Scandinavian team looking for Indo-Europeans in Kazakhstan

An article in the Astana Times. If anyone has any additional information via Kazakh or Scandinavian media, or can find the press release referred to in the article, feel free to share.

  Scandinavian Team Searches for Indo-European Homeland through Kazakhstan DNA

A Scandinavian team has come to Kazakhstan in search of the common homeland of all Indo-European peoples, collecting bone fragments for analysis in the Centre for Geogenetics at the University of Copenhagen.

The researchers are looking for a genetic connection to match the linguistic connections that have already been drawn, Norwegian historian Sturla Ellingvag of the Explico Historical Research Foundation told The Astana Times on Feb. 20. “We’re trying to find a connection in science, in our DNA, to prove that there is indeed a connection, between, for example, Norwegians and the people in Kazakhstan. And also we are looking for a homeland, which is somewhere on the Caspian steppe, or in Russia, or some say it’s in Armenia or Ukraine. There are many different theories.”

The researchers collected about 120 Bronze and early Iron Age bone samples in total from Pavlodar, Kostanai and Karaganda during their week-long trip to Kazakhstan, from Feb. 14 – 21. Kazakhstan is fascinating, the researcher says, because it contains human remains that are “so far back on the DNA map.”

The 4,000 year old samples they’ve found have been very well preserved, Ellingvag said. “I can only speak from meeting archaeologists in Astana and here in Karaganda, but I’m very much impressed by the professionalism and also by the exhibitions they have,” he said.

The project to search for the ancestral homeland of the Indo-European peoples falls under the umbrella of a large grant from the Danish government and is being supported by the Kon-Tiki Museum in Oslo, Gotenburg University in Sweden and the University of Copenhagen in Denmark, which has one of the best historical DNA analysis labs in the world and which is where the analysis on the Kazakh remains will actually be done. Universities in Karaganda, Pavlodar and Kostanai are also involved.

The Kurgan hypothesis posits that the speakers of proto-Indo-European, the hypothesized common ancestor of the massive Indo-European language group, originally lived on the Pontiac-Caspian steppe, an area of land stretching from the Black Sea to the Caspian Sea and including parts of Russia, Ukraine and northwest Kazakhstan, beginning around the fifth millenium B.C. The hypothesis describes the spread of the language family from the steppe in every direction. “Kurgan” is a term for a type of burial mound common in the Caucasus, across Kazakhstan and beyond.

“Two thousand years ago, we started having Kurgan graves in Scandinavia,” said Ellingvag. The commonalities between burial mounds in Norway and Scythian/Saka mounds in Kazakhstan are striking, he said. “[The Scythian people] had these ornaments, these animal ornaments, which are very, very important in Scandinavian art … and the ornaments are actually quite similar, which is striking, it’s very special.”

The Kurgan hypothesis has been somewhat substantiated by genetic evidence so far, according to a press release by the Kon-Tiki Museum on the project, and advances in the technology for doing historical DNA research over the past few years means it is now possible to get closer to finding this genetic and linguistic starting point for most of the peoples of Europe.

“During the past 15 years, the Y-DNA R1a haplogroup has been characterised as a genetic signal of the Proto-Indo-Europeans. The theory now looks more plausible than ever, thanks to recent discoveries about its structure and phylogeography. Moreover, the Y-DNA R1a haplogroup has been found in numerous ancient remains supposedly belonging to early Indo-Europeans,” the press release explains.

A separate but related project is looking into the DNA of ancient horses. The Kurgan culture is credited with being the first to domesticate the horse.

The research team includes Ellingvag, Danish DNA-scientist Peter Damgaard and Bettina Heyerdahl, daughter of Norwegian archaeologist and explorer Thor Heyerdahl. They are also working with Kazakh researcher Emma Usmanova.

I could also find this Youtube video from this expedition.

ISBA 2014 titles

Some interesting talks and posters from the upcoming International Symposium on Biomolecular Archaeology. I don't see any abstracts on the site (yet?) but the titles are intriguing. Some that caught my eye:

• Investigating the maternal lineage diversity from an early medieval site in Southern Italy
• Ancient mitochondrial and Y chromosomal DNA reveals the western Carpathian Basin as a corridor of the Neolithic expansion
• Ancient mitochondrial DNA from the Northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process
• The effect of demography and natural selection on pigmentation heterogeneity in late Pleistocene and early Holocene Europeans
• The genomics of equine speciation and domestication
• Ancient population genetics: new insights on horse domestication
• Species identification and analysis of the Tyrolean Iceman's clothes using next generation sequencing of ancient DNA.
• Early evidence for the use of pottery: extending the ancient lipid record to the Pleistocene.
• Whey to go – first identification of lactose in prehistoric pottery
• Use of the earliest pottery on the Western and Eastern side of the Baltic
• The geographical distribution of the Polynesian cultural complex and its association with P33-C2a1 Y chromosomes: adding data from Aotearoa (New Zealand)
• Interdisciplinary investigation of an archaic hominin femur from the Swabian Jura (South-West Germany)
• Tracing the genetic history of farming populations of El Portalón Cave in the Sierra de Atapuerca, Spain.
• Ancient human genomes suggest three ancestral populations for present-day Europeans
• Ancient DNA from Early Neolithic farmers in Europe
• Genomic diversity and admixture in Stone-Age farmer and hunter-gatherer groups in Scandinavia
• Ancient DNA reveals the complex genetic history of the New World Arctic
• A prediction of the hybridisation potential between Hominin species using mitochondrial DNA
• Population Genomics of Vikings
• Tracing the genetic profile of Sus scrofa on Romanian territory from the Neolithic period until the Middle Ages
• The origins of the Aegean palatial civilizations from a population genetic perspective
• Ancient DNA evidence for a diversified origin of ancestor of Han Chinese

700,000-year old horse sequenced

A 700.000 year old horse gets its genome sequenced

It is nothing short of a world record in DNA research that scientists at the Centre for GeoGenetics at the Natural History Museum of Denmark (University of Copenhagen) have hit. They have sequenced the so far oldest genome from a prehistoric creature. They have done so by sequencing and analyzing short pieces of DNA molecules preserved in bone-remnants from a horse that had been kept frozen for the last 700.000 years in the permafrost of Yukon, Canada. By tracking the genomic changes that transformed prehistoric wild horses into domestic breeds, the researchers have revealed the genetic make-up of modern horses with unprecedented details. The spectacular results are now published in the international scientific journal Nature.

... 

First, by comparing the genome in the 700,000 year old horse with the genome of a 43,000 year old horse, six present day horses and the donkey the researchers could estimate how fast mutations accumulate through time and calibrate a genome-wide mutation rate. This revealed that the last common ancestor of all modern equids was living about 4.0-4.5 million years ago. Therefore, the evolutionary radiation underlying the origin of horses, donkeys and zebras reaches back in time twice as long as previously thought. Additionally, this new clock revealed multiple episodes of severe demographic fluctuation in horse history, in phase with major climatic changes such as the Last Glacial Maximum, some 20,000 years ago.

I'll add the paper abstract later.

Nature (2013) doi:10.1038/nature12323

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse

Ludovic Orlando et al.

The rich fossil record of equids has made them a model for evolutionary processes1. Here we present a 1.12-times coverage draft genome from a horse bone recovered from permafrost dated to approximately 560–780 thousand years before present (kyr BP)2, 3. Our data represent the oldest full genome sequence determined so far by almost an order of magnitude. For comparison, we sequenced the genome of a Late Pleistocene horse (43?kyr BP), and modern genomes of five domestic horse breeds (Equus ferus caballus), a Przewalski’s horse (E. f. przewalskii) and a donkey (E. asinus). Our analyses suggest that the Equus lineage giving rise to all contemporary horses, zebras and donkeys originated 4.0–4.5?million years before present (Myr BP), twice the conventionally accepted time to the most recent common ancestor of the genus Equus4, 5. We also find that horse population size fluctuated multiple times over the past 2?Myr, particularly during periods of severe climatic changes. We estimate that the Przewalski’s and domestic horse populations diverged 38–72?kyr BP, and find no evidence of recent admixture between the domestic horse breeds and the Przewalski’s horse investigated. This supports the contention that Przewalski’s horses represent the last surviving wild horse population6. We find similar levels of genetic variation among Przewalski’s and domestic populations, indicating that the former are genetically viable and worthy of conservation efforts. We also find evidence for continuous selection on the immune system and olfaction throughout horse evolution. Finally, we identify 29 genomic regions among horse breeds that deviate from neutrality and show low levels of genetic variation compared to the Przewalski’s horse. Such regions could correspond to loci selected early during domestication.

Link

Horse Y chromosomes

PLoS ONE 8(4): e60015. doi:10.1371/journal.pone.0060015

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

Barbara Wallner et al.

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.

Link

Genetic diversity of modern horses

Some very distinctive groupings of modern breeds emerge in this survey of modern horse breed genetic variation, and some of these groups have clear geographical associations.

Horses are very mobile, and can also be traded; much of their existing variation may also be the result of artificial breeding which might have included both selection for particular desirable traits as well as mixing different populations.

Now that there is a fairly clear picture of modern variation, it will be useful to explore how this has emerged over time. It'll be interesting to see how ancient horses fit into the modern picture: will they prove ancestral to those living in the same regions, or is there a process of continuous renewal, with multiple episodes of turnover, as good breeds emerge somewhere across the geographical range of the animal, and quickly replace less advantageous ones?

PLoS ONE 8(1): e54997. doi:10.1371/journal.pone.0054997

Genetic Diversity in the Modern Horse Illustrated from Genome-Wide SNP Data

Jessica L. Petersen et al.

Horses were domesticated from the Eurasian steppes 5,000–6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.

Link

Proto-Indo-European homeland in Neolithic Anatolia (Bouckaert et al.)

A new paper in Science uses Bayesian phylogeographic methods to model the spatial expansion of Indo-European languages from their Anatolian homeland. An informative video shows how the authors estimate the process took place across space and time:



There is also a podcast with Q.D. Atkinson on the new study, as well as a website by the authors on their research; the FAQ/Controversies section seems particularly useful.

I don't hold high hopes that, despite the mounting evidence, this will dissuade people from arguing for a steppe PIE origin. And, it shouldn't. Only a vigorous debate will resolve the issue conclusively. And, since IE languages appear on the archaeological record long after their split under any scenario, this may be one of those problems that will never be solved to everyone's satisfaction.

I don't agree with all the details of the authors' model, but certainly they place the PIE homeland near to where I believe it was. Resistance to an Anatolian origin will become more convincing if adherents of different homeland solutions manage to put their ideas in quantitative form. Expert opinion is valuable, but very knowledgeable linguists and/or archaeologists have placed the PIE homeland all the way from Central Europe to Bactria-Sogdiana and from the Pontic-Caspian steppe to Mesopotamia. So, one has to wonder why expert opinion has such a high variance, but every quantitative effort to solve the problem has come up with a single solution.

As I wrote recently:

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).

The current paper suggest a slightly different origin, in Southern Anatolia, perhaps influenced by the distribution of the historical Anatolian languages in the area when they were first put down in writing. But, I suspect that the transposition of Anatolian languages into the areas where they were first attested may have happened late in prehistory. In any case, whether the PIE homeland was in Southern or Eastern Anatolia, the results of this paper explicitly reject the Kurgan Pontic steppe hypothesis.

From the paper:

The distribution for the root location lies in the region of Anatolia in present-day Turkey. To quantify the strength of support for an Anatolian origin, we calculated the Bayes factors (21) comparing the posterior to prior odds ratio of a root location within the hypothesized Anatolian homeland (11) (Fig. 1, yellow polygon) with two versions of the steppe hypothesis—the initial proposed Kurgan steppe homeland (6) and a later refined hypothesis (7) (Table 1). Bayes factors show strong support for the Anatolian hypothesis under a RRW model.  

... 

As the earliest representatives of the main Indo-European lineages, our 20 ancient languages might provide more reliable location information. Conversely, the position of the ancient languages in the tree, particularly the three Anatolian varieties, might have unduly biased our results in favor of an Anatolian origin. We investigated both possibilities by repeating the above analyses separately on only the ancient languages and only the contemporary languages (which excludes Anatolian). Consistent with the analysis of the full data set, both analyses still supported an Anatolian origin (Table 1). 

The West Asian origin of the Proto-Indo-Europeans makes excellent sense in the light of the genetic evidence. But, as I hint at the above paragraph, the tempo of their expansion into Europe remains to be clarified. I strongly suspect, on the basis of the Iceman and Swedish Neolithic TRB farmer (Gok4) whose DNA has been published that the earliest Neolithic was not Indo-European, because these individuals lack the "West Asian" autosomal component.

But, when did the Indo-Europeans first set foot on Europe? Were they already present at the time of Dimini and Vinča in the Balkans? I tend to think that a reasonable proposition, because the 8.2 kiloyear event may have transposed a second set of Neolithic farmers into Europe, of Halafian origin. Or, did they appear later, during the Copper and Bronze Ages with the spread of metallurgy? Until we get ancient DNA from the Balkans and Anatolia, we won't know for sure. But, Y-haplogroups J2, and R1 so conspicuously absent from Neolithic Europe down to 5ka (and in the case of J2, completely missing from the record altogether) must have entered Europe at some point. Did they take the fast train into Europe post-5ka, or did they lurk in both Anatolia and Europe pre-5ka? Thanks to the BEAN project we might find out.

The idea that ~5ka something happened in Europe is also supported by the paper:

Despite support for an Anatolian Indo- European origin, we think it unlikely that agriculture serves as the sole driver of language expansion on the continent. The five major Indo-European subfamilies—Celtic, Germanic, Italic, Balto-Slavic, and Indo-Iranian—all emerged as distinct lineages between 4000 and 6000 years ago (Fig. 2 and fig. S1), contemporaneous with a number of later cultural expansions evident in the archaeological record, including the Kurgan expansion (5–7). 

So, while the deepest prehistory of Indo-European is firmly rooted in Anatolia during the early Neolithic, this is not inconsistent with something important happening in Europe during c. 5ka. But this was a secondary phenomenon, not the earliest seat of the Indo-Europeans. Also, I would not particularly relate this to the Kurgan expansion, but more probably to the arrival of metallurgical "guilds" with higher social complexity.

Both horses and wheeled vehicles quickly spread far and wide because of their simplicity and utility; if they were first adopted by a particular people, they quickly spread beyond it. Metallurgy, on the other hand, requires specialized knowledge about a variety of technical subjects, as well as a complex network of people with distinct roles: miners, metalworkers, traders, warriors, administrators. As such, the people who invented it would have had a distinct advantage until their trade secrets were leaked, or too many Bronze weapons were in the hands of their enemies. During the Bronze Age, more and more people got access to weaponry, and by the end of it, wars were raging all across Western Eurasia.

We tend to think of the Neolithic farmers, but it is quite likely that people kept coming into Europe since its initial colonization. After all, the people who came to the Americas in 1492 were the vanguard of many others who followed them. The same must have happened in Europe as well: a continuous process of settlement by various groups at different times, at least until the Bronze and Iron Ages when everyone, all over West Eurasia, seem to have become very quarrelsome and more than willing to use their swords, spears, axes, and arrows to dissuade newcomers who ventured into their territory.

Coverage of the new paper elsewhere: NY Times, Nature, Gene Expression, John Hawks.

Science 24 August 2012: Vol. 337 no. 6097 pp. 957-960 DOI: 10.1126/science.1219669

Mapping the Origins and Expansion of the Indo-European Language Family 

Remco Bouckaert et al.

ABSTRACT

There are two competing hypotheses for the origin of the Indo-European language family. The conventional view places the homeland in the Pontic steppes about 6000 years ago. An alternative hypothesis claims that the languages spread from Anatolia with the expansion of farming 8000 to 9500 years ago. We used Bayesian phylogeographic approaches, together with basic vocabulary data from 103 ancient and contemporary Indo-European languages, to explicitly model the expansion of the family and test these hypotheses. We found decisive support for an Anatolian origin over a steppe origin. Both the inferred timing and root location of the Indo-European language trees fit with an agricultural expansion from Anatolia beginning 8000 to 9500 years ago. These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory.

Link

SMBE 2012 abstracts (part I)

Some abstracts of interest from SMBE 2012. Part II will follow.

Reconstructing demographic histories from long tracts of DNA sequence identity 

Kelley Harris 1 , Rasmus Nielsen 1,2 1 UC Berkeley, Berkeley, CA, USA,  2 University of Copenhagen, Copenhagen, Denmark 
There has been recent excitement and debate about the details of human demographic history, involving gene flow that  has occurred between populations as well as the extent and timing of bottlenecks and periods of population growth.  Much of the debate concerns the timing of past admixture events; for example, whether Neanderthals exchanged  genetic material with the ancestors of non-Africans before before or after they left Africa. Here, we present a method for  using sequence data to jointly estimate the timing and magnitude of past genetic exchanges, along with population  divergence times and changes in effective population size. To achieve this, we look at the length distribution of regions  that are shared identical by state (IBS) and maximize an analytic composite likelihood that we derive from the  sequentially Markov coalescent (SMC). Recent gene flow between populations leaves behind long tracts of identity by  descent (IBD), and these tracts give our method its power by influencing the distribution of shared IBS tracts. However,  since IBS tracts are directly observable, we do not need to infer the precise locations of IBD tracts. In this way, we can  accurately estimate admixture times for relatively ancient events where admixture mapping is not possible, and in  simulated data we show excellent power to characterize admixture pulses that occurred 100 to several hundred  generations ago. When we study the IBS tracts shared between and within the populations sequenced by the 1000  Genomes consortium, we find evidence that there was no significant gene flow between Europeans and Asians within  the past few hundred generations. It also looks unlikely that the Yorubans of Nigeria interbred with Europeans or Asians  in a population-specific way, though there may have been admixture between Africans and an ancestral non-African  population. 

Which way did they go? Detecting directional migration from genetic data

Benjamin Peter, Montgomery Slatkin University of California, Berkeley, Berkeley, USA  

Range expansions and colonizations are ubiquitous in many species and are studied from many different perspectives in e.g. anthropology, biogeography and invasion biology. It has been well established that these colonization events lead to a loss of genetic diversity and that in many cases it is possible to infer the history of a species' range from present-day genetic data. Previous approaches were mainly based on within-population measures of diversity such as heterozygosity, which then have been compared between populations. However, it is also well established that these statistics are susceptible to confounding demographic factors such as unequal subpopulation sizes or population size changes. In this study, we propose a novel method using data from multiple populations to infer a population's history. Our approach is based on a statistic that detects asymmetries in the 2D-allele frequency spectrum that occur when one population consists mostly of offspring of another population, as we expect in an expanding population. We show that our statistic is able to detect the direction of an expansion using data from multiple populations. Using simulations, we further show that our statistic is generally more powerful than previous approaches and that it is robust to a wide array of confounding demographic factors. We further illustrate the use of our statistic on several data sets for humans, Drosophila and Neurospora and show that we are both able to detect global patterns of colonization and fine-scale population structure.

Populations genetics of the Neolithic transition

Joachim Burger 1 , Mark Thomas 2,3 1  

Johannes Gutenberg University, Institute of Anthropology, D-55128 Mainz, Germany,  2 Research Department of  Genetics, Evolution and Environment, University College London, Wolfson House, 4 Stephenson Way, London NW1  2HE, UK,  3 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE- 752 36 Uppsala, Sweden     

About 11,000 years ago, a change in human lifestyle took place in the territories of present-day western Iran, the Levant  region and south-east Anatolia, which is characterised particularly by four factors: the people founded permanent  settlements with buildings for various functions; plants such as Einkorn and beans were cultivated; goats, sheep, pigs  and cattle were domesticated; a new kind of culture evolved, that became conspicuous with the appearance of a new  material culture including ground stone tools and later, pottery products. The transition from the partly nomadic huntergatherer subsistence strategy to a settled lifestyle based on food production is also known as the “Neolithic Revolution”.  About 8,500 years ago, the Neolithic culture spread to the southeast of Europe and later expanded episodically across  central and northern Europe. The extent to which this movement of a farming culture was accompanied by a movement  of people, as opposed to just a spread of ideas and skills, has been a subject of considerable debate and dispute  over  the last 100 years. Population genetic computer simulations of genetic data from ancient human remains, based on  coalescent theory have shown that the early Neolithic farmers could not have been descended just from the later  hunter-gatherers of central Europe (Bramanti et al. 2009). As the hunter-gatherers had already been settled in Central  Europe since the retreat of the glaciers 20 kya, Neolithic famers must have migrated into this area.   

There is good evidence of cultural contact between hunter-gatherers and early farmers in central Europe. Whether the  exchange of hunting tools also led also to the exchange of men is still not clear, as Y-chromosomal DNA has not yet  been studied systematically in ancient human remains. Moreover, ancient DNA evidence is now emerging that other  regions don/t follow the patterns of population discontinuity observed in Central Europe. While the overall results  support a model of demic diffusion of farmers from southeastern Europe, or even further East, in to Central Europe, it is  very likely that modern populations in most parts of Europe were formed by varying degrees of admixture between  incoming farmers and indigenous hunter-gatherers. Analyses of the appropriate neutral and phenotypically informative  markers using next generation sequencing technologies will provide more information on this in the near future. 

Population genetic properties of time serial data with examples from ancient population-genomic data 

Mattias Jakobsson Uppsala University, Uppsala, Sweden  

Extracting genetic information from ancient material has for long been hampered by numerous difficulties since its first  steps some two decades ago, but in the last few years, many of these problems have been solved and the use of  ancient DNA (aDNA) is now beginning to show its full potential. We will likely see a wealth of genomic data from ancient  populations, but the statistical properties of time-structured genetic samples are considerably less explored than  population genetic patterns arising from spatial structure. Using simulations, we explore and highlight features of  temporal structure and spatial structure, such as an 'isolation-by-time' effect that is similar to isolation-by-distance.  Using model- and simulation-based approaches, we can now make novel inferences about demographic and  evolutionary questions from time serial data. We will discuss examples from the long standing debate about the  introduction of farming in Europe and question about archaic ancestry in East Asia using paleogenomic data.  

Inferences on dog domestication - genetic analysis of the most ancient dogs utilizing DNA capture arrays

Olaf Thalmann 1,2 , Daniel Greenfield 2 , Matthias Meyer 3 , Susanna Sawyer 3 , Pin Cui 3 , Mietje Germonpre 4 , Mikhail V.  Sablin 5 , Francesc Lopez-Giraldez 9 , Daniel LePont 1 , Brian Worthington 10 , Jeff P. Blick 6 , Jeniffer A. Leonard 7 , Richard E.  Green 8 , Robert K. Wayne 2 1 University of Turku, Turku, Finland,  2 University of California, Los Angeles, USA,  3 Max Planck Institute for Evolutionary  Anthropology, Leipzig, Germany,  4 Royal Belgian Institute of Natural Sciences, Brussels, Belgium,  5 Zoological Institute  RAS, Saint-Petersburg, Russia,  6 Georgia College & State University, Milledgeville, USA,  7 Estacion Biologica de  Donana- CSIC, Seville, Spain,  8 University of California, Santa Cruz, USA,  9 Yale University, New Haven, USA, 10 Southeastern Archaeological Research, Inc., Newberry, USA 

The geographical and temporal origin of the dog is controversial. Genetic data suggest a domestication event in Asia or  the Middle East about 15,000 - 30,000 years ago, whereas the oldest dog-like fossils are found in Europe dating to over  30 thousand years ago. We genetically analyzed the remains of 14 prehistoric wolves and dogs including some of the  oldest dog remains described from the New and Old World. Utilizing array based DNA capture techniques coupled with  Illumina double indexed sequencing, we targeted a total of ~750,000 nucleotides in each of the ancient canids and  additional 20 contemporary wolves from North America and Eurasia. The sequence information comprised the complete  mitochondrial genome, 3,000 SNPs previously identified as highly informative for differentiating dogs from wolves,  exonic sequences from 62 potential domestication genes and ~150,000 nucleotides of non-coding regions spread  throughout the genome.   Initial analyses reveal that we have successfully captured and sequenced the complete mitochondrial genome with high  coverage as wells as a substantial number of autosomal fragments from ten prehistoric canids and all contemporary  wolves. Phylogenetic analysis combining the complete mitochondrial genomes of the prehistoric canids with those of a  large collection of modern dogs and wolves result in a statistically well supported tree. While some haplotypes cluster  within modern dogs or wolves, others show a basal placement in the phylogeny. The latter finding might support a  previous notion that an aberrant lineage of dog-like canids might have existed throughout the northern hemisphere  during the late Pleistocene and became globally extinct during the last 20,000 years. We will test this hypothesis by  investigating the autosomal loci and employ sophisticated phylogenetic analyses, demographic modeling and selection  scans to better understand the influence of early human society and artificial selection on the canine genome.

Admixed human genomes reveal complex demographic patterns from early modern humans to the  contemporary era 

Simon Gravel 1 , Jeffrey M Kidd 2 , Jake K Byrnes 1 , Andres Moreno Estrada 1 , Fouad Zakharia 1 , Shaila Musharoff 1 ,  Francisco M De La Vega 1 , Carlos D Bustamante 1 1 Stanford University, Stanford, CA, USA,  2 University of Michigan, Ann Arbor, MI, USA     

A substantial proportion of humans are "admixed", in the sense that their recent ancestors belong to statistically distinct  groups. This needs to be accounted for if unbiased inference and associations are to be performed. We present a  diversity of methods for the analysis of whole-genome sequence data from admixed individuals, and apply them to 50  genomes sequenced by Complete Genomics, including 4 Mexican-Americans, 4 African-Americans and 2 individuals  from Puerto Rico, together with SNP genotype data from hundreds of additional samples.     

Many methods have been presented recently to infer the population of origin of specific loci along the genomes of  admixed individuals, leading to inferred mosaics of ancestry.  We first propose a simple Markov model that relates the  time-dependent migration history to the inferred patterns of local ancestry. We use this framework to infer the timing of  admixture and to differentiate between punctual and continuous models of migration: using demographic models that  are consistent with both historical records and genetic data, we find evidence for continuous migration patterns in both  Mexican and African-American populations.     

We also propose models to study the longer-term evolution of the ancestral populations, by considering the allele  frequency distribution, pairwise TMRCA's, and a simple extension of the recently introduced Pairwise Sequentially  Markovian Coalescent approach for demographic inference. The inferred source population demographic histories are  in broad agreement with previous results for European and West-African populations, and the inferred demography for  the Native source population closely follows the European one until about 20,000 years ago. Taken together, whole  genome sequencing and local ancestry assignment therefore permit inferences about long-term histories of unsampled  ancestral populations and highlights recent historical demographic processes that altered patterns of variation observed  in admixed populations. 

A genomewide map of Neandertal ancestry in modern humans

Sriram Sankararaman 1,2 , Nick Patterson 2 , Swapan Mallick 1,2 , Svante Paabo 3 , David Reich 1,2 1 Harvard Medical School, Boston, USA, 2 Broad Institute of Harvard and MIT, Cambridge, USA, 3 Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 

Analysis of the genomes of archaic hominins, such as Neandertals and Denisovans, has revealed that these groups have contributed to the genetic variation of modern human populations. Yet, we know little about how these ancient mixtures have shaped the genetic structure of human populations and even less about their impact on human evolution. To answer these questions systematically, we need a map of archaic ancestry i.e., a map that labels whether each region of an individual genome is descended from these archaics.

Building such a map is technically challenging because of the antiquity of these gene flow events. We have identified signatures based on patterns of variation at single SNPs as well as haplotypes that are informative of ancient gene flow.

We propose a principled method based on the statistical framework of Conditional Random Fields (CRFs) that integrates these patterns leading to highly accurate predictions. We applied our method to polymorphism data in European and East Asian individuals from the 1000 genomes project, in conjunction with the draft sequence of the Neandertal genome, to obtain the first genomewide map of Neandertal ancestry. Analysis of this map reveals several findings:

1. We identify around 35,000 Neandertal-derived alleles in Europeans and 21,000 in East Asians.

2. The map allows us to identify Neandertal alleles that have been the target of selection since introgression. We identified over 100 regions in which the frequency of Neandertal ancestry is extremely unlikely under a model of neutral evolution. The highest frequency region on chromosome 4 has a frequency of Neandertal ancestry of about 85% in Europe and overlaps CLOCK, a key gene in Circadian function in mammals. The high frequency, Neandertal-derived variant is specific to Europeans; it is not very common in East Asians. This gene has been found in other selection scans in Eurasian populations, but has never before been linked to Neandertal gene flow.

3. Several of the Neandertal-derived alleles identified in 1) above are found in the >6,000 SNPs associated with common diseases listed in the NHGRI catalog. These Neandertal derived variants are found to be risk variants associated with obesity and protective variants against breast cancer.

4. We also investigate the possibility of using this map to reconstruct the genome of the introgressing Neandertal. Using the ancestries in Europe and East Asia, we can reconstruct about 600 Mb which we expect to increase with larger samples and additional populations.

Origins and evolution of the Etruscans’ DNA

Silvia Ghirotto 1 , Francesca Tassi 1 , Erica Fumagalli 2,1 , Vincenza Colonna 3,1 , Anna Sandionigi 4 , Martina Lari 4 , Stefania Vai 4 , Emmanuele Petiti 4 , Giorgio Corti 5 , Ermanno Rizzi 5 , Gianluca De Bellis 5 , David Caramelli 4 , Guido Barbujani 1 1 Department of Biology and Evolution, University of Ferrara, Ferrara, Italy, 2 Department of Biotechnologies and BiosciencesUniversity of Milano-Bicocca, Milano, Italy, 3 Institute of Genetics e Biophysics "Adriano Buzzati-Traverso", National Research Council, Napoli, Italy, 4 Department of Evolutionary Biology, University of Firenze, Firenze, Italy, 5 Institute for Biomedical Technologies (ITB), National Research Council (CNR), Milano, Italy

The Etruscan culture is documented in Etruria, Central Italy, from the 7 th to the 1 st century BC. For more than 2,000 years there has been disagreement on the Etruscans’ biological origins, whether local or in Anatolia. Genetic affinities with both Tuscan and Anatolian populations have been reported, but so far all attempts have failed to fit the Etruscans’ and modern populations in the same genealogy. We extracted and typed mitochondrial DNA of 14 individuals buried in two Etruscan necropoleis, analyzing them along with other Etruscan and Medieval samples, and 4,910 contemporary individuals. Comparing ancient and modern diversity with the results of millions of computer simulations, we show that the Etruscans can be considered ancestral, with a high degree of confidence, to the modern inhabitants of two communities, Casentino and Volterra, but not to most contemporary populations dwelling in the former Etruscan homeland. We also estimate that the genetic links between Tuscany and Anatolia date back to at least 5,000 years ago, strongly suggesting that the Etruscan culture developed locally, without a significant contribution of recent Anatolian immigrants.

Human population genomics in time and space: paleogenomics of populations in Bulgaria

Meredith L. Carpenter 1 , Hannes Schroeder 2 , Nikola Theodossiev 3 , M. Thomas P. Gilbert 2 , Carlos D. Bustamante 1 1 Department of Genetics, Stanford University, Stanford, CA, USA, 2 Centre for Geogenetics, University of Copenhagen, Copenhagen, Denmark, 3 Department of Archaeology, Sofia University, Sofia, Bulgaria

With a few exceptions, most ancient human DNA studies to date have restricted their analysis to the mitochondrial DNA (mtDNA) and Y chromosome. These approaches have led to some interesting theories regarding the spread of human populations; however, they are inherently limited by their use of these two non-recombining markers, which are subject to forces such as genetic drift and natural selection and also represent only the histories of the female and male lines, respectively, from which they descend. Recently, the whole genomes of several ancient individuals have been sequenced. These genomes yielded much more information about the individuals’ ancestry than their mtDNA alone; nevertheless, a single ancient individual is not sufficient for population genetic analyses. Thus, the goal of our study is to sequence the genomes of multiple ancient individuals from the same population. This type of study has the potential to dramatically improve our ability to address demographic questions about ancient human populations. We have begun the low-coverage sequencing of genomic DNA from the teeth of 16 individuals from different time periods (1500 BC-400 BC) in Bulgaria, and we plan to ultimately extend the study to at least 50 ancient Bulgarian individuals from the Neolithic to the Iron Age (6300 BC-400 BC). The results of these initial experiments will be presented, including the identification of mtDNA haplogroups and initial population genetic analyses. Ultimately, we plan to analyze whole-genome sequence variation in these individuals and to compare it to variation present in modern populations. This will be the first systematic population-level study of ancient human genomes and therefore will allow us address demographic questions that have previously been restricted to the realm of theoretical modeling using extant populations.

Horse domestication: a computer simulation approach

Michela Leonardi 1 , Christine Weber 1 , Norbert Benecke 2 , Mark G. Thomas 3,4 , Joachim Burger 1 1 AG Palaeogenetik, Institute of Anthropology, SBII, Johannes Gutenberg University, Colonel Kleinmann-Weg 2, 55128, Mainz, Germany, 2 German Archaeological Institute, Im Dol 4-6, 14165, Berlin, Germany, 3 Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK, 4 Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Uppsala, Sweden

The domestication of horse played a key role in human history. It seems to have happened far both in time and space from the domestication of other ungulates such as cattle, pig, sheep and goat. Archaeological studies, nevertheless, failed in determining exactly the region and modality for horse domestication: several centers have been proposed (at least one in Europe and one in Central Asia) and the relationship between wild and early domestic populations are not clear. From a genetic point of view a phylogenetic approach on modern mitochondrial diversity could not find any structure related with geography or breeds. In the last decade ancient DNA became an important tool to reconstruct past demography. We obtained more than 100 HVR I sequences from pre domestic and domestic specimens found in Europe and Central Asia. After collecting all the previously published ancient and modern comparable sequences from the sub mentioned regions, computer simulations with a Bayesian approach were performed in order to test demographic models related with single or multiple domestications with or without gene flow. A single domestication appears to be unrealistic on the basis of mitochondrial data, while possible model of multiple domestications will be discussed.

The complete mitochondrial genome of a third individual from Denisova Cave

Susanna Sawyer 1 , Bence Viola 1 , Marie-Theres Gansauge 1 , Michael Shunkov 2 , Anatoly Derevianko 2 , Svante Paabo 1 1 Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 2 Paleolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia

A draft genome sequence was determined in 2010 from a small finger bone found in Denisova Cave in southern Siberia and was recently completed to 30-fold coverage. Its analysis reveals that it derived from an individual that belonged to a population related to, but distinct from, Neandertals. A large molar has also been described from Denisova Cave and shown to carry an mtDNA genome closely related to that of the finger bone. A second molar was found in Denisova Cave in 2010. We have captured and sequenced the complete mitochondrial genome of this tooth. While the mtDNAs of the finger bone and the first molar differ at only two nucleotide positions, they carry 86 and 84 differences, respectively, to the second molar. Thus, the maximum amount of mtDNA differences observed among these three Denisovans found within one cave is almost twice as large as the maximum differences seen among six Neandertals for which complete mtDNAs are available. Interestingly, the mtDNA of the second molar has a shorter branch than the other two Denisovan mtDNAs, suggesting that it may be older than the others.

Discovery at al-Magar

An excellent piece by Peter Harrigan on the newly discovered Neolithic site of Saudi Arabia.

Horse domestication mystery solved (?)

I will add the abstract of the paper later when it is "live" on the PNAS site. For the moment, a link to the press release:

New research indicates that domestic horses originated in the steppes of modern-day Ukraine, southwest Russia and west Kazakhstan, mixing with local wild stocks as they spread throughout Europe and Asia. The research was published today, 07 May, in the journal PNAS.

For several decades scientists puzzled over the origin of domesticated horses. Based on archaeological evidence, it had long been thought that horse domestication originated in the western part of the Eurasian Steppe (Ukraine, southwest Russia and west Kazakhstan); however, a single origin in a geographically restricted area appeared at odds with the large number of female lineages in the domestic horse gene pool, commonly thought to reflect multiple domestication "events" across a wide geographic area.

In order to solve the perplexing history of the domestic horse, scientists from the University of Cambridge used a genetic database of more than 300 horses sampled from across the Eurasian Steppe to run a number of different modelling scenarios.

Their research shows that the extinct wild ancestor of domestic horses, Equus ferus, expanded out of East Asia approximately 160,000 years ago. They were also able to demonstrate that Equus ferus was domesticated in the western Eurasian Steppe, and that herds were repeatedly restocked with wild horses as they spread across Eurasia.

ScienceNOW also covers the new research, and reports on a contrasting viewpoint:

Not all researchers are convinced, however. Archaeologist Marsha Levine of the University of Cambridge thinks using modern genetic samples to retrace horses' evolution is a dead end. "There's been mixing of cultures and mixing of horses in this region for many thousands of years," she says. "And so when you're looking at any modern horse, you just don't know where it's from."

Bringing together many kinds of evidence is what will ultimately answer the whens and wheres of horse domestication, Levine says. "What we need to be doing is using material from excavations, sequencing ancient genes, and combining that with what we know from archaeological evidence about how animals were used in the past."

I agree with the idea that ancient DNA will ultimately confirm/reject the model presented in the paper. Of course, it may be the case that the west Eurasian steppe was the place where horse domestication happened, but it is also the place where local horses may be descended from European, West Asian, and Central Asian breeds. I'll have to read the paper to see how the problem of possible admixture between western and eastern horse breeds on the steppe is accounted for in the paper.

PNAS doi: 10.1073/pnas.1111122109

Reconstructing the origin and spread of horse domestication in the Eurasian steppe

Vera Warmuth et al.

Despite decades of research across multiple disciplines, the early history of horse domestication remains poorly understood. On the basis of current evidence from archaeology, mitochondrial DNA, and Y-chromosomal sequencing, a number of different domestication scenarios have been proposed, ranging from the spread of domestic horses out of a restricted primary area of domestication to the domestication of numerous distinct wild horse populations. In this paper, we reconstruct both the population genetic structure of the extinct wild progenitor of domestic horses, Equus ferus, and the origin and spread of horse domestication in the Eurasian steppes by fitting a spatially explicit stepping-stone model to genotype data from >300 horses sampled across northern Eurasia. We find strong evidence for an expansion of E. ferus out of eastern Eurasia about 160 kya, likely reflecting the colonization of Eurasia by this species. Our best-fitting scenario further suggests that horse domestication originated in the western part of the Eurasian steppe and that domestic herds were repeatedly restocked with local wild horses as they spread out of this area. By showing that horse domestication was initiated in the western Eurasian steppe and that the spread of domestic herds across Eurasia involved extensive introgression from the wild, the scenario of horse domestication proposed here unites evidence from archaeology, mitochondrial DNA, and Y-chromosomal DNA.

Link

Frachetti on the multiregional emergence of mobile pastoralism

I had previously posted on horses not being important for the emergence of steppe pastoralism, in which Frachetti and Benecke documented how the early (4,500ky) Begash culture of Kazakhstan had developed full-blown pastoralism without apparently relying on horses.

This is in contradistinction to both the Botai culture where there is abundant evidence for horse use, apparently for food, as well as the Eneolithic cultures of the European steppe where horse bones are much more prevalent than in early Begash.

The simple model of the emergence of pastoral nomadism proposes the spread of this mode of subsistence from the European (Pontic-Caspian) steppe, together with horses and horse-drawn vehicles. Popularized by David Anthony in recent years, this model views horses and wheels as the great enablers of pastoralism, and views the emergence of pastoral cultures across the steppe as the result of movements of mobile pastoralists -atop their horses, and with their herds- across the Eurasian steppe.

Frachetti is a critic of this model, and proposes instead the importance of the (hitherto neglected) Inner Asian Mountain Corridor as important in facilitating prehistoric contacts between east and west. In a new paper in Current Anthropology he elaborates on his proposed "multiregional" model of the emergence of mobile pastoralism.

I have not read the paper's 38 pages carefully yet (including CA comments and response), but this is clearly a seminal work on the studied topic that will be referenced for years to come. I will post any specific comments in updates to this post. For the moment, I will limit myself to a couple of observations:

• Recent work in Y-chromosome phylogeny has established a fairly disjoint division within haplogroup R1a1a; in particular the R-Z93 subhaplogroup seems to abound in the "Asian steppe", as well as Asia in general, while being generally absent in Europe; the R1a1a and Subclades Y-DNA Project is keeping track of new developments in this field.
• My own research on autosomal DNA, suggests the confluence of two "streams" of ancestry onto the steppe: a west-to-east stream emanating from eastern Europe, and associated with the Atlantic_Baltic (K7b) or North_European (K12b) ancestral component; as well as a West_Asian (K7b) or Caucasus/Gedrosia (K12b) component emanating from the highland regions south of the Caspian and south of the steppe (the traditional Silk Road territory).

These lines of evidence certainly appear to be consistent with a "multiregional" model of early mobile pastoralism. In particular they testify to the non-uniformity of ancestry of steppe groups and are inconsistent with their derivation from a single source. The picture is further complicated by the historical movements of nomads across the steppe (including Scytho-Sarmatian type people as well as Turkic-Mongolian ones). Charting the emergence of steppe populations will require a great deal of sleuthing in the genomes of modern steppe inhabitants, as well as a great deal of work on ancient DNA.

In any case, the new paper by Michael Frachetti will provide important new insight to all those who seek to understand "what actually happened" in Eurasian prehistory, and it is a very welcome addition to the ongoing debate.

Current Anthropology Vol. 53, No. 1, February 2012

Multiregional Emergence of Mobile Pastoralism and Nonuniform Institutional Complexity across Eurasia

Michael D. Frachetti


Abstract

In this article I present a new archaeological synthesis concerning the earliest formation of mobile pastoralist economies across central Eurasia. I argue that Eurasian steppe pastoralism developed along distinct local trajectories in the western, central, and (south)eastern steppe, sparking the development of regional networks of interaction in the late fourth and third millennia BC. The “Inner Asian Mountain Corridor” exemplifies the relationship between such incipient regional networks and the process of economic change in the eastern steppe territory. The diverse regional innovations, technologies, and ideologies evident across Eurasia in the mid-third millennium BC are cast as the building blocks of a unique political economy shaped by “nonuniform” institutional alignments among steppe populations throughout the second millennium BC. This theoretical model illustrates how regional channels of interaction between distinct societies positioned Eurasian mobile pastoralists as key players in wide-scale institutional developments among traditionally conceived “core” civilizations while also enabling them to remain strategically independent and small-scale in terms of their own sociopolitical organization. The development of nonuniform institutional complexity among Eurasian pastoralists demonstrates a unique political and economic structure applicable to societies whose variable political and territorial scales are inconsistent with commonly understood evolutionary or corporate sociopolitical typologies such as chiefdoms, states, or empires.

Link

mtDNA of domestic horses: Ancestral Mare ~130-160 thousand years old

The paper is open access.


PNAS doi: 10.1073/pnas.1111637109

Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication

Alessandro Achilli et al.

Archaeological and genetic evidence concerning the time and mode of wild horse (Equus ferus) domestication is still debated. High levels of genetic diversity in horse mtDNA have been detected when analyzing the control region; recurrent mutations, however, tend to blur the structure of the phylogenetic tree. Here, we brought the horse mtDNA phylogeny to the highest level of molecular resolution by analyzing 83 mitochondrial genomes from modern horses across Asia, Europe, the Middle East, and the Americas. Our data reveal 18 major haplogroups (A–R) with radiation times that are mostly confined to the Neolithic and later periods and place the root of the phylogeny corresponding to the Ancestral Mare Mitogenome at ∼130–160 thousand years ago. All haplogroups were detected in modern horses from Asia, but F was only found in E. przewalskii—the only remaining wild horse. Therefore, a wide range of matrilineal lineages from the extinct E. ferus underwent domestication in the Eurasian steppes during the Eneolithic period and were transmitted to modern E. caballus breeds. Importantly, now that the major horse haplogroups have been defined, each with diagnostic mutational motifs (in both the coding and control regions), these haplotypes could be easily used to (i) classify well-preserved ancient remains, (ii) (re)assess the haplogroup variation of modern breeds, including Thoroughbreds, and (iii) evaluate the possible role of mtDNA backgrounds in racehorse performance.

Link

Signals of domestication of wild horses in mtDNA

BMC Evolutionary Biology 2011, 11:328 doi:10.1186/1471-2148-11-328

Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication

Sebastian Lippold et al.

Abstract (provisional)
Background
DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets.

Results
In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds and a single Przewalski horse (Equus przewalski) using a recently described multiplex micro-array capture approach. We found 473 variable positions within the domestic horses, 292 of which are parsimony-informative, providing a well resolved phylogenetic tree. Our divergence time estimate suggests that the mitochondrial genomes of modern horse breeds shared a common ancestor around 93,000 years ago and no later than 38,000 years ago. A Bayesian skyline plot reveals a significant population expansion beginning 6,000-8,000 years ago with an ongoing exponential growth until the present, similar to other domestic animal species. Our data further suggest that a large sample of wild horse diversity was incorporated into the domestic population; specifically, at least 46 of the mtDNA lineages observed in domestic horses (73%) already existed before the beginning of domestication about 5,000 years ago.

Conclusions
Our study provides a window into the maternal origins of extant domestic horses and confirms that modern domestic breeds present a wide sample of the mtDNA diversity found in ancestral, now extinct, wild horse populations. The data obtained allow us to detect a population expansion event coinciding with the beginning of domestication and to estimate both the minimum number of female horses incorporated into the domestic gene pool and the time depth of the domestic horse mtDNA gene pool.

Link

Cave painters painted spotted horses as they saw them.

I am innately skeptical of "symbolism" when it comes to most ancient art (see e.g., the destruction of the "mother goddess" theory). So, an article that shows that ancient artists painted horses as they saw them, and did not put dots on them for some strange symbolic reason, is very welcome.

From ScienceNOW:

About 25,000 years ago, humans began painting a curious creature on the walls of European caves. Among the rhinos, wild cattle, and other animals, they sketched a white horse with black spots. Although such horses are popular breeds today, scientists didn't think they existed before humans domesticated the species about 5000 years ago. Now, a new study of prehistoric horse DNA concludes that spotted horses did indeed roam ancient Europe, suggesting that early artists may have been reproducing what they saw rather than creating imaginary creatures.

Related: Ancient DNA for horse coat color

PNAS doi: 10.1073/pnas.1108982108

Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art

Melanie Pruvost et al.

Archaeologists often argue whether Paleolithic works of art, cave paintings in particular, constitute reflections of the natural environment of humans at the time. They also debate the extent to which these paintings actually contain creative artistic expression, reflect the phenotypic variation of the surrounding environment, or focus on rare phenotypes. The famous paintings “The Dappled Horses of Pech-Merle,” depicting spotted horses on the walls of a cave in Pech-Merle, France, date back ∼25,000 y, but the coat pattern portrayed in these paintings is remarkably similar to a pattern known as “leopard” in modern horses. We have genotyped nine coat-color loci in 31 predomestic horses from Siberia, Eastern and Western Europe, and the Iberian Peninsula. Eighteen horses had bay coat color, seven were black, and six shared an allele associated with the leopard complex spotting (LP), representing the only spotted phenotype that has been discovered in wild, predomestic horses thus far. LP was detected in four Pleistocene and two Copper Age samples from Western and Eastern Europe, respectively. In contrast, this phenotype was absent from predomestic Siberian horses. Thus, all horse color phenotypes that seem to be distinguishable in cave paintings have now been found to exist in prehistoric horse populations, suggesting that cave paintings of this species represent remarkably realistic depictions of the animals shown. This finding lends support to hypotheses arguing that cave paintings might have contained less of a symbolic or transcendental connotation than often assumed.

Link

More on Al-Magar horses

I had covered a news story about the Al-Magar site and its possible early use of the domesticated horse. Now, Horsetalk has some more information, including some pictures:

The discoveries in Al-Magar, in Saudi Arabia, are equally startling.

They not only push evidence of horse domestication back to about 9000 years ago, but may also point to the very roots of the Arabian horse breed.

One statue shows the unique neck and head characteristics of the breed. Two are said to show evidence of harness and a bridle. A nearby cave drawing appears to show a man riding a horse, and other evidence points to horses and other animals being part of the inhabitants' daily lives.

Among more than 80 artifacts found at Al-Magar is a one-metre long statue of a horse, comprising head, neck and chest.

Officials say the statue, which could well be the largest known sculpture of a horse during that period, has features similar to that of the original Arabian horses, characterised by a long neck and unique head shape.

The head of the statue carries what officials say are clear signs of a bridle.

Early horse domestication in Neolithic Arabia (?)

I don't have an opinion on this, but it's something worth keeping an eye on.

Saudis 'find evidence of early horse domestication'

Saudi officials say archaeologists have begun excavating a site that suggests horses were domesticated 9,000 years ago in the Arabian Peninsula.

The vice-president of the Saudi Commission for Tourism and Antiquities said the discovery at al-Maqar challenged the theory it first took place 5,500 years ago in Central Asia.

Ali al-Ghabban said it also changed what was known about the evolution of culture in the late Neolithic period.

A number of artefacts were also found.

They included arrowheads, scrapers, grain grinders, tools for spinning and weaving, and other tools that showed the inhabitants were skilled at handicrafts.

Mr Ghabban said carbon-14 tests on the artefacts, as well as DNA tests on human remains also found there, dated them to about 7,000 BC.

"This discovery will change our knowledge concerning the domestication of horses and the evolution of culture in the late Neolithic period," he told a news conference in Jeddah, according to the Reuters news agency.

"The al-Maqar civilisation is a very advanced civilization of the Neolithic period. This site shows us clearly, the roots of the domestication of horses 9,000 years ago," he added.

Although humans came into contact with horses about 50,000 years ago, they were originally herded for meat, skins, and possibly for milk.

The first undisputed evidence for their domestication dates back to 2,000 BC, when horses were buried with chariots. By 1,000 BC, domestication had spread through Europe, Asia and North Africa.

However, researchers have found evidence suggesting that the animals were used by the Botai culture in northern Kazakhstan 5,500 years ago.

Ancient wild horse Y chromosomes more diverse than those of domesticated horses

The sequenced horses can be found in the supplement, and they all seem to be from Alaska/Yukon/Siberia, probably for reasons having to with DNA preservation.

Hopefully techniques will improve, and the study of ancient wild horse DNA may help identify the wild progenitors of domestic horses, which must have lived in the more western parts of Eurasia, rather than in the studied regions.

With domesticated crops we have been fortunate in still having access to their wild relatives, but wild horses are now all extinct, except Przewalski's horse, which, as as other research has also shown was not the progenitor of domesticated horses.

See also the press release.

Nature Communications 2, Article number: 450 doi:10.1038/ncomms1447

Discovery of lost diversity of paternal horse lineages using ancient DNA

Sebastian Lippold et al.

Abstract

Modern domestic horses display abundant genetic diversity within female-inherited mitochondrial DNA, but practically no sequence diversity on the male-inherited Y chromosome. Several hypotheses have been proposed to explain this discrepancy, but can only be tested through knowledge of the diversity in both the ancestral (pre-domestication) maternal and paternal lineages. As wild horses are practically extinct, ancient DNA studies offer the only means to assess this ancestral diversity. Here we show considerable ancestral diversity in ancient male horses by sequencing 4 kb of Y chromosomal DNA from eight ancient wild horses and one 2,800-year-old domesticated horse. Both ancient and modern domestic horses form a separate branch from the ancient wild horses, with the Przewalski horse at its base. Our methodology establishes the feasibility of re-sequencing long ancient nuclear DNA fragments and demonstrates the power of ancient Y chromosome DNA sequence data to provide insights into the evolutionary history of populations.

Link

Przewalski's horse not progenitor of domesticated horse

Genome Biology and Evolution Advance Access published July 29, 2011 doi:10.1093/gbe/evr067

A MASSIVELY PARALLEL SEQUENCING APPROACH UNCOVERS ANCIENT ORIGINS AND HIGH GENETIC VARIABILITY OF ENDANGERED PRZEWALSKI'S HORSES

Hiroki Goto et al.

The endangered Przewalski’s horse is the closest relative of the domestic horse and is the only true wild horse species surviving today. The question of whether Przewalski’s horse is the direct progenitor of domestic horse has been hotly debated. Studies of DNA diversity within Przewalski’s horses have been sparse, but are urgently needed to ensure their successful reintroduction to the wild. In an attempt to resolve the
controversy surrounding the phylogenetic position and genetic diversity of Przewalski’s horses, we used massively parallel sequencing technology to decipher the complete mitochondrial and partial nuclear genomes for all four surviving maternal lineages of Przewalski’s horses. Unlike SNP typing usually affected by ascertainment bias, the present method is expected to be largely unbiased. Three mitochondrial haplotypes were discovered - two similar ones, haplotypes I/II, and one substantially divergent from the other two, haplotype III. Haplotypes I/II vs. III did not cluster together on a phylogenetic tree, rejecting the monophyly of Przewalski’s horse maternal lineages, and were estimated to split 0.117-0.186 million years ago, significantly preceding horse domestication. In the phylogeny based on autosomal sequences, Przewalski’s horses formed a monophyletic clade, separate from the Thoroughbred domestic horse lineage. Our results suggest that Przewalski’s horses have ancient origins and are not the direct progenitors of domestic horses. The analysis of the vast amount of sequence data presented here suggests that Przewalski’s and domestic horse lineages diverged at least 0.117 million years ago, but since then have retained ancestral genetic polymorphism and/or experienced gene flo

Link

Greek horse breeds

Wikipedia article on Skyros pony

Related:

• Two Holocene refugia for European domestic horses

Genet Mol Biol. 2011 Jan;34(1):68-76. Epub 2011 Mar 1.

Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds.

Bömcke E, Gengler N, Cothran EG.

Abstract

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.

Link

Michael Frachetti on the Inner Asian Mountain Corridor

Here is another video of Michael Frachetti's talk in the Secrets of the Silk Road symposium:

The abstract of the talk:

Abstract - Seeds for the Soul: East/West Diffusion of Domesticated Grains along the Inner Asian Mountain Corridor.
Inner Asia has commonly been conceived as a region of Nomadic societies surrounded by agricultural civilizations throughout Antiquity. Societies of China, SW Asia, and Eastern Europe each developed agriculture in the Neolithic, while the earliest evidence for agriculture from the Eurasian steppe shows it was not a major part of local economies until the Iron Age (c. 700 BC). Newly discovered botanical evidence of ancient domesticated wheat and millet at the site of Begash in Kazakhstan, however, show that mobile pastoralists of the steppe had access to domesticated grains already by 2300 BC and that they were likely essential to the diffusion of wheat into China, as well as millet into SW Asia and Europe in the mid-3rd millennium BC. Currently, Begash provides the only directly dated botanical evidence of these crisscrossed channels of interaction. Whatsmore, the seeds from Begash were found in a ritual cremation context rather than domestic hearths. This fact may suggest that the earliest transmission of domesticated grains between China and SW Asia was sparked by ideological, rather than economic forces. This paper describes the earliest known evidence of wheat in the Eurasian steppes and explores the extent of ritual use of domesticated grains from China to SW Asia, across the Inner Asian mountains.

All in all a very enlightening talk that suggests that the mountain corridor south of the Caspian Sea, lands that would later be part of the Silk Road was the main conduit for cultural exchange between east and west, with Begash having the earliest presence of wheat in the steppe in a ritual context (more below).

His passing remark about the absence of grains east of the Don and all the way to Mongolia is interesting in terms of some of my recent comments.

Frachetti points out how misguided it is to view the Eurasian steppe as a uniform culture area, pointing out that the horse and cattle were more important in the European steppe, whereas goats were much more important in the Asian steppe with a full-blown pastoralist economy that did not depend on horses.

He thinks that domesticated wheat and millet moved in opposite directions (from West Asia and China) and arrived in Central Asia, a land formerly devoid of the cereals that were used in the great civilizations of the Aegean, Near East, South Asia, and China.

His inference that the wheat at Begash and Xiaohe had a ritual funerary use seems very well-argued, although over time wheat acquired an alimentary role as well. They basically find no grains anywhere on the site except at a cremation burial from an early period where wheat was deposited; the existence of a cremation burial is in itself interesting.

During the Q&A an attendee expresses incredulity that wheat would be used in such a context, but really I see no problem with it, as the offering of wheat in that context has a long history, and is, indeed, widely practiced even today.

At Begash we seem to be witnessing the beginnings of the spread of ideology to a steppe population. These steppe pastoralists seem to be adopting the use of wheat as a symbol of life, or "food for the dead", and the fact that they probably traded for this commodity suggests its symbolic importance to them.

Horse not important for the emergence of steppe pastoralism

The earliest horses from the Botai culture of Kazakhstan were used for the mares' milk and were hunted for food. It has also been suggested that the horse has been instrumental in the early emergence of Eurasian pastoralism. If that is true, then we expect to find horse remains in steppe pastoralist cultures in addition to domesticated animals (goats and cattle, the pig is lacking).

A paper by Frachetti and Benecke looked at the chronological sequence of the Begash culture from southeastern Kazakhstan. Surprisingly, they found no horse bones in the earliest period, a few ones in subsequent periods, while 14 per cent of the animals were horses only in the later (post-Mongolian) phase.

From the paper:

The relative frequencies show a steady increase of this species through time, from 2 per cent in Phase 1b to 14 per cent in the Phases 5 and 6. Whether the lack of horses in the earliest phase of occupation (Phase 1a) is an artefact of the small size of the total faunal collection or was a reality remains an open question. The second half of the third millennium BC, which roughly corresponds with Phase 1a, is considered as the period when horse domestication flourished in Western Asia (Benecke & von den Driesch 2003). Nevertheless, percentages of horse remains at Begash remain below 6 per cent until approximately AD 50 (Phase 3b).

...

The steady increase in horses in the faunal record does correlate with documented political and social expansions of eastern Eurasian mobile pastoralists in the mid-first millennium BC. For example, the increase in horses in Phase 3 (750 BC-AD 50) corresponds with the growth of nomadic steppe confederacies such as the Saka and Wusun (Chang et al. 2003; Rogers 2007).

...

The domestic horse is documented at Begash by the start of the second millennium BC, but its impact on pastoralism is not clear. It is true that by increasing their use of the horse throughout the Iron Age and later periods, the inhabitants of Begash likely improved their mobility and access to pastures across various ecological niches for their primary herd animals. Nevertheless, the zooarchaeological record from Begash illustrates that the increase in horses through time correlates first with opportunistic hunting forays at the end of the Bronze Age and then with expanding political engagements that undoubtedly reshaped the organisation of Eurasian pastoralist communities from the first millennium BC onward.

When compared to the relative stability of other domesticates at Begash, the small Bronze Age presence and limited expansion of horses in the faunal record before historic periods demands that we reconsider the degree to which domestic horses played a dominant role in emerging pastoralist lifeways or in aiding the diffusion of regional material culture throughout prehistory. Specifically, there is not ample evidence for extensive horse riding during the second millennium BC at Begash. To the degree that Begash is indicative of other pastoralist settlements in the region, the faunal evidence directly challenges the image of middle to late Bronze Age pastoralists (2000-1000 BC) as derived from migrating horse-riders (Kuz’mina 2008) and suggests that horse riding was not the most significant catalyst for regional diffusion at this point in prehistory. This does not demote the importance of domestic horse riding as a key innovation for Eurasian populations in general or defray its historical impact on the region write large; rather these data suggest there were other mechanisms by which pastoralism, material culture, and ideology developed among regional populations in the third and second millennia BC (Frachetti 2008a).

The early "cowboys of the steppe" paradigm is slowly collapsing. Certainly the horse was known, milked, eaten, and occasionally ridden on the steppes, but its central role in the emergence of Eurasian pastoralism has been ovestated on rather flimsy evidence.

It is only in the 1st millennium BC when it is picked up by Iranic/Turkic warrior confederations that the horse starts to affect Eurasia in a big way, and that is precisely the time when the Scythians appear in West Eurasia from their eastern homeland, followed centuries later by nomadic groups, from the west and north making their presence felt in China.

Antiquity
Volume: 83 Number: 322 Page: 1023–1037

From sheep to (some) horses: 4500 years of herd structure at the pastoralist settlement of Begash (south-eastern Kazakhstan)

Michael Frachetti and Norbert Benecke

Does the riding of horses necessarily go with the emergence of Eurasian pastoralism? Drawing on their fine sequence of animal bones from Begash, the authors think not. While pastoral herding of sheep and goats is evident from the Early Bronze Age, the horse appears only in small numbers before the end of the first millennium BC. Its adoption coincides with an increase in hunting and the advent of larger politically organised

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