Crafty El Sidrón Neandertals exploited plants for food and medicine

Neanderthals in Northern Spain Had Knowledge of Plants' Healing Qualities, Study Reveals 

An international team of researchers, led by the Universitat Autònoma de Barcelona and the University of York, has provided the first molecular evidence that Neanderthals not only ate a range of cooked plant foods, but also understood its nutritional and medicinal qualities.

Until recently Neanderthals, who disappeared between 30,000 and 24,000 years ago, were thought to be predominantly meat-eaters. However, evidence of dietary breadth is growing as more sophisticated analyses are undertaken.

Researchers from Spain, the UK and Australia combined pyrolysis gas-chromatography-mass spectrometry with morphological analysis of plant microfossils to identify material trapped in dental calculus (calcified dental plaque) from five Neanderthals from the north Spanish site of El Sidrón.

...

Dr Stephen Buckley, a Research Fellow at the University of York's BioArCh research facility, said: "The evidence indicating this individual was eating bitter-tasting plants such as yarrow and camomile with little nutritional value is surprising. We know that Neanderthals would find these plants bitter, so it is likely these plants must have been selected for reasons other than taste."

... 

The researchers say evidence for cooked carbohydrates is confirmed by both the cracked/roasted starch granules observed microscopically and the molecular evidence for cooking and exposure to wood smoke or smoked food in the form of a range of chemical markers including methyl esters, phenols, and polynuclear aromatic hydrocarbons found in dental calculus.

...

The study also provides evidence that the starch granules reported from El Sidrón represent the oldest granules ever to be confirmed using a biochemical test, while ancient bacteria found embedded in the calculus offers the potential for future studies in oral health.

The archaeological cave site of El Sidrón, located in the Asturias region of northern Spain, contains the best collection of Neanderthal remains found in the Iberian Peninsula and one of the most important active sites in the world. Discovered in 1994, it contains around 2,000 skeletal remains of at least 13 individuals dating back around 47,300 to 50,600 years.

NATURWISSENSCHAFTEN 2012, DOI: 10.1007/s00114-012-0942-0

Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus

Karen Hardy et al.

Link

Major new ancient DNA project on Southeast Asia and Australia

It seems that I read about a new major project on ancient DNA every other day. There is a lot of activity in this field, which will, no doubt, bear fruit in the coming years.

What I really want to see is a complete genome sequence of early Homo sapiens, e.g., from a sample about as old as Vindija and Denisova. If anyone knows of any such sequencing efforts in the works, write in the comments, or drop me an e-mail.

DNA analysis of ancient remains to uncover origin mysteries
Griffith University leads search for human evolution

In collaboration with the Universities of Auckland, Copenhagen and New South Wales, the researchers will analyse human remains from continental and oceanic Asia and Australia using more powerful newly developed ancient DNA sequencing methods.
Chief Investigator Professor David Lambert from the School of Environment says understanding where the earliest people of Asia and continental Australia came from is critical to understanding modern human evolution.

"The recent sequencing of the Australian Aboriginal genome has identified two waves of human migration through Asia,'' he said.

"Aboriginal Australians descended from an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago.

"This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago, although there is evidence for hybridisation between them."

The researchers aim to identify descendent individuals from both lineages and detect historic patterns of interbreeding among these early people.

Professor Paul Tacon from Griffith University's Place, Evolution & Rock Art Heritage Unit said the research was a world-first study to attempt to recover human DNA sequences from more than 80 ancient human remains collected from a range of time points.
"We aim to identify the mitochondrial DNA lineage of each sample of human remains, the migration wave they represented and evidence of biological interactions, such as hybridisation with other groups.

"Although complete or draft genomes have been recovered from extinct species such as Neandertals and Woolly Mammoths, there are no existing populations of these species available for comparison.

"But an increasing number of complete human genomes in our study provide the foundation for this work."

Professor Tacon said the study was possible because of recent advances in second-generation DNA sequencing and parallel developments in DNA target capture technologies.

"These developments provide extraordinary new possibilities in the field of ancient human genomics."

The study is part of a $550,000 three-year Australian Research Council Linkage Grant.

fastIBD over 2,257 Europeans

Razib points me towards a very interesting new paper that applies fastIBD over the large POPRES dataset of Europeans. The most interesting thing about this is that the authors develop techniques for estimating the time depth of the pattern of common ancestry across Europe, and hence are able to conclude that the Slavic expansion has played a bigger role in European history than the Germanic one.

A worthwhile improvement would be to apply a clustering algorithm like I did back in January over the fastIBD output; that way, one does not have to arbitrarily partition Europe into regions, but have the partitions jump out of the data.

A different idea to confirm the scenario presented in this paper would be to drill into different European populations. For example, in the case of the Italians, it would be worthwhile to identify whether there are particular sub-populations with likely Greek or Albanian ancestry who share an excess of IBD with modern Greeks and Albanians.

Population averages may mask such interesting patterns lurking in the data. For example, sub-clusters within populations can be identified with both fineSTRUCTURE and fastIBD, and the corresponding clusters can be assessed with supervised ADMIXTURE to detect how they differ from each other. For example, using this technique, I was able to infer 3 sub-clusters within the ethnic Greek population:

• pop8 (mainland Greek) with ~23% North_European
• pop11 (Greek Cypriot) with ~5% North_European
• pop14 (Cretan, islander, mainland+Asia Minor) with ~12% North_European
• I have also a strong hunch based on a few half Pontic Greek+half mainland Greek data points that unmixed Pontic Greeks would be related to pop22 (Northeastern Anatolia) with ~5% North_European

Based on these results and the fastIBD analysis of Ralph and Coop (the POPRES Greek sample is from northern Greece), it might appear that a hefty portion of the North_European component in Greeks may date to the medieval period, since it is relatively smaller in eastern Greeks and Cypriots and also in the South Italian/Sicilian cluster pop16 of a different analysis, with Italians as a whole lacking the eastern European affiliations of some Greek groups.

Interestingly, ~5% North_European levels would be similar to those of Armenians who are the closest linguistic cousins of the Greeks within the Indo-European family, as well as the the Anatolian Turkish cluster pop13 at ~9%.

Overall, it would appear that some mainland Greek groups received some input as the result of the medieval Slavic intrusions, since the mainland North_European excess appears as a "wedge" within the South Italy/Sicily/Crete/Anatolia/Armenia arc and the fastIBD pattern of sharing suggests that this is due to fairly recent connections.

As I have pointed out before, one limitation of the method of counting shared blocks of ancestry is that it does not disclose the directionality of gene flow. For example, gene flow between Germans and Slavs is detected in this study, which could be ascribed to Germans living in eastern Europe and/or to Slavs becoming acculturated Germans as a result of living within Germanic states or intermarrying with them prior to the age of the nation state.

Finally -and most interestingly- I hope that similar haplotype-based methods can be applied to a wider dataset, because, as it is becoming clear, Europe has not been isolated from Asia or Africa during its long history. The authors mention "Slavic or Hunnic" as an explanation for the pattern of shared ancestry in eastern Europe, but it is only by including Asian groups that we can detect the existence of real Hunnic (or Avar, or Mongol, or Pecheneg, or, ...) ancestry.

Moreover, I am confident that the Bronze Age is well within the power of haplotype-based methods to detect IBD. For example, South Asian populations clearly show differential patterns of affiliation with modern West Eurasian groups, most of which can date to no later than the Bronze Age. Together with the gradual incorporation of the new ancient DNA genomes that are bound to be coming our way soon, it seems that our picture of not only recent history, but also of late prehistory is bound to become much sharper.

arXiv:1207.3815v1 [q-bio.PE]


The geography of recent genetic ancestry across Europe

Peter Ralph, Graham Coop
(Submitted on 16 Jul 2012)

The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.

Link

From the earliest modern humans to the onset of farming (45,000-4,500 BP)

This is a very exciting new project led by Ron Pinhasi. Together with the BEAN Project it seems that we are about to get a wealth of new data on many of the topics that are of great interest to readers of the blog.

It does seem that there is a cutoff data of 4,500BP for the scope of the project, which may be a little unfortunate if I'm right about the interesting stuff that was taking place place in Europe during the Bronze Age. But, still, getting plenty of new Y-chromosome, mtDNA, autosomal, and craniometric data for the 40 thousand years or so before that will in no doubt inform debates about more recent events as well.

From the earliest modern humans to the onset of farming (45,000-4,500 BP) January 2011-December 2014

This project which is led by Ron Pinhasi and is carried out in collaboration with leading European scientists, investigates the evolution and nature of major prehistoric processes which are key to our understanding of what happened in European prehistory: the origins and spread of modern humans during the Late Pleistocene, their survival during the last Ice Age, post-glacial expansions, the emergence of the first agricultural societies and the decline and eventual disappearance of most hunter-gatherer societies in Europe.

The focus is on the application of state of the art methods in genetics, archaeological sciences and anthropology which allow our team to address for the first time these major processes in sufficient depth and resolution and to yield new knowledge about the interface between human biology, climate , culture and life style. 

The colonisation of Europe by anatomically modern humans (AMHs) ca. 45,000 years before present (BP) and the transition to farming ca. 8,000 BP are two major events in human prehistory. Both events involved certain cultural and biological adaptations, technological innovations, and behavioural plasticity which are unique to our species. 

The reconstruction of these processes and the causality between them has so far remained elusive due to technological, methodological and logistical complexities.
Major developments in our understanding of the anthropology of the Upper Palaeolithic, Mesolithic and Neolithic, and advances in ancient DNA (aDNA) technology and chronometric methods now allow us to assess in sufficient resolution the interface between these evolutionary processes, and changes in human culture and behaviour. 

The project investigates the complex interface between the morphological, genetic, behavioural, and cultural factors that shaped the population history of European AMHs.  

The approach taken include (a) the collection of bioarchaeological, aDNA, stable isotope (for the analysis of ancient diet) and radiometric data on >700 skeletons from key sites/phases across Eurasia, and (b) the application of existing and novel aDNA, bioarchaeological and simulation methodologies.  

This research will yield results that transform our current understanding of major demographic and evolutionary processes and will place Europe at the forefront of anthropological, biological, and genetic research. 

Blood group of pre-Columbian Peruvian highlanders

AJPA DOI: 10.1002/ajpa.22115

Molecular characterization of ABO blood group frequencies in pre-Columbian Peruvian highlanders

Léa Georges et al.

The majority of Native Americans nearly exclusively belong to group O of the ABO blood group system. Several hypotheses have been formulated to explain this observation, primarily differing by the presumption that the observed patterns of ABO diversity are due to the processes of the initial peopling of the Americas or due to subsequent events, especially the demographic consequences in the wake of European contact. A promising strategy to reveal possible diachronic ABO frequency changes is the molecular genetic analysis of relevant genetic markers in precontact populations. A previous study by Halverson and Bolnick [Am J Phys Anthropol 137 (2008) 342-347] already accomplished this for indigenous North American populations. Here we present the first study to analyze ABO blood types from pre-Columbian individuals from South America using molecular genetic methods and comparing them to several extant South American, North American, and Siberian populations. We tried to determine ABO blood types for 59 individuals from the southern Peruvian highlands dating to ∼650 to 1250 AD using a newly developed multiplex PCR/SBE assay coamplifying the fragments relevant for blood type determination and three highly discriminating autosomal STRs. Analysis was successful for 31 individuals and revealed that all are exclusively in the O group, predominantly carrying the O02 (01v) allele. No significant difference could be observed between the ancient and modern Native American populations, while all significantly differed from the extant Siberian populations, supporting the suggestion that low ABO diversity results from founder effects during the initial peopling of the Americas.

Link

5,300-year-old Mongolian statue

5,300-year-old Mongolian statue pieced back together

ARCHAEOLOGISTS of the Chinese Academy of Social Sciences have finished reconstructing a 5,300-year-old pottery statue from fragments unearthed in North China’s Inner Mongolia Autonomous Region, it was announced Saturday. 

The debris of the pottery statue were found at the Xinglonggou relics site in Aohan Banner of Chifeng City in May. 

Experts began to excavate the debris June 30, and finished restoring the statue on Friday, said Liu Guoxiang, leader of the first archaeology team of Inner Mongolia. 

The restored seated figure is 55cm high with bulging eyes, a high nose and vivid facial expression. It was pieced together from 65 fragments. 

“The statue may be of a wizard or leader in the famous Hongshan Culture period (a Neolithic culture dating back 5,000-6,000 years),” added Liu.

Children of lesbians fare worse than children of heterosexual parents

From a related article in Slate by the author:

The rapid pace at which the overall academic discourse surrounding gay and lesbian parents’ comparative competence has swung—from the wide acknowledgement of challenges to “no differences” to more capable than mom and pop families—is notable, and frankly a bit suspect. Scientific truths are seldom reversed in a decade. By comparison, studies of adoption—a common method by which many same-sex couples (but even more heterosexual ones) become parents—have repeatedly and consistently revealed important and wide-ranging differences, on average, between adopted children and biological ones. The differences have been so pervasive and consistent that adoption experts now emphasize that “acknowledgement of difference” is critical for both parents and clinicians when working with adopted children and teens. This ought to give social scientists studying gay-parenting outcomes pause—rather than lockstep unanimity. After all, many children of gay and lesbian couples are adopted. 

... 

The basic results call into question simplistic notions of “no differences,” at least with the generation that is out of the house. On 25 of 40 different outcomes evaluated, the children of women who’ve had same-sex relationships fare quite differently than those in stable, biologically-intact mom-and-pop families, displaying numbers more comparable to those from heterosexual stepfamilies and single parents. Even after including controls for age, race, gender, and things like being bullied as a youth, or the gay-friendliness of the state in which they live, such respondents were more apt to report being unemployed, less healthy, more depressed, more likely to have cheated on a spouse or partner, smoke more pot, had trouble with the law, report more male and female sex partners, more sexual victimization, and were more likely to reflect negatively on their childhood family life, among other things. Why such dramatic differences? I can only speculate, since the data are not poised to pinpoint causes. One notable theme among the adult children of same-sex parents, however, is household instability, and plenty of it. The children of fathers who have had same-sex relationships fare a bit better, but they seldom reported living with their father for very long, and never with his partner for more than three years.

...

So why did this study come up with such different results than previous work in the field? And why should one study alter so much previous sentiment? Basically, better methods. When it comes to assessing how children of gay parents are faring, the careful methods and random sampling approach found in demography has not often been employed by scholars studying this issue, due in part—to be sure—to the challenges in locating and surveying small minorities randomly. In its place, the scholarly community has often been treated to small, nonrandom “convenience” studies of mostly white, well-educated lesbian parents, including plenty of data-collection efforts in which participants knew that they were contributing to important studies with potentially substantial political consequences, elevating the probability of something akin to the “Hawthorne Effect.” This is hardly an optimal environment for collecting unbiased data (and to their credit, many of the researchers admitted these challenges). I’m not claiming that all the previous research on this subject is bunk. But small or nonrandom studies shouldn’t be the gold standard for research, all the more so when we’re dealing with a topic so weighted with public interest and significance.

Social Science Research Volume 41, Issue 4, July 2012, Pages 752–770

How different are the adult children of parents who have same-sex relationships? Findings from the New Family Structures Study

Mark Regnerus

The New Family Structures Study (NFSS) is a social-science data-collection project that fielded a survey to a large, random sample of American young adults (ages 18–39) who were raised in different types of family arrangements. In this debut article of the NFSS, I compare how the young-adult children of a parent who has had a same-sex romantic relationship fare on 40 different social, emotional, and relational outcome variables when compared with six other family-of-origin types. The results reveal numerous, consistent differences, especially between the children of women who have had a lesbian relationship and those with still-married (heterosexual) biological parents. The results are typically robust in multivariate contexts as well, suggesting far greater diversity in lesbian-parent household experiences than convenience-sample studies of lesbian families have revealed. The NFSS proves to be an illuminating, versatile dataset that can assist family scholars in understanding the long reach of family structure and transitions.

Link

The theory that won't die: Chris Stringer on Modern Human Origins

I devoted a whole post on the topic recently, so I won't repeat myself. I'll just say that if modern human behavior evolved in Africa and it was this which facilitated the spread of humans into Eurasia ~60,000 years ago, then they forgot to leave behind any evidence for it.

A Bone Here, a Bead There: On the Trail of Human Origins

There were remarkable things happening in Europe at least 40,000 years ago, with the painted caves, with flutes, with the statuettes and so on. But the seeds of that revolution were sown in Africa more than 100,000 years ago. I would argue that when modern humans came out of Africa, say 60,000 years ago, fundamentally they were behaviorally modern. They took that into Europe. They took that into Asia and into Australia. So there was no single revolutionary event in Europe; this was something that was in modern humans when they came out of Africa, and the ones who stayed behind as well.

The following quote by mousterian is worth highlighting:

What we are dancing around here is an issue more fundamental than simply coastal vs. interior, early vs. late. If it was an expansion (or wave of expansions) during MIS 5 through the interior, these are hunter-gatherers tracking a known ecosystem. If a late expansion during MIS 4 or early MIS 3 along the coast, these represents some innovative cultural adaptation that has enabled them to exploit a new ecosystem and rapidly disperse through it (i.e. the rim of the Indian Ocean). In other words, were we lucky hunter-gatherers in the right place at the right time during the Last Interglacial, or crafty beachcombers struggling for survival across the post-apocalyptic post-Toba landscape? Pushed out of Africa, or pulled into Arabia? In my mind, this is the real disparity between the two models.

Interestingly, all of the Palaeolithic archaeologists working in Arabia unanimously agree on the "lucky hunter-gatherers" MIS 5 scenario. Granted, it’s not as sexy as believing we are somehow fundamentally different, new, and improved. That’s the problem with fact versus fiction.

My chips are on the "lucky hunter-gatherers" MIS 5 scenario and I'm sticking to it until I see any evidence for behaviorally modern people in East Africa or Arabia or the Levant at the time of the postulated 60ky-old migration. But, it's good to see both positions vigorously argued.

Late Minoan IB destructions not followed by Mycenaean immigration

This is an important contribution which falsifies the theory that the destructions of the Minoan palaces associated with the Late Minoan IB involved the coming of Mycenaean elites to Crete, by using a combination of strontium isotope analysis (which captures first-generation migrants) and biodistance analysis (which reveals no pattern of greater affinity of post-LMIB populations to mainland Greek samples.

However, this is interesting:

Therefore these results suggest a gradual rounding of the cranial shape for the Central Cretan population in the course of the Bronze Age, resulting from the increase of the cranial breadth in relation to cranial length. They further provide negative evidence for a disruption of the biological history of the Knossos population following the LMIB destructions due to an increase in the biodistance between the samples dating immediately prior and following the destructions.  

The gradual rounding of the cranial shape of the Central Cretan population over the course of the Bronze Age and the very similar shape of the Gypsades, Sellopoulo and Mavrospelio crania can be more clearly appreciated by plotting the Cranial Index (100*maximum cranial breadth/glabello – occipital length) data. The Cranial Index describes the cranial shape and higher cranial indices reflect a more rounded cranium. In Figure 7, the Cranial Indices for all the above-mentioned Central Cretan population samples are plotted in chronological order, from the Early to Late Bronze Age. Cranial Indices were calculated separately for males and females from each sample.  

The gradual increase in Cranial Index over the Bronze Age most probably reflects gene-flow from population/s biologically different from the Early Bronze Age Cretan population and from inter-population biological interactions (admixture) in the succeeding periods. An alternative interpretation implicating the thermoregulatory model of Beals et al. (1984) and adaptation to colder climatic conditions carries less weight. 

This might be consistent with J. Lawrence Angel's detection of a "Dinaroid-Alpine central trend" of Bronze Age invaders of Greece, as well as the well-known contemporary physiognomy of the historical Hittites and the physical anthropological evidence for them:

Senyurek (1951d, pp. 614-15) concludes that "the majority of the Chalcolithic and Copper Age inhabitants of Anatolia were dolichocephals of mainly Eurafrican and Mediterranean types, and that the brachycephals, probably representing the invaders, were rare in these periods. This study has further supported the conclusion that the earliest inhabitants of Anatolia were longheaded, and that the brachycephals came in subsequently. "The craniological evidence indicates that an invasion of brachycephals into Anatolia took place during the Chalcolithic period and that it was followed by a second invasion, bringing in the brachycephalic elements to Alaca Huyuk and other Copper Age sites, probably at about the middle of the Copper Age. The next invasion of brachycephals, which was more important and extensive than the previous ones, occurred at about 2000 B.C. This was made by the Hittites who were predominantly of the classical Alpine type."  

While there does not appear to be specific evidence for a new population element arriving in Crete after the LMIB destructions, the pattern during the Bronze Age is probably consistent with an intrusive population.

If we accept that the European Neolithic island-hopped to Greece from the East and thence spread north and east into Europe, it is peculiar that ancient DNA from Neolithic Europeans is dominated by Y-haplogroups I2b and G2a (missing the dominant Anatolian J2 haplogroup) and by a "Mediterranean" autosomal makeup (missing the dominant Anatolian West_Asian component). As I have previously argued, this suggests a sea change in the genetic makeup of Anatolia itself since the early Neolithic, and a Bronze Age migration of J2/West_Asian brachycephals into Anatolia, mainland Greece and Crete would be one possible agent for that development.

Late Minoan IB destructions and cultural upheaval on Crete: A bioarchaeological perspective

Nafplioti, Argyro

This paper discusses representative results from strontium isotope ratio (87Sr/86Sr) and biodistance analyses of archaeological human skeletal material carried out to assess the validity of the theory of a LMIB (ca. 1490/1470 BC) Mycenaean invasion of Crete and imposed political domination of Knossos, and thus shed more light onto the question of the LMIB destructions and the subsequent cultural upheaval on the island. These analyses show that the people buried in post- LMIB tombs at Knossos, traditionally associated with Mycenaeans based on material culture evidence, were in fact born locally and not in the Argolid. Further, the analyses presented reject the possibility that these people may represent the descendants of immigrants from the latter region. Additional negative evidence for the theory tested comes from further cranial and dental morphological analyses presented in the author’s doctoral thesis, as well as the material culture itself, briefly discussed here.

Link

Hints of East/Central Asian admixture in Northern Europe

A little more than a year ago, I noticed an interesting pattern in North Europeans: they all tended to be shifted towards East Asians in PCA plots:

With respect to the Asian- and African- shift of West Eurasian populations, I note that northern Europeans (and Basques) are less African-shifted than southern Europeans, and, at the same time they are more Asian-shifted: the 16 least Asian-shifted populations have a coastline in the Mediterranean (excluding the Portuguese), while the 16 least African-shifted populations do not (excluding the French).

The same pattern could also be observed in the arrangement of the ancestral components inferred by the Dodecad Project. The "Atlantic_Baltic" component, which is modal in Northern Europeans, exhibits lowered genetic divergences to the East Eurasian components (Siberian / East_Asian) relative to the "Southern" component which is modal (in Europe) in Southern Europeans.

The fact that Southern European populations were shifted towards the African side relative to Northern European ones across an African-Asian projection, was interpreted by Moorjani et al. (2011) as evidence of African admixture. As I noted at the time, this entailed the assumption that Northern European populations did not have East Asian admixture, which would also produce the observed pattern:

However, this is clearly a case of seeing the glass half full. The authors prefer the hypothesis that some Caucasoid groups have African ancestry, although the hypothesis that other Caucasoid groups have East Asian ancestry can equally well explain the observed pattern. Indeed, both hypotheses may explain the phenomenon they observe.

It now appears that some of the co-authors of the above paper have realised this, and have detected Central/East Asian admixture in northern Europeans. Writing in the supplement of the recent Reich et al. (2012) paper, we read this important aside:

A complication in computing this statistic is that Native American, Siberian, and East Asian  populations are not all equally genetically related to West Eurasian populations, as we can  see empirically from 4 Population Tests of the proposed tree (Yoruba, (French, (East Asian,  Native American))) failing dramatically whether the East Asian population is Han, Chukchi,  Naukan and Koryak. The explanation for this is outside the scope of this study (it has to do  with admixture events in Europe, as we explain in another paper in submission). In practice,  however, it means that we cannot simply use a European population like French to represent  West Eurasians in Equation S3.2, since if we do this, Equation S3.2 may have a non-zero  value for a Native American population, even without recent European admixture.    

To address this complication, we took advantage of the fact that east/central Asian admixture  has affected northern Europeans to a greater extent than Sardinians (in our separate  manuscript in submission, we show that this is a result of the different amounts of central/east  Asian-related gene flow into these groups). To quantify this, we computed the statistic f4(San,  West Eurasian; Pop1, Pop2) for West Eurasian = Sardinian and West Eurasian = French,  and for 24 Siberian and Native American populations (Pop1 and Pop2) (Figure S3.2). Figure  S3.2 shows a scatterplot for all 190=20?19/2 possible pairs of these populations. Within nonArctic Native populations, and within Arctic populations (East Greenland Inuit, Chukchi,  Naukan and Koryak), the statistics are close to zero, consistent with their being (approximate)  clades relative to West Eurasians. In contrast, there are deviations from zero when the comparisons are between non-Arctic Native and Arctic populations, with non-Arctic Native  populations showing consistent evidence of being genetically closer to West Eurasians.   

David Reich has hinted about ancient admixture in Europeans before, and is apparently working on the South Asian admixture event. It would appear that the new works might be using the newer techniques employed in the Reich et al (2012) paper, which allows one to consider multiple admixture events rather than the more simple ones of Reich et al. (2009) and Moorjani et al. (2011) that considered only two ancestral populations.

I will, of course, eagerly wait the publication of the mentioned manuscript, but it appears that this is not the only piece of evidence of gene flow from Central Asia into Europe. In an SMBE 2012 abstract by Palstra et al. we read:

Using an approximate Bayesian framework, we find that present patterns of genetic diversity in Central Asia may be  best explained by a demographic history which combines long-term presence of some ethnic groups (Indo-Iranians)  with a more recent admixed origin of other groups (Turco-Mongols). Interestingly, the results also provide indications  that this region might have genetically influenced Western European populations, rather than vice versa. A further  evaluation in MCMC-based Bayesian analyses of isolation-with-migration models confirms the different times of  establishment of ethnic groups, and suggests gene flow into Central Asia from the east. The results from the  approximate Bayesian and full Bayesian analyses are thus largely congruent. In conclusion, these analyses illustrate  the power of Bayesian inference on genetic data and suggest that the high genetic diversity in Central Asia reflects both  long-term presence and admixture in more recent historical times. 

Neither of these two upcoming pieces of work mention the timing of the Central Asian element in Europe: 

• One possibility is that the Mesolithic Europeans were Asian-shifted themselves. 
• Another one would relate it to the emerging ancient mtDNA picture of deep penetration of Mongoloid elements into west Eurasia at the dawn of history, although the western limit of this penetration has not been conclusively ascertained. 
• Finally, the elements may be a legacy of the Bronze Age Indo-European invasion of Europe, piggy-backing on the spread of the latter from their eastern homeland

In two of the existing models of how the latter event took place (the Armenian plateau hypothesis of Gamkrlidze and Ivanov and the Bactria Sogdiana hypothesis of Johanna Nichols), the Indo-Europeans followed separate streams from their eastern homeland into Europe, with some groups following a path north of the Black and Caspian seas, while others followed a southern path from Anatolia to the Balkans. The northern dispersal route would have brought them into contact with the mixed Caucasoid/Mongoloid population of West Siberia and Eastern Europe, and they may have carried some of this DNA across their sweep over Northern Europe.

My own working hypothesis would derive the earliest Proto-Indo-Europeans with groups living in Neolithic eastern Anatolia and northern Mesopotamia. There are details to be fleshed out, such as when this group of people reached the Balkans (pending ancient DNA from the region), and how they interfaced with the populations living in the north of the Black and Caspian seas (e.g., via a trans-Caucasus movement or a counterclockwise spread around the Caspian).

We will know soon enough how and when Northern Europeans ended up with an extra slice of Central/East Asian ancestry. Things are looking good for our understanding of events in Eurasian prehistory.

Population strata in the West Siberian plain (Baraba forest steppe)

Also from the Population Dynamics in Prehistory and Early History (2012) volume, this is an awesome ancient DNA study which dissects a succession of archaeological cultures stretching from the beginning of the metal ages to the beginning of the Iron Age in a small region of West Siberia. As the authors write:

Our work is devoted to the analysis of human migration processes that occurred during the Bronze Age (4th–early 1st millennium BC) in the forest steppe zone between the Ob and Irtysh rivers (about 800 km from west to east). This area, known as Baraba forest steppe, stretches over 200 km from the taiga zone in the north to the steppes in the south.

The careful examination of the sequence of cultures, combining ancient mtDNA and physical anthropology paints a very compelling picture of the changes that occurred in the span of a few millennia in the Baraba forest steppe. The authors give the map on the left, with the caption: "Fig. 5 | Location of ancient human groups with a high frequency of mtDNA haplogroups U5, U4 and U2e lineages. The area of Northern Eurasian anthropological formation is marked by yellow region on the map (References: 1 Bramanti et al., 2009; 2Malmstrom et al., 2009; 3 Krause et al., 2010; 4 this study)".


The northern Eurasian anthropological formation actually combines eastern and western Eurasian features and may correspond to the Proto-Uralic type. Researchers have clashed about the origins of this population element, with some considering it a third Eurasian race that evolved independently of Caucasoids and Mongoloids, others assigning it to a much diverged branch of one of the two major Eurasian races, and still others considering it the product of admixture between east and west.


All indications are that the type, unlike the Caucasoid-Mongoloid mixtures that took place in Central Asia in the last 2 millennia, is of more ancient vintage, and represents an anthropological element that was indeed of Caucasoid-Mongoloid origins, but in the rather remote past. The authors write with respect to the most ancient periods:

In contrast to the occupation of the southern region of West Siberia, modern humans arrived in the Ob-Irtysh interfluve relatively late, at the end of the Pleistocene, about 13–14 thousand years ago (Okladnikov, Molodin, 1983; Petrin, 1986). The absence of burials dating back to this period in the region does not allow us to conduct a biological investigation of this earliest population. The most ancient anthropological material available is from the Neolithic period (4th–5th millennium BC). 

And, what of the earliest available material?

The anthropological analysis of the material allowed us to detect a specific craniological type in the Baraba population, which was assigned to one of the anthropological formations discovered by V.V. Bunak in 1956 through the analysis of Neolithic materials from the northern forest zone of the East European Plain. Bunak called it the “northern Eurasian anthropological formation” (Bunak, 1956).

This anthropological type developed in a zone that is intermediate to the geographic areas occupied by the classic Caucasoids and the Mongoloids. The exists substantial anthropological evidence showing a wide geographic distribution of this anthropological formation: from the Trans-Urals forest and the Barabian province of Western Siberia in the east to Karelia and the Baltic in the west (Chikisheva, 2010).

The mtDNA evidence seems to support the anthropological assessment:

We have analyzed 18 mtDNA samples from the Ust-Tartas population to date (Fig. 3). The results obtained thus far allow us to draw several preliminary conclusions about the genetic background in the region in the beginning of the Bronze Age. By the Early Metal Period the mtDNA pool structure was already mixed and consisted of both Western and Eastern Eurasian haplogroups in nearly equal proportions. The eastern Eurasian mtDNA cluster was represented by Haplogroups A, C, Z, D, which are most typical of modern and perhaps ancient populations located in the east of the region studied. Haplogroups C and D were predominantly represented by widely distributed root haplotypes. A lineage of Haplogroup A that was detected in two Ust-Tartas samples represents a subcluster that is apparently characteristic of West Siberia and the Volga-Ural Region. The observed presence of Haplogroup Z lineages with a high frequency in the Ust-Tartas group was unexpected, since these lineages are nearly absent in the gene pool of modern indigenous West Siberian populations.

It is worth noting that the Western Eurasian mtDNA haplogroups in the Ust-Tartas series were represented only by Haplogroup U lineages, and specifically by the three subgroups – U2e, U4, U5a1. These results are in agreement with previous data indicating that Haplogroup U lineages (particularly Subgroups U5 and U4) predominated in Eastern, Central and Northern European hunter-gatherer groups from 14000 to 4000 years ago (Bramanti et al., 2009; Malmstrom et al., 2009), and possibly in earlier periods (Krause et al., 2010). The geographic area within which this genetic feature is observed appears to be broad (Fig. 5). Apparently, Baraba was near the eastern periphery of this area.

We now have evidence of the zone of U dominance extending from Iberia in the west and all the way to Lake Baikal in the east. But, this zone is not homogeneous: its western, European, end appears to have lacked the East Eurasian lineages, while starting from Ukraine and to the East the U types were supplemented by the Mongoloid lineages.

But, there was structure within the U zone itself: according to Lillie et al. (same volume) in Ukraine during the 6th millennium BC, the West Eurasian types were represented by U1 and U3, a different mix than in the Baraba forest steppe, and haplogroup T was also present, while of the Mongoloid haplogroups only C was present.

As we head into the Bronze Age, the population of the region displayed signs of continuity:

The genetic analysis of the Odinovo and Krotovo groups (10 and 6 samples, respectively) (Fig. 3) did not reveal any differences between them and the previous Ust-Tartas group, such as the presence of new mtDNA haplogroups. The mtDNA pool structure was still mixed. The East Eurasian haplogroups were represented by the D, C, Z (in both the Odinovo and Krotovo groups) and A (in the Krotovo group) haplogroups. The East Eurasian lineages identified were phylogenetically close (lineages of haplogroups A, C, Z) or even identical (D haplogroup, 16223–16362 lineages) to the samples from the Ust-Tartas group. The West Eurasian part of the samples were represented by the U5a1 (Odinovo group) and U2e (Krotovo group) haplogroup lineages.  

Although only a small series of samples have been investigated thus far, the data obtained reveal continuity between the Odinovo and Krotovo populations and the earlier Ust-Tartas group. These findings are consistent with the autochthonous development of the Baraba populations during the Early and the beginning of the Middle Bronze Age, as well as with the anthropological evidence.  

It is during the Middle and Late Bronze ages that we begin to say the first intrusive lineage into the native population mix:

The anthropological analysis of the West Siberian Andronovo population shows at least four craniological types. Three types are related to the Palaeocaucasian race and are represented by proto-European anthropological type variants. The fourth, Mongoloid, component is autochthonous. The most intensive interactions between the Andronovo migrants and the indigenous populations apparently occurred in the Baraba forest steppe and the right bank of the upper Ob River (Chikisheva and Pozdnyakov, 2003).  

To investigate the putative impact of Andronovo migrants on the mtDNA pool structure of the indigenous populations in Baraba, mtDNA samples from the Late Krotovo (n=20) and Andronovo (n=20) groups in this region were analyzed (Fig. 3) and compared to recently published data (n=10) (Keyser et al., 2009) and our own unpublished data (n=6) on mtDNA lineages from West Siberian Andronovo populations located outside the Baraba forest steppe.  

The genetic influence of migrants can be detected by the appearance of a new mtDNA haplogroup that was absent in the populations preceding the migration wave. This new mtDNA haplogroup, a West Eurasian T haplogroup, was detected in the Late Krotovo population. The T haplogroup appears simultaneously (with a 15 % frequency) in the Krotovo and Andronovo groups, but was completely absent in all preceding Baraba populations. We therefore consider the appearance of the Haplogroup T-lineage as the most likely genetic marker of the Andronovo migration wave to the region.  

This assumption is confirmed by mtDNA studies of Andronovo groups from other West Siberian areas. Haplogroup T lineages were found, with a frequency of 25 %, in the samples (n=16) taken from two Andronovo groups from the Krasnoyarsk and upper Ob River areas.  

We also detected another remarkable feature in the mtDNA pool of the Andronovo group from Baraba. Most mtDNA samples belonged to haplogroups, such as the East Eurasian A and C haplogroups, that are typical of preceding Baraba indigenous populations. Still, these haplogroups were not found in the other West Siberian Andronovo groups. Apparently, the Andronovo group from Baraba assimilated the aboriginal Krotovo population, from which it obtained these East-Eurasian mtDNA haplogroups. Obviously, there was reciprocal genetic contact between the migrant and indigenous groups in the region. 

...

A small but informative series of mtDNA samples from the Baraba Late Bronze Age culture population (n=5) was analyzed (Fig. 3), revealing the presence of MtDNA lineages (East Eurasian A and C lineages) that mark the genetic continuity with aboriginal Baraba groups. At the same time, the series includes the Haplogroup-T lineage, which we believe marks the Andronovo migration wave to West Siberia. Our data is therefore consistent with the putative origin of the West Siberian Late Bronze Culture population as the result of interaction between the Baraba indigenous genetic substrate and the newly arrived group.

It is now clear that the Andronovo groups moving into the area possessed mtDNA haplogroup T and assimilated the locals with their U+East Eurasian mix. It is of course interesting that haplogroup T is the only non-U lineage found in the aforementioned study of Mariupol-type cemeteries from Neolithic Ukraine.

The earliest occurrence of haplogroup T is in the Pre-Pottery Neolithic B of the Near East (Tell Hallula), and this haplogroup appears all over the place in Neolithic Europe. While a recent article has suggested a pre-Neolithic dispersal of T subclades into Europe, on the basis of modern populations, this hypothesis is difficult to reconcile with the ancient DNA data.


Pending new discoveries, it appears likely that mtDNA haplogroup T represents a Neolithic entrant into the boreal zone of U dominance. This has, of course, substantial implications in the context of J.P. Mallory's concept of fault lines, as it demonstrates that the steppe populations did not evolve in isolation, but the dominant lineage in the Andronovo groups was a late entrant into the indigenous U-zone of the eastern European plain.

But, the story doesn't end here:

The analysis of mtDNA samples from the Chicha-1 population revealed some interesting patterns. Crucial changes in the composition of mtDNA haplogroups in the gene pool were observed as compared to the earlier Baraba groups studied (Fig. 3). Dominance of Western Eurasian haplogroups and the near absence of East Eurasian were observed. Additionally, several new West Eurasian haplogroups appeared in the region, including Haplogroups U1a, U3, U5b, K, H, J and W.  

The phylogeographic analysis suggests that the distribution and diversification centres of several of these mtDNA haplogroups and specific lineages are located on the west and south west of the Baraba forest steppe region, on the territory corresponding to modern-day Kazakhstan and Western Central Asia (Fig. 10). Apparently, the migration wave from the south strongly influenced the gene pool of the Baraba population in the transitional period from the Bronze to the Early Iron Age. The impact of the northern human groups was probably less evident in the south of the Baraba forest steppe, at least at the mtDNA level. 

The drastic appearance of a purely Caucasoid population at the Iron Age from a southern, east-Caspian origin perhaps corresponds to the arrival of the first steppe Iranians. The vector of proposed migration is reasonable, if we consider both the likely Indo-Iranian homeland east of the Caspian, as well as the literary evidence for Scythian mobility during this period.

All in all, this is commendable research which allows us to intuit a sequence of events:

• An early mixture zone between Caucasoids and Mongoloids
• The Bronze Age arrival of mtDNA-T bearing Andronovo groups, the first pastoralists entering the zone of U+East Eurasian boreal hunter-gatherers; these Caucasoid peoples admixed with the natives of the mixture zone.
• The early Iron Age arrival of a full-blown set of Caucasoid mtDNA lineages from the south paving the way for the Iranian Scytho-Sarmatian period

Human migrations in the southern region of the West Siberian Plain during the Bronze Age: Archaeological, palaeogenetic and anthropological data


Molodin, Vyacheslav I. et al.


In this paper we present archaeological and anthropological data on human migrations in the Western Siberian foreststeppe region during the Bronze Age (4th–beginning of 1st millennium BC). These data, accumulated over forty years of intensive research in the region, are compared to new results showing the diversity of mitochondrial DNA (mtDNA) lineages in this region during that period (92 mtDNA samples from seven ancient human groups). Preliminary analyses have demonstrated the usefulness of ancient DNA in tracing and unravelling patterns of past human migrations.  


Link


Prehistoric populations of Ukraine: Migration at the later Mesolithic to Neolithic transition


Lillie, Malcolm C. et al.


This paper focuses on the identification of population movements during the Mesolithic and Neolithic periods in the Dnieper Basin region of Ukraine. We assess the evidence for migration from the perspective of individual life histories using a combination of palaeoanthropology/pathology, radiocarbon dating, stable isotopic studies of diet, and mtDNA. 


Link

Y chromosomes and mtDNA from late antique Bavaria

One of the papers in the aforementioned volume includes Y-STR and mtDNA data on a burial cemetery from Bavaria dating to the Imperial Roman age. I reproduce the DNA results below; the haplogroup assignments in red are my own and have been estimated with Whit Athey's haplogroup predictor using both Northwest European and Equal priors.

The number of Y-STRs is not sufficient to make very strong haplogroup assignments in some cases. Still, we can probably say that R1b, E1b1b, and I1 were present in the population. I1 might seem more likely than G2a in a few cases, but remember that a couple of G2a men were found in 7th c. Bavaria. E1b1b, another non-typical German haplogroup has also been found in Usedom from the medieval period.

Christina Sofeso, Marina Vohberger, Annika Wisnowsky, Bernd Päffgen, Michaela Harbeck, *

Verifying archaeological hypotheses: Investigations on origin and genealogical lineages of a privileged society in Upper Bavaria from Imperial Roman times (Erding, Kletthamer Feld)



During the years 2005 and 2006 approximately 2000 archaeological

finds ranging from the Neolithic Period to Late Antiquity 

were found on the Kletthamer Feld (Erding, Upper Bavaria). 

Out of this context a burial site was examined comprising 

13 individuals, some of them rich in precious grave goods. The 

inhumations were dated to the second half of the 4th to the first 

half of the 5th century – a time of upheavals in relation to the 

demographic structure of the former Roman province Raetia (today southern Bavaria).

The high proportion of male individuals within the skeletal population as well as the finding of a Roman fibula, which is seen as part of Roman military clothing, led to distinct hypotheses which we have attempted to support in this study. The hypothesis that the skeletal remains reflect a founder population from a Germanic region north of the Danube River could be rejected on the basis of stable isotope analyses. The theory of a buried family clan had to be dismissed as well, or rather, be extended to the scenario of several families being buried there with their servants. The results obtained fit the third presumption best, namely that the buried individuals were the members of a military unit interred with their families.

Population Dynamics in Prehistory and Early History (2012)

This is a great open access volume. I'll update this post if I read something in it that seems novel.

Population Dynamics in Prehistory and Early History (2012)

Ed. by Kaiser, Elke / Burger, Joachim / Schier, Wolfram

ISBN: 978-3-11-026630-6

DOI: 10.1515/9783110266306

Link

Petty identity politics indeed, or, holding a grudge is no excuse for anti-science

Living Anthropologically takes issue with my contention that the "big hole" in genetic sampling of Native groups in the US is due to "petty identity politics contra science":

1. Contemporary Native Americans have very good reasons to not participate in these studies of earliest Americans. 

Just like in “Battle of the Bones”–which attempts to make a science-versus-creationism argument for studying Native American remains–people take this “paucity of samples from North America” as an opportunity to bash contemporary Native Americans for opting out of these studies. Dienekes blog asks if this is “Petty identity politics contra science?” and commenters on various articles condemn Native groups for this supposedly “petty” refusal. 

For many years I’ve been showing the BBC production, Bones of Contention: Native American Archaeology for Introduction to Anthropology. Produced in 1995, this film is even older than “Battle of the Bones,” but it takes a BBC perspective to give a fairer presentation of U.S. politics and Native issues. What this film at least makes clear–and seems lost on so many–is that Native Americans have plenty of good reasons to still be suspicious of genetic investigation. 

Genocide. Treaty abrogation. Children sent to boarding school to be stripped of language and identity. Contemporary inequalities. The fact that every time I assign “Battle of the Bones” and screen Bones of Contention, some students openly snicker or rant about Native Americans holding back science. It’s one of the factors that went undiscussed in that re-study of Stephen Jay Gould’s Mismeasure of Man–how did Morton get all those skulls anyway?
Petty identity politics indeed.

In my opinion that is a lot of hooey to justify the unjustifiable. I won't argue about the veracity or details of this version of history, but surely native Americans from the US were not especially mistreated compared to other people colonized by Europeans?

I mean, there are now samples from Native Australians, East Indians, Sub-Saharan Africans, Native Americans from all over the Americas except the US. Why don't all these people not "hold a grudge" for their bad treatment at the hands of Europeans, but, apparently, are perfectly willing to participate in genetic research if it's explained to them how they might learn more about their ancestors from it?

And, why limit ourselves to people colonized by Europeans? Surely, Slavs, for example, have a lot of things to say about German Rassenkunde scientists belittling them, studying their skulls to "prove" they are an inferior race, and hatching up and executing plans for their annihilation. So, why do the Russians give the Denisova fingerbone to ze Max Planck folks to study, or allow them to study ancient DNA from all over their territory?

Scour the literature for a while, and you'll find plenty of (modern) Germans studying Jews, and Jews studying pretty much everybody, including many not-so-friendly Muslim populations. You'll find Russians too, studying all the subjugated ethnic groups of their former Empire, and plenty of Han Chinese scientists studying some of the 57 ethnic groups of their country. You'll find Serbs and Turks forgetting about the Battle of Kosovo or the Balkan Wars to participate in joint research about the origins of the Neolithic. You'll find Roma and Saami being studied by their native European "oppressors."

And, how about those African Americans whose ancestors were dragged across the Atlantic in chains, and forced to work as slaves, surely they have as good a reason, if not better, to be suspicious of being made an object of study by people outside their community? But, last time I checked, there were plenty of studies on that population, informing them about the sources of their African ancestors and the timing and extent of admixture with their European ones.

In short: you'll find plenty of groups with historical or even contemporary sources of conflict setting aside their differences in the interest of science.

The anti-scientific attitude of certain Native American groups cannot be ascribed to a history of oppression or conflict with the ancestors of the scientists wishing to study them. And, indeed, if Native Americans were once oppressed by the Palefaces, why don't they let themselves be studied by Chinese or Japanese researchers, or indeed by their own scientists: there are Native American geneticists after all!

There are two answers to this question:

• The cultural relativist nonsense about science being a "white man's way of knowing" that is of no use to Native groups who already know who their ancestors were.
• "petty identity politics" indeed.

If one can think of a better explanation, I'm willing to listen. But, please, no more of that "oppressed people mistrusting Western scientists" tripe.

Clovis people had Western Stemmed Tradition company

A day after the paper by Reich et al. on the three waves of colonization of the Americas in Nature, there is another paper in Science which adds to the complexity of the period of the continent's early settlement.

While the genetics of modern populations can presently identify only one wave of 'First Americans' followed by two much less important waves associated with the later spread of Na-Dene and Eskimo-Aleut, we have known for some time that there were pre-Clovis people living in America. The new research suggests that at the time of the Clovis culture itself, or even prior to it, there was another distinctive archaeological culture.

From the NY Times coverage:

Stone spearheads and human DNA found in Oregon caves, anthropologists say, have produced firmer evidence that these are the oldest directly dated remains of people in North America. They also show that at least two cultures with distinct technologies — not a single one, as had been supposed — shared the continent more than 13,000 years ago. 

In other words, the Clovis people, long known for their graceful fluted projectile points, were not alone in the New World. The occupants of Paisley Caves, on the east side of the Cascade Range, near the town of Paisley, left narrow-stemmed spear points shaped by different flaking techniques. These hunting implements are classified as the Western Stemmed Tradition, previously thought to be younger than the Clovis technology.

From the press release:

Dr. Jenkins says of the paradigm shifting results: 

"One of the central questions has been whether the technological evolution of hunting tools such as dart and spearheads can be attributed solely to the Clovis culture and the knowledge that these people brought from the Old World. During our excavations in the Paisley Caves we've found a completely different type of dart points. But these new points are of a completely different construction from those found in the Clovis culture. As our radiocarbon dating shows, the new finds are as old, or possibly older than the Clovis finds, which proves that the Clovis culture cannot have been the 'Mother technology' for all other technologies in America. Our results show that America was colonized by multiple cultures at the same time. And some perhaps even earlier than Clovis."

The genetic results are themselves quite interesting:

The 26 new specimens attributed to humans were radiocarbon dated byaccelerator mass spectrometry, and they range in age from 2295 ± 15 to 12,265 ± 2514Cyr., confirming the previously established range of occupation of these caves from beforeClovis in the late Pleistocene, to the late Holocene. Twenty-one specimens belonged to mitochondrial founder haplogroup A, screened for the presence of the A – G SNP atnucleotide position (np) 663 (all positions given with reference to the revised CambridgeReference Sequence). Five belonged to haplogroup B, characterized by a 9 base-pair (bp)deletion following np 8281, also present in eight of the coprolites assigned to haplogroupA (Table S17). The presence of this 9bp deletion after nucleotide 8281 has beenpreviously reported for haplogroup A (42-43), but it has also been reported forhaplogroups C and D. Therefore our results are not likely a product of crosscontamination both at the excavation site or in the lab.

There is also a podcast on the Science website.


Science 13 July 2012: Vol. 337 no. 6091 pp. 223-228 DOI: 10.1126/science.1218443

Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves

Dennis L. Jenkins

The Paisley Caves in Oregon record the oldest directly dated human remains (DNA) in the Western Hemisphere. More than 100 high-precision radiocarbon dates show that deposits containing artifacts and coprolites ranging in age from 12,450 to 2295 14C years ago are well stratified. Western Stemmed projectile points were recovered in deposits dated to 11,070 to 11,340 14C years ago, a time contemporaneous with or preceding the Clovis technology. There is no evidence of diagnostic Clovis technology at the site. These two distinct technologies were parallel developments, not the product of a unilinear technological evolution. “Blind testing” analysis of coprolites by an independent laboratory confirms the presence of human DNA in specimens of pre-Clovis age. The colonization of the Americas involved multiple technologically divergent, and possibly genetically divergent, founding groups.

Link

Reconstructing the origin of Native American populations

A new paper by Reich et al., which echoes the title of a previous one by many of the same authors on India looks at the issue of Native American origins. Nicholas Wade has some good coverage of the new research at the NY Times:

North and South America were first populated by three waves of migrants from Siberia rather than just a single migration, say researchers who have studied the whole genomes of Native Americans in South America and Canada.

I have an informed hunch that this will not be the last paper in the Reconstructing... series.

The supplementary material (pdf) is open access, and lists the data used, some of which has been taken from the literature and some of which is new. There is apparently also a new ADMIXTUREGRAPH software used in a paper which seems to parallel a little the functionality of TreeMix. I don't see a download option for this software yet; perhaps Joe Pickrell who co-authored TreeMix and is now in Harvard may chime in about the differences/applicability of the two pieces of code.

UPDATE: And here is the press release:

Two striking exceptions to this simple dispersal were also discovered. First, Central American Chibchan-speakers have ancestry from both North and South America, reflecting back-migration from South America and mixture of two widely separated strands of Native ancestry. Second, the Naukan and coastal Chukchi from north-eastern Siberia carry 'First American' DNA. Thus, Eskimo-Aleut speakers migrated back to Asia, bringing Native American genes.

Interestingly, I have detected some of this "Native American" component in the Chukchi as part of my world9 calculator.

UPDATE II: Of course, if you look at the map of the sampled populations, you'll notice one big hole: the USA. Petty identity politics contra science? Data on Native groups outside the US have been studied for years, and I doubt that the sky will fall over the heads of the new Canadian and South American groups that participated in this particular study. Hopefully, one day the big hole will be filled, although I'm not holding my breath of that happening anytime soon.

Nature (2012) doi:10.1038/nature11258

Reconstructing Native American population history

David Reich et al.

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1, 2, 3, 4, 5. One contentious issue is whether the settlement occurred by means of a single6, 7, 8 migration or multiple streams of migration from Siberia9, 10, 11, 12, 13, 14, 15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call ‘First American’. However, speakers of Eskimo–Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

Link