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Sunday, March 26, 2017

The Medieval pilgrim

Recently at PLoS Neglected Tropical Diseases:

Abstract: We have examined the remains of a Pilgrim burial from St Mary Magdalen, Winchester. The individual was a young adult male, aged around 18–25 years at the time of death. Radiocarbon dating showed the remains dated to the late 11th–early 12th centuries, a time when pilgrimages were at their height in Europe. Several lines of evidence in connection with the burial suggested this was an individual of some means and prestige. Although buried within the leprosarium cemetery, the skeleton showed only minimal skeletal evidence for leprosy, which was confined to the bones of the feet and legs. Nonetheless, molecular testing of several skeletal elements, including uninvolved bones all showed robust evidence of DNA from Mycobacterium leprae, consistent with the lepromatous or multibacillary form of the disease. We infer that in life, this individual almost certainly suffered with multiple soft tissue lesions. Genotyping of the M.leprae strain showed this belonged to the 2F lineage, today associated with cases from South-Central and Western Asia. During osteological examination it was noted that the cranium and facial features displayed atypical morphology for northern European populations. Subsequently, geochemical isotopic analyses carried out on tooth enamel indicated that this individual was indeed not local to the Winchester region, although it was not possible to be more specific about their geographic origin.


During analysis, the cranial morphology of the individual was noted as being of an unusual type and unlike other individuals from the cemetery (Fig 4). Therefore, the cranial measurements (S1 Table) were inputted into FORDISC and CRANID, with additional measurements being taken where necessary. The individual was found not to have an affinity with any of the populations contained within the program databases, which do include some from northern Europe, although not Britain. Therefore, the individual could be said not to share a physical affinity with these northern European samples, although this should not be taken as implying anything about their specific identity or origin. Populations that are poorly represented in the database include those from southern Europe and northern Africa (with the exception of Egypt), so there is a possibility that the individual could share physical cranial affinities with such populations, as his cranial morphology does bear similarities to other individuals from British archaeological populations who were also unclassifiable by FORDISC and have been suggested, on isotopic data, to originate from these areas [20]; (Stephany Leach personal communication, 2012).

Citation: Roffey S, Tucker K, Filipek-Ogden K, Montgomery J, Cameron J, O’Connell T, et al. (2017) Investigation of a Medieval Pilgrim Burial Excavated from the Leprosarium of St Mary Magdalen Winchester, UK. PLoS Negl Trop Dis 11(1): e0005186. doi:10.1371/journal.pntd.0005186

Wednesday, March 22, 2017

Trouble in early Mesolithic Iberia

Humans may have dined on other humans during the Epipalaeolithic-Mesolithic transition in Iberia, according to a new paper at the Journal of Anthropological Archaeology.

If true, I wonder if this had anything to do with the spread of the so called Villabruna cluster across Europe at around that time? I'm not suggesting that Villabruna forager bands ate most of the other European foragers, but rather that they coped best with the stresses associated with the Epipalaeolithic-Mesolithic transition.

The paper is behind a pay wall, but the figures can be viewed here.

Abstract: The identification of unarticulated human remains with anthropic marks in archaeological contexts normally involves solving two issues: a general one associated with the analysis and description of the anthropic manipulation marks, and another with regard to the interpretation of their purpose. In this paper we present new evidence of anthropophagic behaviour amongst hunter-gatherer groups of the Mediterranean Mesolithic. A total of 30 human remains with anthropic manipulation marks have been found in the Mesolithic layers of Coves de Santa Maira (Castell de Castells, Alicante, Spain), dating from ca. 10.2–9 cal ky BP. We describe the different marks identified on both human and faunal remains at the site (lithic, tooth, percussion and fire marks on bone cortex). As well as describing these marks, and considering that both human and faunal remains at the site present similar depositional and taphonomic features, this paper also contextualizes them within the archaeological context and subsistence patterns described for Mesolithic groups in the region. We cannot entirely rule out the possibility that these practices may be the result of periodic food stress suffered by the human populations. These anthropophagic events at the site coincide with a cultural change at the regional Epipalaeolithic-Mesolithic transition.

Morales-Pérez et al., Funerary practices or food delicatessen? Human remains with anthropic marks from the Western Mediterranean Mesolithic, Journal of Anthropological Archaeology, Volume 45, March 2017, Pages 115–130,

Southern European blues

Not sold on this; not unless we see direct evidence from ancient DNA:

Abstract: Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.

Pereira et al., Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe, Proceedings of the Royal Society B, Published 22 March 2017.DOI: 10.1098/rspb.2016.1976

Saturday, March 18, 2017

Greek confirmation bias

A new paper at the EJHG claims that Slavic admixture in Peloponnesean Greeks averages a few per cent at best (see abstract below). However, I'd say the authors are making two potentially erroneous assumptions: 1) that Slavic invaders arrived in Greece straight from the Slavic homeland, probably located somewhere in East Central or Eastern Europe, and 2) modern-day Northern Slavs (Belarusians, Poles, Russians and Ukrainians) are accurate proxies for these ancient invaders.

Keep in mind that when the Slavs moved into the Balkans during the Early Middle Ages, they routinely absorbed the natives into their bands as free men and women (excellent paper on the topic here). So their numbers swelled thanks to this more southerly, local input, and, at the same time, their genetic structure shifted in a big way, probably from more or less Northern Slavic to modern-day Southern Slavic. Indeed, it's likely that by the time they arrived in the Peloponnese, they were less like this and more like this, or even this.

So was Fallmerayer correct when he theorized that the Peloponnese was totally re-populated by Slavs during the Medieval period? Probably not, but the population shift may still have been profound, and totaling much more than a few per cent.

I can't wait for more ancient DNA from Greece and Italy, especially from the Bronze and Iron Ages. Based on my experiences with many Greeks and Italians, it's sure to be a big eye opener for them, and a beautiful thing.

Abstract: Peloponnese has been one of the cradles of the Classical European civilization and an important contributor to the ancient European history. It has also been the subject of a controversy about the ancestry of its population. In a theory hotly debated by scholars for over 170 years, the German historian Jacob Philipp Fallmerayer proposed that the medieval Peloponneseans were totally extinguished by Slavic and Avar invaders and replaced by Slavic settlers during the 6th century CE. Here we use 2.5 million single-nucleotide polymorphisms to investigate the genetic structure of Peloponnesean populations in a sample of 241 individuals originating from all districts of the peninsula and to examine predictions of the theory of replacement of the medieval Peloponneseans by Slavs. We find considerable heterogeneity of Peloponnesean populations exemplified by genetically distinct subpopulations and by gene flow gradients within Peloponnese. By principal component analysis (PCA) and ADMIXTURE analysis the Peloponneseans are clearly distinguishable from the populations of the Slavic homeland and are very similar to Sicilians and Italians. Using a novel method of quantitative analysis of ADMIXTURE output we find that the Slavic ancestry of Peloponnesean subpopulations ranges from 0.2 to 14.4%. Subpopulations considered by Fallmerayer to be Slavic tribes or to have Near Eastern origin, have no significant ancestry of either. This study rejects the theory of extinction of medieval Peloponneseans and illustrates how genetics can clarify important aspects of the history of a human population.

Stamatoyannopoulos et al., Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks, European Journal of Human Genetics advance online publication 8 March 2017; doi: 10.1038/ejhg.2017.18

Friday, March 17, 2017

Yamnaya X chromosomes

In this analysis I'm using the same qpAdm method and almost the same reference samples as Lazaridis & Reich 2017. However, to improve the resolution, in the right pops (or outgroups) I added European Late Upper Paleolithic forager Villabruna, and dropped the low quality Siberian Late Upper Paleolithic forager AfontovaGora3. Also, I ran tests with and without the allsnps: YES flag.

In the left pops, apart from test group Steppe_EMBA (Early Middle Bronze Age steppe conglomerate made up of closely related Afanasievo, Poltavka and Yamnaya samples), we have the putative ancestral populations: Eastern European Hunter-Gatherers (EHG), Caucasus Hunter-Gatherers (CHG), Kura-Araxes (Armenia_EBA), a Chalcolithic Anatolian (Anatolia_ChL), Chalcolithic Armenians (Armenia_ChL), and/or Chalcolithic farmers from Iran (Iran_ChL).

As far as I can tell, these are the best statistical fits with the X chromosome and genome-wide data, respectively. Feel free to set me straight; the full output is in a zip file here.


Steppe_EMBA X
CHG 0.617±0.178
EHG 0.383±0.178
chisq 1.868 taildiff 0.93139015
allsnps: YES

Anatolia_ChL 0.139±0.050
CHG 0.356±0.063
EHG 0.505±0.025
chisq 5.084 taildiff 0.405658017
allsnps: YES

In my opinion, despite the relatively low resolution of the X chromosome analysis, the Steppe_EMBA X chromosomes show a strong southern, in particular CHG, character, which suggests that CHG admixture into Steppe_EMBA was mediated largely via female gene flow.

Interestingly, in one of the models, the Steppe_EMBA X chromosomes are fitted successfully as a two-way mixture of CHG and Iran_ChL (see here). It's impossible to model Steppe_EMBA in such a way with genome-wide data (for instance, see here and here).

Wednesday, March 15, 2017

Failure to replicate

Just in at bioRxiv:

We fail to replicate a genetic signal for sex bias in the steppe migration to central Europe after ~5,000 years proposed by Goldberg et al. PNAS 114(10):2657-2662. Estimation of X-chromosome steppe ancestry in the Bronze Age central European population with the qpAdm method (Haak et al. Nature 522, 207-11) does not indicate lower steppe ancestry on the X-chromosome than in the autosomes. We perform a simulation which indicates presence of estimation bias of -19.5% in the inference of X-chromosome admixture proportions using the method used by Goldberg et al., largely eliminating the observed sex bias.

Iosif Lazaridis, David Reich, Failure to Replicate a Genetic Signal for Sex Bias in the Steppe Migration into Central Europe, Posted March 14, 2017, doi:

Tuesday, March 14, 2017

Epic fail

This is the somewhat dubious conclusion from a new paper by Balanovsky et al. at Human Genetics dealing with, amongst other things, Y-chromosomes of the Early Bronze Age Yamnaya people:

The currently available dataset does not contradict the hypothesis that R-GG400 marks a link between the East European steppe dwellers and West Asians, though the route and even direction of this migration is disputable. It does, however, demonstrate that present-day West European R1b chromosomes do not originate from the Yamnaya populations analyzed in (Haak et al. 2015; Mathieson et al. 2015) and raises the question of their origin. A Bronze Age origin is more likely than a Neolithic one (Balaresque et al. 2010), but further ancient DNA studies may be necessary to identify this source.

More to the point, the authors are trying to argue the following two rather far-fetched and tenuous positions:

- R1b-GG400, the most common Y-haplogroup in Yamnaya samples sequenced to date, moved into Eastern Europe from West Asia, and therefore the Indo-European homeland was in West Asia

- there was no massive Kurgan expansion deep into Europe from the Pontic-Caspian Steppe, because the most common type of R1b in much of Europe is R1b-L51 and not R1b-GG400.

What they're ignoring is that a wide range of European Upper Paleolithic and Mesolithic foragers, mostly from Eastern Europe, belong to R1b, including R1b-P297, the ancestral lineage to both R1b-GG400 and R1b-L51 (see here and here). On the other hand, not a single West Asian forager or even Neolithic farmer as yet belongs to R1b (see here).

Hence, even though it's still possible that R1b-GG400 moved into Eastern Europe from West Asia, it's no longer a parsimonious or convincing theory because it's contradicted by direct evidence from currently available ancient DNA.

The authors are also ignoring very solid evidence from genome-wide data that Yamnaya, or closely related populations from the Pontic-Caspian Steppe, contributed in a big way to the ethnogenesis of modern-day Europeans. Considering that R1b-L51 is a sister clade of R1b-GG400, it's only logical to think that it could have been one of the main Y-chromosome haplogroups associated with this event.

The paper has some nice data and maps, but it's an epic fail as a whole, because it's basically an exercise in confirmation bias.


Balanovsky, O., Chukhryaeva, M., Zaporozhchenko, V. et al., Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia, Hum Genet (2017). doi:10.1007/s00439-017-1770-2

Monday, March 13, 2017

Ancient Egyptians less Sub-Saharan than modern-day Egyptians

SAA 2017 abstracts are now online (see here). Thanks to Sarkoboros for the remainder. I reckon dead cat bounce man Johannes Krause is gonna steal the show this year, unless Afrocentrics get him beforehand. Stay alert Johannes.

Ancient Egyptian Mummy Genomes Suggest an Increase of Sub-Saharan African Ancestry in Post-Roman Periods

Krause et al.

Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia, and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we mtDNA and nuclear DNA from mummified humans recovered from Middle Egypt that span around 1,300 years of ancient Egyptian history from the Third Intermediate to the Roman Period. Our analyses reveal that ancient Egyptians shared more Near Eastern ancestry than present-day Egyptians, who received additional Sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt’s past at a genome-wide level.

Sunday, March 12, 2017

Eastern Scythians = Steppe_MLBA + East Eurasians

OK, I said I wasn't going to make any bold statements in regards to this issue until we see more ancient genomes from Central Asia, but I'm pretty sure now that the steppe ancestry in the eastern Scythians from Unterländer et al. is mostly of the Steppe Middle Late Bronze Age (Steppe_MLBA) kind, rather than the Steppe Early Middle Bronze Age (Steppe_EMBA) kind.

For background info, refer to the discussion in the comments here. Now, check out the graph below (based on the datasheet here). I see four things when I look at this model:

- Steppe_MLBA and Steppe_EMBA are different because the former show excess Central European Middle Neolithic (Central_MN) affinity, and thus cluster at the top of the graph and above the line of best fit, while the latter show excess Caucasus Hunter-Gatherer (Caucasus_HG) affinity, and so cluster at the top of the graph but below the line of best fit

- Indo-Aryan-speaking South Asians fall below the line of best fit, which suggests that they don't have much, if any, Central_MN ancestry, so they're probably largely of Steppe_EMBA origin (though their Iran Neolithic-related farmer ancestry might be skewing things to some extent here, because it's more closely related to Caucasus_HG than to Central_MN)

- Both the ancient and most modern-day Eastern Iranian-speakers (Sarmatians and Pamir Tajiks, respectively) more or less hug the line of best fit, suggesting that they're a mixture of Steppe_MLBA and Steppe_EMBA

- all of the Scythians fall above the line of best fit, suggesting that their steppe ancestry largely derives from Steppe_MLBA.

As per point 2, it's possible that the outcomes for the South and also Central Asians are skewed by their Iran Neolithic-related farmer ancestry, but this shouldn't be much of an issue for the eastern Scythians, and if it is, then in fact their Central_MN/Steppe_MLBA affinity is being underestimated here.

Moreover, word around the campfire is that the R1a-Z93 in the eastern Scythian bam files is of the same type as in the Sintashta samples (Z2124+). Not 100% sure if that's true, but it might well be, because it lines up very nicely with the above graph.


Unterländer et al., Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe, Nature Communications 8, Article number: 14615 (2017), doi:10.1038/ncomms14615

Friday, March 10, 2017

Bring it on

AdmixTools 5 is now available at GitHub (see here). I'm messing around with the latest version of qpAdm as I await the expected flood of new ancient samples. Based on first impressions, I'd say it's sharper than previous versions. Here's an attempt to hone in on Yamnaya's ancestral makeup; note that the best statistical fits are clearly those with the spatiotemporally closest genomes.


Caucasus_HG 0.534±0.022
Eastern_HG 0.466±0.022
chisq 42.494 taildiff 2.66849158e-06

Eastern_HG 0.569±0.016
Iran_Chalcolithic 0.431±0.016
chisq 31.790 taildiff 0.000216504253

Eastern_HG 0.572±0.018
Iran_Neolithic 0.233±0.027
Lengyel_LN 0.195±0.019
chisq 26.291 taildiff 0.0009363224

Caucasus_HG 0.361±0.036
Eastern_HG 0.518±0.021
Lengyel_LN 0.121±0.023
chisq 12.737 taildiff 0.121217144

Kotias_HG 0.367±0.047
Lengyel_LN 0.103±0.031
Samara_HG 0.530±0.027
chisq 9.531 taildiff 0.299484439

I also had a quick look at South Asia. The likely Eastern Iranian-speaking early Sarmatians from Pokrovka, Russia, recently published along with Unterländer et al., look like a decent enough reference for modern-day Eastern Iranians, but not for Indo-Aryans like the Kalasha and North Indian Brahmins. The latter prefer Ulan IV, the late Yamnaya/early Catacomb sample from Allentoft et al. 2015. It's an intriguing question why.


Iran_Neolithic 0.302±0.038
Onge 0.168±0.015
Sarmatian_Pokrovka 0.529±0.035
chisq 10.424 taildiff 0.107885899

Han 0.056±0.020
Iran_Neolithic 0.309±0.047
Onge 0.135±0.030
Ulan_IV 0.500±0.039
chisq 15.316 taildiff 0.00909576308

Han 0.059±0.015
Iran_Neolithic 0.276±0.045
Sarmatian_Pokrovka 0.665±0.048
chisq 4.603 taildiff 0.595657656

Han 0.098±0.015
Iran_Neolithic 0.266±0.052
Ulan_IV 0.637±0.052
chisq 12.971 taildiff 0.0434993304

Han 0.062±0.023
Iran_Neolithic 0.202±0.052
Onge 0.257±0.036
Ulan_IV 0.479±0.043
chisq 5.475 taildiff 0.360663358

Han 0.024±0.027
Iran_Neolithic 0.205±0.057
Onge 0.274±0.038
Sarmatian_Pokrovka 0.497±0.050
chisq 12.517 taildiff 0.0283534925

Han 0.045±0.022
Iran_Neolithic 0.263±0.052
Onge 0.145±0.034
Ulan_IV 0.547±0.043
chisq 8.424 taildiff 0.134346014

Han 0.004±0.026
Iran_Neolithic 0.261±0.055
Onge 0.159±0.036
Sarmatian_Pokrovka 0.576±0.048
chisq 15.002 taildiff 0.0103520115

As far as I can tell right now, the eastern Scythians from Unterländer et al. aren't all that relevant for South Asians. I'll wind things up here with models for a few more populations from Pakistan and India.

Han 0.023±0.021
Iran_Neolithic 0.520±0.047
Onge 0.081±0.033
Ulan_IV 0.376±0.039
chisq 6.495 taildiff 0.261028178

Han 0.028±0.022
Iran_Neolithic 0.563±0.047
Onge 0.061±0.034
Ulan_IV 0.348±0.039
chisq 4.247 taildiff 0.514456854

Han 0.095±0.032
Iran_Neolithic 0.151±0.064
Onge 0.696±0.047
Ulan_IV 0.058±0.053
chisq 5.942 taildiff 0.311882057

Han 0.060±0.033
Iran_Neolithic 0.333±0.066
Onge 0.464±0.049
Ulan_IV 0.144±0.054
chisq 2.644 taildiff 0.754673075

Han 0.022±0.024
Iran_Neolithic 0.692±0.068
Onge 0.013±0.037
Ulan_IV 0.269±0.052
Yoruba 0.004±0.009
chisq 3.455 taildiff 0.484741716

Han 0.020±0.022
Iran_Neolithic 0.202±0.047
Onge 0.421±0.033
Ulan_IV 0.356±0.039
chisq 8.263 taildiff 0.142329696

Han 0.023±0.020
Iran_Neolithic 0.320±0.044
Onge 0.229±0.032
Ulan_IV 0.429±0.036
chisq 6.431 taildiff 0.266528271