Dodecad project submission opportunity

If you do not subscribe to the Dodecad feed, you might want to know about the submission opportunity that is under way for about a day more. Check to see if your group is included in the latest call.

Marital residence in Indo-European and Austronesian societies

Philos Trans R Soc Lond B Biol Sci. 2010 Dec 12;365(1559):3913-22.

Your place or mine? A phylogenetic comparative analysis of marital residence in Indo-European and Austronesian societies.

Fortunato L, Jordan F.

Abstract

Accurate reconstruction of prehistoric social organization is important if we are to put together satisfactory multidisciplinary scenarios about, for example, the dispersal of human groups. Such considerations apply in the case of Indo-European and Austronesian, two large-scale language families that are thought to represent Neolithic expansions. Ancestral kinship patterns have mostly been inferred through reconstruction of kin terminologies in ancestral proto-languages using the linguistic comparative method, and through geographical or distributional arguments based on the comparative patterns of kin terms and ethnographic kinship 'facts'. While these approaches are detailed and valuable, the processes through which conclusions have been drawn from the data fail to provide explicit criteria for systematic testing of alternative hypotheses. Here, we use language trees derived using phylogenetic tree-building techniques on Indo-European and Austronesian vocabulary data. With these trees, ethnographic data and Bayesian phylogenetic comparative methods, we statistically reconstruct past marital residence and infer rates of cultural change between different residence forms, showing Proto-Indo-European to be virilocal and Proto-Malayo-Polynesian uxorilocal. The instability of uxorilocality and the rare loss of virilocality once gained emerge as common features of both families.

Link

Near Eastern origin of European Neolithic farmers

(Last Update Nov 10)

I first became aware of this research in an ISBA4 abstract, and now it seems that a full article has been published in PLoS Biology.

Today, a fascinating new paper has appeared which completes the picture by studying for the first time both mtDNA and Y-chromosomes from a Central European Linearbandkeramik site, Derenburg Meerenstieg II in Germany.

From the paper:

We successfully typed 17 individuals for mtDNA, which together with a previous study [19] provided data for 22 individuals from the Derenburg graveyard (71% of all samples collected for genetic analysis; Tables 1 and S1), and significantly extended the genetic dataset of the LBK (n = 42), to our knowledge the largest Neolithic database available.

Table 1 has a summary of the new data.

Two individuals belonged to Y-chromosome paragroup F*(xG,H,I,J,K), and one to haplogroup G2a3.

From the paper:

The multiplexed single base extension (SBE) approach with its shortened flanking regions around targeted SNPs significantly increases the chance of successful Y-chromosomal amplifications, which have remained problematic for aDNA studies, as have nuclear loci in general, because of the much lower cellular copy number compared to mitochondrial loci. The multiplexed SBE approach promises to open the way to studying the paternal history of past populations, which is of paramount importance in determining how the social organization of prehistoric societies impacted the population dynamics of the past.

The mtDNA data is more plentiful, and the authors write:

Out of 25 different haplotypes present in 42 LBK samples, 11 are found at high frequency in nearly all present-day populations under study, a further ten have limited geographic distribution, and the remaining four haplotypes are unique to Neolithic LBK populations (Table S4).

This suggests to me that there has not been massive extinction (due to selection or any other factor) of the Neolithic gene pool, as only four unique haplotypes to LBK individuals were found. Moreover, even these could potentially still exist, although they might not have been sampled yet.

From the paper:

The 11 widespread haplotypes are mainly basal (i.e., constituting a basal node within the corresponding hg) for Western Eurasian mitochondrial hgs H, HV, V, K, T, and W. While these haplotypes are relatively uninformative for identifying genetic affiliations to extant populations, this finding is consistent within an ancient population (5,500–4,900 cal B.C., i.e., prior to recent population expansions), in which basal haplotypes might be expected to be more frequent than derived haplotypes (e.g., end tips of branches within hgs).

From the paper:

The next ten LBK haplotypes were unequally spread among present-day populations and for this reason potentially contain information about geographical affinities. We found nine modern-day population pools in which the percentage of these haplotypes is significantly higher than in other population pools (p>0.01, two-tailed z test; Figure 1; Table S4): (a) North and Central English, (b) Croatians and Slovenians, (c) Czechs and Slovaks, (d) Hungarians and Romanians, (e) Turkish, Kurds, and Armenians, (f) Iraqis, Syrians, Palestinians, and Cypriotes, (g) Caucasus (Ossetians and Georgians), (h) Southern Russians, and (i) Iranians. Three of these pools (b–d) originate near the proposed geographic center of the earliest LBK in Central Europe and presumably represent a genetic legacy from the Neolithic. However, the other matching population pools are from Near East regions (except [a] and [h]), which is consistent with this area representing the origin of the European Neolithic, an idea that is further supported by Iranians sharing the highest number of informative haplotypes with the LBK (7.2%; Table S4). The remaining pool (a) from North and Central England shares an elevated frequency of mtDNA T2 haplotypes with the LBK, but otherwise appears inconsistent with the proposed origin of the Neolithic in the Near East. It has been shown that certain alleles (here hgs) can accumulate in frequency while surfing on the wave of expansion, eventually resulting in higher frequencies relative to the proposed origin [29],[30]. Several of the other population pools also show a low but nonsignificant level of matches, which may relate to pre-Neolithic distributions or subsequent demographic movements (Figure 1).

As I have noted before, frequency is an uncertain guide to where a lineage has originated, as Neolithic founders may have left more descendants in freshly colonized regions than in their homelands. Nonetheless, with the exception of the English, the "high match" populations are all within the broad trajectory of Neolithic populations from the Fertile Crescent to Central Europe.

With respect to the Y-chromosomal evidence:

The Y chromosome hgs obtained from the three Derenburg early Neolithic individuals are generally concordant with the mtDNA data (Table 1). Interestingly, we do not find the most common Y chromosome hgs in modern Europe (e.g., R1b, R1a, I, and E1b1), which parallels the low frequency of the very common modern European mtDNA hg H (now at 20%–50% across Western Eurasia) in the Neolithic samples. Also, while both Neolithic Y chromosome hgs G2a3 and F* are rather rare in modern-day Europe, they have slightly higher frequencies in populations of the Near East, and the highest frequency of hg G2a is seen in the Caucasus today [15]. The few published ancient Y chromosome results from Central Europe come from late Neolithic sites and were exclusively hg R1a [31]. While speculative, we suggest this supports the idea that R1a may have spread with late Neolithic cultures from the east [31].

Hopefully more Y-chromosome results from different Neolithic sites will turn up more derived haplogroups. Haplogroup G has been implicated as a Neolithic lineage as early as Semino et al. (2010), but clearly this is just the beginning of the reconstruction of Neolithic Y-DNA gene pools, and hopefully Y-DNA can be extracted from Mesolithic samples of similar age.

PCA (on the left) shows the outlier status of the Neolithic samples with respect to extant populations. Either natural selection, or later demographic events have led to a quite different gene pool today than what existed in central Europe thousands of years ago.

From the paper:

To better understand which particular hgs made the Neolithic populations appear either Near Eastern or (West) European, we compared average hg frequencies of the total LBK (LBK42) and Derenburg (DEB22) datasets to two geographically pooled meta-population sets from Europe and the Near East (Tables 2 and S6; 41 and 14 populations, respectively). PC correlates and component loadings (Figure 2) showed a pattern similar to average hg frequencies (Table 2) in both large meta-population sets, with the LBK dataset grouping with Europeans because of a lack of mitochondrial African hgs (L and M1) and preHV, and elevated frequencies of hg V. In contrast, low frequencies of hg H and higher frequencies for HV, J, and U3 promoted Near Eastern resemblances. Removal of individuals with shared haplotypes within the Derenburg dataset (yielding dataset LBK34) did not noticeably decrease the elevated frequencies of J and especially HV in the Neolithic data.

Most importantly, PC correlates of the second component showed that elevated or high frequencies of hgs T, N1a, K, and W were unique to LBK populations, making them appear different from both Europe and Near East. The considerable within-hg diversity of all four of these hgs (especially T and N1a; Table 1) suggests that this observation is unlikely to be an artifact of random genetic drift leading to elevated frequencies in small, isolated populations.

The pooled European and Near Eastern meta-populations are necessarily overgeneralizations, and there are likely to be subsets of Near Eastern populations that are more similar to the Neolithic population. Interestingly, both the PCA and the MDS plots identified Georgians, Ossetians, and Armenians as candidate populations (Figures 2 and S1).

The authors also mapped genetic distances between all 42 Neolithic mtDNA samples (left) and only the Derenburg site (right), with "greener" signifying smaller distance. They write:

In agreement with the PCA and MDS analyses, populations from the area bounding modern-day Turkey, Armenia, Iraq, and Iran demonstrated a clear genetic similarity with the LBK population (Figure 3A). This relationship was even stronger in a second map generated with just the Neolithic Derenburg individuals (Figure 3B). Interestingly, the map of the combined LBK data also suggested a possible geographic route for the dispersal of Neolithic lineages into Central Europe: genetic distances gradually increase from eastern Anatolia westward across the Balkans, and then northwards into Central Europe. The area with lower genetic distances follows the course of the rivers Danube and Dniester, and this natural corridor has been widely accepted as the most likely inland route towards the Carpathian basin as well as the fertile Loess plains further northwest.

How ancient DNA is rewriting theories based on modern populations:

aDNA data offers a powerful new means to test evolutionary models and assumptions. The European lineage with the oldest coalescent age, U5, has indeed been found to prevail in the indigenous hunter–gatherers [12],[35]. However, mtDNA hgs J2a1a and T1, which because of their younger coalescence ages have been suggested to be Neolithic immigrant lineages [8],[12], are so far absent from the samples of early farmers in Central Europe. Similarly, older coalescence ages were used to support hgs K, T2, H, and V as “postglacial/Mesolithic lineages,” and yet these have been revealed to be common only in Neolithic samples. The recent use of whole mitochondrial genomes and the refinement of mutation rate estimates have resulted in a general reduction in coalescence ages [8], which would lead to an improved fit with the aDNA data.

The authors speak about demic diffusion being the best match for their data:

Therefore at a large scale, a demic diffusion model of genetic input from the Near East into Central Europe is the best match for our observations. It is notable that recent anthropological research has come to similar conclusions [40],[41]. On a regional scale, “leap-frog” or “individual pioneer” colonization models, where early farmers initially target the economically favorable Loess plains in Central Europe [33],[42], would explain both the relative speed of the LBK expansion and the clear genetic Near Eastern connections still seen in these pioneer settlements, although the resolving power of the genetic data is currently unable to test the subtleties of these models.

Demic diffusion, at least as it was proposed initially, implies interaction between expanding farmers and local foragers, with gene pools becoming increasingly "forager" the further one goes from the source of the Neolithic. But, this is not really what we observe in the data, and there is no real evidence of forager DNA in Central European Neolithic (1/42 U5a). Whatever the terminology, it appears that genetics is adding extra firepower to the diffusionist camp of archaeological debates, and contradicting the suppositions of the acculturationists.

UPDATE I (Nov 10):

What is most disappointing about the study is that apparently the SNPs defining the Y-clade IJ were not typed in the samples. So, the two F* samples are certainly not I or J, but they could very well already be IJ. Haplogroup IJ largely tracks the path of the farmers from the Near East to the Balkans and Central Europe, and hopefully a re-examination of the Derenburg remains can be made to include the IJ-defining markers.

It is also fascinating that the presence of 33.3% haplogroup G2 in the German Neolithic is matched by a presence of 33.3% haplogroup G2 in 7th c. Bavarian knights, and maybe even the latest French royalty. The Y-DNA landscape of Europe is still largely empty in space and time, and it will be exciting to see it filled out over the next years.

Certainly, the new Haak et al. study has achieved what Haak et al. (2005), and pretty much every ancient DNA study since has achieved: to surprise us.

UPDATE II (November 10):

It is extremely important to note that the authors have not disproved that the F* Y-chromosomes belonged to derived clades (e.g., haplogroup I or haplogroup J) of the phylogeny. For example, haplogroup I is defined by 7 polymorphisms according to ISOGG.

Today only chromosomes that possess all 7 of them seem to be extant, but these polymorphisms occurred in an unknown order in the line of descent leading to modern I men.

The authors typed only M170, one of these 7 polymorphisms, but it could very well be the case that the F* samples were derived for one or more of the remaining 6 ones, and were thus either ancestors or "cousins" of extant European haplogroup-I bearing men.

It is imperative for internal tree markers to be tested in the F* bearing chromosomes to determine their status.

PLoS Biol 8(11): e1000536. doi:10.1371/journal.pbio.1000536

Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities

Wolfgang Haak et al.

In Europe, the Neolithic transition (8,000–4,000 B.C.) from hunting and gathering to agricultural communities was one of the most important demographic events since the initial peopling of Europe by anatomically modern humans in the Upper Paleolithic (40,000 B.C.). However, the nature and speed of this transition is a matter of continuing scientific debate in archaeology, anthropology, and human population genetics. To date, inferences about the genetic make up of past populations have mostly been drawn from studies of modern-day Eurasian populations, but increasingly ancient DNA studies offer a direct view of the genetic past. We genetically characterized a population of the earliest farming culture in Central Europe, the Linear Pottery Culture (LBK; 5,500–4,900 calibrated B.C.) and used comprehensive phylogeographic and population genetic analyses to locate its origins within the broader Eurasian region, and to trace potential dispersal routes into Europe. We cloned and sequenced the mitochondrial hypervariable segment I and designed two powerful SNP multiplex PCR systems to generate new mitochondrial and Y-chromosomal data from 21 individuals from a complete LBK graveyard at Derenburg Meerenstieg II in Germany. These results considerably extend the available genetic dataset for the LBK (n = 42) and permit the first detailed genetic analysis of the earliest Neolithic culture in Central Europe (5,500–4,900 calibrated B.C.). We characterized the Neolithic mitochondrial DNA sequence diversity and geographical affinities of the early farmers using a large database of extant Western Eurasian populations (n = 23,394) and a wide range of population genetic analyses including shared haplotype analyses, principal component analyses, multidimensional scaling, geographic mapping of genetic distances, and Bayesian Serial Simcoal analyses. The results reveal that the LBK population shared an affinity with the modern-day Near East and Anatolia, supporting a major genetic input from this area during the advent of farming in Europe. However, the LBK population also showed unique genetic features including a clearly distinct distribution of mitochondrial haplogroup frequencies, confirming that major demographic events continued to take place in Europe after the early Neolithic.

Link

mtDNA of Napoleon Bonaparte

From the paper:

In a subsequent search of a public database, EMPOP http://www.empop.org webcite, containing data on 4,475 individuals, the 16184C→T mutation was found to be present in three individuals of West Eurasian origin, giving a frequency of 0.0007%. In a personal database comprising about 37,000 control region records (Dr M. Pala, personal communication), the HSV1 sequence with the single mutation 16184C→T was also present in three samples (one from Crete and two from Italy), giving a mutation frequency for 16184C→T of 0.00008%. All three samples belonged to the mtDNA haplogroup H.

On the left, the locks of Napoleon's hair. I am told that full mtDNA sequencing and Y-STR results are in the pipeline.

Investigative Genetics 2010, 1:7 doi:10.1186/2041-2223-1-7

A rare variant of the mtDNA HVS1 sequence in the hairs of Napoléon's family

Gérard Lucotte

This paper describes the finding of a rare variant in the sequence of the hypervariable segment (HVS1) of mitochondrial (mtDNA) extracted from two preserved hairs, authenticated as belonging to the French Emperor Napoléon I (Napoléon Bonaparte). This rare variant is a mutation that changes the base C to T at position 16,184 (16184C→T), and it constitutes the only mutation found in this HVS1 sequence. This mutation is rare, because it was not found in a reference database (P less than 0.05). In a personal database (M. Pala) comprising 37,000 different sequences, the 16184C→T mutation was found in only three samples, thus in this database the mutation frequency was 0.00008%. This mutation 16184C→T was also the only variant found subsequently in the HVS1 sequences of mtDNAs extracted from Napoléon's mother (Letizia) and from his youngest sister (Caroline), confirming that this mutation is maternally inherited. This 16184C→T variant could be used for genetic verification to authenticate any doubtful material and determine whether it should indeed be attributed to Napoléon.

Link

Brain development in modern humans and Neandertals

From the paper:

We find that the modern human pattern of brain development is derived compared to Neanderthals. The pattern of endocranial shape changes between age groups 2 and 6 is similar among modern humans, Neanderthals and chimpanzees [7]. Neanderthals achieved endocranial volumes comparable to modern humans following this presumably ancestral pattern of development. Our results therefore provide an ontogenetic dimension to the findings of Bruner and colleagues [2]. This challenges the view that all morphological characteristics separating modern humans from Neanderthals are already established at the time of birth. However, our results are not incompatible with the findings reported by Ponce de León and colleagues [3,4,5]: when measurements of the face and neurocranium are analyzed together, the human and Neanderthal trajectories appear to be roughly parallel [3,4] because at the time of birth the face of a Neanderthal is already larger than that of a modern human (Figure 1A).

...

The development of cognitive abilities during individual growth is linked to the maturation of the underlying neural circuitry: in humans, major internal brain reorganization has been documented until adolescence, and even subtle alterations of pre- and perinatal brain development have been linked to changes of the neural wiring pattern that affect behavior and cognition [9]. The uniquely modern human pattern of early brain development is particularly interesting in the light of the recent breakthroughs in the Neanderthal genome project [10], which identified genes relevant to cognition that are derived in living humans. We speculate that a shift away from the ancestral pattern of brain development occurring in early Homo sapiens underlies brain reorganization and that the associated cognitive differences made this growth pattern a target for positive selection in modern humans.

Related: Anatomically modern humans

Current Biology, Volume 20, Issue 21, R921-R922, 9 November 2010 doi:10.1016/j.cub.2010.10.018

Brain development after birth differs between Neanderthals and modern humans

Philipp Gunz et al.

Neanderthals had brain sizes comparable to modern humans, but their brain cases were elongated and not globular as in Homo sapiens[1,2]. It has, therefore, been suggested that modern humans and Neanderthals reached large brain sizes along different evolutionary pathways [2]. Here, we assess when during development these adult differences emerge. This is critical for understanding whether differences in the pattern of brain development might underlie potential cognitive differences between these two closely related groups. Previous comparisons of Neanderthal and modern human cranial development have shown that many morphological characteristics separating these two groups are already established at the time of birth [3,4,5], and that the subsequent developmental patterns of the face are similar, though not identical [6]. Here, we show that a globularization phase seen in the neurocranial development of modern humans after birth is absent from Neanderthals.

Link

Multidimensional scaling and ADMIXTURE across Northern Eurasia corresponds to geography and language

Here is a multi-dimensional scaling plot of a number of North Eurasian populations. In comparison to my previous post, I have excluded Americans and Greenlanders, and added several other populations from Central Asia and West Eurasia.

Population labels have been printed in the co-ordinates of the population averages; these largely correspond with identifiable blobs of colored points, but note that some populations have several outliers, so labels appear in white space. Most notable in that respect are the Koryak, Chukchi, and the Nganasan, all of whom have some apparently European-admixed individuals.

"Mongol" corresponds to Rasmussen et al. (2010) Mongol sample, while "Mongola" to the HGDP-CEPH one. The population codes on the left may not be clearly visible as they overlap with each other and are CEU, LT, HU (relatively unadmixed Caucasoids), FI/RU (Uralian-admixed northern Caucasoids), IR/TR (Altaic-admixed southern Caucasoids). The West Eurasian part of the plot can be seen blown up on the right.

The correspondence with geography and language is striking. Siberian isolates from the extreme north and east, Koryak and Chuckhi are on top; HapMap Chinese at the bottom. Between them are Uralians (Selkup, Yukagir, Nganassan) and Altaics (Mongol-Tungus-Turkic people).

Below is ADMIXTURE analysis for the same set of populations, for K=7:

Finns and Russians seem to have an excess of the "Nganasan" component over the Altaic, while Turks have the opposite. Below is a table of Fst distances between components:

The close relationship between the two Caucasoid components is apparent (Fst=0.033), but note fairly large Fst divergences between the morphologically Mongoloid groups. I attribute this mostly to the very low population sizes of these groups, which have probably affected them by drift. For the less demographically constrained Altaic and East Asian components, Fst=0.044.

If you are not familiar with these ethnic groups, the Red Book of the Peoples of the Russian Empire and the Ethnologue indexes on Altaic and Uralic are invaluable, as are the portraits of ethnic groups of China. On the right a picture of a Nganasan.

UPDATE: Also, a past post from the blog, collating Y-haplogroup N frequencies with anthropological descriptions. Nganasans apparently belong to haplogroup N at a frequency of 92.1%!

ADMIXTURE in Siberia, Greenland, and Alaska

I have discovered a great dataset from Rasmussen et al. (2010). The data had been used before in conjunction with an ancient DNA sequence, but for me it is invaluable, as it fills up one of the major holes in Eurasia, namely Siberia, and includes a number of Altaic, Uralic, and other North Eurasian people. I suspect that this will be invaluable in fine-tuning the Northeast Asian ancestry of Dodecad Project members.

To begin with, after I processed the data, I ran ADMIXTURE on it up to K=7. Below you can see the results for K=7:

I'm no expert in linguistics, but it's clear to me that the light blue component corresponds to Altaic speakers. It will be extremely interesting to see what the analysis including other Altaic speakers from my other datasets as well as West Eurasians of Uralic/Altaic language or with "Northeast Asian" admixture will show.

The table below has sample sizes and admixture proportions.

Stay tuned. More to come.

Y chromosomes and mtDNA of Tuareg nomads from the African Sahel

Related:

• mtDNA of Libyan Tuaregs
• mtDNA H1 in North Africa

European Journal of Human Genetics 18, 915-923 (August 2010) | doi:10.1038/ejhg.2010.21

Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel

The Tuareg presently live in the Sahara and the Sahel. Their ancestors are commonly believed to be the Garamantes of the Libyan Fezzan, ever since it was suggested by authors of antiquity. Biological evidence, based on classical genetic markers, however, indicates kinship with the Beja of Eastern Sudan. Our study of mitochondrial DNA (mtDNA) sequences and Y chromosome SNPs of three different southern Tuareg groups from Mali, Burkina Faso and the Republic of Niger reveals a West Eurasian-North African composition of their gene pool. The data show that certain genetic lineages could not have been introduced into this population earlier than ~9000 years ago whereas local expansions establish a minimal date at around 3000 years ago. Some of the mtDNA haplogroups observed in the Tuareg population were involved in the post-Last Glacial Maximum human expansion from Iberian refugia towards both Europe and North Africa. Interestingly, no Near Eastern mtDNA lineages connected with the Neolithic expansion have been observed in our population sample. On the other hand, the Y chromosome SNPs data show that the paternal lineages can very probably be traced to the Near Eastern Neolithic demic expansion towards North Africa, a period that is otherwise concordant with the above-mentioned mtDNA expansion. The time frame for the migration of the Tuareg towards the African Sahel belt overlaps that of early Holocene climatic changes across the Sahara (from the optimal greening ~10 000 YBP to the extant aridity beginning at ~6000 YBP) and the migrations of other African nomadic peoples in the area.

Link

Clustering of European Y-STRs

Roewer et al. had previously discovered structure in European Y-chromosomes with Y-STRs. The new study, five years later, uses a huge database of population samples. While Y-SNPs defining haplogroups are safer due to the avoidance of homoplasy, which can be a problem with a few Y-STR markers, I believe that most major haplogroups can be distinguished even with few Y-STRs, so the paper's results are valid.

From the paper:

In a total of 33,010 males we identified 4176 different haplotypes, 2192 were unique, and 56 corresponded to 42% of the Y chromosomes

Interesting that such a small fraction of haplotypes corresponds to almost half the Y chromosomes. 7 Y-STRs are generally not sufficient to define monophyletic lineages (as the Cohen Modal Haplotype folks well know by now). It would be interesting to see what this fraction is expected to be under an assumption of reproductive equality, to assess the strength of social selection that I've speculated may be behind the mega-haplogroups we observe in the world today.

Here is a synthetic map of Europe showing distribution of different clusters:

(a) Spatial distribution of the most frequent Y-STR haplotype clusters in

Europe and neighboring regions.

(b) Spatial distribution of the Y-STR haplotype clusters accounting for

the second frequency in western Europe.

Now, take a look at a map of predicted language distribution by Finnish scholar Kalevi Wiik for 5,500 BC:

The correspondence is not perfect, but it's pretty close to merit study. The little differences can be ascribed to 7,500 years of history; for example, in 5,500BC there were probably no Germanic speakers in Scandinavia.

Also of interest:

Two clusters were assigned to large areas of the Balkan Peninsula: 1) Croatia, Bosnia and Herzegovina, Serbia, Romania,Western and Eastern Hungary, and Central Ukraine: cluster 18;(2) continental Greece, Bulgaria, and Macedonia: cluster2. Cluster13 was assigned to Albania and to the western area of the Balkans 10 and cluster 11 to the Caucasus.

Forensic Science International: Genetics doi:10.1016/j.fsigen.2010.09.010

Geostatistical inference of main Y-STR-haplotype groups in Europe

Amalia Diaz-Lacava et al.

We examined the multifarious genetic heterogeneity of Europe and neighboring regions from a geographical perspective. We created composite maps outlining the estimated geographical distribution of major groups of genetically similar individuals on the basis of forensic Y-chromosomal markers. We analyzed Y-chromosomal haplotypes composed of 7 highly polymorphic STR loci, genotyped for 33,010 samples, collected at 249 sites in Europe, Western Asia and North Africa, deposited in the YHRD database (www.yhrd.org). The data set comprised 4176 different haplotypes, which we grouped into 20 clusters. For each cluster, the frequency per site was calculated. All geostatistical analysis was performed with the geographic information system GRASS-GIS. We interpolated frequency values across the study area separately for each cluster. Juxtaposing all 20 interpolated surfaces, we point-wisely screened for the highest cluster frequencies and stored it in parallel with the respective cluster label. We combined these two types of data in a composite map. We repeated this procedure for the second highest frequencies in Europe. Major groups were assigned to Northern, Western and Eastern Europe. North Africa built a separate region, Southeastern Europe, Turkey and Near East were divided into several regions. The spatial distribution of the groups accounting for the second highest frequencies in Europe overlapped with the territories of the largest countries. The genetic structure presented in the composite maps fits major historical geopolitical regions and is in agreement with previous studies of genetic frequencies, validating our approach. Our genetic geostatistical approach provides, on the basis of two composite maps, detailed evidence of the geographical distribution and relative frequencies of the most predominant groups of the extant male European population, examined on the basis of forensic Y-STR haplotypes. The existence of considerable genetic differences among geographic subgroups in Europe has important consequences for the statistical inference in forensic Y-STR haplotype analyses.

Link

Brains to Hand-axes

Stone Age Humans Needed More Brain Power to Make Big Leap in Tool Design

Stone Age humans were only able to develop relatively advanced tools after their brains evolved a greater capacity for complex thought, according to a new study that investigates why it took early humans almost two million years to move from razor-sharp stones to a hand-held stone axe.

Wikipedia on Acheulean, and Oldowan.

PLoS ONE 5(11): e13718. doi:10.1371/journal.pone.0013718

The Manipulative Complexity of Lower Paleolithic Stone Toolmaking

Aldo Faisal et al.

Background
Early stone tools provide direct evidence of human cognitive and behavioral evolution that is otherwise unavailable. Proper interpretation of these data requires a robust interpretive framework linking archaeological evidence to specific behavioral and cognitive actions.

Methodology/Principal Findings
Here we employ a data glove to record manual joint angles in a modern experimental toolmaker (the 4th author) replicating ancient tool forms in order to characterize and compare the manipulative complexity of two major Lower Paleolithic technologies (Oldowan and Acheulean). To this end we used a principled and general measure of behavioral complexity based on the statistics of joint movements.

Conclusions/Significance
This allowed us to confirm that previously observed differences in brain activation associated with Oldowan versus Acheulean technologies reflect higher-level behavior organization rather than lower-level differences in manipulative complexity. This conclusion is consistent with a scenario in which the earliest stages of human technological evolution depended on novel perceptual-motor capacities (such as the control of joint stiffness) whereas later developments increasingly relied on enhanced mechanisms for cognitive control. This further suggests possible links between toolmaking and language evolution.

Link

Sickle cell and malaria (Piel et al. 2010)

The authors ascribe the lack of correlation between malaria endemicity and HbS in Asia primarily to either the presence of other protective polymorphisms or the fact that Plasmodium vivax rather than Plasmodium falciparum is the causative agent there.

Nature Communications 1 , Article number: 104 doi:10.1038/ncomms1104

Global distribution of the sickle cell gene and geographical confirmation of the malaria hypothesis

Frédéric B. Piel et al.

It has been 100 years since the first report of sickle haemoglobin (HbS). More than 50 years ago, it was suggested that the gene responsible for this disorder could reach high frequencies because of resistance conferred against malaria by the heterozygous carrier state. This traditional example of balancing selection is known as the 'malaria hypothesis'. However, the geographical relationship between the transmission intensity of malaria and associated HbS burden has never been formally investigated on a global scale. Here, we use a comprehensive data assembly of HbS allele frequencies to generate the first evidence-based map of the worldwide distribution of the gene in a Bayesian geostatistical framework. We compare this map with the pre-intervention distribution of malaria endemicity, using a novel geostatistical area-mean comparison. We find geographical support for the malaria hypothesis globally; the relationship is relatively strong in Africa but cannot be resolved in the Americas or in Asia.

Link

ADMIXTURE analysis of Spencer Wells

One of the people who've entrusted me with their DNA for analysis in the Dodecad Project is none other than the Genographic Project's Spencer Wells. His project ID is DOD162, and he is the very last individual to be included in the project's pilot phase.

I've enjoyed watching the Genographic Project's various documentaries and reading their published articles, often commenting on them in this blog, so it's a nice opportunity to give something back to the leader of one of the few organizations that is really helping advance our knowledge of human origins.

Here are the results of the admixture analysis: Spencer Wells is in the first bar, and admixture proportions of the 10 components I am using are color-coded for both himself and 36 other populations.

His results are uneventful: his bar is very similar to the one next to it, which summarizes the admixture proportions of 25 individuals from the HapMap-3 CEU population. His top component is North European (60.6%) as his appearance and Northwest European ancestry would suggest. Next is South European (24.9%) and West Asian (13.5%). Rounding up his results is a small slice (1%) of Southwest Asian.

Below you can see Spencer followed by the 25 CEU individuals; these are American Whites from Utah, and as you can see, while there is some small variation in proportions and minor components, he "fits right in" this population.

I have also compared him against the 16 Dodecad Project participants who belong to my "American White" category. This is a rather fuzzy category, consisting of European-descended Americans and Canadians whose ancestry was not entirely from one of my other categories. In that population, the average components are: 11.3% West Asian, 0.2% Northwest African, 26.8% South European, 0.1% Northeast Asian, 1.2% SW Asian, 60.4% N European, 0.1% S Asian, also quite close to Spencer's results.

Cranial differences between Japanese Samurai and townsfolk

International Journal of Osteoarchaeology DOI: 10.1002/oa.1215

Evidence for temporal and social differences in cranial dimensions in Edo-period Japanese

Tomohito Nagaoka et al.

This study examined the craniometric traits of the Edo-period (AD1603–1867) human skeletons from the Hitotsubashi site in Tokyo, compared them with temporally and socially various populations, and attempted to detect the morphological differentiation patterns that the Edo-period Japanese exhibited over time and under those social/environmental conditions. The materials measured here were the townsmen's crania from the Hitotsubashi site, which were dated back to the early half of the Edo period. The observations revealed that the Hitotsubashi samples were more dolichocephalic than any other Edo series and were different from subsequent Edo series in terms of larger maximum cranial length and smaller maximum cranial breadth. The Hitotsubashi samples were definitely in contrast with those of Tentokuji and Shirogane, both of which included a samurai (warrior) class of the late to final Edo period and exhibited the most brachycephalic crania. It is reasonable to assume that the temporal and social situations were possibly related to the observed cranial variation and that the temporal changes in cranial dimensions in pre-modern Japan might have reflected the nutritional and environmental conditions.

Link

African Pygmy news

Two new papers, one using mtDNA, one using skulls.

From the paper:

Shape variation indicates that western groups present longer vaults and shorter faces than eastern groups (Fig. 1B). Variation on PC2 involves differentiation in the shape produced mainly by the short distance between bregma and vertex (Fig. 2) being the vertex more anteriorly located in pygmies than in non-pygmies.

...

Differences in CS were significant (p less than0.05) and they concerns Western pygmies which show a smaller cranial size than both Eastern and Western non-pygmies; it is worth to note that Eastern pygmies do not show significant difference in size with any group

Also:

Results of the PCA indicate that the main cranial shape differentiation does not occur between pygmies and non-pygmies but between Eastern and Western populations (pygmies and non-pygmies) (Table 1; Fig. 1A); all comparison between East and West groups reach a high level of significance (p less than 0.01). Eastern non-pygmies appear as the most distinctive group and differentiate from pygmies and Western non-pygmies in relative and absolute values. Since western pygmies show a higher level of admixture than eastern pygmies, it can be expected that the former differentiate less than the latter from non-pygmies.

PLoS ONE 5(10): e13620. doi:10.1371/journal.pone.0013620

Diversity among African Pygmies

Fernando V. Ramírez Rozzi, Marina L. Sardi

Although dissimilarities in cranial and post-cranial morphology among African pygmies groups have been recognized, comparative studies on skull morphology usually pull all pygmies together assuming that morphological characters are similar among them and different with respect to other populations. The main aim of this study is to compare cranial morphology between African pygmies and non-pygmies populations from Equatorial Africa derived from both the Eastern and the Western regions in order to test if the greatest morphological difference is obtained in the comparison between pygmies and non-pygmies. Thirty three-dimensional (3D) landmarks registered with Microscribe in four cranial samples (Western and Eastern pygmies and non-pygmies) were obtained. Multivariate analysis (generalized Procrustes analysis, Mahalanobis distances, multivariate regression) and complementary dimensions of size were evaluated with ANOVA and post hoc LSD. Results suggest that important cranial shape differentiation does occur between pygmies and non-pygmies but also between Eastern and Western populations and that size changes and allometries do not affect similarly Eastern and Western pygmies. Therefore, our findings raise serious doubt about the fact to consider African pygmies as a homogenous group in studies on skull morphology. Differences in cranial morphology among pygmies would suggest differentiation after divergence. Although not directly related to skull differentiation, the diversity among pygmies would probably suggest that the process responsible for reduced stature occurred after the split of the ancestors of modern Eastern and Western pygmies.

Link

Next paper:

Mol Biol Evol (2010) doi: 10.1093/molbev/msq294

Insights into the demographic history of African Pygmies from complete mitochondrial genomes

Chiara Batini et al.

Pygmy populations are among the few hunter-gatherers currently living in sub-Saharan Africa and are mainly represented by two groups, Eastern and Western, according to their current geographical distribution. They are scattered across the Central African belt and surrounded by Bantu-speaking farmers, with whom they have complex social and economic interactions. To investigate the demographic history of Pygmy groups, a population approach was applied to the analysis of 205 complete mitochondrial DNA (mtDNA) sequences from ten central African populations. No sharing of maternal lineages was observed between the two Pygmy groups, with haplogroup L1c being characteristic of the Western group, but most of Eastern Pygmy lineages falling into sub-clades of L0a, L2a and L5. Demographic inferences based on Bayesian coalescent simulations point to an early split among the maternal ancestors of Pygmies and those of Bantu-speaking farmers (∼70,000 ya, years ago). Evidence for population growth in the ancestors of Bantu-speaking farmers has been observed, starting ∼65,000 ya, well before the diffusion of Bantu languages. Subsequently, the effective population size of the ancestors of Pygmies remained constant over time and ∼27,000 ya, coincident with the Last Glacial Maximum, Eastern and Western Pygmies diverged, with evidence of subsequent migration only among the Western group and the Bantu-speaking farmers. Western Pygmies show signs of a recent bottleneck 4,000 – 650 ya, coincident with the diffusion of Bantu languages, while Eastern Pygmies seem to have experienced a more ancient decrease in population size (20,000 - 4,000 ya). In conclusion, the results of this first attempt at analysing complete mtDNA sequences at the population level in sub-Saharan Africa not only support previous findings but also offer new insights into the demographic history of Pygmy populations, shedding new light on the ancient peopling of the African continent.

Link

Ex oriente, Plague!

From a related NYTimes story:

The great waves of plague that twice devastated Europe and changed the course of history had their origins in China, a team of medical geneticists reported Sunday, as did a third plague outbreak that struck less harmfully in the 19th century.

And in separate research, a team of biologists reported conclusively this month that the causative agent of the most deadly plague, the Black Death, was the bacterium known as Yersinia pestis. This agent had always been the favored cause, but a vigorous minority of biologists and historians have argued the Black Death differed from modern cases of plague studied in India, and therefore must have had a different cause.

UPDATE: My Latin failed me, it's ex oriente. It's somewhat difficult to remember a language you don't get to speak :)

PLoS Pathog 6(10): e1001134. doi:10.1371/journal.ppat.1001134

Distinct Clones of Yersinia pestis Caused the Black Death

Stephanie Haensch et al.

From AD 1347 to AD 1353, the Black Death killed tens of millions of people in Europe, leaving misery and devastation in its wake, with successive epidemics ravaging the continent until the 18th century. The etiology of this disease has remained highly controversial, ranging from claims based on genetics and the historical descriptions of symptoms that it was caused by Yersinia pestis to conclusions that it must have been caused by other pathogens. It has also been disputed whether plague had the same etiology in northern and southern Europe. Here we identified DNA and protein signatures specific for Y. pestis in human skeletons from mass graves in northern, central and southern Europe that were associated archaeologically with the Black Death and subsequent resurgences. We confirm that Y. pestis caused the Black Death and later epidemics on the entire European continent over the course of four centuries. Furthermore, on the basis of 17 single nucleotide polymorphisms plus the absence of a deletion in glpD gene, our aDNA results identified two previously unknown but related clades of Y. pestis associated with distinct medieval mass graves. These findings suggest that plague was imported to Europe on two or more occasions, each following a distinct route. These two clades are ancestral to modern isolates of Y. pestis biovars Orientalis and Medievalis. Our results clarify the etiology of the Black Death and provide a paradigm for a detailed historical reconstruction of the infection routes followed by this disease.

Link

Nature Genetics | doi:10.1038/ng.705

Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity

Giovanna Morelli et al.

Plague is a pandemic human invasive disease caused by the bacterial agent Yersinia pestis. We here report a comparison of 17 whole genomes of Y. pestis isolates from global sources. We also screened a global collection of 286 Y. pestis isolates for 933 SNPs using Sequenom MassArray SNP typing. We conducted phylogenetic analyses on this sequence variation dataset, assigned isolates to populations based on maximum parsimony and, from these results, made inferences regarding historical transmission routes. Our phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs. All 626 current isolates from the United States reflect one radiation, and 82 isolates from Madagascar represent a second radiation. Subsequent local microevolution of Y. pestis is marked by sequential, geographically specific SNPs.

Link

Joe Pickrell redux

Joe Pickrell discovers Jewish great-grandparent

Second, Dienekes followed up on his analysis of the ancestry of the GNZ participants with a much larger data set, including individuals of southwest European descent. As expected, when including more data, there was no evidence that Vincent has any Ashkenazi ancestry. Unexpectedly, this was not true for me—even in this larger analysis, the evidence for Ashkenazi ancestry didn’t disappear.

...

As I was mulling over these sorts of issues, I sent the link to my previous analysis to a family member. I didn’t really expect this person to find it that interesting, but hey, you never know. I then got a phone call. I’ll summarize a couple days worth of moderate confusion, second-hand reports of conversations with distant relatives, and family intrigue with this: as it turns out, one of my great-grandparents was indeed a Polish Ashkenazi Jew who immigrated to the United States around the turn of the century. I, obviously, was completely unaware of this.

So to conclude, a tip of my hat to Dienekes and everyone else who looked at these data—this has been the first genuinely unexpected thing to come out of my genetic data.

I've estimated Joe's ancestry here and here.

He is included in the Dodecad Project's spreadsheet as JKP001.

His "Southwest Asian" score of 6.7% is consistent with but not indicative of Jewish ancestry, as this component is found in West Asia and Europe, although it attains its maximum in Saudi Arabia and occurs at about 20% in European Jews.

So, while I wouldn't conclude that he had partial Jewish ancestry based on his data, the issue is no longer relevant due to the emergence of the new genealogical information.

This is an example of what I called "cryptic ancestry" as a possible explanation for people getting unexpected results.