RIP matrilocal egalitarian early European farmers

It seems that Marija Gimbutas' feminist Old Europe fantasy is collapsing like a house of cards.

Michael Balter covers this in Science:

The results of the study, published online today in the Proceedings of the National Academy of Sciences, suggest that men who were buried with adzes—thought to be an indication of higher social status—were more likely to have grown up on loess soils than men who were buried without adzes.
...
A similarly striking pattern was seen when the team looked at the female skeletons, which made up 153 of the total 311 individuals analyzed. The variation in strontium ratios for females was significantly greater than for males, suggesting that a greater number of females than males had grown up in non-fertile areas.
...
The team came to two main conclusions: First, some males had greater access to fertile soils than others, probably because they were the sons of farmers who had inherited access to the best land. And second, LBK societies were "patrilocal," meaning that males tended to stay put in one place while females moved in from other areas to mate with them.

From the press release:

Professor Bentley said: "Our results, along with archaeobotanical studies that indicate the earliest farmers of Neolithic Germany had a system of land tenure, suggest that the origins of differential access to land can be traced back to an early part of the Neolithic era, rather than only to later prehistory when inequality and intergenerational wealth transfers are more clearly evidenced in burials and material culture. 

"It seems the Neolithic era introduced heritable property (land and livestock) into Europe and that wealth inequality got underway when this happened. After that, of course, there was no looking back: through the Bronze Age, Iron Age and Industrial era wealth inequality increased but the 'seeds' of inequality were sown way back in the Neolithic."

PNAS doi: 10.1073/pnas.1113710109

Community differentiation and kinship among Europe’s first farmers

R. Alexander Bentley et al.

Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.

Link

Short-legged Neandertal mystery solved (and other interesting thoughts)

A nice new paper proposes that Neandertal short legs were not due to adaptation to cold but related to gait efficiency in a mountainous environment. A short-legged person usually has to use more strides/time unit to keep up with a long-legged one. What the researchers have shown is that on a slope this is not the case.

An interesting thought came to me as I was reading this: if Neandertal short legs were not due to cold adaptation, could it be that early Homo sapiens long legs were also not due to adaptation for a tropical climate?

It has been generally believed that the longer legs of early Upper Paleolithic humans in Europe compared to Neandertals evidenced their fairly recent arrival from a much warmer region.

But, in an age when there was no alternative to walking, we would expect populations that migrated over long distances to be efficient walkers, or to become so, en route, due to natural selection ("those who can't keep up stayed behind"). Moreover, while all humans are pretty much capable of walking anywhere, we would expect the pioneers in every region colonized by our species to be longer-limbed, since they "got there first".

The reverse could also be true, depending on the environment one walked through: early colonists of mountainous regions might be rather short-legged, and this is exactly what we find in the "hyper-polar" body types of early Neolithic farmers. These had to move across the fairly uneven terrain of southeastern Europe, at an age when there were no maps, no roads, and plenty of forest, making the shortest path between two points something different than a horizontal line.

The press release explains things quite well:

While most studies have concluded that a cold climate led to the short lower legs typical of Neandertals, researchers at Johns Hopkins have found that lower leg lengths shorter than the typical modern human's let them move more efficiently over the mountainous terrain where they lived. The findings reveal a broader trend relating shorter lower leg length to mountainous environments that may help explain the limb proportions of many different animals.

...

"Studies looking at limb length have always concluded that a shorter limb, including in Neandertals, leads to less efficiency of movement, because they had to take more steps to go a given distance," says lead author Ryan Higgins, graduate student in the Johns Hopkins Center of Functional Anatomy and Evolution. "But the other studies only looked at flat land. Our study suggests that the Neandertals' steps were not less efficient than modern humans in the sloped, mountainous environment where they lived."

...

Neandertals, who lived from 40,000 to 200,000 years ago in Europe and Western Asia, mostly during very cold periods, had a smaller stature and shorter lower leg lengths than modern humans. Because mammals in cold areas tend to be more compact, with a smaller surface area, scientists have normally concluded that it was the region's temperature that led to their truncated limbs compared to those of modern humans, who lived in a warmer environment overall.

...

The researchers decided to study different types of bovids--a group of mammals including gazelles, antelopes, goats and sheep--since these animals live in warm and cold environments on both flat and hilly terrain. The group took data from the literature on bovid leg bones and found that they fit the pattern: mountainous bovids, such as sheep and mountain goats, overall had shorter lower leg bones than their relatives on flat land, such as antelopes and gazelles, even when they lived in the same climates.

Investigating closely related bovids brought this trend into even sharper relief. Most gazelles live on flat land, and the one mountainous gazelle species examined had relatively shorter lower legs, despite sharing the same climate. Also, among caprids (goats and sheep), which mostly live on mountains, the one flat land member of the group exhibited relatively longer lower legs than all the others.

"Biologists have Bergman's and Allen's Rules, which predict reduced surface area to body size and shorter limbs in colder environments," says Higgins. "Our evidence suggests that we can also predict certain limb configurations based on topography. We believe adding the topic of terrain to ongoing discussions about limb proportions will allows us to better refine our understanding of how living species adapt to their environments. This improved understanding will help us better interpret the characteristics of many fossil species, not just Neandertals."

Am J Phys Anthropol DOI: 10.1002/ajpa.21575

The effects of distal limb segment shortening on locomotor efficiency in sloped terrain: Implications for Neandertal locomotor behavior

Ryan W. Higgins, Christopher B. Ruff

Past studies of human locomotor efficiency focused on movement over flat surfaces and concluded that Neandertals were less efficient than modern humans due to a truncated limb morphology, which may have developed to aid thermoregulation in cold climates. However, it is not clear whether this potential locomotor disadvantage would also exist in nonflat terrain. This issue takes on added importance since Neandertals likely spent a significant proportion of their locomotor schedule on sloped, mountainous terrains in the Eurasian landscape. Here a model is developed that determines the relationship between lower limb segment lengths, terrain slope, excursion angle at the hip, and step length. The model is applied to Neandertal and modern human lower limb reconstructions. In addition, for a further independent test that also allows more climate-terrain cross comparisons, the same model is applied to bovids living in different terrains and climates. Results indicate that: (1) Neandertals, despite exhibiting shorter lower limbs, would have been able to use similar stride frequencies per speed as longer-limbed modern humans on sloped terrain, due to their lower crural indices; and (2) shortened distal limb segments are characteristic of bovids that inhabit more rugged terrains, regardless of climate. These results suggest that the shortened distal lower limb segments of Neandertals were not a locomotor disadvantage within more rugged environments.

Link

"Comparing Ancient and Modern DNA Variability in Human Populations" abstracts

Excerpts from the conference site.

Temporal differentiation across a West-European Y-chromosomal cline - genealogy as a tool in human population genetics
Maarten H.D. Larmuseau et al.

The pattern of population genetic variation and allele frequencies within a species are unstable and are changing in time according to different evolutionary factors. For humans, it is possible to combine detailed patrilineal genealogical records with deep Y-chromosome genotyping to disentangle signals of historical population genetic structures due to the exponential increase of genetic genealogical data. To test this approach we studied the temporal pattern of the 'autochthonous' micro-geographical genetic structure in the region of Brabant in Belgium and The Netherlands (Northwest-Europe). Genealogical data of 881 individuals from Northwest-Europe were collected from which 634 family trees showed a residence within Brabant for at least one generation. The Y-chromosome genetic variation of the 634 participants was investigated using 110 Y-SNPs and 38 Y-STRs and linked to particular locations within Brabant on specific time periods based on genealogical records. Significant temporal variation in the Y-chromosome distribution was detected through a north-south gradient in the frequencies distribution of subhaplogroup R1b1b2a1 (R-U106), next to an opposite trend for R1b1b2a2g (R-152). The gradient on R-U106 faded in time and became even totally invisible during the Industrial revolution in the first half of the 19th century. Therefore, genealogical data for at least 200 year are required to study small-scale 'autochthonous' population structure in Western-Europe.

The Dutch medieval and post-medieval genetic landscapes
Eveline Altena et al.

Since 2005 many archeological human skeletons have been sampled for DNA research under forensic conditions in The Netherlands. This enables us to perform a large scale genetic survey on reliable genetic data from the prehistory until the present. The majority of the available archaeological DNA samples, though, originate from medieval and post-medieval sites. Here we present preliminary autosomal and Y-chromosomal data from more then 500 archaeological human skeletons, excavated at several medieval and post-medieval sites. We also compare these historical genetic data with data from more then 2000 modern Dutch males.

Comparing ancient and modern DNA variability in North Eastern Iberia: the Neolithic impact of first farmers
Cristina Gamba et al.

Archaeological, anthropological and demographic hypotheses can be tested by comparing ancient and modern DNA from human samples in a diachronical context. In this case, it was possible to evaluate genetic continuity or discontinuity between different periods, and/or to infer ancient human migrations in a set of Iberian samples. We evaluated the demographic impact associated to the spread of the Neolithic in North Eastern Iberia. We recovered mitochondrial DNA from 13 Early Neolithic specimens from three archaeological sites: Can Sadurní, Chaves and Sant Pau. A bayesian simulation approach was performed to compare the obtained results with Middle Neolithic and modern samples from the same region. We tested different scenarios to determine which among them better explained the analyzed data. By comparing simulated and observed FST values, we observed genetic differentiation between Early Neolithic and Middle Neolithic populations, which suggests that at the beginning of the Neolithic, genetic drift played an important role.
Genetic differentiation was also observed between Early Neolithic and modern- day populations. These data are compatible with the arrival of small genetically-distinctive groups at the beginning of the Neolithic, suggesting a pioneer colonization of North Eastern Iberia by first farmers.

The following abstract is interesting as it suggests we should not view the "Neolithic" as a singular event. X2 was also discovered in Megalithic France, as well as a likely immigrant population from the Near East and the Caucasus in the Tarim Basin, and Bronze Age Eulau. From a paper on the Reidla et al. (2003): Overall, it appears that the populations of the Near East, the Caucasus, and Mediterranean Europe harbor subhaplogroup X2 at higher frequencies than those of northern and northeastern Europe (P less than .05) and that X2 is rare in Eastern European as well as Central Asian, Siberian, and Indian populations and is virtually absent in the Finno-Ugric and Turkic-speaking people of the Volga-Ural region.

Where are all the "WIX"? Rare European maternal lineages W, I, and X2 in the past and present
Esther J. Lee et al.

Studies utilizing ancient DNA to examine past populations in Europe have increased dramatically in recent years. Specifically, mitochondrial DNA (mtDNA) sequences for over 100 individuals in prehistoric Europe have been sequenced and published. Scholars have intensively focused on the so-called Neolithic transition in Europe, the transformation from hunter-gatherer lifestyle to agro-pastoralism, and continue to debate whether the process was a result of population movement or cultural dispersion. Both hypotheses continue to be tested and genetics analyses from past and present populations have suggested a complex movement of people and cultures across Eurasia. This work focuses on the mtDNA haplogroups identified in past European populations that are rare in the present, haplogroups W, I, and X2. New data will be presented from Neolithic Funnel Beaker collective burials sites, a late Neolithic Bell Beaker site, and an Iron Age Halstatt site in Germany, in which the three maternal lineages are identified. Among the published European Neolithic data, haplogroup X2 appears in late Neolithic sites in Germany and France but not in the earlier LBK culture. Haplogroup X2 shows an intriguing phylogenetic landscape with a wide geographical distribution at an overall low frequency, but on the other hand, pockets of high diversity and frequency among certain modern western Eurasian populations have been described. The discussion focuses on whether the presence of the three haplogroups in the past is a result of ascertainment bias or some viable population movement.

The following seems to suggest Denisova admixture in the East Asian mainland, and not just the island groups, identified in the recent Reich et al. (2011) paper. The sentence about biased Neandertal similarity with increasing distance to Africa is also interesting; the data that is available so far shows non significant differences in Neandertal similarity among Eurasians, although the published values do seem to show higher (and perplexing) averages in China vs. Europe.

Archaic human ancestry in East Asia
Pontus Skoglund & Mattias Jakobsson

Recent studies of ancient genomes have suggested that gene flow from archaic hominin groups to the ancestors of modern humans occurred on two separate occasions during the modern human expansion out of Africa. At the same time, decreasing levels of human genetic diversity have been found at increasing distance from Africa as a consequence of human expansion out of Africa. We re-analyzed the signal of archaic ancestry in modern human populations and we investigated how serial founder models of human expansion affect the signal of archaic ancestry using simulations. We show that genetic drift coupled with an ascertainment bias for common alleles can cause artificial, but largely predictable, differences in affinity to archaic genomes between descendants of an admixture event. In genotype data from non-African humans, this effect results in a biased genetic similarity to Neandertal with increasing distance from Africa. In addition to the two previously reported connections between non-Africans and Neandertals as well as between Oceanians and a Denisovan archaic human genome from Siberia, we found a significant affinity between East Asians (in particular Southeast Asians) and the Denisovan genome, a pattern that is not expected under a model of solely Neandertal-related admixture in the ancestry of East Asians. This observation could be explained either by substantial migration from Oceania into East Asia, or more common history between anatomically modern- and archaic populations than previously proposed.

The death of "acculturation" as a model for European farming dispersal

Very good open access article that shows how migrationism has returned to fashion and both the laborious wave of advance, as well as the processual "acculturation" model in which Mesolithic people slowly adopt elements of farming culture, transforming themselves into farmers are wrong. My only beef with the article is its treatment of genetics, which is largely based on rehashing of pre-ancient DNA studies and ignores the latest literature.

From the (open access) paper:

In this article I will consider the spread of agriculture from central Europe to the Atlantic (fig. 1). This involves four major “spread events”: the Cardial of the western Mediterranean, the Linienbandkeramik (LBK) of the interior, the Trægtbægerkultur (TRB) of southern Scandinavia, and the Neolithic of Britain and Ireland.

...

Above all, the migrationist scenarios suggested here may account for one thing: why we so rarely see long-term “transitional” stages between foraging and farming. Now we see foragers, now we see farmers; but in Europe we have singularly failed to catch foragers in the act of becoming farmers. The long-term developmental processes we have expected for decades have not materialized. Farmers can evidently trade axes with foragers for centuries or longer without destabilizing them or leading them to adopt farming. “Processes” there undoubtedly are, but we need to look inside the standard deviation of a radiocarbon date to see them in action.

Related:

1. Global demographic expansions followed agricultural spread
2. Human migration and cultural change in the origins of European farmers
3. Near Eastern origin of European Neolithic farmers
4. Migrants introduced farming to Britain
5. Neolithic Expansion was not gradual
6. First farmers in the Mediterranean
7. Earliest evidence for milk in the Near East and Southeastern Europe
8. "First contact" between LBK farmers and foragers
9. Waterways and the Neolithic
10. Reconsideration of the Neolithic of Northwestern Europe

Current Anthropology http://www.jstor.org/stable/10.1086/658368

Westward Ho!
The Spread of Agriculture from Central Europe to the Atlantic

Peter Rowley-Conwy

Recent work on the four major areas of the spread of agriculture in Neolithic western Europe has revealed that they are both chronologically and economically much more abrupt than has hitherto been envisaged. Most claims of a little agriculture in Late Mesolithic communities are shown to be incorrect. In most places, full sedentary agriculture was introduced very rapidly at the start of the Neolithic. “Transitional” economies are virtually absent. Consequently, the long-term processes of internal development from forager to farmer, so often discussed in Mesolithic-Neolithic Europe, are increasingly hard to sustain. The spread of agriculture by immigration is thus an increasingly viable explanation. The crucial role of boats for transport and of dairying for the survival of new farming settlements are both highlighted. Farming migrations were punctuated and sporadic, not a single wave of advance. Consequently, there was much genetic mixing as farming spread, so that agricultural immigrants into any region carried a majority of native European Mesolithic genes, not Near Eastern ones.

Link

Proto-Indo-European monogamy

I had previously linked to a paper by the same author on the subject of marital residence in Indo-European societies, showing Indo-European to be virilocal. In the current paper, the conclusion is reached that Proto-Indo-European and perhaps Proto-Indo-Hittite corresponded to a monogamous society.

Interestingly, the author cites evidence for the presence of a nuclear family in a LBK community, as well as in a successor community of the Corded Ware complex. This is quite interesting, since the LBK probably represents the northern spread of Indo-European peoples from southeast Europe, and, ultimately, West Asia. It will certainly be interesting to infer the presence of the nuclear family in archaeological contexts, as far as this can be determined by archaeology, craniometry, and ancient DNA work.

Hum Biol. 2011 Feb;83(1):87-105.

Reconstructing the history of marriage strategies in indo-European-speaking societies: monogamy and polygyny.

Fortunato L.

Abstract
Explanations for the emergence of monogamous marriage have focused on the cross-cultural distribution of marriage strategies, thus failing to account for their history. In this paper I reconstruct the pattern of change in marriage strategies in the history of societies speaking Indo-European languages, using cross-cultural data in the systematic and explicitly historical framework afforded by the phylogenetic comparative approach. The analysis provides evidence in support of Proto-Indo-European monogamy, and that this pattern may have extended back to Proto-Indo-Hittite. These reconstructions push the origin of monogamous marriage into prehistory, well beyond the earliest instances documented in the historical record; this, in turn, challenges notions that the cross-cultural distribution of monogamous marriage reflects features of social organization typically associated with Eurasian societies, and with "societal complexity" and "modernization" more generally. I discuss implications of these findings in the context of the archaeological and genetic evidence on prehistoric social organization.

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

ISBA4 abstracts

Here are some interesting abstracts from the recent 4th International Symposium on Biomolecular Archaeology.

Naglaa Abu-Mandil1 & Terry Brown

Kinship analysis and sex identification of skeletons from two archaeological sites in Greece

Ancient DNA offers unprecedented opportunities for anthropologists and bioarchaeologists to assess the biological relationships of ancient populations. This study is designed to assess the family relationship among skeletons from two different archaeological sites in Greece which can help in shedding light on the ritual practice in Aegean prehistory. Another aim is to identify the sex of these skeletons genetically to confirm the conventional sexing methods. These sites are called Kouphovouno and Bostani. Kouphovouno is an important Neolithic and Bronze Age archaeological site near Sparta in Lakonia, while Bostani is dated back to the Early Helladic period in Ancient Greek history. In both cases the sites are recently excavated and DNA samples from all people who have handled the skeletons are available. Both mtDNA and nuclear DNA markers are being studied in order to identify maternal relationships and to reveal the sex of the skeletons.

Morten Rasmussen et al.
The nuclear genome of an ancient human

We have sequenced the complete genome from an ancient human. It was obtained from 4,000-year-old permafrost-preserved hair; the genome represents a male individual from the first known culture to settle in Greenland. Sequenced to an average depth of 20, we recover 79% of the diploid genome, and identify 353,151 highconfidence single-nucleotide polymorphisms (SNPs). Comparisons with SNP data from contemporary populations allow us to explore the migrations and kinship of this extinct culture. Analyses provide evidence of a migration from Siberia into the New World, independent of that giving rise to the modern Native Americans and Inuit. The migration was dated to approximately 5,500 years BP and the closest living relatives are found in North-East Siberia showing no signs of admixture with modern Native Americans or Inuit. We use functional SNP assessment to assign possible phenotypic characteristics of the individual.

This is extremely exciting as it speaks of Y-chromosome results from Central European Neolithic sites, which is a first. It seems to me that migrationism is due for a big comeback. If anyone has attended the symposium and/or has more information on this feel free to leave a comment/send me an e-mail.

Wolfgang Haak et al.
Ancient DNA from Early Neolithic Farmers suggests a major genetic input from the Near East

The Neolithic transition (approx. 8000-4000 BC) is considered one of the most important demographic events in Europe’s past since the initial peopling of anatomically modern humans in the Upper Paleolithic (40,000 BC). Whether this transition has been cultural or driven by large-scale population movements is subject of a long-standing scientific debate in archaeology, anthropology and human population genetics. So far, inferences about the genetic make-up of past populations have been drawn from studies of modern-day Eurasian populations, but ancient DNA studies now provide direct snapshots of specific time frames in the past.

We present new mitochondrial and Y-chromosomal data from Neolithic individualsfrom a Central European early farming site, Derenburg (Germany), which significantly extends the genetic dataset of the Linearbandkeramik (LBK; n=42), and provides the first detailed genetic picture of the earliest Neolithic culture in Central Europe (5500-5000 cal BC). Comprehensive population-genetic analyses utilizing a large database of modern-day Western Eurasian populations (n=23,394) reveal unique genetic features of the LBK population and a clearly distinct mitochondrial haplogroup frequency distribution. Importantly however, the LBK population shows an affinity to populations in the modern-day Near East, suggesting a major genetic input from this region at the time of the advent of farming in Europe.

I wish we knew what the haplogroups of the unambiguously defined samples were...

Silja Dillenberger et al.
Parallel tagged amplicon sequencing of highly degraded Ychromosomal DNA from archaeological skeletons

The intent of the study was to develop a Y-SNP multiplex-PCR suitable for genetic analysis of ancient human remains. Therefore 37 SNPs characterizing Eurasian
haplogroups, with a focus on Europe and Central Asia, were selected in order to get a
high phylogeographic resolution. The 37 SNPs, using amplicon lengths between 64 and 107bp, were co-amplified within 2 multiplex PCRs followed by parallel tagged sequencing on the 454 platform. After testing on 3 recent male and 2 recent female individuals it was applied to 8 male prehistoric samples from Central Asia and Europe. One sample was too poorly preserved for haplogroup identification. Another individual could be narrowed down to Q or R*. The haplogroups of the remaining 6 samples could unambiguously be defined. This shows that this approach is adequate for Y-chromosomal typing of highly degraded ancient human remains.

Five years ago I estimated an 11% contribution of Central Asian Turks to modern Anatolians, which seems quite inline with the following estimate. I will simply note that the number of 1.5 million is probably inflated, as the invaders did not have the same reproductive success as the local population; this means that the "original Turks" were fewer than 11%. Moreover, not all of the Anatolian population of the 11th century became present-day Anatolians; the current Muslims of Anatolia are a part of the 11th century population mixed with the invaders, and hence the number of invaders must've been even smaller.

Inci Togan et al.
An Anatolian Trilogy: Arrival of nomadic Turks with their sheep and shepherd dogs

Because of its geographical location, Anatolia was subject to migrations from multiple different regions throughout time. The last, well-known migration was the movement of Turkic speaking, pastoral nomadic group from Central Asia. They invaded Anatolia and then the language of the region was gradually replaced by the Turkic language. Central Asian genetic contribution to Anatolia with respect to the Balkans was estimated as 13% by an admixture analysis implemented in LEA. This estimate was obtained by employing nuclear genetic markers. MtDNA and Y-chromosome estimates confirmed this admixture proportion. Based on the population size estimation for Anatolia in 12th century, it can be calculated that at least 1.5 million nomads might have arrived to Anatolia. History tells us that they have arrived to Central and Eastern Anatolia first and only 150 years later they invaded Western Anatolia. Distributions of genetic diversity of domestic sheep and shepherd dogs in Turkey support that as well the language spoken in Anatolia these nomads have changed the genetic landscape of these two domestic species within Turkey. These observations have implications on conservation strategies of domestic sheep in Anatolia which is known to be the cradle of sheep domestication. Results must be confirmed by ancient DNA studies.

Alicia K Wilbur et al.
Ancient tuberculosis before and after the Age of Exploration

The Age of Exploration resulted in contact between human populations that were previously isolated from each other, initiating exchange of ideas, cultigens, and diseases. The modern biogeography of tuberculosis (TB) strains appears to reflect this with, for example, the presence of European type strains in the Americas and elsewhere. Until recently, it was thought that TB originated in the Old World in the last 10,000 years and the presence of TB in the Americas prior to contact was debated. Current estimates of TB’s origins, however, range from 3-6 million years ago. In our research, we attempt to characterize ancient mycobacterial strains from cases of disseminated bone TB in order to understand the phylogenetic relationships between strains of tuberculosis prior to and after the Age of Exploration. DNA was extracted from over 115 samples exhibiting classic tuberculosis lesions obtained from both the New and Old Worlds and ranging in age from 5800 BCE to A.D. 1800. Then, four quantitative PCR assays were used to gauge the preservation of host and pathogen DNA. Human nuclear and mitochondrial, and mycobacterial repetitive (IS6110) and single copy (rpoB) loci were analyzed. These results show that while approximately one third of the samples contain human nuclear and/or mitochondrial DNA, only 10% were positive for mycobacterial DNA. Mycobacterial DNA was usually recovered in the presence of human DNA (75%). In addition, our results suggest that TB strains in the Americas dating prior to European contact did not contain the IS6110 repeat element. From the samples that tested positive for host and mycobacterial DNA, we first selected two from Peru and one from Canada, for subsequent analyses using highthroughput pyrosequencing. Our analyses indicate that both slow-growing (pathogenic) and fast-growing (environmental) species of mycobacteria are present in the samples. However, our analyses also indicate that new methods for targeting specific sequences of interest are necessary to obtain sufficient genome coverage for evolutionary analyses. We will discuss ways of doing this and our current progress in this effort.

The New Scientist reports that the following study discovered a couple of Africans were present in the crew of Columbus.

Vera Tiesler et al.
Age at death, biological ancestry and provenience of Christopher Columbus’ crew at La Isabela, Santo Domingo, (1493-1498). Histological and biomolecular approaches

The site of La Isabela, in the Dominican Republic, was the first colonial town in the Americas. It was settled by Christopher Columbus and his crew at the beginning of AD 1494, and initially housed some 1,500 individuals from a wide array of social, economic and probably ethnic backgrounds. Its graveyard quickly accumulated the mortal remains of those who succumbed to the harsh conditions of the Atlantic crossing and life in the colony. In this study we present the preliminary results of a series of histological and molecular (isotopic and DNA) studies that expand on the macroscopic skeletal information in combination with detailed historical records on the lives of the deceased. Considered jointly, the data sets provide deepened insights into age at death, disease, nutrition, biological ancestry and geographic origins of 49 individuals unearthed between 1983 and 1991 and currently stored at the Museo del Hombre Dominicano in Santo Domingo, Dominican Republic. The analyses were largely funded by the Universidad Autónoma de Yucatan, Merida, Mexico, and National Geographic Society, Washington D.C., US, and received logistical support form the Museo del Hombre Dominicano, Dominican Republic.

Tracey Pierre et al.
American Southwest prehistory through ancient DNA

The American Southwest is one of the best archaeologically known areas of the world. It is also one of the most ethnically and linguistically diverse regions inhabited by contemporary Native American groups in North America. To what extent are the early and late prehistoric Southwest occupants associated with the Mesa Verde, Chaco Canyon, Mimbres and Basketmaker cultures related to today’s Athapaskan, Puebloan and Uto-Aztecan speakers? Is there genetic evidence for an earlier migration into the Southwest by populations ancestral to today’s Southern Athapaskans? Can the spread of farming into the Southwest region by Uto-Aztecan speakers from Mexico be detected in the gene pools of these earlier cultures? How are the former occupants of Chaco Canyon related to other prehistoric and modern inhabitants of this region? Does the current regional diversity reflect the geographical distribution of Southwest cultures prior to European contact? Previous ancient DNA research from the greater Southwest has demonstrated both regional continuity and discontinuity through the study of short-read mtDNA sequences. With the advent of second generation sequencing technology it is now possible to address in finer resolution these microcontinental migrations questions associated with the spread of language families into the American Southwest.

I don't want to comment too much on the following abstract, but I'm always favorably inclined to the prosaic rather than the ornate interpretations of ancient artifacts, unless there is clear evidence to the contrary.

Lucija Šoberl et al.
On the Beaker trail: Investigating the function of British Beakers through organic residue analysis

Beaker pottery is traditionally regarded as a material symbol of social, material and ideological changes that began in the latest Neolithic – these included the appearance of new ceramic technologies, modes of dress and adornment, the introduction of metallurgy and single burial. As far as the pottery goes, meticulous and numerous typological schemes have been produced in the past, but the function of Beakers has never been established on a larger scale from a scientific point of view.

British Beakers are most commonly found with inhumation burials, laid in pits or cists, and often in association with other objects. It has often been supposed that Beakers were produced specifically for grave deposition, since they differ in terms of fabric quality and decoration from those produced for non-funerary use. Due to their elaborate decoration and innovative fine fabric, Beakers have been considered as prestige items. As a consequence of Sherratt’s interpretation of Beakers as drinking cups, used to consume alcoholic beverages or narcotic substances at ritual gatherings, these vessels have gained almost a legendary status as prestige drinking equipment that has not been scientifically contested. The porous fabric of prehistoric pottery has been known to represent a favourable environment for the long term preservation of organic molecules, such as lipids. Beaker potsherds from funerary and non-funerary contexts have been analysed using solvent extraction, followed by gas chromatography, mass spectrometry and isotope ratio mass spectrometry to provide structure identification, biomolecular fingerprints and compound specific δ13C values.

Through analyses of absorbed lipids we can directly address the function and contents of ceramic vessels. Here we present preliminary results of our research project aimed at addressing the function of Beaker pottery through organic residue analyses. Surprisingly, no support is found for the interpretation of Beakers as vessels used in alcohol consumption, and their very status as prestige items might even be questioned.

Melanie Pruvost et al
Nuclear ancient DNA draws picture of wild and early domesticated horses

Domesticated horses played key roles in the history of mankind providing nutrition and offering unprecedented modes of transportation. If the reasons related to the beginning of horse domestication are still unknown, horses were crucial to the life of nomadic pastoralists on the Eurasian steppe and had always have a particular position among domestic animal (warfare capabilities, symbol of social status, human's nutrition). For these reasons, deciphering the spatial and temporal origin of domestic horses is of key importance for understanding the origin of modern human societies. Due to the high variability of mtDNA among modern and ancient horse populations, the genetic analysis failed to reveal either time or place of horse domestication. In this case, the failure has pushed us to look for other genetic markers and to adapt new sequencing methods to ancient DNA. Thus, we were able for the first time to address the question of horse domestication by analyzing nuclear trait markers directly linked to early breeding practice. Coat color is an easily detectable phenotypic trait, which was likely a major goal of animal breeders since the beginning of domestication. Fortunately, single mutations are often responsible for color variants, which make these mutations very valuable for the analysis of SNP via pyrosequencing. We successfully typed for a dozen nuclear markers in more than 90 horse samples from the Pleistocene to medieval times. Through this example, we will present the advantage and limits of our methodological approach. By comparing mtDNA data and the data for coat color selection of horses, we will open the discussion about the perspective of the analysis of nuclear markers in palaeogenetics.

Linus Girdland Flink et al.
The Mediterranean route: analysing early domestic pigs in Southeast Neolithic France by combining Mitochondrial and Nuclear DNA with Geometric Morphometrics

The Neolithisation of Europe followed two main routes of expansion – the northern so called Danubian or Balkanic route and the southern Mediterranean route. Previous research has shown that the earliest domestic pigs in Europe were of Near Eastern descent, and specifically, that the spatiotemporal occurrence of haplotype Y1-6A is well correlated with the Danubian expansion. Whether domestic pigs along the southern route carried the same or divergent haplotypes remains unknown. A current hypothesis argues that early domestic pigs in the northern Mediterranean basin carried a different haplotype but has up to date lacked sufficient data to test it.

Here we report the results of our analysis of an 80bp d-loop fragment, a MC1R SNP that’s causative of dominant black coat colouring, and 2D geometric morphometric (GMM) data from sus remains in early to middle Neolithic layers in southeast France. Our results support the current hypothesis that divergent mitochondrial lineages accompanied the different routes of expansion as we find high prevalence of the Near eastern haplotype Y2-5A, but not a single Y1-6A. By applying GMM shape analysis we can show that individuals that carried a European d-loop signature (Aside haplotype) were significantly differentiated from individuals that carried the Y2-5A haplotype. This could imply a diverse origin that might represent local wild boar and imported domestic pigs. However, at least one individual that belonged to a European mitochondrial lineage also carried a derived allele at the 0301 locus in the MC1R gene – an allele that is assumed to have originated in domestic stock. Combined with previously published data, these results indicate that by 4000 BC, introgression with wild boar was widespread in Europe. For future analyses we aim to apply the integrated use of DNA and GMM to archaeological wild and domestic pig remains from locations across Europe and the Near East. As we demonstrated here, different analytical techniques can be used to answer a variety of questions and their combined use will make small case studies like this one more easily incorporated into a larger framework.

Ben Krause-Kyora et al.
The flying pig, migration or transfer of ideas in prehistory. Molecular genetic and archaeological investigations of Mesolithic and Neolithic pigs (Sus scrofa).

This study shows the reflection of population dynamics, like mobility and migration, in archaeological evidence from pigs. How did the domestication of the pigs take place in Northern Europe? Did domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic or did local European wild boar were also domesticated by this time?

First goal of this study was the development and establishment of extraction methods suited for extraction of DNA from historical samples, the selection of suitable genetic markers, and the establishment of sensitive, reliable and reproducible detection methods. PCRs were established to amplify pig-specific DNA with high sensitivity down to single molecules. Different primer pairs were used to amplify and sequence highly variable regions of the mitochondrial DNA like the dloop, cytb, XXX to determined specific mtDNA haplotypes. Further on specific nuclear DNA were analysed to determine the sex and the paternal haplotypes. The sequences finally aligned and compared to those already deposited in databases. A SNP analyse were established to determine the coat colour.

The results of over 300 individuals from 25 neolithic sites shows that around 4800- 4000 BC domestic pigs are introduced in the archaeological sites in northern Germany. The study points out that the oldest domestic pig in the sample (4600 BC) has a “Near East” haplotype. All other domestic and wild boars show the same “European” haplotype. The conclusion leads to the opinion that the domestic pigs with a maternal “Near East” ancestor were introduced into central Europe with the linear pottery (LBK) culture. After a short period the domestic pigs with “European” haplotypes coexist with the “Near East” haplotypes in the LBK and the Chaseen culture. An explanation could be that the people of the Ertebølle culture adapt the idea of domestication and permuted it on the indigenous wild boar population. With the established methods it is possible to determine the sex and the coat colour of ancient individuals. Further on the study shows the important of the coat colour as a marker for the domestication.

Josef Caruana & Terry Brown
The Maltese through time: A comparison of prehistoric, Roman and modern Maltese mitochondrial DNA haplotypes

The Maltese islands are a small archipelago situated in the middle of the Mediterranean Sea. Throughout history these islands have been dominated by the Mediterranean power of the era due to their strategic importance in controlling the shipping lanes between the eastern and western Mediterranean Sea. This study compares ancient DNA amplifications from a prehistoric site situated on the island of Gozo, two Roman burial sites in Malta, one of which is found in an urban context whilst the other in a rural context, and a sample group from the modern Maltese population. By analysing mitochondrial DNA Hypervariable Region 1, due to its higher copy number and survivability, this project aimed to study if any changes to the population of the islands can be observed through time. Another aim of the study was to see if any unique haplotypes might have survived these colonisations, and might still be present in the modern population. The modern Maltese population was also compared with other modern populations in the region in order to ascertain who it is most closely related to, and thus, which neighbouring influence most closely affected the matrilineal line of the Maltese population.

Some mtDNA links between Europe and Asia

I was planning on writing up a more complete narrative for this post, but I don't think the evidence is -as of yet- strong enough to support very strong speculation. I will simply say that the recent results of Bramanti et al. for a U-dominated older mtDNA stratum in Central/North-eastern Europe can be reasonably extended to cover both North-western Europe and northern Eurasia up to Lake Baikal, the prehistoric limit between Caucasoids and Mongoloids.

This boreal zone of U dominance contrasts with that of the Neolithic and Bronze Age inhabitants, where the familiar mix of ten or so main Caucasoid haplogroups makes its appearance, in various proportions and in various degrees of admixture at the eastern end of its expansion. The eastern Caucasoids were probably derived from both (i) West Asia via the spread of the Neolithic economy to the east wherever it could be ecologically supported, (ii) in the more northern parts, from migrations across the steppe from Central and Eastern Europe.

More ancient DNA research is needed to establish (i) how complete was the U dominance in the pre-Neolithic northern zone, and (ii) when, and where did the other Caucasoid haplogroups break into it.

Anyway, here is the post as it stands:

Ricaut et al. (2004) discovered the presence of mtDNA haplogroup N1a (16147A, 16172C, 16223T, 16248T, and 16355T) in an Iron Age Scytho-Siberian skeleton from the Altai, reporting the presence of haplogroup N1a among Iranians and upper caste Havik Brahmins from India.

The same sequence was detected in a Neolithic Central European (DER1) of the Linearbandkeramik (LBK) culture, with reported modern matches in Egypt and Armenia. The following haplogroups were detected in the Neolithic LBK gene pool: H*, N1a, K, HV, T2, V, J, W, U3.

A later study by Gokcumen et al. (2008) discovered the presence of N1a in modern Kazakhs from the Altai:

The haplotypic variation within the seven N1a samples was relatively high (Table 2), with these haplotypes belonging to both the European and Central Asian branches of this haplogroup, as recently defined by Haak et al. (2005). Thus, the source of N1a haplotypes in Altaian Kazakhs was unclear, although they seemed to have originated west of this part of Central Asia (Gokcumen et al., 2007).

Haplogroup N1a was found to be a genuine signature of the Central European Neolithic by contrasting its high representation in the LBK with the overwhelming presence of haplogroup U (and especially U5 and U4) mtDNA among the Paleolithic and Mesolithic populations of the region.

A separate Neolithic Funnel Beaker (TRB) sample from Scandinavia (Malmström et al. 2009) included only three individuals belonging to haplogroups H, J, and T. Obviously, a sample of 3 is insufficient, but the absence of haplogroup U in it parallels that of the LBK. By contrast, the contemporaneous Mesolithic Pitted Ware culture, represented by 19 samples had single instances of J, and T (which may be due to admixture with the TRB), a single instance of haplogroup V, one of the few ones thought to be European in origin, and a gene pool that was apparently dominated by haplogroups U4 and U5. The picture emerging from the northmost European hunter-gatherers is one of a restricted set of haplogroups where U subclades were dominant (about 3/4).

N1a was also detected in medieval high-status Hungarians:

Commoners show a predominance of mtDNA haplotypes and haplogroups (H, R, T), common in west Eurasia, while high-status individuals, presumably conquering Hungarians, show a more heterogeneous haplogroup distribution, with haplogroups (N1a, X) which are present at very low frequencies in modern worldwide populations and are absent in recent Hungarian and Sekler populations.

While, as we saw, N1a was frequent among Neolithic Central Europeans, its absence in Hungarian commoners suggests that it was re-introduced -in the high status individuals- from Asia.

Interestingly, there has been European and Asian mtDNA evidence that allows us to have a good idea of the mtDNA landscape on which N1a-bearing people migrated from west to east:

The pre-farming foragers of Europe were dominated by mtDNA haplogroup U. The easternmost sample in the aforementioned study was from Samara, in European Russia and consisted of a U5a, and a U5a1 sample. How far to the west and east did the U-dominated population of pre-Neolithic northern Caucasoids extend?

Neolithic Siberians from Lake Baikal, the eastermost anthropologically attested limit of prehistoric Caucasoid populations had only U5a as a Western Caucasoid element in a population dominated by Eastern Eurasian mtDNA. Similarly, the Lokomotiv Siberian burials from Lake Baikal only had U5a in an other Mongoloid mtDNA gene pool. Yu Hong, a Sogdian in China (1,400 years ago) also belonged to haplogroup U5.

U5a was not limited to the territory of Central Europe to China in ancient times. It was the haplogroup of Cheddar Man, a Paleolithic Briton, and U5a1 or U5a1a has also been detected in a Mycenaean from Bronze Age Greece. Interestingly, U5a1 seems to have decreased in frequency in Britain from the 4th c. to the present.

Is it possible that negative selection is affecting mtDNA frequencies in Europe? U-haplogroup turns up in many ancient DNA samples, but the discovery that it was absent (or non-detectible) in Neolithic farmers raises the possibility that its reduced frequency may be due to demography, i.e., the overwhelming of Paleolithic foragers by Neolithic (and later) intruders.

We know that in the Bronze and subsequent ages, Siberians from Krasnoyarsk belonged to a rich assortment of Caucasoid haplogroups. It seems that newcomers from the West joined the U-dominated earliest settlers:

Twenty samples were found to belong to west Eurasian haplogroups (U2, U4,
U5a1, T1, T3, T4, H5a, H6, HV, K, and I), whereas the 6 remaining samples were attributed to east Eurasian haplogroups (Z, G2a, C, F1b and N9a).

At the other end of the Eurasiatic steppe, in the Bronze Age site of Eulau in Germany, the gene pool was also quite different from that of the Paleolithic inhabitants, with haplogroups K1b, U5b, I, H, X2, K1a2 detected.

Haplogroup X2 represents another link between the west and Siberia according to Reidla et al. (2003):

Overall, it appears that the populations of the Near East, the Caucasus, and Mediterranean Europe harbor subhaplogroup X2 at higher frequencies than those of northern and northeastern Europe (P less than .05) and that X2 is rare in Eastern European as well as Central Asian, Siberian, and Indian populations and is virtually absent in the Finno-Ugric and Turkic-speaking people of the Volga-Ural region. [...] the few Altaian (Derenko et al. 2001) and Siberian haplogroup X lineages are not related to the Native American cluster, and they are more likely explained by recent gene flow from Europe or from West Asia.

The Tubalar, Altaic speakers from the northeastern Altai showed a mixed Caucasoid-Mongoloid mtDNA gene pool, with the western component consisting of haplogroups H8, U4b, U5a1, and X2e:

Specifically, northeastern Altai appears to be a good candidate for the ancestral homeland of the haplogroup U4b, which is apparently ancient European. For some haplogroups, such as X2e, the relatively recent arrival to the Altai region is more likely.

Derenko et al. (2002) discovered a rich assortment of Caucasoid haplogroups in several populations from the Altai, including all aforementioned ones (H, HV1, J*, J1, J1b1, T1, T4, U1a, U2, U3, U4, U5a1, I, X and N1a):

The applied approach permitted identification of 60% of mtDNA types the majority of which had southern Caucasoid origin. Less than 10% of mtDNA types were of eastern European origin.

Derenko et al. (2003) also studied several populations from South Siberia where the Caucasoid component was much diminished (17%) with the following haplogroups present: H, U, J, T, I, N1a, X.

Lactase persistence spread with Neolithic Linearbandkeramik

From the paper:

Following acceptance at the 0.5% level and regression adjustment we found that the most probable location where an LP allele first underwent selection among dairying farmers lies in a region between the central Balkans and central Europe (see Figure 3). It should be noted that, as simulated, we did not attempt to identify the location where the LP −13,910*T allele first arose. Instead we assumed that it started to rise to appreciable frequencies only after selection began among dairying farmers, initially at the particular location we estimated. The timing of the start of this gene-culture coevolution process was therefore strongly influenced by the arrival time of dairying farmers at the location where selection began in simulations. Since we selected simulations that give a good fit to the timing of the arrival of farming at different locations [31], we estimated a narrow range of dates for when selection began (95% CI 6,256 to 8,683 years BP;

...

Although not strictly a parameter of the model presented we have applied the ABC approach to estimate the genetic contribution of people living in the deme where LP-dairying gene-culture coevolution began, and its 8 surrounding demes, to the modern European gene-pool (95% CI 2.83 to 27.4%; mode = 7.47%; see Figure 4B) ... We then compared the distributions of genetic contribution (of people living in and around the LP-dairying start deme to the modern European genepool) with and without selection acting. To our surprise the two distributions are nearly identical.

In other words, selection for the lactase persistence allele did not result in modern Europeans having a larger proportion of their ancestry from the place where this process began.

From the paper:

Perhaps the most interesting result presented here is our estimation of the geographic and temporal origins of LP-dairying co-evolution. We find the highest posterior probabilities for a region between the central Balkans and central Europe (see Figure 3). At first sight such a location of origin may seem counter intuitive since it is far-removed from Northwest Europe, where the −13,910*T allele is found at highest frequency. However, previous simulations have shown that the geographic centroid of allele can be offset from its location of origin, particularly when it occurs on the wave front of a demographic expansion [29],[30]. The lactase-dairying coevolution origin region inferred here is consistent with a number of archaeologically attested patterns concerning the emergence and spread of dairying. Recent carbon isotope ratios from lipids extracted from archaeological sherds show the presence of milk fats in present-day western Turkey and connect these findings to an increased importance of cattle herding [26], [45]–[48]. In general, the spread of the Neolithic lifestyle from the Aegean to Central Europe goes hand in hand with the decline of the importance of sheep and goat and the rise in frequency of cattle bones in archaeological assemblages. While the Balkans at the beginning of the Neolithic still shows a variety of subsistence strategies [49], the middle Neolithic in SE-Europe and the earliest Neolithic in Central Europe after 7,500 BP show a clear preponderance of cattle.

A related recent study: Demography and selection in the spread of Lactase persistence in Europe (Gerbault et al. 2009)

UPDATE (Aug 29):

John Hawks raises two objections to the current paper:

There's only one little problem: It's hard to see how the same scenario gets the allele to India. Or, for that matter, Ireland. The authors posit that Indian lactase persistence will be found to be caused by a "diversity" of alleles. They seem to have missed this paper that found a greater diversity of lactase-associated haplotypes "north of the Caucasus" -- consistent with an initial steppe dispersal. OK, that's two problems, and they're not little.

I don't really see a problem with the spread of the allele to Ireland or to India. What the authors of this paper claim is that the allele began to be selected in Central Europe, not that it originated there. Its presence in Ireland or India does not strictly require any population movements from Central Europe. But there is also a plausible case for gene flow from Central Europe to either direction (Celts in the case of Ireland, and small-scale European admixture routinely detected in admixture studies that include South Asian populations).

As for the cited paper, it completely lacks samples from Central Europe, the Balkans, and Anatolia, hence its conclusion that the allele originated "north of the Caucasus" is spurious, and is not incompatible with the current paper which proposes a Balkan/Central European beginning of its selection process.

UPDATE (Aug 31)

John Hawks suggests in the comments that inclusion of South Asia into the model would shift the place of origin of the allele towards the east, and away from Central Europe. I do agree that a full model should account for the presence of allele as far as India or Central Asia. However, I doubt that their inclusion would have a major effect, for two reasons:

• Higher allele frequency in northwestern Europe compared to India suggests that the "point of origin" ought to be closer to the former than to the latter, or that the allele's selection began earlier in the former than in the latter.
• We must account for terrain and mode of transmission. The steppelands stretching from eastern Europe to the outskirts of China, combined with the invention of full pastoral nomadism made it possible for the spread of genes at a speed impossible for regular "demic diffusion". Moreover, a great part of this territory was essentially devoid of previous populations, and, the economy of the nomads necessitated its continued positive selection. Thus, the allele's frequency would not have been diluted by the time it reached the eastern ends of its expansion.

Thus, once the allele spreads to eastern Europe, the rest of the trip is -by comparison- a free ride.

The opposite trip (introduction to Europe from eastern European nomads) is also possible, but there are reasons to doubt this:

• The beginning of selection inferred in the current study is much older than the invention of pastoral nomadism. Inclusion of more populations could only push the time further into the past; it could not make it more recent. Thus, advocates of an "eastern" solution must explain how an allele appears to have started experiencing selection in the geographical region examined in the current paper thousands of years before it was introduced from the east.
• An eastern-western mode of transmission would result in an eastern-western cline, not a northern-southern one. An additional mechanism would need to be invoked to explain the latter.

PLoS Comput Biol 5(8): e1000491. doi:10.1371/journal.pcbi.1000491

The Origins of Lactase Persistence in Europe

Yuval Itan et al.

Abstract

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model where lactase persistence is only favoured in cultures practicing dairying, and dairying is more favoured in lactase persistent populations. We have developed a flexible demic computer simulation model to explore the spread of lactase persistence, dairying, other subsistence practices and unlinked genetic markers in Europe and western Asia's geographic space. Using data on −13,910*T allele frequency and farming arrival dates across Europe, and approximate Bayesian computation to estimate parameters of interest, we infer that the −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly in association with the dissemination of the Neolithic Linearbandkeramik culture over Central Europe. Furthermore, our results suggest that natural selection favouring a lactase persistence allele was not higher in northern latitudes through an increased requirement for dietary vitamin D. Our results provide a coherent and spatially explicit picture of the coevolution of lactase persistence and dairying in Europe.

Link

"First contact" between LBK farmers and foragers

From the paper:

To conclude, the following model can be put forward. During the 6th Millennium cal BC, major parts of the loess region are exploited by a low density of hunter–gatherers. The LBK communities settle at arrival in locations fitting their preferred physical characteristics, but void of hunter–gatherer activity. Evidently,
multiple processes and contact situations may have occurred simultaneously, but in general the arrival of the LBK did not attract hunter–gatherer hunting activity. Their presence rather restrained native activity to regions located farther away from the newly constructed settlements or triggered fundamental changes in the socio-
economic organisation and activity of local hunter–gatherers. Evidence for the subsequent step in the transition dates to approximately one millennium later (Crombé and Vanmontfort, 2007; Vanmontfort, 2007).

It is important to determine how long it took for indigenous populations and immigrant farmers to warm up to each other. The rate of spread (in km/year; and here) of the Neolithic may imply that by the time the farmer/forager societies started to blend, the wave of advance had already moved far away; the implication of this would be that the Neolithic bearers at the edge would have a smaller contribution from the indigenous populations of the regions they had already passed through.

There are two competing models, which I name the Rolling Snowball, and the Skipping Stone:

• In the Rolling Snowball model, the farmers pick up indigenous genetic elements as they move across space; gradually the genetic impact of the initiators of the movement is diminished.
• In the Skipping Stone model, farmers move out in search of new territories before they have started to blend with the local foragers; the genetic impact of the initiators of the movement is preserved.
  

It would be interesting to see more evidence of forager-farmer relationships in different regions.

Journal of Anthropological Archaeology doi:10.1016/j.jaa.2008.03.002

Forager–farmer connections in an ‘unoccupied’ land: First contact on the western edge of LBK territory

Bart Vanmontfort et al.

Abstract

The interaction between local foragers and incoming farmers is one of the hot topics in the study of Europe’s recent prehistory. In Central and Western Europe’s loam region, occupied by the first farmers of the Linearbandkeramik (LBK), hunter–gatherer remains are scarce and consist mostly of surface finds. Hence, the hunter–gatherer occupation and activity on the loess has never been studied in detail. This paper tackles the problem of the visibility of hunter–gatherer activity on the loess belt. An interregional comparison of microlith datasets allows identifying behavioural changes and differences in exploitation intensity. With regard to forager–farmer interaction, a mutual influence in the spatial patterning of activity or settlement is demonstrated.

Link

Oppenheimer on British Origins

I have glanced through many popular books on human population genetics (HPG), and I find most of them to be worthless. Unlike physics or other established sciences, where popularizers work against the background of well-established theories, HPG popularizers are working with a field that is fairly new, and where many theories are fiercely debated. As a result, they run the constant risk of either presenting elaborate theories that are demolished by newer findings, reading more to the evidence than is warranted by the facts, or dumbing down the material to such a degree, that anyone with even a superficial knowledge of the field loses all interest.

I had enjoyed reading Stephen Oppenheimer's previous book The Real Eve; even though I disagreed with many of the things written in it, at least it was a thoughtful and informative read, which really tried to interpret and present the best available evidence. Even though Oppenheimer is not a professional geneticist, his book was more thoughtful and "deep" than most of the high-profile figures of the field.

Oppenheimer has a new book out about the origins of the British, and a new article in Prospect magazine:

Given the distribution of Celtic languages in southwest Europe, it is most likely that they were spread by a wave of agriculturalists who dispersed 7,000 years ago from Anatolia, travelling along the north coast of the Mediterranean to Italy, France, Spain and then up the Atlantic coast to the British Isles. There is a dated archaeological trail for this. My genetic analysis shows exact counterparts for this trail both in the male Y chromosome and the maternally transmitted mitochondrial DNA right up to Cornwall, Wales, Ireland and the English south coast.

Further evidence for the Mediterranean origins of Celtic invaders is preserved in medieval Gaelic literature. According to the orthodox academic view of "iron-age Celtic invasions" from central Europe, Celtic cultural history should start in the British Isles no earlier than 300 BC. Yet Irish legend tells us that all six of the cycles of invasion came from the Mediterranean via Spain, during the late Neolithic to bronze age, and were completed 3,700 years ago.

I have mostly accepted the traditional theory of Central European origins of the Celts, even though I know (or care) very little about that subject. I am not sure how Oppenheimer derives them from Southwest Europe, but that idea makes some excellent sense. After all, the Celts were first identified by classical writers in Southwestern, not Central Europe, and that is where their languages survived to this day.

The idea that the Celts were drawn from the same dispersal out of the southeast into southwest Europe is also attractive because it explains readily the commonalities between Celtic and Italic languages; it also harmonizes with the relative lack of DNA "signals" that would link the inhabitants of Western Europe with those of Central Europe. It fits quite well into the emerging picture of Indo-European dispersals out of Southeastern Europe, with Italo-Celts being responsible for maritime pioneer colonization across the northern Mediterranean, Germanics being responsible for northward movements from Central European descendants of the Linearbandkeramik, and Balto-Slavs derived from northeastern movements of the Bronze Age which brought Corded Ware type people into contact with the Finno-Ugric substratum of eastern Europe.

Oppenheimer also addresses the idea of an Anglo-Saxon imposed apartheid in Britain:

Some geneticists still cling to the genocide story. Research by several genetics teams associated with University College London has concentrated in recent years on proving the wipeout view on the basis of similarities of male Y chromosome gene group frequency between Frisia/north Germany and England. One of the London groups attracted press attention in July by claiming that the close similarities were the result of genocide followed by a social-sexual apartheid that enhanced Anglo-Saxon reproductive success over Celtic.

The problem is that the English resemble in this way all the other countries of northwest Europe as well as the Frisians and Germans. Using the same method (principal components analysis, see note below), I have found greater similarities of this kind between the southern English and Belgians than the supposedly Anglo-Saxon homelands at the base of the Danish peninsula. These different regions could not all have been waiting their turn to commit genocide on the former Celtic population of England. The most likely reason for the genetic similarities between these neighbouring countries and England is that they all had similar prehistoric settlement histories.

...

The orthodox view is that the entire population of the British Isles, including England, was Celtic-speaking when Caesar invaded. But if that were the case, a modest Anglo-Saxon invasion is unlikely to have swept away all traces of Celtic language from the pre-existing population of England. Yet there are only half a dozen Celtic words in English, the rest being mainly Germanic, Norman or medieval Latin. One explanation is that England was not mainly Celtic-speaking before the Anglo-Saxons. Consider, for example, the near-total absence of Celtic inscriptions in England (outside Cornwall), although they are abundant in Ireland, Wales, Scotland and Brittany.

I like the idea that England was not mainly Celtic speaking before the invasion of Anglo-Saxons. For one thing, the native inhabitants of the British Isles were not identified as Celts by the ancient writers; this is puzzling if they were kinsmen of the continental Celts. The existence of Celts in the British Isles is of course proven on linguistic grounds, but their dominance is very speculative. It is probably due to the fact that the Celts are the only identifiable non-Germanic inhabitants of the Isles who have left a linguistic and cultural legacy (to some extent), so pre-Anglo-Saxons are assumed -wrongly- to have been Celtic.