December 30, 2011

Climate and body composition

Am J Phys Anthropol DOI: 10.1002/ajpa.21591

Ecogeographical associations between climate and human body composition: Analyses based on anthropometry and skinfolds

Jonathan C.K. Wells et al.


In the 19th century, two “ecogeographical rules” were proposed hypothesizing associations of climate with mammalian body size and proportions. Data on human body weight and relative leg length support these rules; however, it is unknown whether such associations are attributable to lean tissue (the heat-producing component) or fat (energy stores). Data on weight, height, and two skinfold thickness were obtained from the literature for 137 nonindustrialized populations, providing 145 male and 115 female individual samples. A variety of indices of adiposity and lean mass were analyzed. Preliminary analyses indicated secular increases in skinfolds in men but not women, and associations of age and height with lean mass in both sexes. Decreasing annual temperature was associated with increasing body mass index (BMI), and increasing triceps but not subscapular skinfold. After adjusting for skinfolds, decreasing temperature remained associated with increasing BMI. These results indicate that colder environments favor both greater peripheral energy stores, and greater lean mass. Contrasting results for triceps and subscapular skinfolds might be due to adaptive strategies either constraining central adiposity in cold environments to reduce cardiovascular risk, or favoring central adiposity in warmer environments to maintain energetic support of the immune system. Polynesian populations were analyzed separately and contradicted all of the climate trends, indicating support for the hypothesis that they are cold-adapted despite occupying a tropical region. It is unclear whether such associations emerge through natural selection or through trans-generational and life-course plasticity. These findings nevertheless aid understanding of the wide variability in human physique and adiposity.


December 29, 2011

Chinese, Korean, Japanese (genetic edition)

My 2006 post on facial composites of Chinese, Korean, and Japanese women is, surprisingly, the most widely read single entry of this blog. People still occasionally guess "who is who" in that post, five years later.

As I was going through the list of the Dodecad populations, I realized that there are 5+ participants in each of the Korean, Japanese, and Chinese groups. So, it seemed like a simple exercise to see whether the relatively high success rate of people's guesses could be corroborated using the DNA data.

Below is the MDS plot; there are 9 Chinese, 5 Japanese, 5 Koreans in the Dodecad Project; I have also added 30 HapMap Chinese (CHB) and Japanese (JPT):
Only the first MDS dimension showed deviation from normality according to a Shapiro-Wilk test. Using MCLUST, that dimension was enough (as can be seen from the above figure) to infer the presence of 3 clusters which corresponded to the 3 groups, with 100% correct assignments.

Interestingly, when I did not use the extra HapMap individuals, MCLUST did not split Koreans from Chinese. This goes to show that the absence of apparent structure does not imply absence of structure. The extra Chinese and Japanese individuals helped flesh out the existing structure in these East Asian groups.

Below is the list of the Dodecad populations that are below the 5-individual limit:

Algerian_D 4 East_African_Various_D 3 Greek_Italian_D 2 Belgian_D 1
North_African_Jews_D 4 Danish_D 3 Swiss_German_D 2 Latvian_D 1
Slovenian_D 4 Tunisian_D 3 Szekler_D 2 Estonian_D 1
Mixed_Scandinavian_D 4 Austrian_D 3 Mandaean_D 2 Bangladesh_D 1
Moroccan_D 4 Saudi_D 3 Azeri_D 2 Yemenese_D 1
Serb_D 4 Pakistani_D 3 Czech_D 2 Sri_Lanka_D 1
Tatar_Various_D 3 Georgian_D 2 Hungarian_D 1
Palestinian_D 3 Kazakh_D 2 Basque_D 1
Romanian_D 3 Udmurt_D 1
Ukrainian_D 1
Egyptian_D 1

If you belong to one of the above groups (all 4 grandparents) and have tested with either 23andMe or Family Finder, you are especially invited to contact me at (but do not send data right away!), about possible inclusion in the project. 

For example, in the most recent Clusters Galore analysis, there was a generic "Balkan" cluster. Does this imply that Balkan ethnic groups cannot be distinguished from each other, or that sample sizes are simply not yet sufficient to make manifest the existing structure?

Forensic analysis of King Tut and his relatives

DNA Tribes has released an analysis, based on 8 forensic autosomal STR markers, of the "Amarna Pharaohs". The analysis is based on data from Ancestry and Pathology in King Tutankhamun's Family.

The results of the DNA Tribes analysis can be seen below:

They seem to indicate that there is something definitely "African" about this collection of mummies. I have previously used PopAffiliator and STRUCTURE with CODIS markers. The results of that analysis suggest that even this small number of markers is sufficient to place a sample in a continental group with high accuracy, but insufficient to estimate levels of admixture. There is a new version of PopAffiliator, which, unfortunately, does not allow for incomplete data entry, and hence cannot be used to verify the results of the DNA Tribes analysis.

The DNA Tribes results are interesting, but may hinge upon a few marker values that are more prevalent in Africa than in Eurasia. Also, it is not clear which population(s) make up the "North African" group. It would be interesting to extract full genome sequences from Egyptian mummies in order to properly place them in the global genetic landscape.

Pictorial evidence in Egyptian art, as well as the statements of classical Greco-Roman authors strongly suggest that the ancient Egyptians occupied an intermediate position in the phenotypic continuum between Near Eastern and "Ethiopian" people. It is also clear that there was variation within ancient Egypt itself: geographic, temporal, and even perhaps social aspects of this variation may have existed. But these qualitative observations are no substitute for the harder type of evidence that can be provided by authentic ancient DNA.

Hopefully, the debate on the genetic identity of the ancient Egyptians can proceed on the basis of new data, although I am not holding my breath that this will happen anytime soon, both because of the fluid state of politics in Egypt itself, the existence of various fringe theories outside of Egypt, and, the rather controversial state of mummy DNA analysis itself.

December 28, 2011

Genetic structure in China

After my experiment on Spain, I decided to carry out a similar experiment in China, for which there is a large number of regional/ethnic sub-populations.15 clusters were inferred with 22 MDS dimensions.

The Uygur are the clear outlier population, doubtlessly due to their substantial Caucasoid admixture and geographical position in Central Asia, a region that was traditionally at the outskirts of Chinese civilization. Other Altaic speakers (both Mongolic and Tungusic) are also divergent, as are the Dai/Lahu people from the China/Thailand/Laos area.

Interestingly, the Tujia people from Central China seem to be the ones most like the Han overall, with Hmongic Miaozu/She more like the southern Han.

Craniofacial Differences Between Modern and Archaeological Asian Skeletal Populations (Ph.D. thesis)

From p. 169:
Since physical changes have been documented in these Asian populations, principal components analyses were conducted for certain variable groupings in each population to understand how crania shape were related. Based on visual inspection, ancient crania appears to be long and narrower compared to their more modern counterparts, and these tests will illustrate which portions of the crania are changing over time.
p. 181:
Since physical differences were shown to be present between the two ethnic groups, shape and size changes were calculated to understand how the crania have changed over time. Principal components analysis was calculated using transformed log variables of the dataset to determine which measurements were changing. All populations appeared to be extremely divergent from one another, resulting in unequal variancecovariance matrices. Modern Chinese individuals appear to have a shorter head than their ancient counterpart while modern Thais tend to have narrower faces and heads than their ancestral group.
p. 187:
None of the variable groupings show a close biological relationship between modern populations. However, the modern Thai population did show a closer biological relationship with the modern Chinese than with either archaeological population. One possible reason for this outcome is due to the influx of Chinese immigrants to Thailand that eventually became part of the gene pool. However, gene flow did not work in reverse with Thai people moving into China. For the most part Thai people remained ethnically Thai and Chinese people remained Chinese.
p. 197:
Modern Chinese individuals appear to have narrower and longer crania, which is opposite than expected. Ancient Chinese crania have higher cranial vaults than their modern counterparts, which contributes to their divergence. Facial variables that appear to be most divergent are ones that measure for prognathism and upper facial height. Modern Chinese individuals have longer upper facial height but are not as prognathic as their ancient counterparts.

Craniofacial Differences Between Modern and Archaeological Asian Skeletal Populations

Chan, Wing Nam Joyce

The principal objective of this study is to perform a biological distance analysis of two Asian ethnic groups to better understand environmental factors influencing cranial shape and size. Cranial shape and size are influenced by both epigenetic and genetic factors, resulting in differences in crania over time. Cranial measurements can be used as a proxy for genetic data and to understand epigenetic factors affecting crania. Therefore, craniometrics can be used to determine differences between populations.

Ancient and modern Chinese and Thai skeletal populations were used for this biological distance analysis. The ancient Chinese population is from northern China at Anyang dating to the Shang Dynasty (1600BC-1046BC) while its modern counterpart is located in Hong Kong dating from 1977-1983. Individuals from both populations are thought to have belonged to the Han ethnic group and are possibly biologically related. Both Thai populations are located in northeastern Thailand, known as the Isaan region. The ancient Thai population from the Ban Chiang site is dated through the Pre-metal to Iron Age periods (2000 B.C.- 200 A.D.) while the modern population dates from 1970s to present. Data were collected on crania at 29 anthropologically accepted measurements to explore epigenetic and biological relationships between modern and ancient populations. Data were subjected to multiple multivariate statistical tests to understand causative agents for change and differences between populations.

These results suggest that modern and ancient Thai and Chinese populations have markedly different crania, especially in shape. However, correlated factors could not be identified in this study, primarily due to lack of historical data. Geographical, temporal, and climate variables such as temperature were tested against measures of biological distance with little to no correlation discovered. Interestingly, modern and ancient Chinese populations displayed the closest biological affinity, possibly due to similar environments and lack of genetic changes. Ban Chiang individuals were the most biologically distant from other populations, indicating possible genetic differences not yet understood. These genetic differences could indicate either that Ban Chiang individuals are not recently ancestral to the modern Thai population or a mass migration movement into northeast Thailand had occurred.

These results are interpreted to indicate that environmental factors have played a large role in altering cranial shape in these two ethnically Asian populations since genetic alteration in the areas has not been documented. Environmental factors have caused isometric changes in cranial shape as crania have become distinct from their ancestral counterparts. Cultural changes, such as diet shifts and modernization, are possible causative agents for these changes witnessed in these populations.

The findings of this study contribute to our understanding of human cranial variation for these two Asian groups, and to broader discussions of epigenetic and genetic relationships in the expression of cranial morphology. This research also contributes to the discussions of how biological distance in the crania has been influenced by epigenetic factors and ultimately how the peopling of modern Asia occurred.


Southeast Asian origin of dogs (again)

PLoS ONE 6(12): e28496. doi:10.1371/journal.pone.0028496

Phylogenetic Distinctiveness of Middle Eastern and Southeast Asian Village Dog Y Chromosomes Illuminates Dog Origins

Sarah K. Brown et al.

Modern genetic samples are commonly used to trace dog origins, which entails untested assumptions that village dogs reflect indigenous ancestry or that breed origins can be reliably traced to particular regions. We used high-resolution Y chromosome markers (SNP and STR) and mitochondrial DNA to analyze 495 village dogs/dingoes from the Middle East and Southeast Asia, along with 138 dogs from >35 modern breeds to 1) assess genetic divergence between Middle Eastern and Southeast Asian village dogs and their phylogenetic affinities to Australian dingoes and gray wolves (Canis lupus) and 2) compare the genetic affinities of modern breeds to regional indigenous village dog populations. The Y chromosome markers indicated that village dogs in the two regions corresponded to reciprocally monophyletic clades, reflecting several to many thousand years divergence, predating the Neolithic ages, and indicating long-indigenous roots to those regions. As expected, breeds of the Middle East and East Asia clustered within the respective regional village dog clade. Australian dingoes also clustered in the Southeast Asian clade. However, the European and American breeds clustered almost entirely within the Southeast Asian clade, even sharing many haplotypes, suggesting a substantial and recent influence of East Asian dogs in the creation of European breeds. Comparison to 818 published breed dog Y STR haplotypes confirmed this conclusion and indicated that some African breeds reflect another distinct patrilineal origin. The lower-resolution mtDNA marker consistently supported Y-chromosome results. Both marker types confirmed previous findings of higher genetic diversity in dogs from Southeast Asia than the Middle East. Our findings demonstrate the importance of village dogs as windows into the past and provide a reference against which ancient DNA can be used to further elucidate origins and spread of the domestic dog.


The function of the Aterian

From the paper:
The ability of human hunters to ‘kill at a distance’ [1], [2] is often considered one of the hallmarks of modern human behavior. Such an ability embodies the cultural transcendence of the human body's condition with the aid of technology and has deep implications for the self-understanding of our species's uniqueness in the animal kingdom. For this reason, the search for evidence of projectile weapon technologies in the Stone Age has superseded the search for evidence of mere hunting activities, the latter having slid in the background of pre-human hominin behavioral repertoire [3]–[5]. Because ‘safe hunting’ is considered to have given anatomically-modern humans a competitive advantage against Neandertals during the last Out-of-Africa event (e.g., [6], [7]), it is extremely important to rigorously examine claims for the existence of such technologies, even when the superficial examination of the morphology of a particular tool suggests a clear functional determination. Such is the case of the Aterian tanged (or stemmed) point, a type of stone tool found throughout North Africa in a variety of ecological, geographical, and chronological contexts within the African Middle Stone Age (MSA), and which exhibits a simple form that is sometimes reminiscent of stemmed arrowheads or spear points from much later time periods (Figure 1). ... The importance of correctly interpreting the function of Aterian stemmed tools is underlined by recent dating results, which suggests that, contrary to early assumptions, it could date to as early as MIS 5 and before [29]. More specifically, new dates from a series of sites, such Mugharet el-Aliya [30], Rhafas [31], Ifri n'Ammar [29], Dar-es-Soltan [32], and Contrebandiers [33] have demonstrated that tanged tools can be found in the earliest part of the North African Middle Stone Age, making them potentially the earliest evidence of prehistoric stone-tipped weaponry. However, the precise way in which they actually fit within a prehistoric technological system, including whether or not they were part of flying projectile armatures or thrusting spears, has never been rigorously determined, despite the crucial role that both projectiles and hafting are thought to play in the evolution of human cultural adaptations.
Several lines of evidence point in the direction of progressive resharpening of Aterian tools in the same manner as edge-tools such as scrapers and cutting-tools. This does not per se rule out an initial use for some Aterian pieces as weapon tips, because the ultimate use of each individual tool must be determined by the examination of use-traces, and because each episode of retouch likely wipes out previous uses of the tool. However, the data presented here make a strong case for the claim that, in general, these tools were probably hafted and used repeatedly for tasks that resulted in the need to rejuvenate edges rather than point-tips. The comparison between excavated, mostly cave contexts, and surface sites reveals that they both contain similar reduction trajectories and shape variabilities of tanged tools. This indicates that the functional emphasis on the tools was similar during their use-life in the landscape and at the repeated-occupation sites, which contradicts the expectations of breakage and repair patterns associated with a use as projectile tips [62], [63].
It is thus possible that hafting was practiced on both sides of the Mediterranean Sea, but in different ways. Although some of the differences in technological innovation between archaic and modern humans that we observe at the continental and species level may be due to cognitive differences or to demographic factors influencing the spread and accumulation of information [79], [80], we must not forget the essentially functional character of toolkits. Especially when comparing and evaluating technologies at very large scales, functional responses to specific technological problems (such as prey size and behavior [1] or increased risk associated with prey frequency and ease of hunting (e.g., [81]–[84])) may trump other factors. Even if the ultimate cause underpinning technological change is a large-scale environmental phenomenon, such as a rapid cooling event, or the aridity of a newly-colonized area, we can understand these associated changes only by unraveling the constraints imposed on toolkits by the subjects of the actions for which the tools themselves were used. Thus, perhaps the better question to answer regarding the Aterian might not be if it represents the earliest hunting weapons technology, but rather, in what way it arose out of new challenges posed by the environments that characterized North Africa since MIS 5, and how it adapted during the almost 100 thousand years of occupation of this region.
PLoS ONE 6(12): e29029. doi:10.1371/journal.pone.0029029

Shape Variation in Aterian Tanged Tools and the Origins of Projectile Technology: A Morphometric Perspective on Stone Tool Function

Radu Iovita


Recent findings suggest that the North African Middle Stone Age technocomplex known as the Aterian is both much older than previously assumed, and certainly associated with fossils exhibiting anatomically modern human morphology and behavior. The Aterian is defined by the presence of ‘tanged’ or ‘stemmed’ tools, which have been widely assumed to be among the earliest projectile weapon tips. The present study systematically investigates morphological variation in a large sample of Aterian tools to test the hypothesis that these tools were hafted and/or used as projectile weapons.

Methodology/Principal Findings Both classical morphometrics and Elliptical Fourier Analysis of tool outlines are used to show that the shape variation in the sample exhibits size-dependent patterns consistent with a reduction of the tools from the tip down, with the tang remaining intact. Additionally, the process of reduction led to increasing side-to-side asymmetries as the tools got smaller. Finally, a comparison of shape-change trajectories between Aterian tools and Late Paleolithic arrowheads from the North German site of Stellmoor reveal significant differences in terms of the amount and location of the variation.

Conclusions/Significance The patterns of size-dependent shape variation strongly support the functional hypothesis of Aterian tools as hafted knives or scrapers with alternating active edges, rather than as weapon tips. Nevertheless, the same morphological patterns are interpreted as one of the earliest evidences for a hafting modification, and for the successful combination of different raw materials (haft and stone tip) into one implement, in itself an important achievement in the evolution of hominin technologies.


December 27, 2011

Y-chromosome of Emperor Cao Cao: O2

Thanks to the wonders of population genetics, not only do we have a good inference of the Y-haplogroups of Cao Cao and Cao Shen, but we can also falsify (?) the claim of descent of a Chinese emperor from 18-19 centuries ago.

That's 4x deeper in time than the Y-haplogroup of Nurhaci. It would be great if a similar study could produce conclusive results for Confucius descendants.

And, I'm sure that the burial sites of many important European historical figures are well-known, as are the lines of descent of many descendants of the old nobility.  In a roundabout way, we obtained the Y-DNA of Louis XVI, and Tsar Nicholas II, but there is plenty more to be discovered.

 J Hum Genet. 2011 Dec 22. doi: 10.1038/jhg.2011.147. [Epub ahead of print]

Present Y chromosomes reveal the ancestry of Emperor CAO Cao of 1800 years ago.

Wang C, Yan S, Hou Z, Fu W, Xiong M, Han S, Jin L, Li H.

Abstract Emperor CAO Cao (155AD-220AD) is one of the most famous persons in Chinese history that had changed the history of East Asia. He claimed to be a descendant of Marquis CAO Can and therefore was of aristocratic ancestry. However, this claim has been suspected for around 1800 years. Here, we collected some present clans with full records of 70-100 generations claimed to be descendants of CAO Cao or CAO Can, and validated them by comparing their Y chromosomes. Haplotype O2-M268 is the only one that is enriched significantly in the Emperor's claimed descendant clans (P=9.323 × 10(-5), odds ratio=12.72) and, therefore, is most likely to be that of the Emperor. Moreover, our analysis showed that the Y chromosome haplotype of the Emperor is different from that of the Marquis (Haplotype O3-002611). Therefore, Emperor CAO Cao's claim was not supported by genetic evidence. This study offers a successful showcase of the utility of genetics in studying the ancient history.

Stature of prehistoric Europeans






Lack of significant population structure in Spain





December 25, 2011

Merry Christmas

Ἡ Παρθένος σήμερον, τὸν ὑπερούσιον τίκτει,

καὶ ἡ γῆ τὸ Σπήλαιον, τῷ ἀπροσίτῳ προσάγει.

Ἄγγελοι μετὰ Ποιμένων δοξολογοῦσι.

Μάγοι δὲ μετὰ ἀστέρος ὁδοιποροῦσι.

δι' ἡμᾶς γὰρ ἐγεννήθη, Παιδίον νέον, ὁ πρὸ αἰώνων Θεός.

December 23, 2011

Multiple origins of Russian mtDNA

Am J Phys Anthropol DOI: 10.1002/ajpa.21649

Russian ethnic history inferred from mitochondrial DNA diversity

Irina Morozova et al.



Cranial nonmetric traits of Garamantes

Am J Phys Anthropol DOI: 10.1002/ajpa.21645

Sahara: Barrier or corridor? Nonmetric cranial traits and biological affinities of North African late holocene populations

Efthymia Nikita et al.

The Garamantes flourished in southwestern Libya, in the core of the Sahara Desert ∼3,000 years ago and largely controlled trans-Saharan trade. Their biological affinities to other North African populations, including the Egyptian, Algerian, Tunisian and Sudanese, roughly contemporary to them, are examined by means of cranial nonmetric traits using the Mean Measure of Divergence and Mahalanobis D2 distance. The aim is to shed light on the extent to which the Sahara Desert inhibited extensive population movements and gene flow. Our results show that the Garamantes possess distant affinities to their neighbors. This relationship may be due to the Central Sahara forming a barrier among groups, despite the archaeological evidence for extended networks of contact. The role of the Sahara as a barrier is further corroborated by the significant correlation between the Mahalanobis D2 distance and geographic distance between the Garamantes and the other populations under study. In contrast, no clear pattern was observed when all North African populations were examined, indicating that there was no uniform gene flow in the region.


December 22, 2011

Voice pitch and semen quality




Leigh W. Simmons et al.



December 20, 2011

Non-destructive extraction of ancient nuclear and mitochondrial DNA



Am J Phys Anthropol DOI: 10.1002/ajpa.21647

Nondestructive sampling of human skeletal remains yields ancient nuclear and mitochondrial DNA

Deborah A. Bolnick et al.



2012 looking good for my predictions

I wrote:
From LiveScience via Razib:
Some of these archaics have indeed been found.



Syphilis spread from the Americas in the last 500 years




Yrbk Phys Anthropol 54:99–133, 2011.


Kristin N. Harper et al.



December 19, 2011

Neandertal admixture: why I remain skeptical

The announcement by 23andMe of a Neandertal admixture feature of their commercial test gives me an opportunity to revisit the question of Neandertal admixture in general. At the outset, let me state that I'm still on the fence on whether there has been such admixture in Eurasians. The evidence that has appeared since the publication of Green et al. (2010) provides arguments both in favor and against the Neandertal admixture hypothesis.

Let's begin by examining the case for Neandertal introgression into Eurasians. This case boils down to the fact that modern Eurasians are more similar to Neandertals than modern Africans are. If Neandertals were an irrelevant outgroup, this is an unexpected finding.

The above statement in bold is the fact. But, this fact does not admit to the single interpretation of Neandertal admixture in the ancestors of Eurasians.

At the very beginning, I suggested that this fact could be explained by archaic admixture in Africans. Both genetics and paleoanthropology has furnished evidence in favor of my idea. It is no longer tenable to propose that Eurasians are shifted towards Neandertals only because of Neandertal admixture: in fact some of the shift may be due to Africans being shifted away from Neandertals because of admixture with archaic African hominins. Any future work on the issue must take this possibility into account.

A different pitfall is in the direction of gene flow: whether Neandertals donated genes to the Eurasian gene pool or vice versa. Again, I have contended that it is more likely for a successful expanding species to donate to a contracting species, rather than opposite. However, Green et al. proposed an ingenuous argument against that direction of gene flow:

The main idea is the following:

- Yoruba Nigerians are closer to Eurasians than San are.
- If the Neandertal genome is Proto-Eurasian-admixed, then it should be shifted towards Yoruba relative to San
- It does not appear to be, hence, on balance, gene flow was from Neandertals to modern humans, rather than the opposite.

The idea is fleshed out in the supplement of the Green et al. paper. It exploits the fact that modern human populations are not equidistant to each other, to show that an archaic hominin that was admixed with a subset of modern humans (Eurasians) would not only be shifted towards that population, but would also appear closer to populations close to Eurasians (=Yoruba), rather to those who are not (=San).

All this depends, of course, on the idea that the people who interbred with Neandertals were Proto-Eurasians, i.e., a subset of Africans who left the continent and went on to become modern Eurasians.

This idea is not as secure as it formerly appeared to be. The recognition of the real possibility of Out-of-Arabia means that the people who admixed with Neandertals may not have been Proto-Eurasians, but, rather undifferentiated Proto-Humans. In other words, they were not necessarily closer to modern Eurasians than to modern Africans, but, rather, common ancestors to both.

In conclusion:
  • The inference of Neandertal admixture in modern Eurasians in terms of the D-statistic is proven to be a simplification that ignores archaic admixture in Africa
  • The inference of Neandertal-to-modern admixture is based on the assumption that moderns admixing with Neandertals were already Eurasian-like, but the mounting evidence for a major human expansion Out-of-Arabia may mean that they were not. 



It may very well be that some level of Neandertal admixture will remain part of the story. We shall see.

December 18, 2011

Modern human vs. Neandertal brains



Evolution of the base of the brain in highly encephalized human species

Markus Bastir et al.



December 16, 2011

First assessment of 1000 Genomes Iberian Spanish (IBS) sub-populations

As promised, I have taken the IBS sample from the latest available 1000 Genomes data and split it into sub-populations. There are at present 147 IBS individuals, and 108 of them have regional information about them:
  • Canarias_1KG 2 
  • Galicia_1KG 8 
  • Aragon_1KG 6 
  • Valencia_1KG 12 
  • Andalucia_1KG 4 
  • Murcia_1KG 8 
  • Baleares_1KG 7 
  • Cataluna_1KG 9 
  • Pais_Vasco_1KG 8 
  • Cantabria_1KG 6 
  • Extremadura_1KG 8 
  • Castilla_La_Mancha_1KG 6 
  • Castilla_Y_Leon_1KG 12
I estimated the admixture proportions of these individuals in terms of the K12a calculator. I do not report averages at this time, as I will repeat the analysis that created K12a, but using new reference individuals from the 1000 Genomes project. Nonetheless, the following figure of the ADMIXTURE analysis gives a visual taste of the makeup of the different populations:

The one population that stands out in this set is that of the Basque Country (Pais_Vasco_1KG) which appears, like the HGDP French_Basque population to differ from its neighbors in having near zero of the "Caucasus" component.

I first speculated that some of the IBS sample were of Basque origin during the summer, and it seems that this was indeed the case.

The paucity of the "Caucasus" component in Dodecad, HGDP, and now 1000 Genomes Basques, together with the paucity of the "Caucasus"/"Gedrosia" components in Finns compared to northern Balto-Slavs and Scandinavians respectively is very suggestive, since these are the two major non-Indo-European speaking populations of Europe. (*)

In my opinion, these comparisons add weight to the growing body of evidence that the PIE Urheimat is to be sought in the territory of West Asia, as a secondary movement, about 8,000 years, ago of the broader series of expansions that began from this area 12,000 years ago.

(*) Hungarians are also non-Indo-European, but they seem to have received their language in historical times through a process of elite dominance.

1000 Genomes at 2,100+ and counting

The latest working data on 1000 Genomes data include 2,123 individuals. I had already included some Khmer Vietnamese (KHV) from the previous working data for use with my K12a calculator. The list of populations in the datafile currently include:


I will probably take the time to extract anew the population data from the newest file, as well as split some (such as IBS) for which I have some more regional information. By my last count, I now have about ~10,600 individuals to work with (some are duplicates, e.g., between the HapMap and 1000 Genomes Project).

In other news, I see some 23/11/2011 data on Y-chromosome SNPs. I haven't worked on those myself, but I know that many hobbyists are interested in the Y-chromosome aspect of the project, so those might be useful.

Finally, there are slides from the ICHG seminar on the 1000 Genomes Project, which should be interesting reading.

Mega-study on Mexican admixture

There have been other studies on Mexican admixture patterns before, but this one breaks new ground, by determining the more specific origin of the three major components of the Mexican population. From the paper:
The paper is also methodologically interesting:


Ancestral Components of Admixed Genomes in a Mexican Cohort

Nicholas A. Johnson et al.



December 14, 2011

Clusters Galore analysis of West Eurasians

It's been a while since the last Clusters Galore analysis, so I've decided to use my recently assembled dataset and run such an analysis over the individuals who belonged to the Six main West Eurasian components.

Hence, at the beginning, I identified 945 individuals in my set who had more than 95% combined admixture proportions in the Six. Subsequently, I ran MDS on this set, keeping 50 dimensions.

One of the open issues in Clusters Galore analysis is how to choose how many MDS dimensions to retain. So far, I've applied a heuristic by choosing the number of MDS dimensions that maximizes the number of inferred clusters by MCLUST. However, when I actually inspect the MDS plots, it often turns out that meaningful information seems present at even higher number of MDS dimensions. As a result, I've decided to pick the number of dimensions in the following manner.

The main idea is that data points in uninformative MDS dimensions will appear as largely Gaussian noise. So, we can use a test of normality (I've chosen the Shapiro-Wilk test) to detect dimensions that appear not to be noise. Below is the p-value of this test for different MDS dimensions:
Up to 22 dimensions, there is a strong non-Gaussian signal (all p-values less than 0.001). Hence, I would use the first 22 dimensions in MCLUST analysis. With these dimensions, the number of inferred clusters was estimated as 35. So, this is something like a 6-fold increase in resolution over the Six components inferred by ADMIXTURE.

The cluster totals for the different populations can be seen in the spreadsheet.

Important Caveat: Some populations (e.g., Finnish_D, or Turkish_D) have a great number of individuals who do not meet the "95% in the Six" inclusion threshold. Hence, results are not representative for them, and simply indicate the cluster assignment of their subsets that do meet the threshold. You can check whether individuals have been removed from the original dataset by comparing sample sizes in the Clusters Galore spreadsheet with the K12a one.

Here are some observations on the 35 cluster. I will mention the modal population (or region) for each one:
  1. Ashkenazi
  2. Scandinavian
  3. French
  4. British Isles
  5. Armenian
  6. S Italian/Sicilian
  7. Kurd
  8. Greek
  9. Cypriot
  10. Balto-Slavic
  11. Hungarian
  12. Balkan
  13. Sephardic
  14. Spanish
  15. Iberian
  16. North Italian/Tuscan
  17. Morocco Jews (main)
  18. Saudis
  19. Georgian/Abkhazian
  20. Basque
  21. Bedouin
  22. Druze #1
  23. Druze #2
  24. Druze (main)
  25. Mozabite (main)
  26. Mozabite #1
  27. Orkney
  28. Sardinian
  29. Azerbaijan Jews
  30. Iran/Iraq Jews
  31. Lezgins
  32. Morocco Jews #1
  33. Samaritan
  34. Yemen Jews
  35. Abkhazian

Segmented HAPlotype Estimation and Imputation Tool (Delaneau et al. 2011)

The ShapeIT website seems to be very well-designed and informative.

Nature Methods (2011) doi:10.1038/nmeth.1785

A linear complexity phasing method for thousands of genomes

Olivier Delaneau et al.

Human-disease etiology can be better understood with phase information about diploid sequences. We present a method for estimating haplotypes, using genotype data from unrelated samples or small nuclear families, that leads to improved accuracy and speed compared to several widely used methods. The method, segmented haplotype estimation and imputation tool (SHAPEIT), scales linearly with the number of haplotypes used in each iteration and can be run efficiently on whole chromosomes.


December 13, 2011

Of Elephants and Men

The same team described dental remains from Qesem cave.

The press release:





Miki Ben-Dor et al.



December 12, 2011

The womb of nations: how West Eurasians came to be

One of the most interesting observations about the genetic structure of the Old World, is the fact that distantly located populations are often more similar to each other than to their more immediate geographic neighbors.

For example, in my recent K12a admixture experiment, the six components. I named Mediterranean, North_European, Caucasus, Gedrosia, Southwest_Asian, and Northwest_African have a maximum Fst between any two of them of 0.073 (between Gedrosia and Northwest_African), and a mimimum Fst between any of them and any of the others of 0.075 (between Gedrosia and South_Asian). Henceforth, I will call these six components simply "the Six."

It is remarkable that "Gedrosia", the component peaking in present-day Balochistan is about equidistant to the component peaking in Mozabite Berbers ("Northwest_African") and that peaking in South Indian Dravidian speakers ("South_Asian"). Going by geography alone, and even if we calculated distances "as the crow flies" and ignored all natural obstacles between Balochistan and the Sahara, we would have expected "Gedrosia" to be about 3 times more distant to "Northwest_African" than to "South_Asian".

Divergence between populations across the entire genome builds up mainly by two processes:
  • Genetic drift
  • Admixture
Over time, two populations stemming from the same root will shift in their overall allele frequencies because of random factors (drift). These differences may become even more pronounced by new mutations arising in each population, and by natural selection operating in different environments.

Moreover, if these populations migrate from their original homeland and absorb the indigenous inhabitants wherever they go, then they will diverge even more, depending on how much admixture they undergo, and how distantly related the aboriginal inhabitants are.

It is clear that admixture has played a role in the overall divergence of the Six. For example, the Northwest_African component is shifted (relative to the remaining five) towards the other African components; the Southwest_Asian is also thus shifted, but less noticeably. The Gedrosia component is shifted towards the South_Asian one; and the easternmost components, the North_European, and Gedrosia ones, are shifted towards the Asian components.

All these shifts are quite salient in the MDS plot, and there is ample evidence for the aboriginal populations being shifted in the expected direction in each region.

We can calculate the median Fst within the Six: it is 0.053, as well as the median Fst between members of the Six and all the rest: it is 0.13. The ratio of the two is ~40%. Of course, the various components have diverged from each other at different times: West and East Eurasians, for example, began diverging shortly after both diverged from Africans. Nonetheless, we can (conservatively) place the divergence time of the ancestors of the Six from East Asians, Ancestral South Indians, and Sub-Saharan Africans, at around 40,000 years ago, the time when the Upper Paleolithic (and modern man) makes its appearance all over the Old World.

Actual divergence times may be lower, and this is why 40k is a conservative estimate. The point of this back-of-a-napkin calculation is to give a rough estimate, rather than a precise date.

Assuming that Fst builds up roughly linearly with time due to drift (again a simplification), we can estimate that divergence within the Six dates to less than 16 thousand years ago. This may be an overestimate for two reasons:
  • Divergence between Proto-West Eurasians and the rest of mankind may be less than 40k years
  • Each of the Six have partially absorbed aboriginal inhabitants (e.g., Palaeo-Europeans, Ancestral South Indians, Pre-Berber North Africans, etc.) that spent most of the Paleolithic diverging from the common ancestors of the Six.
It is therefore clear, that the common ancestors of the Six may have been a people living in some small area of Eurasia until well after 16 thousand years ago. Much like a bubble of space in cosmological inflation, their living space multiplied by orders of magnitude, coming to encompass a huge region of space within most of West Eurasia and North Africa. Within that region a fairly homogeneous population was established, the people traditionally called "Caucasoids."

The womb of nations

The Neolithic of West Eurasia started, by most accounts, c. 12 thousand years ago. Its origin was in the area framed by the Armenian Plateau in the north, the Anatolian Plateau in the west, the Zagros Range in the east, and the lowlands of southern Mesopotamia and the Levant in the south. Intriguingly, the prehistoric site of Göbekli Tepe sits right at the center of this important area, in eastern Anatolia/northern Mesopotamia.

If there is a candidate for where the ur-population that became the modern Six lived, the early Neolithic of the Near East is surely it. This hypothesis makes the most sense chronologically, archaeologically, genetically, and geographically.

Migrants out of the core area would have spread their genes in all directions, becoming differentiated by a combination of drift, admixture, and the selection pressures they faced in different natural and cultural environments; some of them would acquire lighter pigmentation, others lactase persistence, malaria resistence, the ability to process the dry desert air or to survive the long winter nights of the arctic. These spreads were sometimes gradual, sometimes dramatic: they took place over thousands of years and from a multitude of secondary and tertiary staging points.

In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.

It is, perhaps, in the ancient land of the Colchi, protected by the Black and Caspian seas, and by tall mountains on the remaining sides, that something resembling the ur-population survived. The great linguistic diversity of the Caucasian peoples, the central position of the Caucasus component among the Six (see MDS plot), and the fact that theirs was a remote region, ignored by the empires of the Near East to the south, and the frequent travellers of the Eurasiatic steppe to the north, may all indicate the plausibility of this assertion. Through a peculiar coincidence, old Blumenbach may have been onto something, although for reasons he could scarcely have imagined.

We don't have to suppose that a single process drove the dispersal of genes from the core area of the Near East. Agriculture was definitely an early facilitator of dispersal, but a variety of technological developments may have been instrumental in further spurts of dispersal: the invention of pottery, metalworking, pastoralism, sea navigation, the engines of war, all the way to the recent past, when ocean-going vessels from Western Europe sailed to the New World, Arab merchants and warriors spread their new religion to the continent of Africa, and Russian hunters and farmers began the conquest of Siberia.

There are hints that scientists are beginning to realize that this story may describe what happened during prehistory. The next few years will help resolve this grand puzzle of "how West Eurasians came to be."

December 10, 2011

First analysis of Metspalu et al. (2011) data (plus K12a admixture calculator)

Here are the results of my first analysis of the new Metspalu et al. (2011) data (populations with _M endings), together with a large number of other samples from various sources, including Chaubey et al. (2011) (_Ch endings), that I had not used before.

Uploaded with

Spreadsheet of population averages; no outliers removed in source datasets. I'll defer all the technical and other details for when I release Dodecad v4, which will (most likely) be based on the same dataset.

Fst divergences:

MDS plot of first two dimensions based on above table.

You can use DIYDodecad 2.1 with the 'K12a' calculator, which incorporates the K=12 inferred clusters of the above analysis.

Instructions: uncompress the contents of the K12a bundle to your working directory, and follow the instructions of the DIYDodecad 2.1 README file, substituting 'K12a' for 'dv3' in all those instructions. Terms of use: 'K12a', including all files in the downloaded RAR file is free for non-commercial personal use. Commercial uses are forbidden. Contact me for non-personal uses of the calculator.