Skulls and genes tell the same story for humans

The temporal bone seems to be most correlated with neutral genetic variation, the zygomatic and occipital least. The occipital is often affected by cradling or artificial modification, and the zygomatic may be more strongly influenced by nutrition and patterns of chewing, which may explain their greater deviation from neutrality.

American Journal of Physical Anthropology doi:10.1002/ajpa.21041

Congruence of individual cranial bone morphology and neutral molecular affinity patterns in modern humans

Noreen von Cramon-Taubadel

Abstract

Recent studies have demonstrated that the shape of the human temporal bone is particularly strongly correlated with neutral genetic expectation, when compared against other cranial regions, such as the vault, face, and basicranium. In turn, this has led to suggestions that the temporal bone is particularly reliable in analyses of primate phylogeny and human population history. While several reasons have been suggested to explain the temporal bone's strong fit with neutral expectation, the temporal bone has never systematically been compared against other individual cranial bones defined using the same biological criteria. Therefore, it is currently unknown whether the shapes of all cranial bones possess reliable information regarding neutral genetic evolution, or whether the temporal bone is unique in this respect. This study tests the hypothesis that the human temporal bone is more congruent with neutral expectation than six other individual cranial bones by correlating population affinity matrices generated using neutral genetic and 3D craniometric data. The results demonstrate that while the temporal bone shows the absolute strongest correlation with neutral genetic data compared with all other bones, it is not statistically differentiated from the sphenoid, frontal, and parietal bones in this regard. Potential reasons for the temporal bone's consistently strong fit with neutral expectation, such as its overall anatomical complexity and/or its contribution to the architecture of the basicranium, are examined. The results suggest that future phylogenetic and taxonomic studies would benefit from considering the shape of the entire cranium minus those regions that deviate most from neutrality.

Link

Genetic variation in Cameroon

American Journal of Physical Anthropology doi:10.1002/ajpa.21088

A multi-perspective view of genetic variation in Cameroon

V. Coia et al.

Abstract

In this study, we report the genetic variation of autosomal and Y-chromosomal microsatellites in a large Cameroon population dataset (a total of 11 populations) and jointly analyze novel and previous genetic data (mitochondrial DNA and protein coding loci) taking geographic and cultural factors into consideration. The complex pattern of genetic variation of Cameroon can in part be described by contrasting two geographic areas (corresponding to the northern and southern part of the country), which differ substantially in environmental, biological, and cultural aspects. Northern Cameroon populations show a greater within- and among-group diversity, a finding that reflects the complex migratory patterns and the linguistic heterogeneity of this area. A striking reduction of Y-chromosomal genetic diversity was observed in some populations of the northern part of the country (Podokwo and Uldeme), a result that seems to be related to their demographic history rather than to sampling issues. By exploring patterns of genetic, geographic, and linguistic variation, we detect a preferential correlation between genetics and geography for mtDNA. This finding could reflect a female matrimonial mobility that is less constrained by linguistic factors than in males. Finally, we apply the island model to mitochondrial and Y-chromosomal data and obtain a female-to-male migration N ratio that was more than double in the northern part of the country. The combined effect of the propensity to inter-populational admixture of females, favored by cultural contacts, and of genetic drift acting on Y-chromosomal diversity could account for the peculiar genetic pattern observed in northern Cameroon.

Link

X chromosomes and settling of Americas

Related:

• Concurrent but distinctive migrations into the Americas
• Three-stage colonization model for Americas reconsidered
• Craniofacial shape variation and Native American origins
• New synthesis on the first arrivals into the New World

American Journal of Physical Anthropology doi:10.1002/ajpa.21084

X-chromosome lineages and the settlement of the Americas

Stephane Bourgeois et al.

Abstract

Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y-chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X-chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8-kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X-chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s).

Link

Cranial diversity in Pleistocene Africa and Europe

From the paper:

The results of the bootstrap analyses conducted in this study are compatible with the suggestion from genetic studies that living humans represent only a restricted part of past modern human variation (Underhill et al., 2000; Excoffier, 2002; Marth et al., 2003; Fagundes et al., 2007). Certainly the European and North African Upper Paleolithic samples appear to exhibit greater craniometric variability than recent human samples. Our results appear to accord with the conclusions reached by Manica et al. (2007), von Cramon-Taubadel and Lycett (2008), and Betti et al. (2009) regarding the proportional relationship between recent within-population craniometric diversity and geographic distance from eastern Africa.

Very related:

• Variability of anatomically modern humans and Out of Africa
• Reduction of human cranial diversity and distance from Africa
• Population bottlenecks in human history (paper in favor of Out of Africa Only theory)

American Journal of Physical Anthropology doi:10.1002/ajpa.21080

Modern human cranial diversity in the Late Pleistocene of Africa and Eurasia: Evidence from Nazlet Khater, Pestera cu Oase, and Hofmeyr

Isabelle Crevecoeur et al.

Abstract

The origin and evolutionary history of modern humans is of considerable interest to paleoanthropologists and geneticists alike. Paleontological evidence suggests that recent humans originated and expanded from an African lineage that may have undergone demographic crises in the Late Pleistocene according to archaeological and genetic data. This would suggest that extant human populations derive from, and perhaps sample a restricted part of the genetic and morphological variation that was present in the Late Pleistocene. Crania that date to Marine Isotope Stage 3 should yield information pertaining to the level of Late Pleistocene human phenotypic diversity and its evolution in modern humans. The Nazlet Khater (NK) and Hofmeyr (HOF) crania from Egypt and South Africa, together with penecontemporaneous specimens from the Petera cu Oase in Romania, permit preliminary assessment of variation among modern humans from geographically disparate regions at this time. Morphometric and morphological comparisons with other Late Pleistocene modern human specimens, and with 23 recent human population samples, reveal that elevated levels of variation are present throughout the Late Pleistocene. Comparison of Holocene and Late Pleistocene craniometric variation through resampling analyses supports hypotheses derived from genetic data suggesting that present phenotypic variation may represent only a restricted part of Late Pleistocene human diversity. The Nazlet Khater, Hofmeyr, and Oase specimens provide a unique glimpse of that diversity.

Link

Y chromosomes and mtDNA in Egyptian West Desert

Notice that all Y-chromosomes belong to either E-subclades or to J1. I would definitely not equate J1 with the Neolithic in this case; it is more likely to be due to historical movements of Semitic/Arabic populations into Egypt. The complete absence of J2 is noteworthy and resembles Arabian peninsula populations where the J2/J1 ratio reaches its minimum.

American Journal of Physical Anthropology doi:10.1002/ajpa.21078

Near Eastern Neolithic genetic input in a small oasis of the Egyptian Western Desert

Martina Kujanová et al.

Abstract

The Egyptian Western Desert lies on an important geographic intersection between Africa and Asia. Genetic diversity of this region has been shaped, in part, by climatic changes in the Late Pleistocene and Holocene epochs marked by oscillating humid and arid periods. We present here a whole genome analysis of mitochondrial DNA (mtDNA) and high-resolution molecular analysis of nonrecombining Y-chromosomal (NRY) gene pools of a demographically small but autochthonous population from the Egyptian Western Desert oasis el-Hayez. Notwithstanding signs of expected genetic drift, we still found clear genetic evidence of a strong Near Eastern input that can be dated into the Neolithic. This is revealed by high frequencies and high internal variability of several mtDNA lineages from haplogroup T. The whole genome sequencing strategy and molecular dating allowed us to detect the accumulation of local mtDNA diversity to 5,138 ± 3,633 YBP. Similarly, theY-chromosome gene pool reveals high frequencies of the Near Eastern J1 and the North African E1b1b1b lineages, both generally known to have expanded within North Africa during the Neolithic. These results provide another piece of evidence of the relatively young population history of North Africa.

Link

mtDNA in East African Bantu

The admixture detected here is consistent with the autosomal results of Tishkoff et al., according to which the Tutsi/Hutu population had 66% membership in the Niger-Kordofani, and 18% in the Cushitic cluster (Table S8).

American Journal of Physical Anthropology doi:10.1002/ajpa.21070

mtDNA variability in two Bantu-speaking populations (Shona and Hutu) from Eastern Africa: Implications for peopling and migration patterns in sub-Saharan Africa

Loredana Castrì et al.

Abstract

In this study, we report novel data on mitochondrial DNA in two of the largest eastern Bantu-speaking populations, the Shona from Zimbabwe and the Hutu from Rwanda. The goal is to evaluate the genetic relationships of these two ethnic groups with other Bantu-speaking populations. Moreover, by comparing our data with those from other Niger-Congo speaking populations, we aim to clarify some aspects of evolutionary and demographic processes accompanying the spread of Bantu languages in sub-Saharan Africa and to test if patterns of genetic variation fit with models of population expansion based on linguistic and archeological data. The results indicate that the Shona and Hutu are closely related to the other Bantu-speaking populations. However, there are some differences in haplogroup composition between the two populations, mainly due to different genetic contributions from neighboring populations. This result is confirmed by estimates of migration rates which show high levels of gene flow not only between pairs of Bantu-speaking populations, but also between Bantu and non-Bantu speakers. The observed pattern of genetic variability (high genetic homogeneity and high levels of gene flow) supports a linguistic model suggesting a gradual spread of Bantu-speakers, with strong interactions between the different lines of Bantu-speaker descent, and is also in agreement with recent archeological findings. In conclusion, our data emphasize the role that population admixture has played at different times and to varying degrees in the dispersal of Bantu languages.

Link

Gender differences in reproductive success (Brown et al. 2009)

This is a wonderful paper which gathers data to address the issue of how sexual selection operates in men and women. Bateman's principles as presented here are:

1. greater mating variance in men than women;
2. greater reproductive variance in men than women;
3. correlation between mating and reproductive success.

Each man and woman has a certain number of lifetimes sexual mates and a certain number of offspring. While women are more similar to each other, with relatively fewer having too few (or too many) partners/offspring compared to the average, men are more variable, with a few of them having no or many offspring/partners.

The authors bring up the interesting point that greater male variance does not -in itself- substantiate sexual selection as it is often assumed. This is because variance can be either due to selection or to random genetic drift.

A good way to see this (not found in the paper), is to imagine the same set of people living their lives either (a) in the peaceful countryside, or (b) in a big city during a series of air raids. In case (b) variance will be greater, as those killed or maimed by the raids will not mate or reproduce, and the survivors will, whereas in case (a) everyone will have the same a priori opportunities.

So, if everyone has the same number of offspring as everyone else does imply a lack of sexual selection; but, variability in reproductive success does not in itself imply selection. Only when mating and reproductive success (Bateman's third rule) are correlated do we have a good case for sexual selection.

The authors collect data on the male- and female- specific variance in mating and reproductive success, although they note a dearth of data in favor of the third principle. One can't disagree with their call for the collection of relevant data to investigate whether the three principles apply in humans, nor with their observation that what is applicable to fruit flies (the subject of Bateman's original research) does not necessarily apply to humans, and certainly not to all societies (*)

(*) An interesting observation from the paper is that although monogamous societies are a minority of human societies, they tend to encompass the largest number of people. Moreover, in about half of nominally polygamous societies, in practice monogamy is practiced by the great majority of the population.

Below is Table 1 from the paper.


Not related to the subject of this paper, but this gives us the opportunity to examine realistic demographic parameters in simulations such as these, where an assumption of Poisson distributed number of offspring (with mean m) is used. In the Poisson distribution, the variance is also m. As the table above shows, the variance is almost equal to the mean in some populations (e.g., USA), but quite different in others (e.g., 19th c. Sweden); indeed the latter seems more common.

Departure from the Poisson assumption in the direction of greater reproductive variance is entirely consistent with my observations in the above-linked post on the importance of reproductive inequality.

Trends in Ecology & Evolution doi:10.1016/j.tree.2009.02.005

Bateman’s principles and human sex roles

Gillian R. Brown et al.

Abstract

In 1948, Angus J. Bateman reported a stronger relationship between mating and reproductive success in male fruit flies compared with females, and concluded that selection should universally favour ‘an undiscriminating eagerness in the males and a discriminating passivity in the females’ to obtain mates. The conventional view of promiscuous, undiscriminating males and coy, choosy females has also been applied to our own species. Here, we challenge the view that evolutionary theory prescribes stereotyped sex roles in human beings, firstly by reviewing Bateman's principles and recent sexual selection theory and, secondly, by examining data on mating behaviour and reproductive success in current and historic human populations. We argue that human mating strategies are unlikely to conform to a single universal pattern.

Link

Archaic admixture in modern humans? (Wall et al. 2009)

John Hawks points me towards a new paper which aims to estimate the presence of archaic admixture (from Neandertals, Indonesian "hobbits", and assorted candidates) in the modern human genome. I highly recommend reading that post for an analysis of the paper; while Dr. Hawks is probably on the "admixture happened" side of the debate, he offers both reasons to like and dislike the new study.

There is, however, what I think is a more important weakness of the paper. To substantiate the case for admixture, the authors compare West African Yorubans separately with Europeans and with East Asians.

Let's assume that they do in fact detect what is genuine archaic admixture, i.e., the introgression of chunks of DNA into regional humans from a species other than modern Homo sapiens. They can achieve this by detecting regions where Yoruban DNA sequence differs from European DNA sequence in a manner suggestive of a very ancient time depth.

But, is there a reason to ascribe these differences to Neandertal introgression?

Actually, there is not, as Europeans are derived from a specific East African population: they are not derived from Sub-Saharan Africans in general, or West Africans in particular. Indeed, this very paper finds evidence of archaic admixture in Africa itself!

Thus, what appears as a piece of Neandertal DNA in Europeans, could in fact be a piece of ancestral East African DNA which differs from Yoruba DNA because of population structure in Africa itself, for which there is more than enough evidence.

So, what this paper does, is tell us that a chunk of DNA in Europeans, and the corresponding chunk in Yorubans don't share ancestry within a conventional Out-of-Africa time frame. It does not, however, tell us that this is because of archaic introgression in Europeans. The culprit could equally well be long-term population structure in Africa, i.e., the presence of "modern" and "archaic" populations in Africa itself.

The way forward is to compare Europeans with Middle Eastern Caucasoids and East Africans. If the "archaic" European DNA is found across many of these populations, then the case for Neandertal introgression will weaken, and the hypothesis presented in this post (ancient African population structure) will be supported.

UPDATE (May 9): John Hawks has updated his blog entry in response to this post. He makes two points:

The East Asian and European comparisons come up with different genes showing evidence of putative introgression.

What we don't know at this point is whether either (or both) of the European/East Asian introgression candidate genes are found in East Africa. If so, then the presence of different sets of genes in Europe and East Asia could be the result of random survivals of the diversity of the initial African population. Or, introgression happened in either Europe or East Asia, and one region preserves archaic DNA inherited from Africa and the other archaic DNA that introgressed in East Asia or Europe, which is why the two are different.

Furthermore, while Out-of-Africa is conventionally seen as one migration c. 40Kya which eventually spawned both Europeans and East Asians, there is Y-chromosomal evidence for a separate process linking Western Eurasia and East Africa (Y-chromosome haplogroup E). Thus, a later movement may have spread "archaic" East African genes into Western Eurasia but not in East Asia.

John's second point:

The entire point of the out-of-Africa replacement idea is to draw humans from an unstructured ancient population. Humans have to be inbred to explain the low genetic variation today. A long bottleneck in Africa is one explanation for this inbreeding

We do know that there was substantial variation in Africa at the time when modern Homo sapiens emerged. A long period of inbreeding in Africa would indeed create the fairly homogeneous species we discover when we look at most genes. This species would, however, during its population expansion -within Africa- come into contact with other previously isolated African populations, some of which would go extinct, while others might be absorbed, their genes persisting at low frequency in the expanding species.

This requires no great leap of faith. It parallels directly what happened in Africa in the last few thousand years, where previously isolated Pygmy and Khoi-San populations came into contact with expanding farmer-pastoralists, and contributing a little bit to the farmers' genomes.

Thus, the expanding African population that eventually spilled over into Eurasia, would indeed be quite inbred and homogeneous, but its gene pool would also contain traces of the smaller, less successful African populations it had absorbed. Because of their low frequency, these traces would be more susceptible to extinction in the series of bottlenecks that led to Europeans on one side and East Asians on the other, with different sets of archaic genes preserved in either region.


Molecular Biology and Evolution, doi:10.1093/molbev/msp096

Detecting ancient admixture and estimating demographic parameters in multiple human populations

Jeffrey D. Wall et al.

Abstract

We analyze patterns of genetic variation in extant human polymorphism data from the NIEHS SNPs project to estimate human demographic parameters. We update our previous work by considering a larger data set (more genes and more populations), and by explicitly estimating the amount of putative admixture between modern humans and archaic human groups (e.g., Neandertals, Homo erectus, H. floresiensis). We find evidence for this ancient admixture in European, East Asian and West African samples, suggesting that admixture between diverged hominin groups may be a general feature of recent human evolution.

Link

Genetic structure in Europeans (Nelis et al. 2009)

Yet another study on Europeans, this time with ~3K individuals and ~270K SNPs. The studied populations now include a wide assortment of Slavs, Balts, as well as Estonians and several other populations from all over Europe.

The most interesting new fact from this study:

Estonia is a small country with no geographic barriers and its Estonian population is merely one million. In order to study the genetic structure of Estonia in more detail, all Estonian individuals were grouped here by their county of birth. Then, PCA was performed and the mean values of the two first PC of the counties were plotted onto the Estonian regional map (Figure 2). Surprisingly, the resulting genetic map correlates almost perfectly with the geographic map, although Estonia is only 43,400 km2 in size, and the mean area of a county only 2,900 km2. Thus, fine-scale genetic difference can be revealed by PC analysis, and the results can be useful for identification of the distant relatives.

Figure 2 is reproduced here; the Estonian map is on the bottom right.

What seems very interesting is how Swedes and Estonians both deviate towards Finns but from different "starting points", a North German-Central European one and Baltic-West Russian one respectively. This is quite reasonable, as Swedes are Germanics who absorbed some Finnish elements, while Estonians are Finno-Ugrians surrounded by Balto-Slavs.

As the authors note, the multi-dimensional scaling plot is quite similar to the results of the PCA analysis:


Also of interest is the result of PCA within individual countries for which more than one geographical sample were available.


as the authors note:

Interestingly, PC analysis was also capable of highlighting intra-population differences, such as between the two Finnish and the two Italian samples, respectively. A low level of intra-population differentiation in Germany has been reported previously [18], and was confirmed here. In addition, we detected intra-population differences within the Czech and Estonian samples (Figure S3).

The two Finnish samples were from Helsinki and Kuusamo. The German ones from Schleswig-Holstein and Augsburg. The Italian ones from Borbera valley in the Piedmont and Apulia.

PLoS ONE doi:10.1371/journal.pone.0005472

Genetic Structure of Europeans: A View from the North–East

Mari Nelis et al.

Abstract

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (F_st) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Link

Basques are not a genetic isolate

This paper shows that Basques, who are viewed by some as a relatively isolated remnant of the European Paleolithic population, do not in fact show any signs of being a genetic isolate, having similar levels of heterozygosity, i.e., tendency to have different alleles in any particular locus, and linkage disequilibrium, i.e, the tendency of alleles in big blocks of DNA to be inherited together.

The MDS plot of the Fst distances is also quite interesting, showing Catalans, Extremadura, Basques, and Andalusians on the left, and Moroccans and Saharans on the right. As the authors note:

The MDS plot shows that genetic variation can be described with a single component, namely, Iberian vs North African populations (note the huge difference in scale between components 1 and 2), and Basques are not differentiated from other Iberian populations.

European Journal of Human Genetics doi:10.1038/ejhg.2009.69

Isolated populations as treasure troves in genetic epidemiology: the case of the Basques

Paolo Garagnani et al.

Abstract

The Basques are a culturally isolated population, living across the western border between France and Spain and speaking a non-Indo-European language. They show outlier allele frequencies in the ABO, RH, and HLA loci. To test whether Basques are a genetic isolate with the features that would make them good candidates in genetic association studies, we genotyped 123 SNPs in a 1-Mb region in chromosome 22 in Basque samples from France and Spain, as well as in samples from northern and southern Spain, and in three North African samples. Both Basque samples showed similar levels of heterozygosity to the other populations, and the decay of linkage disequilibrium with physical distance was not different between Basques and non-Basques. Thus, Basques do not show the genetic properties expected in population isolates.

Link

Phylogeography of macrohaplogroup M in India

A nice little open access review paper from the Indian Journal of Genetics.

Journal of Genetics Volume 88, Number 1, April 2009

Phylogeographic distribution of mitochondrial DNA macrohaplogroup M in India

Suvendu Maji, S. Krithika and T. S. Vasulu

Abstract

Indian subcontinent harbours both the human mtDNA macrohaplogroups M and N, of which M is the most prevalent. In this study, we discuss the overall distribution of the various haplogroups and sub-haplogroups of M among the different castes and tribes to understand their diverse pattern with respect to geographical location and linguistic affiliation of the populations. An overview of about 170 studied populations, belonging to four distinct linguistic families and inhabiting different geographic zones, revealed wide diversity of about 22 major haplogroups of M. The tribal populations belonging to the same linguistic family but inhabiting different geographical regions (Dravidian and Austro–Asiatic speakers) exhibited differences in their haplogroup diversity. The northern and southern region castes showed greater diversity than the castes of other regions.

Link (pdf)

Citation of my Y-STR mutation rate criticism

I was reading Tuuli Lappalainen Ph.D. dissertation, at the University of Helsinki: "Human genetic variation in the Baltic Sea region: Features of population history and natural selection," and, to my surprise, I noticed that my post on How Y-STR variance accumulates: a comment on Zhivotovsky, Underhill and Feldman (2006) was cited:

Estimating the age of haplogroups is important for connecting genetic patterns to historical phenomena. However, it is dependent on the correct estimation of the mutation rate, which has proven to be difficult. Rates calculated from pedigrees are 3-4 times higher than evolutionary rates (Parsons et al. 1997, Howell et al. 2003, Dupuy et al. 2004, Zhivotovsky et al. 2004, Zhivotovsky et al. 2006), and it is unclear which should be used for the calculation of the most recent common ancestor for major haplogroups in large geographic regions. It has recently been suggested (Pontikos 2008) that the widely used evolutionary rate of the Y chromosome (Zhivotovsky et al. 2004) is strongly underestimating the effective mutation rate due to not accounting for population growth and the bias of analyzing the biggest haplogroups that have grown at rates exceeding the general growth rate of the population. These analyses have not been published in a peer-reviewed journal, but they appear to correctly point out at least some problems of the commonly used models. Thus, the appropriate mutation rate to use for analyzing the temporal scale of the Y-chromosomal haplogroup variation may be a few times lower than was used in II – close to the pedigree rate. The same bias should apply to mitochondrial DNA, too. If the revised rates (Pontikos 2008) were used instead, TMRCAs for the main Y-chromosomal haplogroups I1a, N3 and R1a1 would be in the order of 3000-4000 years before present. These dates would imply that instead of the proposed Neolithic arrival of these haplogroups, their upper age limit would be in late Neolithic or early Bronze Age. Interestingly, the revised age of N3 variation in the Baltic Sea region would actually correspond nicely with the recently suggested Bronze Age arrival of the Finno-Ugric language (Häkkinen 2009). However, given the current uncertainty of the appropriate mutation rates, all time estimates should be used with great caution.

The cited post was the first one in the now extensive Y-STR series in which I have tried to dissect various aspects Y-STR based age estimation.

Genetic admixture in eastern Indonesia

From the paper:

Although less pronounced in EI compared to other regions, we observed a higher eastern Asian component with mtDNA than with NRY-DNA, and conversely a higher Melanesian component with NRY-DNA than with mtDNA in EI, similar to what has been described for Island Melanesia (Kayser et al. 2008) and Polynesia (Kayser et al. 2006). As described elsewhere, a history of sex-biased admixture between Austronesians and non- Austronesians might explain this result, confirming previous surveys in Near and Remote Oceania on the modality of the Austronesian migration (Hage and Marck 2003; Kayser et al. 2006; Kayser et al. 2008; Kayser, Lao, and Stoneking 2008).

Molecular Biology and Evolution, doi:10.1093/molbev/msp097

Genetic admixture history of eastern Indonesia as revealed by Y-chromosome and mitochondrial DNA analysis

Stefano Mona et al.

Abstract

Eastern Indonesia possesses more linguistic diversity than any other region in Southeast Asia, with both Austronesian (AN) languages that are of East Asian origin, as well as non-Austronesian (NAN) languages of likely Melanesian origin. Here, we investigated the genetic history of human populations from seven eastern Indonesian islands, including AN- and NAN-speakers, as well as the relationship between languages and genes, by means of non-recombining Y-chromosomal (NRY) and mitochondrial DNA (mtDNA) analysis. We found that the eastern Indonesian gene pool consists of East Asian as well as Melanesian components, as might be expected based on linguistic evidence, but also harbours putative indigenous eastern Indonesian signatures that perhaps reflect the initial occupation of the Wallacea by aboriginal hunter-gatherers already in Palaeolithic times. Furthermore, both NRY and mtDNA data showed a complete lack of correlation between linguistic and genetic relationships, most likely reflecting genetic admixture and/or language shift. In addition, we noted a small fraction of the NRY and mtDNA data shared between eastern Indonesians and Australian Aborigines likely reflecting an ancient link between Asia and Australia. Our data thus provide insights into the complex genetic ancestry history of eastern Indonesian islanders characterized by several admixture episodes, and demonstrate a clear example of the lack of the often-assumed correlation between the genes and languages of human populations.

Link

Mediterranean diet and coronary heart disease

From the paper:

As shown in Table 4, sufficient support from RCTs to satisfy the criterion for experimental evidence is observed only for marine or total ω-3 fatty acid intake and a Mediterranean dietary pattern. Little or weak evidence from RCTs is found for consumption of fruits, vegetables, fish, fiber, polyunsaturated fatty acids, and total fat and supplemental intake of beta carotene, vitamin E, ascorbic acid, and folate. Other factors have not been evaluated singly in clinical trials (Table 4). The evidence from RCTs agrees with the Bradford Hill results from cohort studies for intake of ascorbic acid and vitamin E supplements, polyunsaturated fatty acids, and total fats and a Mediterranean dietary pattern, but disagree for fish consumption, which shows moderate evidence of a causal link with CHD in cohort studies but virtually no effect in RCTs.

Covered elsewhere:

Eating a Mediterranean diet rich in vegetables and nuts does help protect the heart, a new review concludes.

"We took this on because there is a lot of confusion out in the public about what we should eat and what we should avoid eating in terms of preventing a heart attack," study co-author Dr. Sonia Anand of McMaster University in Hamilton, Ont., told CBC News on Tuesday.

"So the good thing is, we can say try and eat more like someone who would live in Greece or Italy, the Mediterranean diet, and try and avoid a Western-type of diet, which is your eggs and bacon breakfast or your hot dogs for lunch."

Related:

• Mediterranean diet reduces risk of dying, heart disease, cancer, Parkinson's, and Alzheimer's
• Traditional Mediterranean diet protects against diabetes
• Mediterranean diet lowers risk of Alzheimer's
• Mediterranean diet in Greco-Roman and Byzantine writers

Arch Intern Med. 2009;169(7):659-669.

A Systematic Review of the Evidence Supporting a Causal Link Between Dietary Factors and Coronary Heart Disease

Andrew Mente, PhD; Lawrence de Koning, MSc; Harry S. Shannon, PhD; Sonia S. Anand, MD, PhD, FRCPC

Abstract

Background Although a wealth of literature links dietary factors and coronary heart disease (CHD), the strength of the evidence supporting valid associations has not been evaluated systematically in a single investigation.

Methods We conducted a systematic search of MEDLINE for prospective cohort studies or randomized trials investigating dietary exposures in relation to CHD. We used the Bradford Hill guidelines to derive a causation score based on 4 criteria (strength, consistency, temporality, and coherence) for each dietary exposure in cohort studies and examined for consistency with the findings of randomized trials.

Results Strong evidence supports valid associations (4 criteria satisfied) of protective factors, including intake of vegetables, nuts, and "Mediterranean" and high-quality dietary patterns with CHD, and associations of harmful factors, including intake of trans–fatty acids and foods with a high glycemic index or load. Among studies of higher methodologic quality, there was also strong evidence for monounsaturated fatty acids and "prudent" and "western" dietary patterns. Moderate evidence (3 criteria) of associations exists for intake of fish, marine -3 fatty acids, folate, whole grains, dietary vitamins E and C, beta carotene, alcohol, fruit, and fiber. Insufficient evidence (2 criteria) of association is present for intake of supplementary vitamin E and ascorbic acid (vitamin C); saturated and polyunsaturated fatty acids; total fat; -linolenic acid; meat; eggs; and milk. Among the dietary exposures with strong evidence of causation from cohort studies, only a Mediterranean dietary pattern is related to CHD in randomized trials.

Conclusions The evidence supports a valid association of a limited number of dietary factors and dietary patterns with CHD. Future evaluation of dietary patterns, including their nutrient and food components, in cohort studies and randomized trials is recommended.

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Alternate mtDNA phylogeny of N and M clades

I would be very interested in hearing from readers who are more up-to-date on mtDNA phylogenetics than myself on what they think of this paper. Until now, we knew that West Eurasians belonged almost entirely in macro-haplogroup N, with the exception of low-frequency haplogroup M1 and a few erratics representing more recent admixture. On the other hand, East Eurasians belonged to both macro-haplogroups N and M. What this paper seems to suggest is that haplogroup N itself has its own East vs. West structure, and the common West (or East) Eurasian haplogroups within N are phylogenetically related in addition to geographically co-existing.

J Mol Evol. 2008 Nov;67(5):465-87. Epub 2008 Oct 15.

PCA and clustering reveal alternate mtDNA phylogeny of N and M clades.

Alexe G, Satya RV, Seiler M, Platt D, Bhanot T, Hui S, Tanaka M, Levine AJ, Bhanot G.

Phylogenetic trees based on mtDNA polymorphisms are often used to infer the history of recent human migrations. However, there is no consensus on which method to use. Most methods make strong assumptions which may bias the choice of polymorphisms and result in computational complexity which limits the analysis to a few samples/polymorphisms. For example, parsimony minimizes the number of mutations, which biases the results to minimizing homoplasy events. Such biases may miss the global structure of the polymorphisms altogether, with the risk of identifying a "common" polymorphism as ancient without an internal check on whether it either is homoplasic or is identified as ancient because of sampling bias (from oversampling the population with the polymorphism). A signature of this problem is that different methods applied to the same data or the same method applied to different datasets results in different tree topologies. When the results of such analyses are combined, the consensus trees have a low internal branch consensus. We determine human mtDNA phylogeny from 1737 complete sequences using a new, direct method based on principal component analysis (PCA) and unsupervised consensus ensemble clustering. PCA identifies polymorphisms representing robust variations in the data and consensus ensemble clustering creates stable haplogroup clusters. The tree is obtained from the bifurcating network obtained when the data are split into k = 2,3,4,...,kmax clusters, with equal sampling from each haplogroup. Our method assumes only that the data can be clustered into groups based on mutations, is fast, is stable to sample perturbation, uses all significant polymorphisms in the data, works for arbitrary sample sizes, and avoids sample choice and haplogroup size bias. The internal branches of our tree have a 90% consensus accuracy. In conclusion, our tree recreates the standard phylogeny of the N, M, L0/L1, L2, and L3 clades, confirming the African origin of modern humans and showing that the M and N clades arose in almost coincident migrations. However, the N clade haplogroups split along an East-West geographic divide, with a "European R clade" containing the haplogroups H, V, H/V, J, T, and U and a "Eurasian N subclade" including haplogroups B, R5, F, A, N9, I, W, and X. The haplogroup pairs (N9a, N9b) and (M7a, M7b) within N and M are placed in nonnearest locations in agreement with their expected large TMRCA from studies of their migrations into Japan. For comparison, we also construct consensus maximum likelihood, parsimony, neighbor joining, and UPGMA-based trees using the same polymorphisms and show that these methods give consistent results only for the clade tree. For recent branches, the consensus accuracy for these methods is in the range of 1-20%. From a comparison of our haplogroups to two chimp and one bonobo sequences, and assuming a chimp-human coalescent time of 5 million years before present, we find a human mtDNA TMRCA of 206,000 +/- 14,000 years before present.

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Supplement on "Geographical structure and differential natural selection amongst North European populations" (McEvoy et al. 2009)

From the supplemental material of a paper I covered in March, here are a couple of PCA plots of the first two principal components of the studied populations, with or without the Finns.


In the plot without the Finns, we see the expected British Isles -> Continental Europe differentiation in the order of Ireland, UK, Netherlands, along PC1. Swedes, and to a much lesser extent Danes deviate from this gradient in an orthogonal direction.
When Finns are included, PC1 now captures the major difference between them and the other Celto-Germanic populations which appear strikingly homogeneous along this component. The reason for the Swedes' divergence is now clear, as they are seemingly drawn towards the Finns, although the two clusters can be cleanly separated by a line at around PC1=-0.03.

It is fairly clear by now, that in northern Europe, there are two major distinctions (in that order): (i) between the Finns, and Finno-Ugrian influenced populations on the one hand, and the rest, and (b) a less important West-East gradient from Ireland to the Baltic.

The fact that factor (i) is the most important one pretty much vindicates the views of traditional physical anthropology since the time of Deniker at least. Despite the lack of data and statistical knowledge available at his time, Deniker, in the late 19th century, divided the light-pigmented northern European xanthochrooi of earlier classifications into two: the race nordique, associated primarily with the Germanic peoples, and the race orientale associated primarily with the eastern Slavs and Finns.

This classification scheme was continued by the better writers that followed, e.g., as razza nordica and razza baltica by Renato Biasutti, and as Атланто-балтийская раса (Atlanto-Baltic race) and Беломорско-балтийская раса (White Sea-Baltic race) in works written in Russian.