Neandertal shoulder blades and the direction of gene flow

John Hawks points me to a new paper by Di Vicenzo et al. What is most interesting to me is the following figure:

What is most striking about it is the position of Vindija, an Upper Paleolithic Neandertal specimen which is clearly closer to Homo sapiens specimens than any of the Neandertal or archaic humans.

The first component is one of increasing (left-to-right) modernity, with Australopithecus on the left, and modern humans on the right. Apart from Vindija, the two West Asian samples from Kebara and Shanidar also appear quite "modern" in terms of their component 1 position.

There are two possible options: that Neandertals and modern humans were evolving in parallel towards a "modern" scapular glenoid fossa shape; or, that these Neandertals may have experienced gene flow from modern humans.

I am inclined to accept the idea of gene flow: Kebara and Shanidar are from the time when genetic evidence suggests that the major expansion of modern humans was well under way, and Vindija from a time when they had most probably already arrived in Europe. If there was AMH-to-Neandertal gene flow, these are exactly the Neandertal specimens that might be affected, and not, e.g., the >100ka European Neandertals that can be safely assumed to lack any modern human ancestry on a variety of grounds.

Dr. Hawks writes:

There is as yet no evidence that the Vindija Neandertal genomes have genetic introgression from the African populations from which present non-Africans derive most of their genetic heritage. Green and colleagues [4] tested explicitly for this kind of gene flow, from "modern" into Neandertal populations and found none.

I am not convinced by the strength of that test, as it is based on the assumption that modern-to-Neandertal gene flow would Eurasianize the sequence we got from Vindija. That assumption is not secure, since:

1. It seems increasingly likely that the major Upper Paleolithic expansion of humans originated in Asia and not in Africa, in which case the expanding moderns would be Proto-Human rather than Proto-Eurasian
2. We've now had enough contrasts between Mesolithic/Neolithic and present-day DNA to cure us of the illusion that populations are largely static: we simply have no evidence (until we actually test them) as to what early modern humans in the Near East and Europe were like genetically.

Regardless of what one thinks about the recent Out of Africa hypothesis, the fact that the one sample on which the "Neandertal genome" is based appears to be so close to modern humans compared to other Neandertals should give us pause about the reasons for its apparent involvement (in some way) in the story of mankind.

I remain skeptical about the mainstream story about what this involvement is (Neandertal-to-Eurasian gene flow), and this analysis certainly seems consistent with the alternative (AMH-to-Neandertal gene flow during the expansion of modern humans out of the Near East). I can definitely co-sign the following statement by Dr. Hawks:

Frankly, I expect that the admixture estimates presented thus far will prove to be wrong. I could be wrong in this expectation, but there are many assumptions underlying genetic analyses of admixture, and it's easy for an incorrect assumption to give rise to an incorrect conclusion. I take the morphological evidence very seriously as a possible "reality-check" about the validity of genetic comparisons. After all, the morphological comparisons predicted introgression from Neandertals in the first place...

UPDATE:


The scenario of gene flow from the paper can be seen below:

I want to highlight a couple of facts:

In the Levant, Tabun (120ky) is less modern than Kebara (60ky). This is exactly as we expect if there was a major human expansion c. 70ky, as I have argued for in my blog post on L3 and here. The same difference between Krapina (130ky) and Vindija (40ky), the latter just at the time when modern humans were getting there.

Notice also how "natural" Out-of-Arabia fits with the rest of the scenario: a group of expanding humans from Arabia (south-to-north) forms a natural extension that would affect Kebara, Shanidar, and ultimately Vindija. I won't even bother with the Coastal Migration Theory that seems utterly unable to explain modern-Neandertal interbreeding.

Journal of Human Evolution 


The Vindija Neanderthal scapular glenoid fossa: Comparative shape analysis suggests evo-devo changes among Neanderthals

Fabio Di Vincenzo et al.

Although the shape of the scapular glenoid fossa (SGF) may be influenced by epigenetic and developmental factors, there appears to be strong genetic control over its overall form, such that variation within and between hominin taxa in SGF shape may contain information about their evolutionary histories. Here we present the results of a geometric morphometric study of the SGF of the Neanderthal Vi-209 from Vindjia Cave (Croatia), relative to samples of Plio-Pleistocene, later Pleistocene, and recent hominins. Variation in overall SGF shape follows a chronological trend from the plesiomorphic condition seen in Australopithecus to modern humans, with pre-modern species of the genus Homo exhibiting intermediate morphologies. Change in body size across this temporal series is not linearly directional, which argues against static allometry as an explanation. However, life history and developmental rates change directionally across the series, suggesting an ontogenetic effect on the observed changes in shape (ontogenetic allometry). Within this framework, the morphospace occupied by the Neanderthals exhibits a discontinuous distribution. The Vindija SGF and those of the later Near Eastern Neanderthals (Kebara and Shanidar) approach the modern condition and are somewhat segregated from both northwestern European (Neandertal and La Ferrassie) and early Mediterranean Neanderthals (Krapina and Tabun). Although more than one scenario may account for the pattern seen in the Neanderthals, the data is consistent with palaeogenetic evidence suggesting low levels of gene flow between Neanderthals and modern humans in the Near East after ca. 120–100 ka (thousands of years ago) (with subsequent introgression of modern human alleles into eastern and central Europe). Thus, in keeping with previous analyses that document some modern human features in the Vindija Neanderthals, the Vindija G3 sample should not be seen as representative of ‘classic’ – that is, unadmixed, pre-contact – Neanderthal morphology. 

Link

Dodecad submission opportunity

I took some time to re-organize some of the Dodecad populations, as part of the current submission opportunity.

For example, I extracted an English_D population out of the previous British_D one; the latter now contains all British individuals that don't have four English grandparents.

Many ethnic groups were represented in the Indian_D population, and I extracted at least two samples, Iyer_D, and Jatt_D with at least 5 participants each.

I've also identified a few other smaller populations, such as Breton_D, Turkish_Cypriot_D, which haven't reached 5 participants yet, but I'm hopeful that they will.

In any case, here is the list of current Dodecad populations. Do consider submitting your data to the Project, especially if you belong in one of the populations that haven't reached 5 participants yet, or in one of the eligible groups that are not represented in the Project. Even groups with relatively large sample sizes could use more participants: more data = better ability to discover patterns of human variation.

Ashkenazi_D	34		English_D	12		Lithuanian_D	7
Indian_D	28		British_D	12		Iyer_D	6
Turkish_D	27		French_D	11		Brazilian_D	6
Armenian_D	23		Norwegian_D	11		O_Italian_D	5
Russian_D	22		Portuguese_D	10		Japanese_D	5
Irish_D	22		Mixed_Germanic_D	9		N_Italian_D	5
Polish_D	21		Chinese_D	9		Korean_D	5
Spanish_D	20		S_Italian_Sicilian_D	9		Moroccan_D	5
German_D	20		Somali_D	9		Jatt_D	5
Greek_D	18		British_Isles_D	8		Algerian_D	4
Finnish_D	17		Dutch_D	8		North_African_Jews_D	4
Sicilian_D	14		Kurd_D	8		Slovenian_D	4
Assyrian_D	13		Iranian_D	8		Mixed_Scandinavian_D	4
C_Italian_D	13		Bulgarian_D	7		Serb_D	4
Swedish_D	13		S_Italian_D	7		Romanian_D	4
East_African_Various_D	3		Azeri_D	2		Mixed_Arab_D	1
Danish_D	3		Georgian_D	2		Yoruba_D	1
Tunisian_D	3		Kazakh_D	2		Egyptian_D	1
Austrian_D	3		Iraqi_D	2
Saudi_D	3		Breton_D	2
Pakistani_D	3		Belgian_D	1
Tatar_Various_D	3		Latvian_D	1
Palestinian_D	3		Estonian_D	1
Philippines_D	3		Bangladesh_D	1
Czech_D	3		Yemenese_D	1
Turkish_Cypriot_D	3		Sri_Lanka_D	1
Greek_Italian_D	2		Hungarian_D	1
Swiss_German_D	2		Basque_D	1
Szekler_D	2		Udmurt_D	1
Mandaean_D	2		Ukrainian_D	1

Diving Into Noah's Flood

A new National Geographic documentary featuring Jeffrey Rose and the Gulf Oasis hypothesis. I wish that Noah would be left out of it -he was also featured in a recent talk about the flooding of the Black Sea- but I understand how invoking a well-known biblical figure is not bad for publicity, and if it's the hook that will get people to watch a program about cutting-edge archaeology, why should we complain?

I wasn't able to find a full page on the documentary, but here's a description from NatGeo:

Diving into Noah's Flood
Archaeologist Jeff Rose embarks on a journey to understand how the destructive forces of water might have inspired the biblical story of Noahs Ark and the great flood. Dr. Rose believes that a massive flood once swallowed a landmass as big as Great Britain, created the Persian Gulf and sent tribes of Neolithic people into constant retreat from the ever-rising waters.

You can probably find the program online if you missed its broadcast, or you can check National Geographic channel for airdates. I'll update this entry with any noteworthy information from the documentary.

Trailer:



UPDATE: In a sense, this is the antithesis of the Black Sea Flood theory as inspiration of the Gilgamesh Flood and later Biblical Flood story, in that it has people moving south-to-north, staying close to freshwater sources created by the river that once flowed in the Gulf, as the Indian Ocean rose and saltwater claimed land after land of the Gulf Oasis.

Another interesting lesson from the documentary is just how hard underwater archaeology actually is. In the earlier Black Sea talk (linked above), it was shown that thousands of years of sediments have covered most traces of any human habitation that may have existed along the pre-Flood coastline, dead organisms dropping to the sea floor like snow.

In the new NatGeo documentary it was shown how many false positives archaeologists have to contend with: things that look anomalous on the bottom of the sea often tend to be man-made, but not necessarily from the period in question; people have been dumping stuff on the sea for quite a long time.

The documentary also shows the precarious manner in which archaeologists have to work in Iraq, as the documentary host and his local contact visit various Ubaid and Sumerian sites, as well as pay a visit to the Marsh Arabs.

So, what's my opinion of the overall theory? The ideas of the Gulf Oasis theory seem plausible, and the idea that the earliest flood myth in Mesopotamia may have been related to the flooding of the Gulf seems much more plausible than the idea that it may have been related to the inundation of the Black Sea.

I am not so willing to believe, however, that people from the north played no role in the formation of the Ubaid and then the early Sumerian civilization. As I explain in the Womb of Nations, there are good arguments why most West Eurasians share relatively recent common ancestry from the northern tip of the Fertile Crescent. That does not preclude the absorption of Gulf Oasis denizens, indeed of a great number of them, depending on how close genetically they were with the proto-agriculturalists to begin with, but some substantial role must be maintained for the latter: the emergence of Ubaid/Sumerian culture cannot simply have been a local development.

Perhaps a case can be made that some of the languages of the Gulf were the descendants of the languages spoken in the Gulf Oasis. Sumerian and Elamite are the obvious candidates, although the two are not related to each other.

The advancement of the sea may have pushed Gulf Oasis denizens northward, eastward, and westward, into Mesopotamia, Arabia, and Iran, but the later gradual expansion of the land by fluvial depositions of sediments by the Tigris and Euphrates provided the added land and irrigation to motivate people to move southward. So, it is perhaps through a blending of cultures that the Proto-Sumerian civilization was born: a marsh-adapted southern element, and an agriculture-bearing northern element joining to exploit the harsh but profitable environment that was formed as a result of these two processes.

Epistasis and phantom heritability

A few years ago, I proposed the "lego-block" model of genetic variation. The main idea of this model is that the search for genes that "do" something is often misguided, because most genes don't actually do much of anything in themselves: they are commodity blocks (like lego pieces), and it is the way they are put together that influences the complex phenotypic outcome of an organism.

(By not "doing" something, I do not, of course, mean that they have no biological effect. Rather, I mean that they have no effect at a higher-order phenotypic trait, in the same way that the luminosity of pixels is irrelevant to the depicted image, it is rather the combination of pixels of different luminosity that produces an image)

I am not, of course, denying that there are genes with large positive/negative effects, but these traverse one of two possible trajectories during evolution:

• Flicker: alleles of large negative effect arise, may persist for a few generations, but ultimately die out. They never amount to much of anything
• Shine: alleles of large positive effect spread through the population quickly and become fixed

Alleles that flicker are much more common than alleles that shine. This is a simple consequence of the random nature of mutation: there are many more ways to break a system than to improve it, and the mutation mechanism is excellent in breaking down organisms: the survivors are the ones who carry a "manageable" mutation load, and, once in a very long while, adaptive alleles arise that quickly become fixed.

An alternative to the "lego-block" model of commodity alleles that produce positive/negative phenotypes due to the way they work together (epistasis) is the model of additive variation. According to this model, there is a plethora of genes of small positive/negative effect for a trait, and the final phenotypic expression is influenced by the sum of positive/negative alleles one inherits from their parents.

A new paper in PNAS provides strong evidence that the missing heritability is not due to our inability of finding loci of small effect, but rather to the fact that we've overestimated the heritability of traits. 

At the limit (a perfect "lego-block" world) there are absolutely no alleles that are individually associated with any traits. That does not mean that all individuals will be phenotypically indistinguishable! A great deal of phenotypic variation can still persist even in this case.

Here is a simple example:

	C	D
A	10	0
B	0	10

The value of a trait depending on the alleles in two loci is shown, e.g., AC=10, AD=0, BC=0, BD=10.

It can be easily seen (due to symmetry) that whether one inherits A/B in one locus, or C/D in the other has no effect -in itself- on the trait. It is the combination of alleles that has a (huge) effect on the trait.

The paper is open access.

PNAS doi: 10.1073/pnas.1119675109

The mystery of missing heritability: Genetic interactions create phantom heritability

Or Zuk et al.

Human genetics has been haunted by the mystery of “missing heritability” of common traits. Although studies have discovered >1,200 variants associated with common diseases and traits, these variants typically appear to explain only a minority of the heritability. The proportion of heritability explained by a set of variants is the ratio of (i) the heritability due to these variants (numerator), estimated directly from their observed effects, to (ii) the total heritability (denominator), inferred indirectly from population data. The prevailing view has been that the explanation for missing heritability lies in the numerator—that is, in as-yet undiscovered variants. While many variants surely remain to be found, we show here that a substantial portion of missing heritability could arise from overestimation of the denominator, creating “phantom heritability.” Specifically, (i) estimates of total heritability implicitly assume the trait involves no genetic interactions (epistasis) among loci; (ii) this assumption is not justified, because models with interactions are also consistent with observable data; and (iii) under such models, the total heritability may be much smaller and thus the proportion of heritability explained much larger. For example, 80% of the currently missing heritability for Crohn's disease could be due to genetic interactions, if the disease involves interaction among three pathways. In short, missing heritability need not directly correspond to missing variants, because current estimates of total heritability may be significantly inflated by genetic interactions. Finally, we describe a method for estimating heritability from isolated populations that is not inflated by genetic interactions.

Link

Chimpanzee Y-chromosome gene diversity explained

In short (as I understand it):

• Gorilla females tend to have one man, hence there is no sperm competition between different males' sperm
• Orangutan females tend to choose their man, so, once again, there is no sperm competition between different males' sperm
• Bonobos are matriarchal and have concealed ovulation, hence they can also choose the father of their children
• Male chimpanzees pick their female partners, but female partners are not necessarily faithful, hence a race sometimes takes place within female chimps to determine which sperm will impregnate them.

From the paper:

In conclusion, the major findings of this study are: (i) That the contrasting patterns of DAZ and CDY variability in chimpanzees (P. troglodytes) and bonobos (P. paniscus), initially suggested by comparative FISH [11], are similarly reflected by real-time qPCR data. (ii) Although chimpanzee and bonobo share promiscuous mating behaviors, it is only in chimpanzees that male dominance is sufficiently developed to influence sperm competition [62], [63]. This results in high selective pressure on male fertility genes. Bonobos on the other hand, are characterized by a matriarch-dominated societal structure [63,64, reviewed in 65] which, coupled to concealed ovulation [66], permits female mate choice, thus rendering sperm competition redundant. (iii) That monoandrous mating in gorillas (G. gorilla) [37]–[41] and female mate choice in orangutans (P. pygmaeus and P. abelii) [18], [49], [50] similarly accounts for the dearth of intraspecific Y-chromosomal variation in the ampliconic fertility genes DAZ and CDY among Y-chromosomal lineages in these species.

PLoS ONE 6(12): e29311. doi:10.1371/journal.pone.0029311

Y-Chromosome Variation in Hominids: Intraspecific Variation Is Limited to the Polygamous Chimpanzee

Gabriele Greve et al.

Abstract Background

We have previously demonstrated that the Y-specific ampliconic fertility genes DAZ (deleted in azoospermia) and CDY (chromodomain protein Y) varied with respect to copy number and position among chimpanzees (Pan troglodytes). In comparison, seven Y-chromosomal lineages of the bonobo (Pan paniscus), the chimpanzee's closest living relative, showed no variation. We extend our earlier comparative investigation to include an analysis of the intraspecific variation of these genes in gorillas (Gorilla gorilla) and orangutans (Pongo pygmaeus), and examine the resulting patterns in the light of the species' markedly different social and mating behaviors.

Methodology/Principal Findings

Fluorescence in situ hybridization analysis (FISH) of DAZ and CDY in 12 Y-chromosomal lineages of western lowland gorilla (G. gorilla gorilla) and a single lineage of the eastern lowland gorilla (G. beringei graueri) showed no variation among lineages. Similar findings were noted for the 10 Y-chromosomal lineages examined in the Bornean orangutan (Pongo pygmaeus), and 11 Y-chromosomal lineages of the Sumatran orangutan (P. abelii). We validated the contrasting DAZ and CDY patterns using quantitative real-time polymerase chain reaction (qPCR) in chimpanzee and bonobo.

Conclusion/Significance

High intraspecific variation in copy number and position of the DAZ and CDY genes is seen only in the chimpanzee. We hypothesize that this is best explained by sperm competition that results in the variant DAZ and CDY haplotypes detected in this species. In contrast, bonobos, gorillas and orangutans—species that are not subject to sperm competition—showed no intraspecific variation in DAZ and CDY suggesting that monoandry in gorillas, and preferential female mate choice in bonobos and orangutans, probably permitted the fixation of a single Y variant in each taxon. These data support the notion that the evolutionary history of a primate Y chromosome is not simply encrypted in its DNA sequences, but is also shaped by the social and behavioral circumstances under which the specific species has evolved.

Link

Huge differences in personality between men and women

From the paper's conclusion:

In conclusion, we believe we made it clear that the true extent of sex differences in human personality has been consistently underestimated. While our current estimate represents a substantial improvement on the existing literature, we urge researchers to replicate this type of analysis with other datasets and different personality measures. An especially critical task will be to compare self-reported personality with observer ratings and other, more objective evaluation methods. Of course, the methodological guidelines presented in this paper can and should be applied to domains of individual differences other than personality, including vocational interests, cognitive abilities, creativity, and so forth. Moreover, the pattern of global sex differences in these domains may help elucidate the meaning and generality of the broad dimension of individual differences known as “masculinity-femininity” [11]. In this way, it will be possible to build a solid foundation for the scientific study of psychological sex differences and their biological and cultural origins.

From the press release:

The researchers used personality measurements from more than 10,000 people, approximately half men and half women. The personality test included 15 personality scales, including such traits as warmth, sensitivity, and perfectionism. When comparing men's and women's overall personality profiles, which take multiple traits into account, very large differences between the sexes became apparent, even though differences look much smaller when each trait is considered separately. However, the study indicates that previous methods to measure such differences have been inadequate, both because they focused on one trait at a time and because they failed to correct for measurement error.

PLoS ONE 7(1): e29265. doi:10.1371/journal.pone.0029265

The Distance Between Mars and Venus: Measuring Global Sex Differences in Personality

Marco Del Giudice et al.

Abstract

Background

Sex differences in personality are believed to be comparatively small. However, research in this area has suffered from significant methodological limitations. We advance a set of guidelines for overcoming those limitations: (a) measure personality with a higher resolution than that afforded by the Big Five; (b) estimate sex differences on latent factors; and (c) assess global sex differences with multivariate effect sizes. We then apply these guidelines to a large, representative adult sample, and obtain what is presently the best estimate of global sex differences in personality.

Methodology/Principal Findings

Personality measures were obtained from a large US sample (N = 10,261) with the 16PF Questionnaire. Multigroup latent variable modeling was used to estimate sex differences on individual personality dimensions, which were then aggregated to yield a multivariate effect size (Mahalanobis D). We found a global effect size D = 2.71, corresponding to an overlap of only 10% between the male and female distributions. Even excluding the factor showing the largest univariate ES, the global effect size was D = 1.71 (24% overlap). These are extremely large differences by psychological standards.

Significance

The idea that there are only minor differences between the personality profiles of males and females should be rejected as based on inadequate methodology.

Link

Relatives in HUGO Pan-Asian SNP data

I haven't used the Pan-Asian SNP data much since discovering them, because of the low number of common SNPs with all my main Illumina-based datasets, but this should be useful to anyone using this important data resource.

PLoS ONE 6(12): e29502. doi:10.1371/journal.pone.0029502

Identification of Close Relatives in the HUGO Pan-Asian SNP Database

Xiong Yang et al.

The HUGO Pan-Asian SNP Consortium has recently released a genome-wide dataset, which consists of 1,719 DNA samples collected from 71 Asian populations. For studies of human population genetics such as genetic structure and migration history, this provided the most comprehensive large-scale survey of genetic variation to date in East and Southeast Asia. However, although considered in the analysis, close relatives were not clearly reported in the original paper. Here we performed a systematic analysis of genetic relationships among individuals from the Pan-Asian SNP (PASNP) database and identified 3 pairs of monozygotic twins or duplicate samples, 100 pairs of first-degree and 161 second-degree of relationships. Three standardized subsets with different levels of unrelated individuals were suggested here for future applications of the samples in most types of population-genetics studies (denoted by PASNP1716, PASNP1640 and PASNP1583 respectively) based on the relationships inferred in this study. In addition, we provided gender information for PASNP samples, which were not included in the original dataset, based on analysis of X chromosome data.

Link

Activity patterns of Garamantes

A different paper on cranial nonmetric traits from the same team and on the same population (Garamantes).

From the current paper:

The study of the activity patterns of the Garamantes, a population that flourished at Central Sahara approximately 3,000 years ago, offers some interesting insights on the levels of stress imposed by a sedentary life in a hyper-arid environment. The population showed low bilateral asymmetry, possibly due to limited task specialization. Moreover, the Garamantes exhibited low sexual dimorphism in the upper limbs, which is consistent to the pattern found in agricultural populations and implies that the engagement of males in warfare  and construction works was not particularly intense. In the lower limbs, males were stronger in TA possibly as a result of their involvement in herding and mobility on the uneven terrain of Fezzan. Finally, the Garamantes did not appear systematically more robust than other North African populations occupying less harsh environments, indicating that life in the Sahara did not require particularly strenuous daily activities.

AJPA DOI: 10.1002/ajpa.21597

Activity patterns in the Sahara Desert: An interpretation based on cross-sectional geometric properties

Efthymia Nikita et al.

The Garamantian civilization flourished in modern Fezzan, Libya, between 900 BC and 500 AD, during which the aridification of the Sahara was well established. Study of the archaeological remains suggests a population successful at coping with a harsh environment of high and fluctuating temperatures and reduced water and food resources. This study explores the activity patterns of the Garamantes by means of cross-sectional geometric properties. Long bone diaphyseal shape and rigidity are compared between the Garamantes and populations from Egypt and Sudan, namely from the sites of Kerma, el-Badari, and Jebel Moya, to determine whether the Garamantian daily activities were more strenuous than those of other North African populations. Moreover, sexual dimorphism and bilateral asymmetry are assessed at an intra- and inter-population level. The inter-population comparisons showed the Garamantes not to be more robust than the comparative populations, suggesting that the daily Garamantian activities necessary for survival in the Sahara Desert did not generally impose greater loads than those of other North African populations. Sexual dimorphism and bilateral asymmetry in almost all geometric properties of the long limbs were comparatively low among the Garamantes. Only the lower limbs were significantly stronger among males than females, possibly due to higher levels of mobility associated with herding. The lack of systematic bilateral asymmetry in cross-sectional geometric properties may relate to the involvement of the population in bilaterally intensive activities or the lack of regular repetition of unilateral activities.

Link

Happy New Year 2012

All the best wishes for readers of the blog.

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.

Abstract

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.

Link

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 dodecad@gmail.com (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.

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.

Link

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.

Link

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

Abstract

Background 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.

Link