PLoS ONE 5(5): e10639. doi:10.1371/journal.pone.0010639

The Origin and Genetic Variation of Domestic Chickens with Special Reference to Junglefowls Gallus g. gallus and G. varius

Hiromi Sawai et al.

It is postulated that chickens (Gallus gallus domesticus) became domesticated from wild junglefowls in Southeast Asia nearly 10,000 years ago. Based on 19 individual samples covering various chicken breeds, red junglefowl (G. g. gallus), and green junglefowl (G. varius), we address the origin of domestic chickens, the relative roles of ancestral polymorphisms and introgression, and the effects of artificial selection on the domestic chicken genome. DNA sequences from 30 introns at 25 nuclear loci are determined for both diploid chromosomes from a majority of samples. The phylogenetic analysis shows that the DNA sequences of chickens, red and green junglefowls formed reciprocally monophyletic clusters. The Markov chain Monte Carlo simulation further reveals that domestic chickens diverged from red junglefowl 58,000±16,000 years ago, well before the archeological dating of domestication, and that their common ancestor in turn diverged from green junglefowl 3.6 million years ago. Several shared haplotypes nonetheless found between green junglefowl and chickens are attributed to recent unidirectional introgression of chickens into green junglefowl. Shared haplotypes are more frequently found between red junglefowl and chickens, which are attributed to both introgression and ancestral polymorphisms. Within each chicken breed, there is an excess of homozygosity, but there is no significant reduction in the nucleotide diversity. Phenotypic modifications of chicken breeds as a result of artificial selection appear to stem from ancestral polymorphisms at a limited number of genetic loci.

Link

BMC Genomics 2010, 11:326doi:10.1186/1471-2164-11-326

Genetic Structure of the Spanish Population

Javier Gayan et al.

Abstract

Background
Genetic admixture is a common caveat for genetic association analysis. Therefore, it is important to characterize the genetic structure of the population under study to control for this kind of potential bias.

Results
In this study we have sampled over 800 unrelated individuals from the population of Spain, and have genotyped them with a genome-wide coverage. We have carried out linkage disequilibrium, haplotype, population structure and copy-number variation (CNV) analyses, and have compared these estimates of the Spanish population with existing data from similar efforts.

Conclusions
In general, the Spanish population is similar to the Western and Northern Europeans, but has a more diverse haplotypic structure. Moreover, the Spanish population is also largely homogeneous within itself, although patterns of micro-structure may be able to predict locations of origin from distant regions. Finally, we also present the first characterization of a CNV map of the Spanish population. These results and original data are made available to the scientific community.

Link

Related:

• The script of the Philistines
• Tayinat Dark Age temple

Journal of Archaeological Science doi:10.1016/j.jas.2010.05.008

Lathyrus Consumption in Late Bronze and Iron Age Sites in Israel: An Aegean Affinity

Yael Mahler-Slasky et al.

Abstract

This paper presents new evidence, together with previous findings, for the appearance of charred seeds of Lathyrus sativus (grass pea)/L. cicera. This grain legume was a food staple in ancient times, principally in the Aegean region, but also appeared sporadically and in a limited way in the archaeological record of the southern Levant. It is encountered there first in the Late Bronze Age but disappears in the record at the end of the Iron Age. Although a palatable, nutritious plant adapted for growing under adverse conditions, its seeds can be toxic when consumed in large quantities. Apparently L. sativus/cicera made its way to the lowlands of the southern Levant, either by trade or with Philistine immigrants. It is absent at other south Levantine Bronze Age (i.e., Canaanite) and Iron Age sites and it remained a food component in the southern coastal region (i.e., Philistia, the region associated with the biblical Philistines) up to the end of Iron Age II, suggesting a possible ethnic association. Evidence of L. sativus/cicera joins that of another Aegean archaeobotanical import from an earlier, Middle Bronze Age II context, L. clymenum, found at Tel Nami, a coastal site farther to the north of the region.

Link

Forensic Sci Int Genet. 2010 May 20. [Epub ahead of print]

Mitochondrial DNA polymorphisms in Gelao ethnic group residing in Southwest China.

Liu C, Wang SY, Zhao M, Xu ZY, Hu YH, Chen F, Zhang RZ, Gao GF, Yu YS, Kong QP.

Abstract

Gelao ethnic group, an aboriginal population residing in southwest China, has undergone a long and complex evolutionary process. To investigate the genetic structure of this ancient ethnic group, mitochondrial DNA (mtDNA) polymorphisms of 102 Gelao individuals were collected and analyzed in this study. With the aid of the information extracted from control-region hypervariable segments (HVSs) I and II as well as some necessary coding-region segments, phylogenetic status of all mtDNAs under study were determined by means of classifying into various defined haplogroups. The southern-prevalent haplogroups B, R9, and M7 account for 45.1% of the gene pool, whereas northern-prevalent haplogroups A, D, G, N9, and M8 consist of 39.2%. Haplogroup distribution indicates that the Gelao bears signatures of southern populations and possesses some regional characters. In the PC map, Gelao clusters together with populations with Bai-Yue tribe origin as well as the local Han and the Miao. The results demonstrate the complexity of Gelao population and the data can well supplement the China mtDNA database.

Link

Related: Portraits of ethnic groups of China including a portrait of Gelao, the mainland relatives of the Gelong and Li who are an indigenous group of Hainan.
Note that Hlai is the Li's own self-appellation. Wikipedia article on Kadai (Daic) languages. Note that haplogroup O1 has been linked to Daic languages, which would agree with the results on the Gelong people. Tai-Kadai people form their own autosomal cluster, demonstrated their common genetic origins.

J Hum Genet. doi:10.1038/jhg.2010.50.

Genetic origin of Kadai-speaking Gelong people on Hainan island viewed from Y chromosomes.

Li D, Sun Y, Lu Y, Mustavich LF, Ou C, Zhou Z, Li S, Jin L, Li H.

The government of China defined 56 official ethnicities for the ethnic groups in China for political purposes; however, there are many more than 56 ethnic groups. Therefore, similar groups must be pooled for registry, and the so-called ethnicity identification is an important official mission in China. Here, we showed how genetics can help in the ethnicity identification for the Gelong people on Hainan Island. The Gelong speak a Kadai language whose other speakers (officially of the Gelao ethnicity) are all far in the southwest of China. Being registered as a Han ethnicity, the Gelong lost all the benefits assigned to the minorities. Y-chromosome typing was performed in a sample of 78 individuals. Twenty single nucleotide polymorphisms (SNPs) and seven short tandem repeats (STRs) were typed and eight haplogroups were detected, among which haplogroup O1a(*) was the most dominant. Compared with the Y haplogroups of the populations in south China, the Gelong were found to be closest to the Gelao and the Hlai using principal components (PCs) analysis, dendrogram clustering and STR networks. The genetic similarity between the Gelong and the Hlai may have resulted from the gene flow during thousands of years of neighboring history on Hainan Island, whereas the similarity between the Gelong and the Gelao may have resulted from their common ancestry because there is less possibility of gene flow over such a far distance. As both linguistic and genetic evidence support the similarity between the Gelong and the Gelao, we suggest that the Gelong register as Gelao for their official ethnicity. However, this identification is invalid until it is accepted by the Gelong people themselves and the Hainan government.

Link

On the left Figure S5: Proportion of each individual’s ancestry derived using the linkage model in STRUCTURE for the optimal number of ancestral populations (K = 4) (TIFF 102 kb)

Related:

• Genetic ancestry of Coloured South Africans
• Origin of South African Couloured population

Human Genetics doi:10.1007/s00439-010-0836-1

Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape

Erika de Wit et al.

Admixed populations present unique opportunities to discover the genetic factors underlying many multifactorial diseases. The geographical position and complex history of South Africa has led to the establishment of the unique admixed population known as the South African Coloured. Not much is known about the genetic make-up of this population, and the historical record is patchy. We genotyped 959 individuals from the Western Cape area, self-identified as belonging to this population, using the Affymetrix 500k genotyping platform. This resulted in nearly 75,000 autosomal SNPs that could be compared with populations represented in the International HapMap Project and the Human Genome Diversity Project. Analysis by means of both the admixture and linkage models in STRUCTURE revealed that the major ancestral components of this population are predominantly Khoesan (32–43%), Bantu-speaking Africans (20–36%), European (21–28%) and a smaller Asian contribution (9–11%), depending on the model used. This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population.
Link

Figure 1 (on the left) Modelled “suitability” (probability of occurrence, Maxent) for (A) agriculture, (B) sedentary animal husbandry, (C) nomadic pastoralism, and (D) hunting and gathering.

From the paper:
Our simplistic exercise showed that a “geo-deterministic” approach can predict surprisingly many features of human cultural geography without any explicit cultural or historical assumptions. Although many deviations require further factors for a satisfying explanation, the nature of these deviations invite the generation of hypotheses for further research. Our ‘null model’ offers a highly parsimonious, empirically supported explanation to the question of why some regions are more “powerful” than others, supplementing the idea of a historical effect operating through the timing of transition to agriculture [2].

In some instances, our model may actually provide a simpler explanation. Putterman [10], for example, suggested that the dominance of Western European cultures indicates the transmission of “civilization” traits (other than knowledge on agriculture) from regions of first domestication. Our data indicate that higher climatic suitability may have been sufficient for Europe to “catch up”, allowing for much higher population densities than, e.g., the “fertile crescent” region. Models of “suitability” under past climatic scenarios may be helpful to evaluate this. Similarly, models applied to predicted future climatic scenarios may be useful to anticipate changes of the economic suitability of landuse types.

However, our model has clear deviations in some regions that may well be explicable by the availability of animals and plants suitable for domestication (e.g., central Africa). Apart from that, and more importantly, we know that human societies and economies went through historical development, so ignoring history may not always be the best strategy to understand causalities. This problem occurs also with other research questions in biogeography, e.g. when investigating global biodiversity patterns [45]–[47]. Nevertheless, our ‘null model’ will be a useful tool in identifying regions that require further investigation to understand additional processes that shape the distribution and performance of human economic traits.I really like this type of paper that looks at a simple explanation for a phenomenon, in this case, economic output as a product of soil/climate quality and suitability. As the authors point out, their "null" model has its limitations, and it is precisely in regions of the world where its predictions do not match the observations, that we should look for additional factors (besides soil and climate) to explain economic traits.

Related: Soil and Greek temples.

PLoS ONE 5(5): e10416. doi:10.1371/journal.pone.0010416

Is the Spatial Distribution of Mankind's Most Basic Economic Traits Determined by Climate and Soil Alone?

Jan Beck, Andrea Sieber

Abstract

Background
Several authors, most prominently Jared Diamond (1997, Guns, Germs and Steel), have investigated biogeographic determinants of human history and civilization. The timing of the transition to an agricultural lifestyle, associated with steep population growth and consequent societal change, has been suggested to be affected by the availability of suitable organisms for domestication. These factors were shown to quantitatively explain some of the current global inequalities of economy and political power. Here, we advance this approach one step further by looking at climate and soil as sole determining factors.

Methodology/Principal Findings
As a simplistic ‘null model’, we assume that only climate and soil conditions affect the suitability of four basic landuse types – agriculture, sedentary animal husbandry, nomadic pastoralism and hunting-and-gathering. Using ecological niche modelling (ENM), we derive spatial predictions of the suitability for these four landuse traits and apply these to the Old World and Australia. We explore two aspects of the properties of these predictions, conflict potential and population density. In a calculation of overlap of landuse suitability, we map regions of potential conflict between landuse types. Results are congruent with a number of real, present or historical, regions of conflict between ethnic groups associated with different landuse traditions. Furthermore, we found that our model of agricultural suitability explains a considerable portion of population density variability. We mapped residuals from this correlation, finding geographically highly structured deviations that invite further investigation. We also found that ENM of agricultural suitability correlates with a metric of local wealth generation (Gross Domestic Product, Purchasing Power Parity).

Conclusions/Significance
From simplified assumptions on the links between climate, soil and landuse we are able to provide good predictions on complex features of human geography. The spatial distribution of deviations from ENM predictions identifies those regions requiring further investigation of potential explanations. Our findings and methodological approaches may be of applied interest, e.g., in the context of climate change.

Link

Evans et al. had previously proposed that the derived MCPH1 allele had entered the modern human gene pool by Neandertals. This paper tests this by looking at a 50,000 year BP Neandertal, finding them to have the ancestral allele, thus weakening the case for introgression.

The authors write:
Evans and colleagues proposed that haplogroup D originated from a lineage separated from modern humans for 1.1 million years and introgressed into the human gene pool by 37,000 years ago, probably from a Neanderthal stock [4].

However, simulation approaches have shown that two key hypotheses of this model, namely positive selection and admixture, can be relaxed as long as Eurasia was settled from an African population that was both subdivided and under expansion [5]. Interestingly, variation in neurocranial geometry have recently suggested significant levels of geographic structure among early modern humans from Africa [6]. In addition, no direct empirical evidence supports a third key component of the model, ie. that Neanderthals carried alleles of the D haplogroup.This is a great paper in view of the recent controversy about modern human-Neandertal admixture. I have been on the skeptic camp, and this certainly strengthens my African structure thesis.
Here is how the authors try to explain the deep divergence between the ancestral and derived haplotypes:
There is a broad agreement that the contribution of archaic Homo populations to the modern gene pool, if any, must have been very limited [33], [34]. Different lines of evidence concur to suggest that the dispersal of anatomically modern humans from Africa was accompanied by repeated founder effects [35]–[38]. If these founder effects were drastic, most or all gene genealogies should actually be shallow, and hence the occurrence of ancient splits would imply some degree of introgression from archaic human forms. However, different consequences would be expected if only mild founder effects occurred when anatomically modern humans moved out of Africa. Under these conditions, gene trees would have a strong random component, and a certain fraction thereof, even in the absence of selection, would show two highly divergent major lineages [39]. The likelihood of finding gene genealogies with a very old common ancestor and very differentiated lineages would be even higher if the source African population was subdivided and structured genetically before dispersal, which is what most studies clearly suggest [40]–[43]. These theoretical considerations are actually matched by consistent results in simulation studies [5], [34], [44] and by variation in neurocranial geometry, suggesting significant levels of geographic structure among early modern humans from Africa [6]. One more piece of evidence in favor of the idea that seemingly archaic DNA in modern Eurasians is not due to the more fashionable "Neandertal introgression" but to ancient African population structure.
PLoS ONE 10.1371/journal.pone.0010648

The Microcephalin Ancestral Allele in a Neanderthal Individual

Martina Lari et al.

Background
The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal.

Methodology/Principal Findings
Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination.

Conclusions/Significance
The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

Link

A very limited number of markers, but a relatively wide assortment of populations.

BMC Evolutionary Biology 2010, 10:84doi:10.1186/1471-2148-10-84

The Mediterranean Sea as a barrier to gene flow: evidence from variation in and around the F7 and F12 genomic regions

Georgios Athanasiadis et al.

Abstract

Background
The Mediterranean has a long history of interactions among different peoples. In this study, we investigate the genetic relationships among thirteen population samples from the broader Mediterranean region together with three other groups from the Ivory Coast and Bolivia with a particular focus on the genetic structure between North Africa and South Europe. Analyses were carried out on a diverse set of neutral and functional polymorphisms located in and around the coagulation factor VII and XII genomic regions (F7 and F12).

Results
Principal component analysis revealed a significant clustering of the Mediterranean samples into North African and South European groups consistent with the results from the hierarchical AMOVA, which showed a low but significant differentiation between groups from the two shores. For the same range of geographic distances, populations from each side of the Mediterranean were found to differ genetically more than populations within the same side. To further investigate this differentiation, we carried out haplotype analyses, which provided partial evidence that sub-Saharan gene flow was higher towards North Africa than South Europe.

Conclusions
As there is no consensus between the two genomic regions regarding gene flow through the Sahara, it is hard to reach a solid conclusion about its role in the differentiation between the two Mediterranean shores and more data are necessary to reach a definite conclusion. However our data suggest that the Mediterranean Sea was at least partially a barrier to gene flow between the two shores.

Link

The main trans-Saharan slave routes are shown in Figure 1 (on the left). The paper also contains quite useful interpolation maps of the main Sub-Saharan African mtDNA haplogroups, who should be useful for future reference.

BMC Evolutionary Biology 2010, 10:138 doi:10.1186/1471-2148-10-138


The trans-Saharan slave trade - clues from interpolation analyses and high-resolution characterization of mitochondrial DNA lineages
Abstract
Background
A proportion of 1/4 to 1/2 of North African female pool is made of typical sub-Saharan lineages, in higher frequencies as geographic proximity to sub-Saharan Africa increases. The Sahara was a strong geographical barrier against gene flow, at least since 5,000 years ago, when desertification affected a larger region, but the Arab trans-Saharan slave trade could have facilitate enormously this migration of lineages. Till now, the genetic consequences of these forced trans-Saharan movements of people have not been ascertained.

Results
The distribution of the main L haplogroups in North Africa clearly reflects the known trans-Saharan slave routes: West is dominated by L1b, L2b, L2c, L2d, L3b and L3d; the Center by L3e and some L3f and L3w; the East by L0a, L3h, L3i, L3x and, in common with the Center, L3f and L3w; while, L2a is almost everywhere. Ages for the haplogroups observed in both sides of the Saharan desert testify the recent origin (holocenic) of these haplogroups in sub-Saharan Africa, claiming a recent introduction in North Africa, further strengthened by the no detection of local expansions.

Conclusions
The interpolation analyses and complete sequencing of present mtDNA sub-Saharan lineages observed in North Africa support the genetic impact of recent trans-Saharan migrations, namely the slave trade initiated by the Arab conquest of North Africa in the seventh century. Sub-Saharan people did not leave traces in the North African maternal gene pool for the time of its settlement, some 40,000 years ago.

Link

Wikipedia article on Volga Tatars. Some pictures of Kazan Tatars, which look just about what you would expect for 16% eastern Asian mtDNA, i.e., primarily Caucasoid but with visible traces of Mongoloid admixture

Molecular Biology and Evolution, doi:10.1093/molbev/msq065

Mitogenomic diversity in Tatars from the Volga-Ural region of Russia

B. Malyarchuk et al.

To investigate diversity of mitochondrial gene pool of Tatars inhabiting the territory of the middle Volga River basin, 197 individuals from two populations representing Kazan Tatars and Mishars were subjected for analysis of mitochondrial DNA (mtDNA) control region variation. In addition, 73 mitochondrial genomes of individuals from Mishar population were sequenced completely. It was found that mitochondrial gene pool of the Volga Tatars consists of two parts, but western Eurasian component prevails considerably (84% on average) over eastern Asian one (16%). Eastern Asian mtDNAs detected in Tatars belonged to a heterogeneous set of haplogroups (A, C, D, G, M7, M10, N9a, Y, Z), although only haplogroups A and D were revealed simultaneously in both populations. Complete mtDNA variation study revealed that the age of western Eurasian haplogroups (such as U4, HV0a and H) is less than 18,000 years, thus suggesting re-expansion of Eastern Europeans soon after the Last Glacial Maximum.

Link

A very interesting abstract from the HAPLOID DNA MARKERS IN FORENSIC GENETICS workshop that took place in April. I will scour the abstract volume (pdf) for other interesting pieces of research, but I wanted to give an early heads-up on this abstract, given the recent interest on this haplogroup, and the controversy regarding its origin. It is also exciting to see the issue of the mutation rate finally addressed, I hope the authors take my side on the debate.
We'll have to wait and see what the authors propose when their paper is actually published, but I am guessing that my post on Haplotype outliers and Y-chromosome age estimation will be vindicated. Therein, I argued that Y-STR age estimation sometimes leads to young ages if "relics of a bygone age" are not identified, and the age estimation is dominated by the dominant (and more recent) expansion. As far as I can intuit from the abstract, the authors seem to propose such a model, in which an expanding Neolithic R-M269 population interacted with pre-existing European R-M269. Let's hope the details surface soon.


Increased Resolution Within Y-Chromosome Haplogroup R1b M269 Sheds Light On The Neolithic Transition In Europe

George Busby et al.
Early studies on classical polymorphisms have largely been vindicated by the growing tome of information on the genetic structure of European populations, with mtDNA, Y-Chromosome and autosomal markers all combining to give a fundamental pattern of migration from the East. The processes behind this pattern are however, less clear, particularly with regard to uniparental markers. Much debate still rages about how best to use Y and mtDNA to date particular historical movements, or indeed if it is appropriate at all. For example, whilst some progress has been made recently in calibrating the mtDNA clock, the selection of a mutation rate with which to date the Y-Chromosome is contentious, as the two most favoured values can give dates that differ by a factor of three. In order to address this we have investigated the sub-lineages of the common European haplogroup R1b-M269. This haplogroup has been shown to be clinal in Europe, and more recently has been posited to be the result of the Neolithic expansion from the Near East. Here, we use newly characterised SNPs downstream of M269 to produce a refined picture of the haplogroup in Europe, and further show that the diversity of this lineage cannot be entirely attributed to Neolithic migration out of Anatolia. We use simple coalescent simulations to estimate an absolute lower bound for the age of the sub-haplogoups. Rather than originating with the farmers from the East, we suggest that the sub-structure of R1b-M269 visible in Europe today, and thus the great majority of European paternal ancestry, is the result of the interaction between the Neolithic wave of expansion and populations of early Europeans already present in the path of the wave.

I was wary of this paper's conclusion as soon as I realized that the authors contended that Europeans and East Asians did not differ significantly in their levels of Neanderthal admixture. You see, Neandertals were absent from East Asia, so there is no reason for East Asians to have such admixture at all, or to have much less of it than West Eurasians do.
Even if we assumed that undifferentiated Eurasians picked up Neandertal admixture in West Asia, the fact would remain that Europeans co-existed with Neandertals after the ancestors of East Asians had moved on towards the Pacific. So, they ought to have more Neandertal admixture -if such admixture ever took place. Indeed, one of the main arguments for introgression of Neandertal genes in modern humans is the long co-existence of modern humans with Neandertals in Europe.
It could be argued that Neandertal admixture was indeed higher in West Eurasians initially, but the difference was evened out by gene flow across Eurasia. This, however, makes no sense, as the history of Eurasians post-Out of Africa was one of genetic differentiation, which suggests barriers to gene flow, and it would be difficult to imagine a scenario in which the Neandertal component would even out in Eurasia across populations from the Atlantic to the Pacific.
We should also note that the present paper's line of genetic evidence is not really complementary to the palaeoanthropological argument for admixture, as that argument is based on observing phenotypic continuities between Neandertals and modern Caucasoids that could not (according to the argument's proponents) be explained by the simple Out of Africa model and/or observing phenotypic traits of Upper Paleolithic Europeans that seem to be shared with Neandertals but not with UP sapiens outside Europe.
In short: those who use skulls to argue Neandertal introgression predict that Europeans should be somehow closer to Neandertals than East Asians are, but this paper fails to find evidence of this.
So what really happened: an alternative hypothesis
The authors do make an important observation: Neandertal genomes were closer to those of modern Eurasians than to modern Africans. This is an important finding that is incompatible with pure Out-of-Africa. But, Neandertal admixture is not the only way to explain the data.
There is an alternative explanation. It involves the emergence of Homo sapiens and Homo neanderthalensis from a common ancestor and the subsequent admixture of Homo sapiens with populations that have branched out before this divergence. This would account for increased similarity between Eurasians and Neandertals, but without the problem of explaining how "Neandertal" ancestry is so similar in Europeans and East Asians.
What about Africans? Why do they stand further away from Neandertals? The answer is simple: low-level of admixture with archaic humans in Africa itself. It is fairly clear to me that the sapiens line whose earliest examples are in East/South Africa must have been an offshoot of an older African set of populations. We are lucky that Neandertals lived in a climate conducive to bone (or even DNA) preservation, while the African populations inhabiting the tropics left no traces of their existence.
In conclusion: I am not at all convinced that the authors have uncovered evidence of Neanderthal admixture in Eurasians; the alternative explanation is that modern humans and Neandertals were related, modern humans spread from East Africa/West Asia and as they entered deeper into Africa, they interacted with archaic human populations there.
PS: The only potential argument in favor of the authors' hypothesis is the following:Non-Africans haplotypes match Neandertals unexpectedly often. An alternative approach to detect gene flow from Neandertals into modern humans is to focus on patterns of variation in present-day humans—blinded to information from the Neandertal genome—in order to identify regions that are the strongest candidates for being derived from Neandertals. If these candidate regions match the Neandertals at a higher rate than is expected by chance, this provides additional evidence for gene flow from Neandertals into modern humans.We thus identified regions in which there is considerably more diversity outside Africa than inside Africa, as might be expected in regions that have experienced gene flow from Neandertals to non-Africans. We used 1,263,750 Perlegen Class A SNPs, identified in individuals of diverse ancestry (78), and found 13 candidate regions of Neandertal ancestry (SOM Text 17). A prediction of Neandertal-to-modern human gene flow is that DNA sequences that entered the human gene pool from Neandertals will tend to match Neandertal more often than their frequency in the present-day human population. To test this prediction, we identified 166 "tag SNPs" that separate 12 of the haplotype clades in non-Africans (OOA) from the cosmopolitan haplotype clades shared between Africans and non-Africans (COS) and for which we had data from the Neandertals. Overall, the Neandertals match the deep clade unique to non- Africans at 133 of the 166 tag SNPs, and 10 of the 12 regions where tag SNPs occur show an excess of OOA over COS sites. Given that the OOA alleles occur at a frequency of much less than 50% in non-Africans (average of 13%, and all less than 30%) (Table 5), the fact that the candidate regions match the Neandertals in 10 of 12 cases (P = 0.019) suggests that they largely derive from Neandertals. The proportion of matches is also larger than can be explained by contamination, even if all Neandertal data were composed of present-day non-African DNA (P = 0.0025) (SOM Text 17).
The problem with the above analysis is in the underlined portion. The deep clade is rather unique to non-Americans of African ancestry, as per reference (78), i.e., a very limited sample of Africans. In short, there is no reason to believe that the identified deep clades matching the Neandertals are really unique to non-Africans, and the pattern can be easily explained by geographical structure within Africa itself.
Related: for a contrary view see John Hawks.
UPDATE: To their credit, the authors consider the scenario I am advocating it here, labeling it Scenario 4. They write:
Although gene flow from Neandertals into modern humans when they first left sub-Saharan Africa seems to be the most parsimonious model compatible with the current data, other scenarios are also possible. For example, we cannot currently rule out a scenario in which the ancestral population of present-day non-Africans was more closely related to Neandertals than the ancestral population of present-day Africans due to ancient substructure within Africa (Fig. 6). If after the divergence of Neandertals there was incomplete genetic homogenization between what were to become the ancestors of non-Africans and Africans, present-day non-Africans would be more closely related to Neandertals than are Africans. In fact, old population substructure in Africa has been suggested based on genetic (81) as well as paleontological data (86).
Whether their model is more parsimonious than Scenario 4 is up to the reader. We know that there is population structure in Africa today, and as the authors note there are reasons why this ought to have been true in the past. So, while Scenario 4 makes up a reasonable xtra assumption (the one I describe in my post), the authors' favored scenario does not explain easily how a species that inhabited Western Eurasia (Neandertals) ended up contributing not-too different amounts of DNA to Europeans and Chinese. So, for the time being, I'm sticking to my guns and saying that the paper has uncovered something important, but probably not Neandertal admixture.

UPDATE II (May 11): Direction of gene flow (to or from Neanderthals, or ...?)

Science 7 May 2010:
Vol. 328. no. 5979, pp. 710 - 722

A Draft Sequence of the Neandertal Genome

Richard E. Green et al.

Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.

Link

In my first post on Green et al. (2010) I bring up a couple of red flags to the tale of Neandertal admixture that has appeared in the media:

1. The uniformity of alleged Neandertal admixture outside Africa is suspect, given that Neandertals were a West Eurasian species
2. The observed pattern of Neandertals being closer to non-Africans than to Africans can be well explained by structure in Africa itself, a point which the authors concede (as their Scenario 4), but which has received zero play in the media which -as usual- have jumped on the more easily digestible ("caveman sex") explanation.

Now I want to address another major red flag that I hinted at before, namely the direction of gene flow, if gene flow did in fact occur between modern humans and Neandertals.
The authors reject that gene flow into the Neandertals took place; I immediately got suspicious of this claim because it is not consistent with what we know from historical cases of contact.
Whether it is Europeans meeting Native Americans, Yayoi meeting Jomon, or Bantu farmers meeting Pygmy hunters, the story is always the same: the dominant intrusive population ends up with admixture from the native one, but admixture goes both ways.
If modern humans and Neandertals interbred, then there is absolutely no reason to think that "we" got Neandertal genes, but "they" didn't get ours. To think that requires extra assumptions, e.g., that modern-Neandertal kids were shunned by Neandertal societies, i.e., that Neandertals were a sort of prehistoric Samaritans that practiced strict endogamy. I find that hard to believe.
There is an alternative explanation for why no modern admixture in Neandertals would be detected, namely the early age of the bones tested in the paper, which are from Europe and date from the Early Upper Paleolithic, when modern humans had not yet arrived in Europe. It is worthwhile to consider this explanation:
If admixture occurred primarily in Europe itself, then we would expect Neandertal admixture to be higher in modern Europeans or Caucasoids. But we don't see that at all, so, unless we postulate that Papua New Guinean and Chinese ancestors reached their final destination with a detour through Europe after 40ky or so, we can safely conclude that Neandertal-modern admixture was earlier and occurred in the Middle East.
So, we have a population of moderns and Neandertals mixing in the Near East. According to the authors' scenario, episodes of admixture between the two species gave "us" enough Neandertal admixture that was carried by our (modern) ancestors throughout the world, creating a fairly uniform (but small) component of "Neandertal" ancestry.
But, why wouldn't the (modern) admixture in Near Eastern Neandertals also be carried a couple of thousand km into Europe? In short: we are supposed to think that Neandertal admixture in modern humans made it to the ends of the earth, but modern admixture in Neandertals could not move a short distance from West Asia into Europe. The explanation of pristine European Neandertals presented in the paper just doesn't fly in the context of the authors' broad model.
It is also worthwhile to consider the actual genetic argument for no modern-to-Neandertal introgression. This goes something like this: we observe closer proximity between modern non-Africans and Neandertals than between modern Africans and Neandertals. This can be explained by either Neandertal-to-non-African gene flow or vice versa.
The authors observe that modern non-Africans are closer to Yoruba than to San. They argue that if Neandertals had modern non-African admixture, then they would also be closer to Yoruba than to San. But, they observe that they are about equidistant to Yoruba and San. Ergo, they couldn't have substantial non-African admixture.
The error in this syllogism is the equation of modern non-Africans (who are closer to Yoruba than to San) with ancient non-Africans for which this was not necessarily the case.
Perhaps a case could be made that this was true for late Out-of-Africans, as these split off from other moderns after the Yoruba-San split. But, the late Out-of-Africans were not the only anatomically modern humans who left Africa, and we have good evidence of anatomically modern humans outside Africa before the exodus that gave rise to modern Eurasians (at sites like Qafzeh).
Note that this observation nicely addresses the argument presented by John Hawks on the young coalescence dates between some Neandertal and Eurasian DNA, which supposedly disqualifies the African structure scenario I presented (and which the authors labeled as "Scenario 4" in their paper). These young coalescence ages can be easily explained as modern-to-Neandertal gene flow within the context of the African structure model.
Finally, I want to remind readers of a very interesting paper I blogged about last year. Here are the relevant quotes:Our data on neighbors and variability is unsupportive of the strict forms of a single-origin model but does not conflict with another approach, the model of ‘‘isolation by distance,’’ which predicts that genetic and phenotypic dissimilarity increases with geographic distance (24, 29–31). The metapopulation framework would predict the same because frequency and magnitude of genetic exchange would follow the likelihood of 2 populations to meet, which declines with geographical distance from the early AMH epicenter in Africa. Our fossil AMH data, however, suggest that before there was isolation by distance from Africa, there already existed (at least temporally) isolation by distance within Africa during the Pleistocene.

Seemingly ancient contributions to the modern human gene pool (36) have been explained by admixture with archaic forms of Homo, e.g., Neanderthals. Although we cannot rule out such admixture (37), the clear morphological distinction between
AMH and archaic forms of Homo in the light of the proposed ancestral population structure of early AMH to us suggests another underestimated possibility: the genetic exchange between subdivided populations of early AMH as a potential source for ‘‘ancient’’ contributions to the modern human gene pool (9, 36).I won't present the reasoning behind these conclusions (the paper is open access anyway), but they have an important implication: seemingly "ancient" contributions to modern humans need not have been acquired by either Neandertals or other archaic (pre-sapiens) populations, but they could also have been acquired by admixture with different branches of anatomically modern humans.
Given that anatomically modern humans appear on the record ~200ky ago, so they probably existed at an even earlier date, while extant sapiens populations trace their earlier split much later (the authors date the Yoruba-San split at most 164ky or as late as 67ky), we can reasonably assume that there were anatomically modern sapiens populations that are not ancestral to any modern humans, and which may have contributed seemingly "ancient" genes to our expanding ancestors.
There you have it: structure in Africa, modern-to-Neandertal admixture, or even sapiens-to-sapiens admixture, there are plenty of alternatives to the story dominating the media.

A beautiful new paper has appeared that tackles the distribution and substructure of Y chromosome haplogroup C, a widely dispersed lineage that binds Asia, Oceania, and the Americas. This will be invaluable as a resource for students of East Eurasian anthropology and genetics. My only problem with the paper is in its use of the evolutionary mutation rate that I have criticized elsewhere.
From the paper:
Hg C is prevalent in various geographical areas (Figures 1 and 2), including Australia (65.74%), Polynesia (40.52%), Heilongjiang of northeastern China (Manchu, 44.00%), Inner Mongolia (Mongolian, 52.17%; Oroqen, 61.29%), Xinjiang of northwestern China (Hazak, 75.47%), Outer Mongolia (52.80%) and northeastern Siberia (37.41%). Hg C is also present in other regions, extending longitudinally from Sardinia in Southern Europe all the way to Northern Colombia, and latitudinally from Yakutia of Northern Siberia and Alaska of Northern America to India, Indonesia and Polynesia, but absent in Africa.On the structure of haplogroup C:
As shown in Figure 1, most of the subhaplogroups of Hg C have a geographically pronounced distribution. Hg C6, which is defined by a recently identified marker, was not detected in our samples. Hg C1 and C4 are completely restricted to Japan and Australia, respectively, and not detected in the other samples from East Asia and Southeast Asia. Hg C5 occurs in India and its neighboring regions Pakistan and Nepal. In mainland East Asia, four Hg C5 individuals were detected, including two in Xibe, one in Uygur and one in Shanxi Han. Although the dispersal of Hg C2 is relatively wide, its distribution remains limited to Oceania and its neighboring regions, except Australia. In our samples, only three Hg C2 individuals were observed in Eastern Indonesia, which is consistent with previous reports. Hg C3 is the most widespread subhaplogroup, which was detected in Central Asia, South Asia, Southeast Asia, East Asia, Siberia and the Americas, but absent in Oceania. Different subhaplogroups of Hg C that do not overlap between the regions suggest that these individuals have undergone long-time isolation. As these subhaplogroups have a common origin by sharing the M130-derived allele, their geographical distributions enable us to infer the prehistoric migration routes of this lineage.The MDS plot is quite instructive. Notice the duality of Japanese C chromosomes, which parallels what we know about the dual origins of the Japanese. It would be instructive to test European haplogroup C outliers to see where they fall within haplogroup C diversity.The C3 MDS is quite instructive, and shows quite well the distribution of C3 diversity in Chinese ethnic populations.
Off the top of my head, I detect a top-right Mongolian-Manchu-Tibetan quadrant (note that Mongolians and Tibetans are also linked by the rare haplogroup D) and a left Central/Southern Chinese ethnic quadrant. Notice the closeness of Hani to Yi, which may validate the former's oral traditions.
Finally, getting back to the controversial issue of Y-chromosome age estimation, here are the dates proposed by the authors for the age of STR variation within haplogroups and their divergence times. In my opinion these are overestimates due to the use of the evolutionary rate.
A case in point is haplogroup C3b-P39; according to the authors' date, this ought to be related to the early arrival of the ancestors of Amerindians, but haplogroup C in the Americans has a strong relationship with Na-Dene speakers such as Athapaskans, and it seems to me that a late spread of this haplogroup is more consistent with its limited geographical distribution and strong linguistic associations.
Related: the Southern origin of O3

Journal of Human Genetics doi: 10.1038/jhg.2010.40

Global distribution of Y-chromosome haplogroup C reveals the prehistoric migration routes of African exodus and early settlement in East Asia

Hua Zhong et al.

The regional distribution of an ancient Y-chromosome haplogroup C-M130 (Hg C) in Asia provides an ideal tool of dissecting prehistoric migration events. We identified 465 Hg C individuals out of 4284 males from 140 East and Southeast Asian populations. We genotyped these Hg C individuals using 12 Y-chromosome biallelic markers and 8 commonly used Y-short tandem repeats (Y-STRs), and performed phylogeographic analysis in combination with the published data. The results show that most of the Hg C subhaplogroups have distinct geographical distribution and have undergone long-time isolation, although Hg C individuals are distributed widely across Eurasia. Furthermore, a general south-to-north and east-to-west cline of Y-STR diversity is observed with the highest diversity in Southeast Asia. The phylogeographic distribution pattern of Hg C supports a single coastal ‘Out-of-Africa’ route by way of the Indian subcontinent, which eventually led to the early settlement of modern humans in mainland Southeast Asia. The northward expansion of Hg C in East Asia started ~40 thousand of years ago (KYA) along the coastline of mainland China and reached Siberia ~15 KYA and finally made its way to the Americas.

Link

From the public release:The study, published in the May 3 online issue of the Proceedings of the National Academy of Sciences, tested the genetic makeup of 100 individuals of Hispanic/Latino background in the New York tri-state area, including Dominicans, Columbians and Ecuadorians, as well as Mexicans and Puerto Ricans, the two largest Hispanic/Latino ethnic groups in the United States. Currently, Hispanic/Latino Americans comprise 15.4% of the total United States population, or 46.9 million people, and account for the largest ethnic minority in the United States.

"It is important to quantify the relative contributions of ancestry in relation to disease outcome in the Hispanic/Latino population," says study co-author Christopher Velez, a medical student at NYU School of Medicine. "This ethnically appropriate genetic research will be critical to the understanding of disease onset and severity in the United States and in Latin America. It will allow for the development of appropriate genetic tests for this population."

Through their analysis of the entire genome, the researchers found evidence of a significant sex bias consistent with the disproportionate contribution of European male and Native American female ancestry to present day populations. The scientists also found that the patterns of genes in the Hispanic/Latino populations were impacted by proximity to the African slave trade. In fact, Puerto Ricans, Dominicans and Columbians from the Caribbean coast had higher proportions of African ancestry, while Mexicans and Ecuadorians showed the lowest level of African ancestry and the highest Native American ancestry.

European migrant contributors were mostly from the Iberian Peninsula and Southern Europe. Evidence was also found for Middle Eastern and North African ancestry, reflecting the Moorish and Jewish (as well as European) origins of the Iberian populations at the time of colonization of the New World. The Native Americans that most influenced the Hispanic/Latino populations were primarily from local indigenous populations.The paper has plentiful supplementary material online. Here is the result of the frappe analysis in a broader context:

As we can see, Hispanic individuals are a variable mix of Caucasoid (red/orange), Amerindian/Mongoloid (blue, teal) and Sub-Saharan (green) components. The orange Caucasoid component seems centered on Sardinia while the red one in NE Europe.
PNAS doi:10.1073/pnas.0914618107

Genome-wide patterns of population structure and admixture among Hispanic/Latino populations

Katarzyna Bryc et al.

Abstract

Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.

Link

A great series of portraits of Chinese ethnic groups. I think this may be a great resource when reading papers on Chinese genetics and anthropology, as it provides a direct visual snapshot of the groups involved, most of which are probably not familiar to Western readers.
Several of the groups have familiar names, so feel free to use the search (on the right of the blog), or click on the labels. to look up posts on them.
Jing, Korean, Blang


Dongxiang, Pumi, Hani

Bouyei, Tatar, Dai

Russian, Ewenki, Naxi

Mongol, Zhuang, Han

Lahu, Yi, Bai

Hui, Mulam, Li

Achang, Salar, Jino

Jingpo, Miao, Manchu

Tujia, Monba, Lisu

Nu, Yugur, Dong

Tibetan, Sui, Bonan

Yao, Va, She

Hezhen, Lhoba, Maonan

Oroqen, Daur, Uygur

Kirgiz, Xibe, Derung

Ozbek, Gelao, De'ang

Tajik, Kazak, Qiang

Minorities in Taiwan, Tu

The inset barplot (left) shows the proportions of European (blue) and African ancestry in the studied sample of African Americans. As can be seen, African Americans are quite similar in their admixture of the various "African" clusters (at least the ones included here), but differ from each other primarily in their level of European ancestry.
Figure 4 shows quite well how the various African components in African Americans are uniformly distributed.
From the paper:
The largest African ancestral contribution comes from the Yoruba, with an average of 47.1% ± 8.7% (range, 18% to 64%), followed by the Bantu at 14.8% ± 5.0% (range, 3% to 28%) and Mandenka at 13.8% ± 4.5% (range, 3% to 29%). The contributions from the other three African groups were quite modest, with an average of 1.7% from the Biaka, 0.5% from the Mbuti, and 0.3% from the San.
Table 1 has a breakdown of the ancestral components of African Americans from different geographical regions.
Genome Biology 2009, 10:R141doi:10.1186/gb-2009-10-12-r141

Characterizing the admixed African ancestry of African Americans

Fouad Zakharia et al.
Abstract

Background
Accurate, high-throughput genotyping allows the fine characterization of genetic ancestry. Here we applied recently developed statistical and computational techniques to the question of African ancestry in African Americans by using data on more than 450,000 single-nucleotide polymorphisms (SNPs) genotyped in 94 Africans of diverse geographic origins included in the HGDP, as well as 136 African Americans and 38 European Americans participating in the Atherosclerotic Disease Vascular Function and Genetic Epidemiology (ADVANCE) study. To focus on African ancestry, we reduced the data to include only those genotypes in each African American determined statistically to be African in origin.

Results
From cluster analysis, we found that all the African Americans are admixed in their African components of ancestry, with the majority contributions being from West and West-Central Africa, and only modest variation in these African-ancestry proportions among individuals. Furthermore, by principal components analysis, we found little evidence of genetic structure within the African component of ancestry in African Americans.

Conclusions
These results are consistent with historic mating patterns among African Americans that are largely uncorrelated to African ancestral origins, and they cast doubt on the general utility of mtDNA or Y-chromosome markers alone to delineate the full African ancestry of African Americans. Our results also indicate that the genetic architecture of African Americans is distinct from that of Africans, and that the greatest source of potential genetic stratification bias in case-control studies of African Americans derives from the proportion of European ancestry.

Link

From the related public release:
Previous models of cooperation assumed that punishment of free-riders was uncoordinated and unconditional. One problem with these models was that the costs associated with punishment were often higher than the gains of cooperation. Thus, the cost of one group member's punishing a free-rider would be substantial and would not overweigh the gains achieved through increased cooperation.

Costs may be defined as loss of friendship or loss of relational closeness with other members of the group.

To address the problem, Boyd and his colleagues changed the assumptions built into previous cooperation/punishment models. First, they allowed for punishment to be coordinated among group members. In their model, group members could signal their willingness to punish someone who was not participating in the group, but punishment would only occur if it was coordinated. This meant the cost of punishing a free-rider would be distributed across members and would not be higher than the cost of gains achieved through increased cooperation.

Second, the researchers allowed for the cost of punishing a free-rider to decline as the number of punishers increased. Boyd explained that this new model was "catching up with common sense" because these two assumptions exist in reality.

Their model had three stages in which a large group of unrelated individuals interacted repeatedly. The first stage was a signaling stage where group members could signal their intent to punish. In the second stage, group members could choose to cooperate or not. The final stage was a punishment stage when group members could punish other group members.

The results of their model look a lot like what is seen in most human societies, where individuals meet and decide whether and how to punish group members who are not cooperating. This is coordinated punishment where group members signal their intent to punish, only punish when a threshold has been met and share the costs of punishing.

Boyd argues that even in societies without formal institutions for establishing rules and methods of punishment, group punishment appears to be effective at maintaining cooperation.
Here is an example of what the authors are talking about. Imagine you are living in the Old West and a gang has just robbed your neighbor's store. Clearly, if you went out to punish the perpetrators you would pay a high cost (they would be likely to kill you) and it wouldn't be successful. So, it doesn't make sense to punish individually. But, the sheriff could assemble a posse to go after the criminals. This would immediately reduce your risk (since you would be one target among many) and it would also increase your chance of success (as more punishers are more likely to achieve their goal).
Related posts:

• The evolution of altruistic punishment
• Moralistic punishment in front of an audience
• Strong Reciprocity and the Emergence of Large-Scale Societies
• Altruistic punishment in Papua New Guinea

Science, Vol. 328. no. 5978, pp. 617 - 620

Coordinated Punishment of Defectors Sustains Cooperation and Can Proliferate When Rare

Robert Boyd et al.

Abstract

Because mutually beneficial cooperation may unravel unless most members of a group contribute, people often gang up on free-riders, punishing them when this is cost-effective in sustaining cooperation. In contrast, current models of the evolution of cooperation assume that punishment is uncoordinated and unconditional. These models have difficulty explaining the evolutionary emergence of punishment because rare unconditional punishers bear substantial costs and hence are eliminated. Moreover, in human behavioral experiments in which punishment is uncoordinated, the sum of costs to punishers and their targets often exceeds the benefits of the increased cooperation that results from the punishment of free-riders. As a result, cooperation sustained by punishment may actually reduce the average payoffs of group members in comparison with groups in which punishment of free-riders is not an option. Here, we present a model of coordinated punishment that is calibrated for ancestral human conditions and captures a further aspect of reality missing from both models and experiments: The total cost of punishing a free-rider declines as the number of punishers increases. We show that punishment can proliferate when rare, and when it does, it enhances group-average payoffs.

Link

I had previously posted on a paper which proposed a Neolithic origin of European R1b1b2 (R-M269) chromosomes. In my criticism for that paper I noted that:
Equally flawed is the inference that R1b1b2 is clinal (Figure 2A). Microsatellite variance is not significantly higher in Turkey than in Europe -- even if one makes the questionable questionable assumption that modern Anatolian Turks are patrilineal descendants of Neolithic Anatolians. The significance of the regression line disappears if 1 or 2 data points are excluded, and the plot has a quite visible "gap" between Turkey and Italy corresponding to the entirety of eastern Europe and the Balkans, i.e. the routes that any putative Neolithic lineages would have entered Europe.
The current paper does not sample the gap I noted in my earlier post, but it looks at Sardinian Y chromosomes, casting doubt on the alleged reduction of diversity from West Asia to Western Europe.

The new paper however has flaws of its own. Its most significant error is its use of the infamous "evolutionary" mutation rate.
Second, Balaresque et al. [17] used a STR specific germ-line mutation rate that placed the TMRCA in the Neolithic age. In contrast we used a unique prior for the microsatellite mutation rate estimates as 6.9×10−4 as recommended by Zhivotovsky and co-workers [24]–[26], see also [27]–[31], that, as reported above, placed the haplogroups TMRCA values in pre-Neolithic times. The difference between the former, evolutionarily effective, and the latter, germ line mutation rates is critical. In fact the haplogroups that survive the stochastic processes of drift and extinction accumulate STR variation at a lower rate than predicted from corresponding pedigree estimates. In particular, under constant population size, the accumulated variance is on average 3–4 times smaller [26]. Hence germ line mutation rates provide evolutionary estimates for haplogroups biased toward much younger age [26].
The degree of blindness required to use the evolutionary rate never ceases to amaze me. I will direct the reader to my earlier post on the evolutionary rate, but let us consider what the assumption of "constant population size" means. Sardinia has a male effective population size numbering in the hundreds of thousands, while the Paleolithic population of the entire European continent numbered at most to a few tens of thousands.
We can thus safely assume 2-3 orders of magnitude of population growth since the Paleolithic. Thus, the assumption of "constant population size" is nonsense, population increase occurred at a faster rate, and correspondingly Y-STR variance accumulated at a faster rate, close to the germline rate.
It is sad to see that geneticists have disagreed for years about what the proper mutation rate should be for evolutionary studies. Most of the work on how the evolutionary rate changes with population growth dynamics was already done by Zhivotovsky et al. (2006), but a group of geneticists seem to have discarded all those observations and uncritically used the simple case of constant population size which corresponds to the "slow" rate of Zhivotovsky et al. (2004) and leads to substantial age overestimates.
It's downright bizarre how neither authors nor peer reviewers can put 2+2 together and figure out that applying a model of constant population size for a population that grew 1,000-fold is muddle-headed oversimplification.
In conclusion, the age estimates of the new paper are wrong and should be divided by 3 or so to provide better estimates. However, I should also point out that age estimation with Y-STRs is associated with wide error margins, even if the number of Y-STRs is quite large. The authors are quite right to point out that the inclusion of an additional Y-STR marker upsets the orderly westward diminution of diversity observed in the previous paper; however, neither they (with their pre-Neolithic estimate), nor the authors of the previous paper (with their Neolithic one) have much of a case.
Where does that leave us? We have no clue as to the origin of R-M269 in Western Europe. I can think of several reasons why this is likely to remain the case:

1. Modern populations are not good representatives of ancient, Neolithic, let alone pre-Neolithic populations from the same vicinities as ancient mtDNA studies have repeatedly shown. Y-chromosome studies are more scant, but there is no reason to think that Y-chromosome distributions are more geographically stable; if anything, strong regional differentiation, and greater historical male mobility may suggest that the opposite is the case.
2. Inferences of diversity clines are based on a patchy collection of convenience samples where most of Europe (let alone West Asia) is underrepresented or sampled non-systematically and at a very small number of markers.
3. Indeed, confidence intervals of Y-STR based age estimates are so wide, that small differences in Y-STR diversity are almost never sufficient to infer greater or lesser antiquity of a population: in short, the odds that a population exhibiting lower Y-STR variance may be older than one exhibiting higher variance are too high to ignore, even with many Y-STR markers, let alone the 10 or so of most scientific studies.

It's about time that geneticists face up to the limitations of their craft. I suppose it's more impressive to make grand statements about European prehistory than to admit to the limitations of the available data.
So, is R-M269 Neolithic or Paleolithic in Europe? I have no idea and I haven't seen any data to convince me one way or another. So, while I welcome new data on its distribution and diversity, and acknowledge that all new data is useful, my own position remains agnostic. A single validated ancient DNA sample would mean more to me than all modern population studies put together.
Related: my Y-STR series.
PLoS ONE doi:10.1371/journal.pone.0010419

A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture

Laura Morelli et al.

Abstract

Two alternative models have been proposed to explain the spread of agriculture in Europe during the Neolithic period. The demic diffusion model postulates the spreading of farmers from the Middle East along a Southeast to Northeast axis. Conversely, the cultural diffusion model assumes transmission of agricultural techniques without substantial movements of people. Support for the demic model derives largely from the observation of frequency gradients among some genetic variants, in particular haplogroups defined by single nucleotide polymorphisms (SNPs) in the Y-chromosome. A recent network analysis of the R-M269 Y chromosome lineage has purportedly corroborated Neolithic expansion from Anatolia, the site of diffusion of agriculture. However, the data are still controversial and the analyses so far performed are prone to a number of biases. In the present study we show that the addition of a single marker, DYSA7.2, dramatically changes the shape of the R-M269 network into a topology showing a clear Western-Eastern dichotomy not consistent with a radial diffusion of people from the Middle East. We have also assessed other Y-chromosome haplogroups proposed to be markers of the Neolithic diffusion of farmers and compared their intra-lineage variation—defined by short tandem repeats (STRs)—in Anatolia and in Sardinia, the only Western population where these lineages are present at appreciable frequencies and where there is substantial archaeological and genetic evidence of pre-Neolithic human occupation. The data indicate that Sardinia does not contain a subset of the variability present in Anatolia and that the shared variability between these populations is best explained by an earlier, pre-Neolithic dispersal of haplogroups from a common ancestral gene pool. Overall, these results are consistent with the cultural diffusion and do not support the demic model of agriculture diffusion.

Link