February 28, 2014

4.2 kiloyear event and the demise of Indus Valley megacities

From the paper:
The 4.2 ka aridification event is regarded as one of the most severe climatic changes in the Holocene, and affected several Early Bronze Age populations from the Aegean to the ancient Near East (Cullen et al., 2000; Weiss and Brad- ley, 2001). This study demonstrates that the cli- mate changes at that time extended to the plains of northwestern India. The Kotla Dahar record alone cannot fully explain the role of climate change in the cultural evolution of the Indus civilization. The Indus settlements spanned a diverse range of environmental and ecological zones (Wright, 2010; Petrie, 2013); therefore, correlation of evidence for climate change and the decline of Indus urbanism requires a comprehensive assessment of the relationship between settlement and climate across a sub- stantial area (Weiss and Bradley, 2001; Petrie, 2013). The impact of the abrupt climate event in India and West Asia records, and that observed at Kotla Dahar, on settled life in the Indus region warrants further investigation.
Plato (or rather the Egyptian priest speaking through Plato) may have been the first one to note the differential survival of people as a result of natural catastrophes. It is hard to imagine that such an extreme event would not unbalance agricultural economies leading to famine and also endanger the supply systems on which early cities were based. The failure of cities would in turn lead to a failure of governing elites centered on them and a power vacuum which new elites (armed with bronze weapons at this time) might take advantage of. Climate may have ended the Bronze Age civilization itself 1000 years later.

Geology doi: 10.1130/G35236.1

Abrupt weakening of the summer monsoon in northwest India ∼4100 yr ago

Yama Dixit et al.

Climate change has been suggested as a possible cause for the decline of urban centers of the Indus Civilization ∼4000 yr ago, but extant paleoclimatic evidence has been derived from locations well outside the distribution of Indus settlements. Here we report an oxygen isotope record of gastropod aragonite (δ18Oa) from Holocene sediments of paleolake Kotla Dahar (Haryana, India), which is adjacent to Indus settlements and documents Indian summer monsoon (ISM) variability for the past 6.5 k.y. A 4‰ increase in δ18Oa occurred at ca. 4.1 ka marking a peak in the evaporation/precipitation ratio in the lake catchment related to weakening of the ISM. Although dating uncertainty exists in both climate and archaeological records, the drought event 4.1 ka on the northwestern Indian plains is within the radiocarbon age range for the beginning of Indus de-urbanization, suggesting that climate may have played a role in the Indus cultural transformation.


February 25, 2014

Recent radiation of R-M269 males in Europe

From the paper:
As such it is not possible to predict the subhaplogroup within R-M269 to which an individual belongs based on his YSTR haplotype, in contrast to the situation with higher level haplogroups for which haplotypes do have predictive power(Athey, 2005; Schlecht et al., 2008).
The explosion of R-M269 descendants who (seemingly) went from zero to a solid majority in much of Western Europe over the last few thousand years is probably one of the most interesting events in recent European history. Not many would have entertained such a possibility until a few years ago, but truth is often stranger than fiction.

Annals of Human Genetics DOI: 10.1111/ahg.12050

Recent Radiation within Y-chromosomal Haplogroup R-M269 Resulted in High Y-STR Haplotype Resemblance

Maarten H. D. Larmuseau et al.

Y-chromosomal short tandem repeats (Y-STRs) are often used in addition to Y-chromosomal single-nucleotide polymorphisms (Y-SNP) to detect subtle patterns in a population genetic structure. There are, however, indications for Y-STR haplotype resemblance across different subhaplogroups within haplogroup R1b1b2 (R-M269) which may lead to erosion in the observation of the population genetic pattern. Hence the question arises whether Y-STR haplotypes are still informative beyond high-resolution Y-SNP genotyping for population genetic studies. To address this question, we genotyped the Y chromosomes of more than 1000 males originating from the West-European regions of Flanders (Belgium), North-Brabant and Limburg (the Netherlands) at the highest resolution of the current Y-SNP tree together with 38 commonly used Y-STRs. We observed high resemblance of Y-STR haplotypes between males belonging to different subhaplogroups of haplogroup R-M269. Several subhaplogroups within R-M269 could not be distinguished from each other based on differences in Y-STR haplotype variation. The most likely hypothesis to explain this similarity of Y-STR haplotypes within the population of R-M269 members is a recent radiation where various subhaplogroups originated within a relatively short time period. We conclude that high-resolution Y-SNP typing rather than Y-STR typing might be more useful to study population genetic patterns in (Western) Europe.


February 21, 2014

AIMs and fine structure in 15 European populations

This is an open access article.

European Journal of Human Genetics advance online publication 19 February 2014; doi: 10.1038/ejhg.2014.1

Using ancestry-informative markers to identify fine structure across 15 populations of European origin

Laura M Huckins et al.

The Wellcome Trust Case Control Consortium 3 anorexia nervosa genome-wide association scan includes 2907 cases from 15 different populations of European origin genotyped on the Illumina 670K chip. We compared methods for identifying population stratification, and suggest list of markers that may help to counter this problem. It is usual to identify population structure in such studies using only common variants with minor allele frequency (MAF) >5%; we find that this may result in highly informative SNPs being discarded, and suggest that instead all SNPs with MAF >1% may be used. We established informative axes of variation identified via principal component analysis and highlight important features of the genetic structure of diverse European-descent populations, some studied for the first time at this scale. Finally, we investigated the substructure within each of these 15 populations and identified SNPs that help capture hidden stratification. This work can provide information regarding the designing and interpretation of association results in the International Consortia.


Evolution equally efficient in removing deleterious variants in Europeans and West Africans

...but apparently not in Denisovans who accumulated deleterious mutations at a higher rate than modern humans. This may account for the fact that we haven't been able to find many Denisovans in the archaeological record as they may simply be a population that "failed" -- although apparently some distant relatives of the single Denisovan genome did admix into Australasians.

arXiv:1402.4896 [q-bio.PE]

No evidence that natural selection has been less effective at removing deleterious mutations in Europeans than in West Africans

Ron Do et al.

Non-African populations have experienced major bottlenecks in the time since their split from West Africans, which has led to the hypothesis that natural selection to remove weakly deleterious mutations may have been less effective in non-Africans. To directly test this hypothesis, we measure the per-genome accumulation of deleterious mutations across diverse humans. We fail to detect any significant differences, but find that archaic Denisovans accumulated non-synonymous mutations at a higher rate than modern humans, consistent with the longer separation time of modern and archaic humans. We also revisit the empirical patterns that have been interpreted as evidence for less effective removal of deleterious mutations in non-Africans than in West Africans, and show they are not driven by differences in selection after population separation, but by neutral evolution.


February 17, 2014

mtDNA of Okladnikov Neandertal

PNAS February 11, 2014 vol. 111 no. 6

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

Pontus Skoglund et al.

One of the main impediments for obtaining DNA sequences from ancient human skeletons is the presence of contaminating modern human DNA molecules in many fossil samples and laboratory reagents. However, DNA fragments isolated from ancient specimens show a characteristic DNA damage pattern caused by miscoding lesions that differs from present day DNA sequences. Here, we develop a framework for evaluating the likelihood of a sequence originating from a model with postmortem degradation—summarized in a postmortem degradation score—which allows the identification of DNA fragments that are unlikely to originate from present day sources. We apply this approach to a contaminated Neandertal specimen from Okladnikov Cave in Siberia to isolate its endogenous DNA from modern human contaminants and show that the reconstructed mitochondrial genome sequence is more closely related to the variation of Western Neandertals than what was discernible from previous analyses. Our method opens up the potential for genomic analysis of contaminated fossil material.


February 14, 2014

AAPA 2014 abstracts

The program of the 83rd Annual Meeting of the American Association of Physical Anthropologists is online (pdf). I list some interesting titles:

  • Ancient DNA sequencing on the Ion Torrent PGM and Proton Platforms: Genetic diversity of haplotype D4b1a2a1a at Nuvuk, an ancient Thule Village
  • Preliminary analysis of ancient DNA on a late Neolithic population in Northeast China
  • Ancient DNA analysis of human remains from Halahaigou, a Neolithic cemetery in China
  • Mitochondrial DNA analysis reveals substantial population structure in Hecun, a shell mound in South China
  • Kinship analysis of ancient samples in the Noble Family cemetery of the Yuan Dynasty
  • Ancient DNA analysis of an infant from Sudanese Nubia (ca 500-1400 C.E.)
  • Ancient DNA analysis of human skeletal remains from pre-Columbian Puerto Rico
  • Ancient DNA from Early to Mid-Holocene Burials in Northwestern Argentina: Implications for understanding the colonization and early populations of South America
  • Ancient DNA from the Schild site in Illinois: Implications for the Mississippian transition in the Lower Illinois River Valley
  • Patterns of sequence variation at the pigmentation loci ASIP and OCA2 in Melanesian and African populations
  • Evolution of the HERC2 eye color gene in Europeans using linkage disequilibrium analysis in four human populations
  • Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa
  • The Qesem Cave mandibular premolars and molar from a morphometric perspective.
  • Exploring the relationship of Neanderthals and modern humans at various population levels through an analysis of body proportion indices
  • Early human dispersal from Africa: A model-based test of two hypotheses

February 13, 2014

Human admixture common in human history (Hellenthal et al. 2014)

A string of recent papers argued for admixture in human populations at time scales from the Middle Pleistocene to recent centuries. A new paper in Science makes the point convincingly for extensive admixture in humans over the last few thousand years. The authors include the creators of Chromopainter/fineStructure software; the new "Globetrotter" method appears to be a natural extension of that method that seemed to work wonderfully well except for the limitation of producing only a tree of the studied populations.

The paper has a companion website in which you can look up the admixture history of individual populations.

While reading this study, it is important to remember its limitations. Two are immediately obvious: (i) admixture events can only be detected for the last few thousand years, as this method depends on pattern of linkage disequilibrium which decays exponentially with time due to recombination, and (ii) detection of admixture seems to depend on the presence of maximally differentiated populations from the edges of the human geographical range; for example, the Japanese appear unadmixed even though they are clearly of dual Jomon/Yayoi ancestry. On the other hand, the method does detect the admixture present in the San at a similar time scale.

The case of Northwestern Europe appears especially striking as none of the populations from the region show evidence of admixture. This may be because the mixtures taking place there (e.g., between "Celts" and "Anglo-Saxons" in Great Britain) involved populations that were not strongly differentiated. Alternatively, population admixture history may have preceded the last few thousand years and is thus beyond the temporal scope of this method.

An exception to the rule that populations at the edges of the human range appear to be unadmixed are the Armenians who appear to be the only * between the Atlantic and Pacific in Figure 2D (shown at the beginning of this post). The companion site lists their status as "uncertain".

Other results are more questionable; for example, the authors assert that Sardinians are an admixed population with one side being "Egyptian-like" and the other "French-like" whereas the ancient DNA evidence as it stands would rather indicate that Sardinians are the best approximation of Neolithic Europeans currently in existence and so are more likely to (mostly) possess a gene pool that traces back to ~8-9 thousand years in Europe. It will be quite the surprise if so many Europeans from 5kya or earlier look like modern Sardinians and ancient Sardinians don't!

The analysis of Eastern Europe is particularly interesting as it documents three way admixture (Northern/Southern/NE Asian) in most populations but two way admixture (Northern/Southern) in Greeks, estimated at ~37%. The authors claim that this is related to the Slavs, which seems reasonable given the 1,054AD age estimate. On the other hand, according to the companion website, the southern element in Greeks is inferred to be Cypriot-like and it's far from clear that the pre-Slavic population of Greece was Cypriot-like or indeed represented by any of the populations in the authors' dataset.

The three-way admixture in much of eastern Europe is not particularly surprising as history furnishes ample evidence for groups of steppe origin in the region during historical times. Some bequeathed their both language and name (e.g., Magyars), others only their name (e.g., Bulgarians) on the local Europeans, but records indicate a widespread presence of "eastern" groups in Europe from the time of the Huns to that of the Ottomans. A study of late Antique eastern Europeans from the Baltic to the Aegean may help better document how the twin phenomena of the eastern invasions and the spread of the Slavs shaped the present-day genetic diversity of the region.

I suspect that a few ancient samples will be far more informative for understanding the recent history of our species than the most sophisticated modeling of modern populations. Nonetheless, it's great to have a new method that maximizes what can be learned about the past from the messy palimpsest of the present.

Science 14 February 2014: Vol. 343 no. 6172 pp. 747-751 DOI: 10.1126/science.1243518

A Genetic Atlas of Human Admixture History

Garrett Hellenthal et al.

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.


February 12, 2014

Ancient Clovis genome from Montana yields no surprises (Rasmussen et al. 2014)

Ancient DNA has consistently managed to surprise us, with pretty much no direct genetic continuity revealed between Pleistocene and modern populations anywhere in the world. So, it is refreshing to see that at least in the case of the Americas the people who lived there ~13 thousand years ago are clearly related to the people who lived there in pre-Columbian times, with no real evidence of subsequent gene flows from Eurasia (at least in the case of Central/South Americans).

Many people suspected this because of the difficulty to access the Americas from Eurasia: this must have limited gene flow between the two regions to a handful of migrants and a restricted set of time periods where geological and climatic conditions were advantageous. The much reduced genetic diversity of Native Americans also argues in favor of them being a relatively simple population, with low heterozygosity and a handful of unique "founder lineages" in both the Y-chromosome and mtDNA.

Nonetheless, there are also several theories in the realm of alernative history, involving Solutreans from Europe, trans-Pacific boat riders, bearded "White Gods", Minoans/Phoenicians/Atlanteans/Ancient Egyptians, "African" Olmecs, "Caucasoid" Paleo-Indians, lost Israelite tribes, to mention only a few of the most well-known ones.

The new study does not, of course, disprove any of the proposals in the preceding paragraph: one can still claim that diverse groups once inhabited the Americas and  Rasmussen et al. (2014) just happened to chance upon one that looked just like modern native Americans. But, this certainly improves the odds of early "Native American simplicity", offering no evidence for the complexity postulated by many of the alternative theories.

Moreover, while the existence of other human groups in the Americas cannot be disproved by the study of a single ancient individual, what can be proved is the antiquity of the ancestors of Native Americans. Rather than being late arrivals arriving from Asia after the initial colonization, perhaps with derived Mongoloid physical morphology, we now know that they were already there as early as ~13 thousand years ago. It is remarkable that a single ancient DNA sample can sweep away much of the nonsense that has been written on the topic in the past.

A piece in Nature News addresses some of the "ethics" debate that seems ever-present in studies involving Native American remains. I don't know how this study will be perceived by living Native Americans: a possibility is that they'll be more receptive to ancient DNA research now that a team of scientists have stretched the time depth of their ancestry in the Americas to the earliest studied sample, revealing themselves not to be the evil-doers that western scientists are generally assumed to be according to a certain kind of mentality. A different -and more alarming- possibility, is that radical anti-science elements will be emboldened by these findings to claim that continuity with the earliest Americans (which in itself seems true enough) adds support to claims of ownership to pretty much all archaeological samples whose relationship to living Amerindians was hitherto uncertain in light of the many alternative theories.

In any case, it is remarkable that this ~13 thousand year old genome now exists while the genomes of modern native Americans that can be had for a fraction of the cost and technical difficulty do not. Indeed, not even genotype data exist from most Amerindian groups from the USA, which creates the rather bizarre state of affairs that the Anzick-1 genome had to be compared with native groups from several countries in the Western hemisphere except the one in which it was found.

Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025

The genome of a Late Pleistocene human from a Clovis burial site in western Montana

Morten Rasmussen et al.

Clovis, with its distinctive biface, blade and osseous technologies, is the oldest widespread archaeological complex defined in North America, dating from 11,100 to 10,700 14C years before present (BP) (13,000 to 12,600 calendar years BP)1, 2. Nearly 50 years of archaeological research point to the Clovis complex as having developed south of the North American ice sheets from an ancestral technology3. However, both the origins and the genetic legacy of the people who manufactured Clovis tools remain under debate. It is generally believed that these people ultimately derived from Asia and were directly related to contemporary Native Americans2. An alternative, Solutrean, hypothesis posits that the Clovis predecessors emigrated from southwestern Europe during the Last Glacial Maximum4. Here we report the genome sequence of a male infant (Anzick-1) recovered from the Anzick burial site in western Montana. The human bones date to 10,705 ± 35 14C years BP (approximately 12,707–12,556 calendar years BP) and were directly associated with Clovis tools. We sequenced the genome to an average depth of 14.4× and show that the gene flow from the Siberian Upper Palaeolithic Mal’ta population5 into Native American ancestors is also shared by the Anzick-1 individual and thus happened before 12,600 years BP. We also show that the Anzick-1 individual is more closely related to all indigenous American populations than to any other group. Our data are compatible with the hypothesis that Anzick-1 belonged to a population directly ancestral to many contemporary Native Americans. Finally, we find evidence of a deep divergence in Native American populations that predates the Anzick-1 individual.


February 03, 2014

West Eurasian ancestry in eastern and southern Africa (Pickrell et al. 2014)

I had mentioned this when it was in preprint form and now it has appeared in PNAS. The great advantage of preprints (and why I'm all for them) is that they allow us to look at research much earlier (about half a year in this case) and thus help accelerate the pace of information dissemination. One disadvantage is that it is sometimes hard to keep track of how papers change between the preprint stage (and there may be multiple versions) and the final published stage; perhaps we need a diff for scientific papers.

PNAS doi: 10.1073/pnas.1313787111

Ancient west Eurasian ancestry in southern and eastern Africa

Joseph K. Pickrell et al.

The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.