March 01, 2015

8,000 year old wheat in Britain

Britain received farming later than most of Europe, but perhaps it received one of the products of farming well before any farmers set foot on the island. I've always wondered if news (and at least some products) of the agricultural revolution spread far and wide before the revolution itself did. Did foragers at the northwestern end of Europe hear stories of the strange new people that had already appeared 8,000 years ago on the opposite end of the continent?

Was this an isolated incident or will we be finding wheat elsewhere in pre-farming Europe? 

Science 27 February 2015: Vol. 347 no. 6225 pp. 998-1001

Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago 

Oliver Smith et al.

The Mesolithic-to-Neolithic transition marked the time when a hunter-gatherer economy gave way to agriculture, coinciding with rising sea levels. Bouldnor Cliff, is a submarine archaeological site off the Isle of Wight in the United Kingdom that has a well-preserved Mesolithic paleosol dated to 8000 years before the present. We analyzed a core obtained from sealed sediments, combining evidence from microgeomorphology and microfossils with sedimentary ancient DNA (sedaDNA) analyses to reconstruct floral and faunal changes during the occupation of this site, before it was submerged. In agreement with palynological analyses, the sedaDNA sequences suggest a mixed habitat of oak forest and herbaceous plants. However, they also provide evidence of wheat 2000 years earlier than mainland Britain and 400 years earlier than proximate European sites. These results suggest that sophisticated social networks linked the Neolithic front in southern Europe to the Mesolithic peoples of northern Europe.

Link

Two observations on the ancestry of Armenians

I was thinking a bit on how to interpret the findings of the new Haber et al. preprint, and especially the idea that "29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans." I looked at the globe13 proportions, and strangely enough, I had estimated that the three Armenian samples (Armenian_D, Armenians, and Armenians_15_Y) have 28-29% of the Mediterranean component that is modal in Sardinians. This seems like a curious coincidence which has raised my confidence that Haber et al. is picking something real.

Looking back at my inferences of Armenian ancestry, it seems (according to globe13) to come completely from West_Asian, Mediterranean, and Southwest_Asian. The Mediterranean component seems real enough as it seems to match Sardinians/early European farmers well. I am not so sure about the Southwest Asian component which is modal in Yemen Jews and may represent population-specific drift in relatively recent Arabians. The West_Asian component is bimodal in Caucasus and Gedrosia, so it can't be the result of a very drifted population in either region (unless there is spooky action at a distance). 

Another curious finding is the lack of North_European in a latitudinal "column" of populations from the Yemen, through the Levant to the South Caucasus (Georgians and Armenians). It seems that North_European is the only one of the four major Caucasoid components that Armenians lack to any important degree. There is a rather abrupt change between the South Caucasus (~1%) and the North Caucasus (15-20%). It seems that the Greater Caucasus did act like a barrier to gene flow. The K=4 analysis of the same dataset that produced K=13 (globe13) also shows the same barrier: all three Armenian samples and Georgians have ~0% of "Amerindian" (which is surely correlated to "Ancient North Eurasian" ancestry and via it with North_European), but North Caucasians and Europeans have 4-10%.  It's clear that this influence did not cross the Greater Caucasus, as Armenians and Georgians lack it. 

February 27, 2015

The plight of the Assyrians

ISIS Onslaught Engulfs Assyrian Christians as Militants Destroy Ancient Art
ISTANBUL — The reports are like something out of a distant era of ancient conquests: entire villages emptied, with hundreds taken prisoner, others kept as slaves; the destruction of irreplaceable works of art; a tax on religious minorities, payable in gold.

A rampage reminiscent of Tamerlane or Genghis Khan, perhaps, but in reality, according to reports by residents, activist groups and the assailants themselves, a description of the modus operandi of the Islamic State’s self-declared caliphate this week. The militants have prosecuted a relentless campaign in Iraq and Syria against what have historically been religiously and ethnically diverse areas with traces of civilizations dating to ancient Mesopotamia.

The latest to face the militants’ onslaught are the Assyrian Christians of northeastern Syria, one of the world’s oldest Christian communities, some speaking a modern version of Aramaic, the language of Jesus.
The New York Times reporter need not have gone to so distant a past to find parallels to the plight of the Assyrians, as this is merely a repeat of what happened only a hundred years ago.

February 26, 2015

Estonian biocentre high coverage Y chromosome sequences and Turkic data

Courtesy of the good people of the Estonian biocentre:
The Y chromosome data seems particularly exciting (there is a spreadsheet of populations in the download directory). One of the weaknesses of the 1000 Genomes data was that it didn't have any populations between Tuscany and East/South Asia, and the new dataset seems to rectify that.

The Turkic dataset is probably the one used for the preprint The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia. Since I overlooked this when it came out last summer, I'll post about it when the paper is published in a journal.

February 25, 2015

KNM-LH1: a 23,000 year old human from Kenya

From the paper:
KNM-LH 1 and other Pleistocene African specimens, all of which are potentially sampling candidate populations for dispersals across and out of Africa during the Late Pleistocene (12–15, 50, 59), differ substantially not only from recent Africans but also from individuals drawn from Holocene LSA archaeological sites. KNM-LH 1 and other Pleistocene African specimens (found with MSA and LSA artifacts) are also distinct from most EUP individuals.
Things are looking good for my Afrasian-Palaeoafrican admixture hypothesis which postulates that modern Africans are a mixture of "Afrasians" (a group of humans that also spilled over into Eurasia and/or back-migrated to Africa) and various groups of very divergent "Palaeoafrican" populations. In the context of this hypothesis, greater African genetic diversity is understood not as the result of a bottleneck of epic proportions during Out-of-Africa, but rather as a result of admixture between the two groups.

PNAS doi: 10.1073/pnas.1417909112

Late Pleistocene age and archaeological context for the hominin calvaria from GvJm-22 (Lukenya Hill, Kenya)

Christian A. Tryon et al.

Kenya National Museums Lukenya Hill Hominid 1 (KNM-LH 1) is a Homo sapiens partial calvaria from site GvJm-22 at Lukenya Hill, Kenya, associated with Later Stone Age (LSA) archaeological deposits. KNM-LH 1 is securely dated to the Late Pleistocene, and samples a time and region important for understanding the origins of modern human diversity. A revised chronology based on 26 accelerator mass spectrometry radiocarbon dates on ostrich eggshells indicates an age range of 23,576–22,887 y B.P. for KNM-LH 1, confirming prior attribution to the Last Glacial Maximum. Additional dates extend the maximum age for archaeological deposits at GvJm-22 to >46,000 y B.P. (>46 kya). These dates are consistent with new analyses identifying both Middle Stone Age and LSA lithic technologies at the site, making GvJm-22 a rare eastern African record of major human behavioral shifts during the Late Pleistocene. Comparative morphometric analyses of the KNM-LH 1 cranium document the temporal and spatial complexity of early modern human morphological variability. Features of cranial shape distinguish KNM-LH 1 and other Middle and Late Pleistocene African fossils from crania of recent Africans and samples from Holocene LSA and European Upper Paleolithic sites.

Link

February 24, 2015

Mutation rate again (Lipson et al. 2015)

This estimate is in-between 1.2 and 2.5x10-8, the two most quoted values for this parameter. It seems like such an important number that I'm wondering if it would be possible to brute force estimate it. Maybe people who have whole genomes of parents-offspring should get together and do the mother of all meta-analyses to pin down this number.

From the paper:
For example, a recent method for estimating population split times from coalescent rates placed the median split of African from non-African populations at 60–80 ky and the split of Native Americans from East Asians at ∼ 20 ky, both assuming a per-generation mutation rate of 1.25 × 10−8 and an average generation interval of 30 years [28]. [...] Using our inferred rate also makes the dates more recent, but only by a factor of about 1.3 rather than 2, i.e., ∼ 46–61 and 15 ky (with some associated uncertainty both from the model and from our estimated rate), neither of which contradicts external evidence.
The first of these estimated splits overlaps the dates of estimated Neandertal admixture by the Ust' Ishim and Kostenki papers. For a variety of reasons that I've repeated ad nauseam, I think that the split of Africans from non-Africans first happened about 100ka with Out-of-Africa-into-Arabia. But, if there was back-migration into Africa, maybe this can be brought down. The 15ky value for the East Asian/Native America split seems too young: it's as late as could plausibly maintained for the colonization of the Americas, but the split of the two must have happened some time before that (because the ancestors of Native Americans and East Asians would have split long before a group of them made the crossing into the Americas).

bioRxiv http://dx.doi.org/10.1101/015560

Calibrating the Human Mutation Rate via Ancestral Recombination Density in Diploid Genomes

Mark Lipson et al.

The human mutation rate is an essential parameter for studying the evolution of our species, interpreting present-day genetic variation, and understanding the incidence of genetic disease. Nevertheless, our current estimates of the rate are uncertain. Classical methods based on sequence divergence have yielded significantly larger values than more recent approaches based on counting de novo mutations in family pedigrees. Here, we propose a new method that uses the fine-scale human recombination map to calibrate the rate of accumulation of mutations. By comparing local heterozygosity levels in diploid genomes to the genetic distance scale over which these levels change, we are able to estimate a long-term mutation rate averaged over hundreds or thousands of generations. We infer a rate of 1.65 +/- 0.10 x 10^(-8) mutations per base per generation, which falls in between phylogenetic and pedigree-based estimates, and we suggest possible mechanisms to reconcile our estimate with previous studies. Our results support intermediate-age divergences among human populations and between humans and other great apes.

Link

February 23, 2015

Spread of Leprosy into Medieval Europe

Infection, Genetics and Evolution Volume 31, April 2015, Pages 250–256

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe

Helen D. Donoghue et al.

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th–11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th–8th century Northern Italy, 7th–11th century Hungary, 8th–9th century Austria, the Slavic Greater Moravian Empire of the 9th–10th century and 8th–10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.

Link

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.

Italic "Eteocretan" Sea peoples?

Stranger things have happened...

TALANTA XL-XLI (2008-2009), 151-172

AN ‘ETEOCRETAN’ INSCRIPTION FROM PRAISOS AND THE HOMELAND OF THE SEA PEOPLES

Luuk de Ligt

The whereabouts of the homeland or homelands of the so-called Sea Peoples have been endlessly debated. This article re-examines this problem by looking at one of the ‘Eteocretan’ inscriptions from the town of Praisos. It is argued that this text is written in an Indo-European language belonging to the OscanUmbrian branch of the Italic language family. Based on this finding it is suggested that this language must have arrived in eastern Crete during the Late Bronze Age, when Mycenaean rulers recruited groups of mercenaries from Sicily, Sardinia and various parts of the Italian peninsula. When the Mycenaean state system collapsed around 1200 BC, some of these groups moved to the northern Aegean, to Cyprus and to the coastal districts of the Levant. It is also suggested that this reconstruction explains the presence of an Etruscan-speaking community in sixth-century-BC Lemnos. An interesting corollary of this theory is that the Sea Peoples were present in the Mycenaean world some considerable time before its collapse in the early twelfth century

Link (pdf)

February 22, 2015

Y chromosomes and Catalan surnames

Some really rich data in the supplements.

European Journal of Human Genetics advance online publication 18 February 2015; doi: 10.1038/ejhg.2015.14

Y-chromosome diversity in Catalan surname samples: insights into surname origin and frequency

Neus Solé-Morata et al.

The biological behavior of the Y chromosome, which is paternally inherited, implies that males sharing the same surname may also share a similar Y chromosome. However, socio-cultural factors, such as polyphyletism, non-paternity, adoption, or matrilineal surname transmission, may prevent the joint transmission of the surname and the Y chromosome. By genotyping 17 Y-STRs and 68 SNPs in ~2500 male samples that each carried one of the 50 selected Catalan surnames, we could determine sets of descendants of a common ancestor, the population of origin of the common ancestor, and the date when such a common ancestor lived. Haplotype diversity was positively correlated with surname frequency, that is, rarer surnames showed the strongest signals of coancestry. Introgression rates of Y chromosomes into a surname by non-paternity, adoption, and transmission of the maternal surname were estimated at 1.5−2.6% per generation, with some local variation. Average ages for the founders of the surnames were estimated at ~500 years, suggesting a delay between the origin of surnames (twelfth and thirteenth centuries) and the systematization of their paternal transmission. We have found that, in general, a foreign etymology for a surname does not often result in a non-indigenous origin of surname founders; however, bearers of some surnames with an Arabic etymology show an excess of North African haplotypes. Finally, we estimate that surname prediction from a Y-chromosome haplotype, which may have interesting forensic applications, has a ~60% sensitivity but a 17% false discovery rate.

Link

Multiple opportunities for Out-of-Africa

Geology doi: 10.1130/G36401.1

Alluvial fan records from southeast Arabia reveal multiple windows for human dispersal

Ash Parton et al.

The dispersal of human populations out of Africa into Arabia was most likely linked to episodes of climatic amelioration, when increased monsoon rainfall led to the activation of drainage systems, improved freshwater availability, and the development of regional vegetation. Here we present the first dated terrestrial record from southeast Arabia that provides evidence for increased rainfall and the expansion of vegetation during both glacial and interglacial periods. Findings from extensive alluvial fan deposits indicate that drainage system activation occurred during Marine Isotope Stage (MIS) 6 (ca. 160–150 ka), MIS 5 (ca. 130–75 ka), and during early MIS 3 (ca. 55 ka). The development of active freshwater systems during these periods corresponds with monsoon intensity increases during insolation maxima, suggesting that humid periods in Arabia were not confined to eccentricity-paced deglaciations, and providing paleoenvironmental support for multiple windows of opportunity for dispersal out of Africa during the late Pleistocene.

Link

February 20, 2015

Bronze Age mixing of multiple populations => Armenians (?)

As far as I can tell, the hypothesis of "several mixtures" comes from looking at many pairs of populations and seeing that different types of pairs seem like they mixed to make Armenians. Possibility (1) is that Armenians have multiple mixtures, and possibility (2) is that none of the sources work very well.

Hellenthal et al. did not find mixture in Armenians, but they worked with a different methodology and smaller sample size. Either, the N=173 sample size enabled detection of this admixture, or differences in methodology account for differences in conclusions. If true, the admixture dates in this paper would be some of the earliest discovered by looking at modern populations (without the help of ancient DNA).

The TreeMix analysis (Figure 4) is inconclusive about admixture from a population best represented by Neolithic Europeans. There is no plot of residuals in this figure, so this model with one migration event may not be adequate. Prior knowledge suggests that it isn't, as Pakistani and European populations have no admixture in Figure 4.

It's great that the authors will share their data!
ftp://ngs.sanger.ac.uk/scratch/project/team19/Armenian
As of this writing, the data is not "live"; it might appear when the paper is published.

bioRxiv doi: http://dx.doi.org/10.1101/015396

Genetic evidence for an origin of the Armenians from Bronze Age mixing of multiple populations

Marc Haber et al.

The Armenians are a culturally isolated population who historically inhabited a region in the Near East bounded by the Mediterranean and Black seas and the Caucasus, but remain underrepresented in genetic studies and have a complex history including a major geographic displacement during World War One. Here, we analyse genome-wide variation in 173 Armenians and compare them to 78 other worldwide populations. We find that Armenians form a distinctive cluster linking the Near East, Europe, and the Caucasus. We show that Armenian diversity can be explained by several mixtures of Eurasian populations that occurred between ~3,000 and ~2,000 BCE, a period characterized by major population migrations after the domestication of the horse, appearance of chariots, and the rise of advanced civilizations in the Near East. However, genetic signals of population mixture cease after ~1,200 BCE when Bronze Age civilizations in the Eastern Mediterranean world suddenly and violently collapsed. Armenians have since remained isolated and genetic structure within the population developed ~500 years ago when Armenia was divided between the Ottomans and the Safavid Empire in Iran. Finally, we show that Armenians have higher genetic affinity to Neolithic Europeans than other present-day Near Easterners, and that 29% of the Armenian ancestry may originate from an ancestral population best represented by Neolithic Europeans.

Link

February 19, 2015

Late (not necessarily steppe) split of Proto-Indo-European

This is the paper that I saw referenced in a previous study. As I suspected, the paper does not in fact provide support specifically for the steppe hypothesis, but only for a late split of Proto-Indo-European (that is consistent with the steppe hypothesis but not unique to it).

I don't know how well linguists have figured out how to estimate time depth; the fact that a small tweak in the methodology (compared to Bouckaert et al.) results in a 3,000 year drop in the estimated age of the PIE split does not add to my confidence about the robustness of this field. Regardless of which hypothesis one accepts, the PIE split occurred thousands of years before the first written monuments in any Indo-European language. For the time being, the ball is on the other side of the court, which may accept this finding or come up with another tweak in the methodology that gives yet another date.

In any case, accepting provisionally that the Chang et al. date is accurate then it falsifies the Anatolian farmer/IE language hypothesis. So, steppe aficionados can declare a partial victory, because there is one less opponent to worry about. Falsification of the Anatolian first farmer hypothesis is not a complete victory, as the PIE urheimat question is not a boxing match between Kurganists and Anatolianists, but rather a mêlée with many players holding on to their swords. So, if you're willing to believe that the methodology is mature enough and they finally "got it right", you need only find a PIE split around 6,000 years ago, but you need not find it on the steppe. 


ANCESTRY-CONSTRAINED PHYLOGENETIC ANALYSIS SUPPORTS THE INDO-EUROPEAN STEPPE HYPOTHESIS 

Will Chang et al.

Discussion of Indo-European origins and dispersal focuses on two hypotheses. Qualitative evidence from reconstructed vocabulary and correlations with archaeological data suggest that IndoEuropean languages originated in the Pontic-Caspian steppe and spread together with cultural innovations associated with pastoralism, beginning c. 6500–5500 bp. An alternative hypothesis, according to which Indo-European languages spread with the diffusion of farming from Anatolia, beginning c. 9500–8000 bp, is supported by statistical phylogenetic and phylogeographic analyses of lexical traits. The time and place of the Indo-European ancestor language therefore remain disputed. Here we present a phylogenetic analysis in which ancestry constraints permit more accurate inference of rates of change, based on observed changes between ancient or medieval languages and their modern descendants, and we show that the result strongly supports the steppe hypothesis. Positing ancestry constraints also reveals that homoplasy is common in lexical traits, contrary to the assumptions of previous work. We show that lexical traits undergo recurrent evolution due to recurring patterns of semantic and morphological change.



February 16, 2015

Turkic language family time depth: 204BC

From the paper:
The regular-sound-change tree estimates a mean divergence time between the outgroup Chuvash and other Turkic languages of 204 BCE, with a 95% credible interval of 605 BCE to 81 CE. This compares to proposals from glottochronological analyses that suggest dates of 30 BCE to 0 CE [21] and 500 BCE to 50 CE from historical data [18, 21 and 22]. The sporadic-sound-change model estimates the mean age of the tree to be more than two millennia older (2408 BCE, 95% CI = 3994–1279 BCE), because it wrongly assumes that the many occurrences of regular sound change along the outgroup Chuvash branch are multiple instances of independent phonological change.
Current Biology Volume 25, Issue 1, 5 January 2015, Pages 1–9

Detecting Regular Sound Changes in Linguistics as Events of Concerted Evolution

Daniel J. Hruschka et al.

Summary

Background

Concerted evolution is normally used to describe parallel changes at different sites in a genome, but it is also observed in languages where a specific phoneme changes to the same other phoneme in many words in the lexicon—a phenomenon known as regular sound change. We develop a general statistical model that can detect concerted changes in aligned sequence data and apply it to study regular sound changes in the Turkic language family.

Results

Linguistic evolution, unlike the genetic substitutional process, is dominated by events of concerted evolutionary change. Our model identified more than 70 historical events of regular sound change that occurred throughout the evolution of the Turkic language family, while simultaneously inferring a dated phylogenetic tree. Including regular sound changes yielded an approximately 4-fold improvement in the characterization of linguistic change over a simpler model of sporadic change, improved phylogenetic inference, and returned more reliable and plausible dates for events on the phylogenies. The historical timings of the concerted changes closely follow a Poisson process model, and the sound transition networks derived from our model mirror linguistic expectations.

Conclusions

We demonstrate that a model with no prior knowledge of complex concerted or regular changes can nevertheless infer the historical timings and genealogical placements of events of concerted change from the signals left in contemporary data. Our model can be applied wherever discrete elements—such as genes, words, cultural trends, technologies, or morphological traits—can change in parallel within an organism or other evolving group.

Link

February 13, 2015

Why do East Asians have more Neandertal ancestry than Europeans?

This is quite the paradox, because even though Neandertals are now known to have existed all the way to the Altai, they were still overall a West Eurasian-distributed species. As far as I can tell, three explanations have been proposed: (1) East Asians have at least one extra Neandertal admixture event on top of what all Eurasians share, (2) West Eurasians have at least one admixture event that reduces their Neandertal ancestry relative to what all Eurasians share, (3) Neither of them have any such events, but natural selection has acted to reduce Neandertal alleles more in Europeans than East Asians.

I don't really have an opinion on this highly technical subject, but a couple of papers in AJHG make the case for (1 or 2) and 2, and against (3).

AJHG doi:10.1016/j.ajhg.2015.01.006

Complex History of Admixture between Modern Humans and Neandertals

Benjamin Vernot, Joshua M. Akey

Recent analyses have found that a substantial amount of the Neandertal genome persists in the genomes of contemporary non-African individuals. East Asians have, on average, higher levels of Neandertal ancestry than do Europeans, which might be due to differences in the efficiency of purifying selection, an additional pulse of introgression into East Asians, or other unexplored scenarios. To better define the scope of plausible models of archaic admixture between Neandertals and anatomically modern humans, we analyzed patterns of introgressed sequence in whole-genome data of 379 Europeans and 286 East Asians. We found that inferences of demographic history restricted to neutrally evolving genomic regions allowed a simple one-pulse model to be robustly rejected, suggesting that differences in selection cannot explain the differences in Neandertal ancestry. We show that two additional demographic models, involving either a second pulse of Neandertal gene flow into the ancestors of East Asians or a dilution of Neandertal lineages in Europeans by admixture with an unknown ancestral population, are consistent with the data. Thus, the history of admixture between modern humans and Neandertals is most likely more complex than previously thought.

Link

AJHG doi:10.1016/j.ajhg.2014.12.029

Selection and Reduced Population Size Cannot Explain Higher Amounts of Neandertal Ancestry in East Asian than in European Human Populations

Bernard Y. Kim, Kirk E. Lohmueller

It has been hypothesized that the greater proportion of Neandertal ancestry in East Asians than in Europeans is due to the fact that purifying selection is less effective at removing weakly deleterious Neandertal alleles from East Asian populations. Using simulations of a broad range of models of selection and demography, we have shown that this hypothesis cannot account for the higher proportion of Neandertal ancestry in East Asians than in Europeans. Instead, more complex demographic scenarios, most likely involving multiple pulses of Neandertal admixture, are required to explain the data.

Link

February 12, 2015

A story of 69 ancient Europeans

A new study on the bioRxiv includes data on 69 ancient Europeans (remember when we got excited in anticipation for the single genome of the Iceman? that was only three years ago) and adds plenty of new info to chew on for those of us interested in prehistory. 

Two Near Eastern migrations into Europe

In 2011, I observed that West Eurasian populations were too close (measured by Fst) to allow for long periods of differentiation between them. By implication, there must have been a "common source" of ancestry uniting them, which I placed in a "womb of nations" of the Neolithic Near East. I proposed that migrations out of this core area homogenized West Eurasians, writing:
In Arabia, the migrants would have met aboriginal Arabians, similar to their next door-neighbors in East Africa, undergoing a subtle African shift (Southwest_Asians). In North Africa, they would have encountered denser populations during the favorable conditions of MIS 1, and by absorbing them they would became the Berbers (Northwest_Africans). Their migrations to the southeast brought them into the realm of Indian-leaning people, in the rich agricultural fields of the Mehrgarh and the now deserted oases of Bactria and Margiana. Across the Mediterranean and along the Atlantic facade of Europe, they would have encountered the Mesolithic populations of Europe, and through their blending became the early Neolithic inhabitants of the Mediterranean and Atlantic coasts of Europe (Mediterraneans). And, to the north, from either the Balkans, the Caucasus, or the trans-Caspian region, they would have met the last remaining Proto-Europeoid hunters of the continental zone, becoming the Northern Europeoids who once stretched all the way to the interior of Asia.
The new paper confirms the last two of these migrations. The remainder involve parts of the world from which no ancient DNA has been studied.

The first migration (early Neolithic) is already uncontroversial, but the paper includes data from Spanish early farmers that are also Sardinian- and LBK-like. The "Sardinian" Iceman was no fluke. It is now proven that not only the LBK but also the Spanish Neolithic came from the same expansion of Mediterranean populations which survives in Sardinia. The authors write:
Principal components analysis (PCA) of all ancient individuals along with 777 present-day West Eurasians4 (Fig. 2a, SI5) replicates the positioning of present-day Europeans between the Near East and European hunter-gatherers4,20, and the clustering of early farmers from across Europe with present day Sardinians3,4,27, suggesting that farming expansions across the Mediterranean to Spain and via the Danubian route to Hungary and Germany descended from a common stock.
The second migration went into eastern Europe:
The Yamnaya differ from the EHG by sharing fewer alleles with MA1 (|Z|=6.7) suggesting a dilution of ANE ancestry between 5,000-3,000 BCE on the European steppe. This was likely due to admixture of EHG with a population related to present-day Near Easterners, as the most negative f3-statistic in the Yamnaya (giving unambiguous evidence of admixture) is observed when we model them as a mixture of EHG and present-day Near Eastern populations like Armenians (Z = -6.3; SI7).
The EHG (Eastern European Hunter-Gatherers) are likely Proto-Europeoid foragers and the Yamnaya (a Bronze Age Kurgan culture) were a mixture of the EHG and something akin to Armenians.The "attraction" of later groups to the Near East is clear in the PCA: hunter-gatherers on the left side, the Near East (as grey dots) on the right side, and Neolithic/Bronze Age/modern Europeans in the middle. The second migration may very well be related to the Uruk expansion and the presence of gracile Mediterranoids and robust Proto-Europeoids in the Yamna:
The Yamna population generally belongs to the European race. It was tall (175.5cm), dolichocephalic, with broad faces of medium height. Among them there were, however, more robust elements with high and wide faces of the proto-Europoid type, and also more gracile individuals with narrow and high faces, probably reflecting contacts with the East Mediterranean type (Kurts 1984: 90).
The authors present a table of Fst values which confirms the homogenizing influence of migrations from the Near East. The WHG group has an Fst=0.086 with Armenians, but the LBK farmers have only 0.023. The EHG group has an Fst=0.067 with Armenians, but the Yamnaya steppe people have only 0.030. Someone might argue that it is the Armenians that are receiving genes from Europe, but the same pattern holds even for the Bedouins, for which admixture with Europeans seems far-fetched: 0.106 to 0.043 and 0.093 to 0.060. It is now clear that the "glue" that did not allow West Eurasian populations to drift very far apart were migrations from the Near East.

The (partial) demise of the farmers

It seems that the legacy of the early farmers suffered two hits, which is why only in Sardinia and (to a lesser degree) in southern Europe that they have persisted as the major component of ancestry. The first blow came during the Neolithic:
Middle Neolithic Europeans from Germany, Spain, Hungary, and Sweden from the period ~4,000-3,000 BCE are intermediate between the earlier farmers and the WHG, suggesting an increase of WHG ancestry throughout much of Europe.
And the coup de grâce after the 5kya mark:
We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG. The estimate of Yamnaya related ancestry in the Corded Ware is consistent when using either present populations or ancient Europeans as outgroups (SI9, SI10), and is 73.1 ± 2.2% when both sets are combined (SI10). [...] The magnitude of the population turnover that occurred becomes even more evident if one considers the fact that the steppe migrants may well have mixed with eastern European agriculturalists on their way to central Europe. Thus, we cannot exclude a scenario in which the Corded Ware arriving in today’s Germany had no ancestry at all from local populations.
Confirmation of the Bronze Age Indo-European invasion of Europe

In 2012 I had used the paltry data on a handful ancient DNA samples to observe that in ADMIXTURE modern Europeans had a West Asian genetic component (peaking in "Caucasus" and "Gedrosia") that pre-5kya Europeans didn't. I proposed that the Bronze Age migration of the Indo-Europeans spread this component:
But there is another component present in modern Europe, the West_Asian which is conspicuous in its absence in all the ancient samples so far. This component reaches its highest occurrence in the highlands of West Asia, from Anatolia and the Caucasus all the way to the Indian subcontinent. [...] Nonetheless, some of the legacy of the earliest Indo-European speakers does appear to persist down to the present day in the genomes of their linguistic descendants, and I predict that when we sample later (post 5-4kya) individuals we will finally find the West_Asian piece that is missing from the European puzzle.
This prediction is now confirmed:
This pattern is also seen in ADMIXTURE analysis (Fig. 2b, SI6), which implies that the Yamnaya have ancestry from populations related to the Caucasus and South Asia that is largely absent in 38 Early or Middle Neolithic farmers but present in all 25 Late Neolithic or Bronze Age individuals. This ancestry appears in Central Europe for the first time in our series with the Corded Ware around 2,500 BCE (SI6, Fig. 2b, Extended Data Fig. 1).
I was a little puzzled with the "Ancient North Eurasians" recently proposed as a "third ancestral population" for Europeans: it seemed to be a tertium quid that spread after 5kya, but very different geographically than the "West Asian" component. But:
These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6).
So, it seems that there is no contradiction after all and both EHG (which is related to "Ancient North Eurasians") and another type of Near Eastern ancestry (=West_Asian) arrived after 5kya.

1939 strikes back

It is amazing how well this was anticipated by Carleton Coon in 1939. Back then much of West Eurasia was an archaeological/anthropological terra incognita, there was no radiocarbon dating, no DNA, no computers, not even serious multivariate statistics. And yet:
We shall see, in our survey of prehistoric European racial movements, 8 that the Danubian agriculturalists of the Early Neolithic brought a food-producing economy into central Europe from the East. They perpetuated in the new European setting a physical type which was later supplanted in their original home. Several centuries later the Corded people, in the same way, came from southern Russia but there we first find them intermingled with other peoples, and the cul-tural factors which we think of as distinctively Corded are included in a larger cultural equipment. [...] On the basis of the physical evidence as well, it is likely that the Corded people came from somewhere north or east of the Black Sea. The fully Neolithic crania from southern Russia which we have just studied include such a type, also seen in the midst of Sergi's Kurgan aggregation. Until better evidence is produced from elsewhere, we are entitled to consider southern Russia the most likely way station from which the Corded people moved westward.
And in 2015:
Our results support a view of European pre-history punctuated by two major migrations: first, the arrival of first farmers during the Early Neolithic from the Near East, and second of Yamnaya pastoralists during the Late Neolithic from the steppe (Extended Data Fig. 5).
In 1939:
Linguistically, Indo-European is probably a relatively recent phenomenon, which arose after animals had been tamed and plants cultivated. The latest researches find it to be a derivative of an initially mixed language, whose principal elements were Uralic, called element A, and some undesignated element B which was probably one of the eastern Mediterranean or Caucasic languages. 5 The plants and animals on which the Somewhere in the plains of southern Russia or central Asia, the blending of languages took place which resulted in Indo-European speech. This product in turn spread and split, and was further differentiated by mixture with the languages of peoples upon whom it, in one form or other, was imposed. Some of the present Indo-European languages, in addition to these later accretions from non-Indo-European tongues, contain more of the A element than others, which contain more of the B. The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete. 
In 2015:
These results can be explained if the new genetic material that arrived in Germany was a composite of two elements: EHG and a type of Near Eastern ancestry different from that which was introduced by early farmers (also suggested by PCA and ADMIXTURE; Fig. 2, SI5, SI6). We estimate that these two elements each contributed about half the ancestry each of the Yamnaya (SI6, SI9), explaining why the population turnover inferred using Yamnaya as a source is about twice as high compared to the undiluted EHG.
The EHG is still flimsy as it's only two individuals from Karelia and Samara who are very similar to each other. It's hard not to imagine that the hunter-gatherer from Russian Karelia (outside any proposed PIE homeland) would be speaking a similar language as his Samara counterpart. Did they both speak "element A" and was PIE formed when the "southern" steppe hunter-gatherers came into contact with "element B" people from the Caucasus? Short of a time machine, we can never say for sure. This might very well be an answer to the conundrum of Uralic/Proto-Kartvelian borrowings. There is simply no geographical locale in which these two language families neighbor each other: Northwest, Northeast Caucasian speakers and the pesky Greater Caucasus intervene. But, maybe there was no such locale, and these borrowings aren't due to some "PIE people" living adjacent to Uralic and Proto-Karvelian speakers but the "PIE people" being a mix of an element A (EHG) that was (or interacted with) Uralic and another element B (Armenian-like) that was (or interacted with) Proto-Kartvelian.

Urheimat (or not?)

The authors of the current paper are agnostic about the PIE homeland:
We caution that the location of the Proto-Indo-European9,27,29,30 homeland that also gave rise to the Indo-European languages of Asia, as well as the Indo-European languages of southeastern Europe, cannot be determined from the data reported here (SI11). Studying the mixture in the Yamnaya themselves, and understanding the genetic relationships among a broader set of ancient and present-day Indo-European speakers, may lead to new  insight about the shared homeland.
Whatever the ultimate answer will be, it seems that Coon was right that "The unity of the original " Indo- Europeans," could not have been of long duration, if it was ever complete." If PIE=EHG (as Anthony and Ringe suggest), then "from the crib", PIE got half its ancestry from a non-IE, Near Eastern source. Conversely, if PIE=Near East (as I suggested) then "from the crib", PIE got half of its ancestry from a non-IE, Eastern European source. The "Yamnaya" seems to max out in Norwegians at around half, which means that they are about a quarter Proto-Indo-European genetically, regardless of which theory is right.

These two possibilities (as well as the third one of PIE being neither-nor, but rather a linguistic mixture of the languages of the EHG and Near East) are testable. The Anthony/Ringe version of the steppe hypothesis predicts pre-Yamnaya expansions from the steppe. Whether these happened and what was their makeup can be tested: if they did occur and they did lack "Near Eastern" ancestry, then the steppe hypothesis will be proven. PIE in the Near East, on the other hand, predicts that some PIE languages (certainly the Anatolian ones) will be a "within the Near East" expansion. If such migrations did occur and they lacked "EHG" ancestry, then some variant of the Gamkrelidze/Ivanov model will be proven. Or, the truth might be that everywhere where Indo-Europeans arrive they carry a blend of "West Asian" and "EHG", supporting the third possibility. Time will tell.

In the interim, I am curious about how much Yamnaya ancestry existed in different parts of Europe (all of the post-5kya samples in this study come from Germany, with a couple from Hungary). In northern Europe, all populations seem to have less Yamnaya ancestry than the Corded Ware: there it must have declined. But, modern Hungarians have more than Bronze Age Hungarians: there it must have increased.

Germany and a slice of Hungary is a very narrow window through which to see the whole of Europe and these results must be tested by looking at samples from beyond the "heartland". I do hope that some kind of Moore's law operates in the world of ancient DNA, and in three more years we'll be reading studies about thousands of ancient individuals.

bioRxiv doi: http://dx.doi.org/10.1101/013433
Massive migration from the steppe is a source for Indo-European languages in Europe

Wolfgang Haak , Iosif Lazaridis , Nick Patterson , Nadin Rohland , Swapan Mallick , Bastien Llamas , GuidoBrandt , Susanne Nordenfelt , Eadaoin Harney , Kristin Stewardson , Qiaomei Fu , Alissa Mittnik , Eszter Banffy ,Christos Economou , Michael Francken , Susanne Friederich , Rafael Garrido Pena , Fredrik Hallgren , ValeryKhartanovich , Aleksandr Khokhlov , Michael Kunst , Pavel Kuznetsov , Harald Meller , Oleg Mochalov ,Vayacheslav Moiseyev , Nicole Nicklisch , Sandra L. Pichler , Roberto Risch , Manuel A. Rojo Guerra , ChristinaRoth , Anna Szecsenyi-Nagy , Joachim Wahl , Matthias Meyer , Johannes Krause , Dorcas Brown , DavidAnthony , Alan Cooper , Kurt Werner Alt , David Reich

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6. By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe.

Link