagues obtained nearly 250 Mb of sequence from three 5,000-year-old remains of Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia. Analysis of these sequences in the context of the present day European gene pool suggests that the spread of agriculture involved the northward migrations of farmers. Thus, these data provide the most direct and compelling support for the demic diffusion model of agriculture (as opposed to cultural diffusion) described to date. 

It seems I have my answer to the what's next question. Jakobsson has been doing some interesting work on the demography of human emergence and dispersal, so it will be interesting to see not only the novel sequences from these Neolithic Scandinavians, but also how they fit into existing models of demic diffusion.

The second bit of information:

Similarly, Jeff Wall (University of California San Francisco, USA) described a novel method for inferring archaic admixture, which he applied to publicly available whole-genome sequence data generated by Complete Genomics. Provocatively, he finds higher rates of introgression in Asians compared to Europeans. An advantage of Wall’s method is that it does not require an archaic genome to infer introgression, and thus he was able to also test the hypothesis that contemporary African genomes have signatures of gene flow with archaic human ancestors. Strikingly, Wall indeed did find evidence of archaic admixture in African genomes, suggesting that modest amounts of gene flow were widespread throughout time and space during the evolution of anatomically modern humans.

I guess that I shouldn't throw explanation #1 out the window yet. Wall was involved in the recent paper on archaic African admixture, which only looked at a small subset of the genome, so it is nice to see that he is now working with full genomes, and that the race to data mine complete genomes for archaic admixture is afoot.

The book of abstracts is online at the symposium site. The Jakobsson paper does seem to agree with our emerging picture of a non-local origin of northern European farmers as well as greater survival of pre-farming populations in the northern periphery of Europe, but it will be interesting to see where exactly extant populations fall on the farmer-hunter/gatherer continuum.
Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Northern Europe 
Mattias Jakobsson
Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden 
The prehistoric spread of farming in Europe has garnered intense interest for almost a century, and was one of the first questions to which population genetic data was used to investigate demographic hypotheses. However, the impact of the agricultural revolution on the European gene pool remains largely unknown. We obtained 249 million base pairs of quality-filtered human autosomal sequence data from some 5,000 year-old remains of three Neolithic hunter-gatherers and one Neolithic farmer excavated in Scandinavia, the northernmost fringe of agricultural practice at the time. Applying novel methods to study population structure based on low genome-coverage data, we find that Northern European Neolithic farmers are most similar to modern-day southern Europeans, contrasting sharply to Neolithic hunter-gatherers who are most similar to extant individuals from northern Europe. With most extant European populations appearing genetically intermediate between the two Neolithic groups, our results suggest that migration from the south by a genetically distinct group of humans accompanied the spread of agriculture to geographic regions where hunting and gathering was the mode of subsistence, but that admixture eventually shaped modern-day patterns of genomic variation.

Archaic admixture in the human genome 
Jeff D Wall
We describe a method that uses patterns of linkage disequilibrium in extant human populations to identify regions of the genome that were inherited from ‘archaic’ human ancestors, such as Neandertals, Homo erectus or H. floresiensis. We validate this approach using two recently published archaic human genomes, and show that several ancient admixture events must have occurred, both within and outside of Africa. We also explore differences in the amount of archaic admixture across different contemporary human populations.

Finally, here is the meeting report:

Investigative Genetics 2012, 3:7 doi:10.1186/2041-2223-3-7

Understanding human evolutionary history: a meeting report of the Swedish Royal Academy of Sciences symposium of modern human genetic variation 

Joshua M Akey

Link (pdf)

March 23, 2012

African American athletes have more European mtDNA than the general AA population

Does anyone have a theory why this is the case?



M. Deason et al.






  • 37.8% Southwestern
  • 37.7% Southeastern
  • 22.5% Northwestern
  • 1.9% African
  • 0.1% Far_Asian



  • 47.3% Atlantic_Baltic
  • 46.4% Southern
  • 3.1% Caucasus_Gedrosia
  • 1.7% Australasian
  • 0.9% African
  • 0.6% East_Asian






March 22, 2012

Projecting Sub-Saharan Africans on the European-East Asian axis

Continuing my exploration of Sub-Saharan origins, I projected African populations onto the Principal Components created by a set of European and East Asian populations. The set of SNPs was ascertained on a San individual, as before, and 112 European/110 East Asian individuals were used to avoid sample size issues.

Note that projecting populations onto PCs generated by other populations tends to make the projected populations regress to the mean somewhat. Overall, it appears that African populations are strongly shifted to the European side of the fist principal component.

There is a dearth of haplogroups of Sub-Saharan origin in Europe. Most of them occur as outliers, and in small percentages. Hence, the very strong shift of African populations towards Europeans cannot be ascribed to occasional African admixture in Europe.

Y-haplogroup E is the only major link between Africa and Europe, which is not also shared by Africa and East Asia. But, this haplogroup occurs at very small frequencies in all the included European populations, and at quite variable frequencies overall. As McEvoy et al. correctly observed, even Y-haplogroup E devoid European populations exhibit a closeness with Africans not shared by East Asians.

If admixture with Y-haplogroup E bearing males in Europe cannot account for the relative closeness of Africans to Europeans, what does? As I have mentioned in my review of McEvoy et al., there are two possibilities:

  • An Asian component not shared by Eurafricans is actually pulling East Asians away from Europeans and Africans. With the discovery of Denisovans and archaic-leaning Red Deer Cave people, this is a possibility that must be seriously entertained.
  • Y-haplogroup E bearers were originally closer to West than to East Eurasians. This is also quite likely, since the origins of haplogroup E are traced to East Africa from DE-bearing ancestors who may have well lived in Eurasia; Asia possesses both sister clades E and D, as well as both sister clades DE and CF one level-up. But, even if DE originated in East Africa itself, we must remember that the population there was originally different than many of the current inhabitants of the region, and may very well have been genetically closest to the emerging Proto-Caucasoids of the adjacent regions of Asia, rather than to the more distant human populations that would ultimately evolve into the East Asians of today.
I tend toward the second explanation -because of the relatively shallow divergence times between East Asians and Europeans, and the lack of any archaic Y-chromosomes/mtDNA. It is hard to imagine such a strong divergence being explained by a little archaic admixture in East Asia.

Interpreting the Beaker phenomenon in Mediterranean France

Antiquity Volume: 86 Number: 331 Page: 131–143

Interpreting the Beaker phenomenon in Mediterranean France: an Iron Age analogy

Olivier Lemercier

The author offers a new descriptive explanation of the Beaker phenomenon, by focusing on Mediterranean France and making reference to the Greek influx in the same area 2000 years later. In the Iron Age, the influence began with an exploratory phase, and then went on to create new settlements and colonise new areas away from the coast. The Beaker analogy is striking, with phases of exploration and implantation and acculturation, but adjusted to include a final phase where Beaker practice was more independent. Comparing the numerous models put forward to explain it, the author shows that immigration and a cultural package are both aspects of the Beaker phenomenon.


Keros: maritime sanctuary of the Early Bronze Age

Antiquity Volume: 86 Number: 331 Page: 144–160


Colin Renfrew1, Michael Boyd1 and Christopher Bronk Ramsey2

The sanctuary on the island of Keros takes the form of deposits of broken marble vessels and figurines, probably brought severally for deposition from elsewhere in the Cyclades. These acts of devotion have now been accurately dated, thanks to Bayesian analyses of the contemporary stratigraphic sequence on the neighbouring islet of Dhaskalio. The period of use—from 2750 to 2300 cal BC—precedes any identified worship of gods in the Aegean and the site is among the earliest ritual destinations only accessible by sea. The authors offer some preliminary thoughts on the definition of these precocious acts of pilgrimage.


March 20, 2012

Rare mtDNA haplogroups of North Asia

From the paper:


Miroslava Derenko et al.



mtDNA haplogroup HV4a1a from Franco-Cantabria

PLoS ONE 7(3): e32851. doi:10.1371/journal.pone.0032851

Genetic Continuity in the Franco-Cantabrian Region: New Clues from Autochthonous Mitogenomes

Alberto Gómez-Carballa et al.



The Late Glacial Maximum (LGM), ~20 thousand years ago (kya), is thought to have forced the people inhabiting vast areas of northern and central Europe to retreat to southern regions characterized by milder climatic conditions. Archaeological records indicate that Franco-Cantabria might have been the major source for the re-peopling of Europe at the beginning of the Holocene (11.5 kya). However, genetic evidence is still scarce and has been the focus of an intense debate.

Methods/Principal Findings

Based on a survey of more than 345,000 partial control region sequences and the analysis of 53 mitochondrial DNA (mtDNA) genomes, we identified an mtDNA lineage, HV4a1a, which most likely arose in the Franco-Cantabrian area about 5.4 kya and remained confined to northern Iberia.


The HV4a1a lineage and several of its younger branches reveal for the first time genetic continuity in this region and long-term episodes of isolation. This, in turn, could at least in part explain the unique linguistic and cultural features of the Basque region.


Dual origins of Sub-Saharan Africans?

A reader quotes from Coon's The Living Races of Man (1965):
''Meanwhile we may note that a detailed analysis of 571 modern Negro crania, made by advanced mathematical techniques, has shown that these crania gravitate between two poles, a Mediterranean Caucasoid and a Pygmy one. The former type is again divisible into an ordinary Mediterranean and a Western Asian type, which suggests more than a single northern point of origin for the Caucasoid element. As we shall in greater detail in Chapter 8 and 9, the Negroes resemble Caucasoids closely a number of genetic traits that are inherited in a simple fashion. Examples of these are fingerprints, types of earwax, and the major blood groups. The Negroes also have some of the same local, predominantly African, blood types as the Pymies. 
This evidence suggests that the Negroes are not a primary sub-species but rather a product of mixture between invading Caucasoids and Pygmies who lived on the edges of the forest, which at the end of the Pleistocene extended farther north and east than it does now.''
Since I'm not one to reject old theories just because they're old, I decided to test this particular idea. I used the San ascertainment panel of the Harvard HGDP dataset, and plotted all African populations, together with West and East Eurasian ones in a PCA plot:
African populations fall along a cline towards West Eurasian populations, with the most isolated Mbuti Pygmies on one end, and a tight blob of West Eurasian populations on the other. Hence, there is evidence for variable affiliation of Sub-Saharans with West Eurasians, but no real evidence for variable affiliation of West Eurasians with Sub-Saharans, except for the Mozabites and HGDP Arabs, with their well-known African admixture.

Nor can the results be explained in terms of more recent common ancestry of African farmers with Eurasians in general, because African populations fall in a clear cline towards West Eurasian populations.

While I would hesitate to say that the above results prove the correctness of Coon's theory, they're certainly quite consistent with it. It may very well be that Y-haplogroup E1b1 bearers from East Africa, descended from Y-haplogroup DE-YAP from Eurasia are ultimately responsible for the introduction of the Caucasoid component into Africa.

Maghrebi origin of early south Iberian Neolithic

Quaternary Research
Volume 77, Issue 2, March 2012, Pages 221–234

The Mesolithic–Neolithic transition in southern Iberia

Miguel Cortés Sánchez et al.

New data and a review of historiographic information from Neolithic sites of the Malaga and Algarve coasts (southern Iberian Peninsula) and from the Maghreb (North Africa) reveal the existence of a Neolithic settlement at least from 7.5 cal ka BP. The agricultural and pastoralist food producing economy of that population rapidly replaced the coastal economies of the Mesolithic populations. The timing of this population and economic turnover coincided with major changes in the continental and marine ecosystems, including upwelling intensity, sea-level changes and increased aridity in the Sahara and along the Iberian coast. These changes likely impacted the subsistence strategies of the Mesolithic populations along the Iberian seascapes and resulted in abandonments manifested as sedimentary hiatuses in some areas during the Mesolithic–Neolithic transition. The rapid expansion and area of dispersal of the early Neolithic traits suggest the use of marine technology. Different evidences for a Maghrebian origin for the first colonists have been summarized. The recognition of an early North-African Neolithic influence in Southern Iberia and the Maghreb is vital for understanding the appearance and development of the Neolithic in Western Europe. Our review suggests links between climate change, resource allocation, and population turnover.


March 19, 2012

The effects of ascertainment on admixture estimates

In a previous experiment, I discovered a clear signal of West Eurasian-like admixture in Sub-Saharan African populations, using a set of markers ascertained in a San individual. The marker panels of the Harvard HGDP dataset have been ascertained on different individuals from around the world, and so they are very useful in showing the effects of ascertainment on admixture estimates.

I have repeated the same K=5 experiment, using the ascertainment panels on a French, Han, Papuan1, San, and Yoruba individuals. Irrespective of the panel used, the same five components emerged: Asian, West-Eurasian, African, Australasian, and Amerindian. However, there are substantial differences in the inferred admixture proportions. The average admixture proportions can be found in this spreadsheet.

The levels of the "African" component in the HGDP African populations are summarized below:

These are almost the same in the French/Han/Papuan1 ascertainments, despite the different number of markers used. When SNPs are ascertained on Eurasian individuals, many SNPs present in African populations are not discovered, and hence, African populations appear "purer" by having a higher proportion of the "African" ancestral component.

However, when SNPs are ascertained on African populations, a different picture emerges, with clear evidence of West Eurasian admixture:

San ascertainment:
Yoruba ascertanment:

It is now evident that there is Eurasian admixture in African populations that was "hidden" in panels of SNPs ascertained on Eurasian individuals. Moreover, this Eurasian admixture seems to be more related to West Eurasians.

Someone might argue that the observed West Eurasian admixture in African populations is the result of a second migration Out-of-Africa that only affected West Eurasians. This, however, is a weak argument, because -with the exception of a few populations with known recent African admixture, such as the HGDP Arabs- there is no variation in African ancestry in Eurasia: it is everywhere virtually zero. On the contrary, in Africa, there are populations with a lot of West Eurasian admixture (Mozabites), intermediate (Yoruba, Bantu) and minimal (San, Pygmies). If the HGDP included more East African and Saharan populations, we would see an even clearer view of variable West Eurasian admixture throughout Africa. In short: the variable levels of West Eurasian admixture in Africa, coupled with the constant lack of any substantial African admixture in West Eurasia is a tell-tale sign that it was a West Eurasia-to-Africa migration, and not the reverse. 

This migration created a cline of West Eurasian admixture in Africa, with minima in isolated African hunter-gatherer (San/Pygmy populations), maxima in North and East Africa, and sharp transitions across geographical barriers (such as the Sahara), or ethnic differences (e.g., African agriculturalists vs. foragers). It is no longer tenable to view West Eurasian back-migrations as limited events that affected only North and East Africa: their effects are clearly evident throughout Africa, having affected different populations to a different extent.

The existence of Eurasian admixture throughout Africa is an interesting and novel finding. How much such admixture is there? As I explain here, in the case of admixed populations, the proportion of foreign admixture of a population increases if we include "purer" indigenous populations: Mexican Mestizos are less "European" if remote Amazonians are included in the analysis; North Indians appear more "South Asian" if South Indian tribals are excluded.

The African hunter-gatherers (San and Pygmies) are the least admixed Africans currently in existence, but we cannot tell what their proportion of indigenous African vs. Eurasian ancestry actually is. We simply don't have the genomes of pre-back-migration Africans to compare against, although there are strong hints from palaeonathropology that these included forms that do not fit within the present-day Homo sapiens continuum, such as Iwo Eleru.

It is at present unknown what percentage of African genomes is derived from Eurasian back-migrants, anatomically modern humans in Africa, as well as more divergent indigenous African hominins.

Hopefully the techniques of "virtual genomes", inference techniques allowing migration, such as TreeMix, together with full genome sequencing, and (hopefully) ancient African DNA will help elucidate the emerging picture of the multiple origins of the Sub-Saharan Africans. Africa may have been the cradle of H. sapiens but many of her Eurasian sons came back.

Panel for admixture inference in Americas

This is based on only a few hundred AIMs, but nonetheless is quite useful because it reports new data for a variety of South American populations.



Joshua Mark Galanter et al.

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.


March 18, 2012

Neandertal/Denisovan admixture using PCA and ADMIXTURE (and another African surprise)

I have repeated the previous experiment, but this time I created K=5 synthetic populations from the components inferred by ADMIXTURE in the Harvard HGDP set. At K=5, the five inferred components corresponded to Sub-Saharan, West-Eurasian, East-Asian, Amerindian, and Australasian populations.
It is noteworthy, that for the first time, some deep Sub-Saharan African populations show evidence of Eurasian admixture; the type of this admixture is not clear, but it seems to be mostly West rather than East Eurasian. It may, in fact, reflect an element that was already West Eurasian-like, since there is a definite excess of the West Eurasian-centered component in the Sub-Saharan populations.

Note that this element was picked up because the SNP ascertainment was done on a San individual.  The San were not generally used for the ascertainment of SNPs in commercial SNP arrays designed for association studies, and hence their SNP diversity is generally under-reported. But, the panel4 of SNPs was ascertained in a San individual with full genome sequencing (as described in the Harvard HGDP materials).

Hence, it appears that Yoruba are 82.9% of the San-centered component, BantuKenya 78.3%, BantuSouthAfrica 86.9%, BiakaPygmy 94.7%, Mandenka 80.9%, MbutiPygmy 97.9%. San-centered components have appeared before in ADMIXTURE experiments, but the crucial difference here is that the remainder of the African populations' ancestry does not fall in another Sub-Saharan-centered component, but rather in the Eurasian ones.

Remembering that ~0% in an ADMIXTURE component means minimum -in the context of the studied set of populations- not zero, influence, we can reasonably infer that the San and Pygmy groups have minimal Eurasian influence, and not that it is absent entirely. Just as the Eurasian ancestry in other Sub-Saharan Africans turned up when we ascertained SNPs in the San, so could the Eurasian ancestry in the San turn up if we ascertain SNPs in an even more divergent African population. Unfortunately, we're out of luck, because the San are the most divergent African population currently in existence, having barely survived the recent Bantu onslaught.

In order to determine how much, i.e., whether there has indeed been a major episode of admixture between a Eurasian-like and a very divergent (unknown) African hominin, we would have to have the genome of that hominin (like we do with Neandertals and Denisovans), and measure how shifted towards it different populations are. I don't hold high hopes that the African heat will provide such an ancient genome, but if such a population did in fact persist down to the Holocene boundary, there may yet be hope of discovering their DNA directly. Otherwise, it will take ingenuity with full genomes of modern populations to test the hypothesis.

Getting back on topic, below is the projection of the 5 ancestral components onto the PCA created by chimp, Denisova, and Neandertal

The exact average positions of the different groups are:

# Population Sample_Size PC1 PC2

1         Chimp  1  0.815 -0.051
2       Neander  1 -0.452 -0.680
3      Denisova  1 -0.363  0.731
4    East-Asian 50  0.034 -0.011
5 West-Eurasian 50  0.033 -0.013
6   Sub-Saharan 50  0.050 -0.001
7  Australasian 50  0.024  0.000
8    Amerindian 50  0.034 -0.012

So: Neandertals are "bottom left", and Denisova are "top left". The plot of the ancestral components, for the "central" portion of modern human populations:
The results are as expected, and there may even be a hint of a little excess of "Neandertal" influence in  the West Eurasian population -relative to East Asians- in accordance with what John Hawks has reported. Also, if the Yoruba are 17.1% more Eurasian than the San, then the little Neandertal ancestry in them detected by Hawks's experiments is immediately explained.

March 16, 2012

Neandertal/Denisovan admixture using PCA

Eric Durand at 23andMe developed a test of Neandertal ancestry based on PCA. The main idea is to map modern human samples onto a PCA space of Chimpanzee, Neandertal, and Denisova, and see if there are any shifts in direction towards the two archaic hominins.

I tried my hand at replicating this experiment using the Harvard HGDP set. In particular I used the panel4 of SNPs, ascertained on a San individual. Below is the broad-view PCA:

blue (top left) = Neandertal
green (bottom left) = Denisova
red (right) = Chimp

Now, here is a blowup of the middle portion of the figure, on human populations.

As expected, Eurasians deviate from Africans in a Neandertal direction, while, Papuans deviate from Eurasians in a Denisova direction.

TreeMix analysis of North Eurasians (and an African surprise)

I have used my K12b dataset to isolate a set of 537 individuals who had less than 10% membership in the South Asian, Northwest African, Southeast Asian, South Asian, East African, Gedrosia, South Asian, East African, Southwest_Asian, and Sub_Saharan components. Hence, the remaining 537 individuals had 90%+ membership in the remaining Atlantic_Med, North_European, Caucasus, Siberian, and East_Asian components.
  • The Atlantic_Med component is frequent in northwestern Europe
  • The North_European component is dominant in northeastern Europe and forays into Siberia
  • The Caucasus component is dominant in the Caucasus and forays into Central Asia
  • The Siberian component is dominant in North Asia and forays into Europe
  • The East_Asian component is frequent in East Asia and forays into North Asia
This pruning procedure may not be perfect, but it helps isolate a dataset consisting (mostly) of North Eurasian individuals. Furthermore, I removed all populations who had less than 5 remaining individuals after the first pruning step. Hence, in the end, I had a dataset of 38 populations/452 individuals. The remaining populations were:
Russian_D, Polish_D, German_D, Finnish_D, Swedish_D, Mixed_Slav_D, Norwegian_D, Lithuanian_D, Japanese_D, Daur, French, French_Basque, Hezhen, Japanese, Oroqen, Russian, Sardinian, Yakut, CEU30, JPT30, Belorussian, Chuvashs, Hungarians, Lithuanians, Romanians, Selkup, Evenk, Tuva, Yukagir, Nganassan, Dolgan, Buryat, Mongol, FIN30, Kent_1KG, Bulgarians_Y, Ukranians_Y, Mordovians_Y
Additionally, a sample of 30 Yoruba from the HapMap-3 was used as an outgroup.

TreeMix analysis

The TreeMix analysis was performed with default parameters, and allowing for a different number of migration edges.

Nomenclature: The direction of gene flow is best seen in the figure and/or associated treeout files.
For the text, I will put in (), the common ancestor of two populations, e.g., (French_Basque,Sardinian) and also as (X, *) the tree rooted at a particular node X, e.g., (Buryat, *)

0 migration edges:

The West and East Eurasian clusters are identified, with some populations with likely admixture being placed closer to the Eurasian root.

1 migration edge:
64% from (Sardinians/Basques) to Yoruba; this is difficult to interpret, but there has been evidence in the past that Africans and West Eurasians share more ancestry than Africans and East Asians do. In the linked post, I proposed a major episode of back-migration into Africa, and it is perhaps this that is being captured by this migration edge: Sardinians/Basques are the only two South-West Eurasian populations included, and any back-migration into Africa must have originated in the southern parts of West Eurasia.

Such a high level of back-migration may in fact be plausible, since Yoruba are a predominantly Y-haplogroup E bearing population, and the origin of the DE clade of the human Y-chromosome phylogeny is up in the air with both an African and Eurasian case having been advanced. Personally, I favor the Eurasian case, since within the CT clade, we have two subclades: CF (Eurasian) and DE (Eurasian/African).

Interestingly, John Hawks has recently discovered an unanticipated excess of "Neandertal ancestry" in Yoruba. This may also point to a back-migration into Africa and/or admixture of a group of Africans related to Eurasians (whom I've called Afrasians), with groups of Africans (Palaeoafricans) that split before the H. sapiens/H. neandertalensis common ancestor.

There is, however, another detail in the figure that may have escaped your notice: there is now about 0.5 worth of drift in the figure (left-to-right) as opposed to only 0.12 in the tree without migration edges. So, perhaps what we are seeing is indeed the first sign of admixture between modern and archaic humans in Africa, which has been made more likely by recent anthropological discoveries.

It's not clear to me whether TreeMix has stumbled onto something important or not, but it is certainly worth keeping in mind that the above model fits the data better than the simple tree model. Moreover, TreeMix attempts to reverse the polarity of migration edges, and -apparently- the (Sardinian, French_Basque)-to-Yoruba edge is preferable to the reverse.

So, we should keep our minds open to the possibility that the greater similarity of West Eurasians to Africans is not the result of multiple Out-of-Africa waves, one of which affected only West Eurasians, but of an Into-Africa back-migration from West Eurasia.

So far, tree-based models have focused on how diverse African groups are, and hence, the reduced diversity of Eurasians has been interpreted as an Out-of-Africa bottleneck that carried a subset of African variation into Eurasia.

But, there is an alternative interpretation of the evidence, namely that African groups are diverse because they carry a superset of ancient Into-Africa variation, with the African-specific part of their variation being the result of admixture with pre-existing African hominins. Such a scenario cannot be captured by tree models, but is apparently considered and not rejected by TreeMix which allows for lateral gene flow. Let's wait and see what new things come from full genome sequencing.

2 migration edges:

The (French_Basque/Sardinian)-to-Yoruba edge persists (64%) and a new edge was added from  (Buryat, *)-to-Mongol (85%). The "Mongol" sample consists of Siberian Mongols described by Rasmussen et al. (2010). An inspection of their K12b population portrait indicates that they do, in fact, have West Eurasian admixture, which according to the K12b spreadsheet amounts to about 18% in total. 

3 migration edges:
The aforementioned (French_Basque/Sardinian)-to-Yoruba (64%) and (Buryat,*)-toMongol (85%) edges persist, and now we have a 68% Nganasan-to-Selkup edge. 

These are the two Siberian Uralic populations in the dataset. This seems to parallel the K12b results, as Selkups have a North_European element which the Nganasans (Uralic speakers from the Arctic coast of Central Siberia lack), so we are seeing the hybridity of the Selkups here, who, like the Mongol sample are partly of West Eurasian ancestry.

4 migration edges:

The aforementioned (French_Basque,Sardinian)-to-Yoruba (64%), (Buryat,*)-to-Mongol (84%), and Nganasan-to-Selkup (68%) persist, and now we have a 89% (Buryat, *)-to-Tuva edge. According to the K12b the Tuva have 13.3% West Eurasian admixture, so again we have reasonably good agreement between TreeMix and ADMIXTURE. 

Interestingly, the non-"eastern" component of Selkups and Tuvans now forms a clade. It seems that a Nganasan-like and a (Buryat, *)-like population have converged into southern Siberia, absorbed a common local element and became the Selkup and Tuva respectively.

5 migration edges:

The aforementioned (French_Basque,Sardinian)-to-Yoruba (64%), (Buryat,*)-to-Mongol (85%),  Nganasan-to-Selkup (68%) persist, and 90% (Buryat, *)-to-Tuva persist, and now we have a new 18% Oroqen-to-(Yakut, Evenk) edge. The Oroqen and the Evenk are Tungusic speakers, whereas the Yakut are Turkic people from northeastern Siberia, having migrated there from the vicinity of Lake Baikal during the last millennium.

migration edges:

The aforementioned (French_Basque,Sardinian)-to-Yoruba (64%), (Buryat,*)-to-Mongol (85%),  Nganasan-to-Selkup (68%), 90(Buryat, *)-to-Tuva persist, 18% Oroqen-to-(Yakut, Evenk), persist, and a new 16% Nganasan-to-Oroqen edge appears. Interestingly, this has allowed the Oroqen and Hezhen to now form their own clade, which makes sense as these are both Tungusic speakers from northeastern China. The other Tungusic population, the Evenk group with the Turkic Yakut: what they share in common is that they both share origins close to Lake Baikal in Siberia.

migration edges:

The aforementioned (French_Basque,Sardinian)-to-Yoruba (64%), (Buryat,*)-to-Mongol (85%),  Nganasan-to-Selkup (68%), 90(Buryat, *)-to-Tuva persist, 18% Oroqen-to-(Yakut, Evenk),  16% Nganasan-to-Oroqen edges persist, and there is a new 81% Evenk-to-Yukagir edge. The remainder of the Yukagirs' ancestry is derived from the West Eurasian tree. The Yukagir language is rather mysterious, with some links to Uralic having been postulated. Here it pays off to look at the population portraits, since it is apparent that -unlike the Selkup- their West Eurasian ancestry is limited to a few individuals.

It is fairly interesting that Russian anthropologists placed the Yukagirs in the Baikal group of the Central Asian race, the same as the Evenks, who are their biggest donors. So, Yakuts, Evenks, and Yukagirs all seem to share the same Baikal-type of origin.

migration edges:
There is now a 64% Sardinian-to-Yoruba edge, a 16% Oroqen-to-Yukagir edge, 20% (Buryat, *)-to-(Yakut, Evenk), and a 24% Nganasan-to-Chuvash edge, 29% Oroqen-to-(Yakut,Evenk) edge, 88% (Buryat, *)-to-Tuva, 62% Nganasan-to-Selkup, 85% (Buryat, *)-to-Mongol. 

The tree has been rather re-organized, with two main Siberian groups identified: an eastern group (Hezhen, Daur, Oroqen, Buryat), and a central group (Yukagir, Dolgan, Nganasan, Yakut, Evenk, Selkup). The Chuvash, predominantly Europeoid Turkic speakers from Russia show evidence of gene flow from the central group as well, whereas the Selkup, Uralic speakers from Siberia, who belong to the central group, show evidence of gene flow from Europe.

migration edges:

64% (French_Basque,Sardinian)-to-Yoruba, 85% (Buryat, *)-to-Mongol, 68% Nganasan-to-Selkup, 92% (Buryat,*)-to-Tuva, 14% Oroqen-to-(Yakut,Evenk), 14% Nganasan-to-Oroqen, 82% Yakut-to-Yukagir, 90% Evenk-to-Dolgan, 13% Hezhen-to-(Nganasan, *).

10 migration edges:

64% (French_Basque, Sardinian)-to-Yoruba, (85% Nganasan, *)-to-Mongol, 68% Nganasan-to-Selkup, 92% (Nganasan,*)-to-Tuva, 15% Oroqen-to-(Yakut,Evenk), 15% Nganasan-to-Oroqen, 82% Yakut-to-Yukagir, 90% Evenk-to-Dolgan, 43% Hezhen-to-Buryat, 14% Sardinian-to-Bulgarian.

I will stop at this point. I may add more migration edges later to this post, but I'm tired of typing this stuff.

You can download all the plots and *.treeout files here.

UPDATE (March 20): I have repeated the experiment with HGDP San, rather than Yoruba as the outrgroup:

There is now a 63% migration edge from (Basque, Sardinian) to San.

March 15, 2012

Small number of founders of modern Taurine Cattle


Modern Taurine Cattle descended from small number of Near-Eastern founders

Ruth Bollongino et al.




March 14, 2012

Late archaic humans from Longlin and Maludong

This is an extremely important find, as it shows the late persistene of archaic humans in East Asia down to the edge of the Holocene. Archaic humans of the same apparent age have recently been published in Nigeria and there are many finds with a mixture of archaic and modern qualities in Africa, such as the ones from Dar-es-Soltane and Temara mentioned by the authors for North Africa.

The authors propose two different scenaria: one that the archaic specimen from Longlin is derived from a morphologically variable African population; the other that it represents an indigenous archaic remnant.

From the paper:
The evidence is slowly mounting for the place of origin of fully modern H. sapiens, as region after region strikes out by having archaic humans present when they are not supposed to be there. Both Sub-Saharan Africa and East Asia have struck out, and Europe had already struck out because of its documented Neandertal population. Australasia is not a valid option due to the lack of precursors, and the Americas because of the their late settlement.

That leaves two options: northernmost Africa (what is now desert) and Arabia/the Gulf Oasis/Indian subcontinent. I'd say that things are looking good for my two deserts theory.

UPDATE: From the New Scientist:







Darren Curnoe et al.



Methodology/Principal Findings


