Ancient human DNA and proteomes at SAA 2017

I’m looking forward to the 82nd annual meeting of the Society for American Archaeology (Vancouver, BC, Canada: March 29–April 2, 2017) at the end of this month, which will be my first SAA.

Final program.
Individual abstracts.

This is a sprawling conference. I’ve spent a long while going through the entries and have highlighted some abstracts of special interest below — I’ll feature things that caught my eye from other domains of archaeology and non-human aDNA/proteome work in later posts.

Get in touch if you’d like to meet up when I’m there.

Click for index.

Genome-Wide Ancient DNA

“Native Americans” in Bronze Age Siberia?
Neolithic to Bronze Age Baikal
Third Intermediate to Roman Egypt
Refining radiocarbon dating with immediate relatives
LSA Malawi
Cuncaicha: 9–4ka in the high Andes
Demography and migration in Atacama
Coast Tsimshian
Shuar shrunken heads

Ancient Proteomics

Who made the Châtelperronian?

Ancient mtDNA and Y-DNA

California Penutian migrations
Pre-contact Athabaskans
Adunqiaolu, Bronze Age Xinjiang
Pre-Genghisid royal Mongols


GENOME-WIDE ANCIENT DNA

First, a plug for my own talk, which will be at 3:45pm on Thursday, March 30 in the Bioarchaeology and Genetics General Session (West Meeting Room 205, Vancouver Convention Centre):

[92] The Ones Who Stayed Behind? Genome-Wide Affinities of Okunev Remains from Bronze Age South Siberia and the Enduring Dialogue of Ancient DNA and Physical Anthropology

Kim, Alexander (Harvard University, Dept. of Anthropology), Alexander Kozintsev (Peter the Great Museum of Anthropology and Ethnography), Nadin Rohland (Dept. of Genetics, Harvard Medical School), Swapan Mallick (Dept. of Genetics, Harvard Medical School) and David Reich (Dept. of Genetics, Harvard Medical School; Howard Hughes Medical Institute; Broad Institute of MIT and Harvard)

Genome-wide ancient DNA data from Upper Paleolithic Siberians and deep time series in Europe challenge many traditional models of relationships between Native Americans, West Eurasians, and East Asians—commonplace units in physical anthropology—by recasting them as fusions of prehistoric ancestry streams that may unexpectedly cross-cut or fracture these categories. We evaluate new and published genome-wide data from remains attributed to Okunev—an archaeological culture of the Middle Yenisei and eastern steppe in southern Siberia (latter third–first half second millennium BC), famous for slab graves, massive stelae, and fantastic zoomorphic and anthropomorphic petroglyphs—to test an unusual physical anthropological hypothesis. Russian anthropologists have argued Okunev remains to exhibit pronounced affinity to Native Americans, surpassing that of other ancient groups from the region as well as recent Siberians and Central Asians. Kozintsev et al. (1999), in the most systematic investigation, suggested Okunev people to derive much of their ancestry from late-persisting “collateral relatives” of Native Americans who remained in Eurasia. We evaluate this proposal in special light of the “Ancient North Eurasian” concept (sensu Lazaridis 2014) and offer considerations on the future of skeletal morphology in framing and motivating investigations of human population history.


[330] Ancient Genomics of Neolithic to Bronze Age Baikal Hunter-Gatherers

Damgaard, Peter de Barros (Center for GeoGenetics, University of Copenhagen), Jeremy Choin (Center for GeoGenetics, University of Copenhagen), Andrzej Weber (Department of Anthropology, University of Alberta), Martin Sikora (Center for GeoGenetics, University of Copenhagen) and Eske Willerslev (Center for GeoGenetics, University of Copenhagen)

Genome-wide data from hunter-gatherer populations of the Upper Paleolithic to Neolithic has provided unprecedented insight into the human evolutionary and demographic trajectory. However such datasets have hitherto been largely confined to Western Eurasia. The sole representative of Inner Asian past populations post-dating the split between paleolithic Europeans and Asians, as well as paleolithic Siberians and East Asians, are the Mal’ta and Afontova Gora individuals, the Ancient North East Asian (ANE) branch, clouding the dating of the population split, and subsequent admixture events, between ANE and East Asian hunter-gatherers. Our genome data (~1X) reveal that Baikal Hunter-Gatherers (BHG) are an uncharacterized genetically homogeneous branch of Inner Asian hunter-gatherers, displaying highest shared genetic drift with present-day East Asians. Targeted sampling strategies coupled to excellent biomolecule preservation has permitted the generation of an advantageous sample size dataset (n = 31), rendering possible to estimate allele frequencies within these groups, thereby optimizing population tests. BHG model as an excellent proxy for an Inner Asian source population admixing into the late Bronze Age Andronovo groups, becoming Iron Age steppe nomads. With genomes allowing for kinship analyses, pathogen detection and strontium ratios, coupled to archaeological interpretative approaches we extend possible means to elucidate behavioral processes and cultural transformation.

Good to see the Baikal-Hokkaido Archaeological Project collaborating with a first-rate palaeogenomics lab. The Middle Holocene Cis-Baikal region has preserved well-stratified habitation sites and formal hunter-gatherer cemeteries of continental importance, which continue to lend remarkable insights into Neolithic South Siberian social configurations and ecological strategies.

The archaeology and earlier ancient uniparental marker work (mtDNA and Y-DNA from Early Neolithic Kitoi and Late Neolithic–Bronze Age Isakovo/Glazkovo samples) suggested an interesting discontinuity across the Middle Neolithic — maybe involving shifts in relatedness to ancestral Yeniseians. However, if Kitoi and succeeding Late Neolithic groups were both members of a homogeneous “BHG”, these cultural transformations and uniparental lineage turnovers must belie a bigger picture of substantial genome-wide continuity, potentially going as far back as the Mesolithic.

“Andronovo” would be a disagreement with the recent model in Unterländer et al. (2017), Ancestry and demography and descendants of Iron Age nomads of the Eurasian Steppe, doi:10.1038/ncomms14615. Here Iron Age eastern Scythians were instead modeled as “Yamnaya”1 + East Eurasian (Han and Nganasan were adequate stand-ins but it stands to reason that this was something more like BHG).

See earlier post: Y-DNA supports population discontinuity between Early Neolithic & Late Neolithic/Early Bronze Age in Cis-Baikal


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

Krause, Johannes (Max Planck Institute—SHH), Verena Schuenemann (Institute for Archaeological Sciences, University of Tübingen), Alexander Peltzer (Department for Archaeogenetics, Max Planck Inst), Wolfgang Haak (Department for Archaeogenetics, Max Planck Inst) and Stephan Schiffels (Department for Archaeogenetics, Max Planck Inst)

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.

Hopefully a deeper transect, into the Old Kingdom, Early Dynastic, and Predynastic, is to follow. My prediction (I would be happy to be wrong) is that this DNA came from tooth or bone — I think mummified soft tissue has mostly been a source of disappointment. Differential relatedness of modern Copts and non-Copts to the ancient samples would be something to look out for.

If any of these talks is going to really upset some people, it’ll be this one.


[287] Improving Radiocarbon Dating with Ancient DNA Analysis

Sedig, Jakob (Harvard University)

Recent advances in ancient DNA (aDNA) analysis have helped to shed new light on long-standing archaeological questions. Researchers can now study how elites and commoners may have been genetically related, the genetic heritage of the first migrants to a particular area, how ancient populations are related to modern groups, and more. While such revelations have been of critical importance to archaeology, results from recent analyses have implicated that ancient DNA analyses can also be applied to methodological issues in archaeology. In particular, by identifying the relatedness of two or more individuals, aDNA analyses can sometimes be used to improve the dating of specimens and/or sites. This paper discusses recent aDNA research that has identified multiple sets of ancient individuals who are first-degree relatives (parent-offspring or siblings), but have a difference of 100 years or more in radiocarbon age ranges. These case studies are then used to examine how aDNA analysis can be used in to supplement radiocarbon dating in three particular ways: by identifying the need for the re-dating of samples; to help tighten the radiocarbon age ranges for individuals and sites; and possibly help calibrate the radiocarbon curve.

We have a good sense for the bounds on human lifespan and reproductive lifetime. A finding of first-degree relatedness (which is trivial to see with genome-wide data) gives us chronological precision gains somewhat like “wiggle-matching” of tree ring samples.

This is by my friend Jakob, a Southwest US archaeologist who recently earned his PhD from University of Colorado Boulder and has been an “in-house” archaeologist with the Reich Lab for around a year. Follow him on Twitter here.


[146] The Forgotten Significance of the Later Stone Age Sites near Hora Mountain, Mzimba District, Malawi

Thompson, Jessica (Emory University), Alan Morris (University of Cape Town), Flora Schilt (University of Tuebingen), Andrew Zipkin (University of Illinois at Urbana-Champaign) and Kendra Sirak (Emory University)

In 1950, J. Desmond Clark led excavations at a Later Stone Age rockshelter at Hora Mountain, a large inselberg overlooking a modern floodplain in the Mzimba District of northern Malawi. At the Hora 1 site, he recovered two human skeletons, one male and one female, along with a rich—but superficially described and undated—cultural sequence. In 2016, our renewed excavations recovered a wealth of lithic, faunal, and other materials such as mollusk shell beads and ochre. Our reexamination of the skeletons also produced the first ancient DNA from the central African region, which together with previous morphological analysis demonstrates that the LSA foragers of the area cannot be readily fit within the known genetic and phenotypic parameters of living foragers. The significance of the Hora 1 site was made further clear by the relocation of several previously known sites also at the mountain, the discovery of four new rock art sites, and the discovery of four very rich new archaeological sites in the mountains adjacent to the floodplain. Here, we describe our renewed work and how it fits with the original findings to offer unprecedented promise for understanding the lifeways of Holocene foragers in central Africa.

Mota2 will not be lonely for much longer.

Lack of “ready fit” suggests an extinct lineage outside the space of surviving “Pygmy” or “Khoisan” diversity, or some unusual mixture.

Morris and Ribot (2006), DOI: 10.1002/ajpa.20308, suggest from morphological analyses of Holocene crania that pre-agricultural, pre-Bantu Malawians might already have had significant relatedness to present-day West-Central Africans.


[143] Andean Population Dynamics Revealed by Genome-Wide Data from the High Elevation Cuncaicha Rockshelter

Posth, Cosimo (Archaeogenetics Department, Max Planck Institute for Science of Human History), Thiseas Lamnidis (Archaeogenetics Department, Max Planck Institute f), Stephan Schiffels (Archaeogenetics Department, Max Planck Institute f), Kurt Rademaker (Archaeogenetics Department, Max Planck Institute) and Johannes Krause (Department of Anthropology, Northern Illinois Univ)

Present-day Andean human populations harbor a relatively high genetic diversity but a minimal population structure and differentiation among them. Moreover, mitochondrial DNA (mtDNA) and Y chromosome studies on precontact human remains suggest that both modern and ancient Andean populations derive from a single ancestral origin. However, nuclear ancient DNA (aDNA) data from the Andes in particular and South America in general are still too scarce to fully address questions on genetic continuity through time. The employment of enrichment techniques in the aDNA field now provides the opportunity of targeting over a million autosomal variants and increases the resolution on past population dynamics. Here we analyze mtDNA and genome-wide data of five human burials from the Cuncaicha rockshelter spanning between 9,000 and 4,000 years ago. Cuncaicha is an archaeological site at 4,480 m above sea level in the southern Peruvian highlands, which exhibits human occupation from the Late Pleistocene onward. Tracking genomic changes at the same site over a temporal transect will provide insights on the demographic processes shaping Andean populations across the Holocene.

With some interesting exceptions (e.g., Neolithic hunter-gatherers from the Russian Far East: Siska et al. 2017 and the claim for Kennewick Man — not fully convincing to me and unverifiable because the contemporary Colville data are gated), Early Holocene genomes everywhere we’ve looked have been significantly different from modern inhabitants of those regions. Will the same hold true here? The mysterious Australasian-related “Population Y” ancestry that seems to peak in western Amazonia fizzles out when you get into the Andes — was that always true?


[143] The Impact of Climate Dynamics and Cultural Change on the Demography and Population Structure of Precolumbian Populations in the Atacama

Fehren-Schmitz, Lars (UCSC Anthropology) and Kelly Harkins (UCSC Anthropology)

Archaeological studies in the Central Andes have pointed at the temporal coincidence of climatic fluctuations and episodes of cultural transition throughout the precolumbian period. Although most scholars explain the connection between environmental and cultural changes by the impact of climatic alterations on the capacities of the ecosystems inhabited by precolumbian cultures, direct evidence for assumed demographic consequences has been missing so far. Desert margin areas, as we find them at the Andean foothills and along the Pacific coastline of the Atacama are ideal research areas to study the dynamic relationship of climate and demography because they are reactive ecosystems with low resilience. Thus, even minor climatic changes can force these ecosystems into transition potentially altering the ecological conditions for the populations living in them. Here we present a large body of mitochondrial and genome wide genetic data from precolumbian populations living at the fringes of the Atacama. We test demographic models informed by genomic, paleoclimatic, and archaeological data and show that especially in later precolumbian phases climatic changes do coincide with demographic transitions and migration events. We conclude that increasing socioeconomic complexity and agricultural specialization increased the vulnerability of populations living in the desert margin ecosystems of the Atacama.


[176] Eight Years of Partnership with Coast Tsimshian First Nations on Genomic Research

Malhi, Ripan (University of Illinois Urbana-Champaign)

In 2008 a partnership was established with the Coast Tsimshian to use genomics as a novel avenue of research to learn about the population and evolutionary history of these First Nations. Community based research methods were used as a way to establish research goals that were respectful and mutually beneficial to all parties. Through this partnership we have been able to gain insight into the present-day and ancestral Coast Tsimshian genetic structure. Specifically, we have demonstrated a close genetic affinity between present-day members of the Coast Tsimshian community and ancestors through paleogenomics analysis of human skeletal remains from the Prince Rupert Harbour region. We have also showed how ancient peoples of that region adapted to their environments prior to European contact. We estimate the decrease in effective population size as a result of the well-known population decline due, in part, to the introduction of novel pathogens.

Heartening to see this. Some of this work is already out in preprint at bioRxiv: Demographic and immune-based selection shifts before and after European contact inferred from 50 ancient and modern exomes from the Northwest Coast of North America, https://doi.org/10.1101/051078.


[14] Authentication of Museum-Curated Tsantsas Utilizing Next Generation Sequencing Technology

Mower, Courtney (Arcadia University), Anna Dhody (Mütter Museum), Kimberlee S. Moran (Arcadia University) and Shanan S. Tobe (Arcadia University)

The Shuar, native to Northern Peru and Southern Ecuador, prepared shrunken heads to serve as trophies following battle, in response to their cultural beliefs. Authentic shrunken heads (tsantsas) were prepared in a precise manner and exhibit key morphological characteristics. Forgeries, including primates and inauthentic human preparations, were marketed to tourists and private collectors to profit from the “savage” image surrounding the Shuar. Inauthentic shrunken heads were prepared in a nontraditional manner; however, key morphological characteristics may be present highlighting the need for DNA analysis to provide further discrimination. Species identification was conducted to identify a head as human, sloth, or primate. Genetic markers were analyzed using next generation sequencing to determine the provenience of the shrunken heads, as a means of authentication, since forgeries are often European, while tsantsas are of South American ancestry. Maternally and paternally inherited DNA was also analyzed to determine the potential relatedness among authentic tsantsas, due to the taking of women following battle. This method of analysis can be applied more broadly in forensic science to cases involving the identification of human remains and the illegal sale of antiquities on the black market, threatening cultural preservation.


ANCIENT PROTEOMICS

[96] Ancient Hominin Bone Proteomes: Improving our Understanding of Past Human Behavior through the Study of Ancient Bone Proteins

Welker, Frido (Department of Human Evolution, MPI-EVA)

The analysis of ancient proteins is increasingly used to study archaeological and anthropological bone specimens from prehistoric time periods. This ranges from large-scale ZooMS screening (Zooarchaeology by Mass Spectrometry) of morphologically unidentifiable specimens to the targeted analysis of ancient bone proteomes from humans through the application of LC-MS/MS. Here, some biological and phylogenetic results that can be obtained through the analysis of ancient human bone proteomes will be discussed in the light of the Châtelperronian, “transitional,” technocomplex of western Europe. This technocomplex is chronologically placed between Middle Paleolithic (MP) and Upper Paleolithic (UP) lithic industries and displays behavioral aspects interpreted as intermediate between what is typically seen in the MP and UP. Despite intense research interest, the biological association of the Châtelperronian to either Neanderthals and/or Anatomically Modern Humans remains much debated. The analysis of a Pleistocene hominin bone proteome associated to the Châtelperronian allowed us to establish the biological affiliation of this specimen, and this will be presented together with biological insights obtained through the analysis of the same bone proteome.

I wonder if this presentation expands the case for a Neanderthal identification of Châtelperronian beyond Welker et al. 2016. Grotte du Renne is key, but I am concerned about power to exclude or resolve hybrid ancestry. This could be simulated.

From that paper — basically they had just seven characters:

In six cases, we observed the ancestral Hominidae state in the proteome data, which is also present in Denisovan and Neandertal protein sequences (34). These include one position for which a majority of AMHs (93.5%) carry a derived substitution (COL28α1; dbSNP rs17177927) and where our data contain the ancestral position (amino acid P). For the seventh case, COL10α1, we observed an amino acid state present in Denisovans, Neandertals, and 0.9% of modern humans haplotypes (46/5,008 1000 Genomes haplotypes) (SI Appendix, Tables S6 and S9), but not in any other Hominidae

Their ID was IMO more convincingly backed up by the samples’ clearly Neanderthal mtDNA.


ANCIENT mtDNA AND Y-DNA

[92] Ancient Human DNA Analysis from Central California: Interpreting the Penutian Migration through Genetics.

Monroe, Cara (University of Oklahoma-LMAMR), Fernando Villanea (Washington State University-School of Biological), Eric Lenci Jr. (Muwekma Ohlone Tribe), Alan Leventhal (San Jose State University-School of Social Scien) and Rosemary Cambra (Muwekma Ohlone Tribe)

Mitochondrial DNA (mtDNA) data was collected from over 300 individuals to further understand the hypothesized spread of Penutian populations from the Columbian Plateau into Central California around 5,000 BP. While living and ethnographic Ohlone groups—specifically in the San Francisco Bay area—speak Penutian languages, it is unclear what effect immigrating Penutians speakers had on existing Hokan populations between 2500–3000 BP. Distinct maternal lineages that belong to either immigrating Pro-Utian speaking peoples, or to Hokan populations who lived in the area for more than 7,000 years, have been identified and indicates intermarriage post-migration. Bayesian analysis further suggests a major population expansion within the region.


[252] Tochak-McGrath Discovery: Three Precontact Individuals from the Upper Kuskokwim River, Alaska

Sattler, Robert, Thomas Gillispie (Tanana Chiefs Conference), Carrin Halfmann (University of Alaska Fairbanks) and Angela Younie (Tanana Chiefs Conference)

Three precontact individuals inadvertently discovered in the village McGrath, Alaska provide a novel understanding of human history of the Upper Kuskokwim River region of Eastern Beringia. Collaboration between the McGrath Village Council, MTNT, Inc. and Tanana Chiefs Conference enabled a community research endeavor that has yielded a radiocarbon age estimate of c. 600–700 cal BP, isotopic dietary reconstruction suggesting a strong reliance on anadromous salmon, rare dental traits including a two-rooted lower canine and a fourth molar, and a population relationship similar to modern Alaska Natives through mtDNA (A2a and A2 root) and yDNA (Q). The three individuals are intergenerational (c. 30, 20, 2–3 years of age) and shared a similar high marine diet. Additional faunal remains at the multicomponent site include dog (C. lupus familiaris), bear (Ursus sp.), beaver (Castor sp.) and burbot (Coregonus sp.). Situated in the alluvial floodplain or the Kuskokwim River, the context suggests the Tochak family drowned together and were buried rapidly by natural sedimentation processes. The results of interdisciplinary research on the Tochak McGrath site provide rare insights into the precontact lifeways of Alaska Natives in the upper reach of the Kuskokwim River basin.

I have some familiarity with this work, and it’s a very encouraging story of collaborative aDNA research.

I wouldn’t read too much into isolated dental quirks3, but there is a curious argument by Lee and Scott (2011) that two-rooted lower canines are a “European trait”, and “a sensitive indicator of admixture wherever Europeans come in contact with Asian or African populations” — they do for instance seem to track Bronze Age movements from the western steppe into Inner Asia. I think this instance will be a false positive.


[115] Migration and Diversity in Ancient Xinjiang: A Multidisciplinary Approach to the Investigation of Adunqiaolu Population

Wang, Minghui (Institute of Archaeology, CASS) and Dexin Cong

The Adunqiaolu site, located in western Xinjiang, belongs to the early Bronze Age and dates to the nineteenth–seventeenth centuries BC. Archaeological evidence suggests that this group of people may have come from southern and/or southwest Siberia, north of Tianshan. Applying both cranial-metrics and aDNA analysis, this study explores regional variations in western Xinjiang and their relationships to other ancient populations. Ancient DNA analysis indicates that their genes are mainly European, specifically Spanish and German, and the same sequences recovered from human bones dating to the beginning of the Neolithic. However, in the process of migration and through time, there are small amounts of Mongolian gene admixture. Preliminary craniofacial morphological analysis shows that their physical characteristics are very similar to the ancient European type. Compared with modern Eurasian populations, Adunqiaolu ancient population is on a branch of the Europa group, having close genetic affinities with Iranians and Europeans. They show a relatively pure European genetic structure.

This is in the Dzungarian part of Xinjiang, close to the border with Kazakhstan (i.e., not in the Tarim). “Specifically Spanish and German” has to be misconveyed, but continuity of “European-like” (mtDNA?) lineages from the local(?) Neolithic might be saying something interesting about pre-Bronze Age layers of West Eurasian-related ancestry in the region.

Jia et al. 2011 outline some of the relational hypotheses:

In the northwest [of Dzungaria], excavations at a series of cemeteries collectively termed Qiemu’erqieke (Shamirshak) revealed pottery and burial practices that have parallels in the Okunevo culture of the Altai region of southern Siberia and the Yenisei Valley (Xinjiang Institute of Archaeology 1981; Lin Yun 2008; Jia and Betts 2010). To the southwest, and a little later in date, are the Sazicun and Adunqiaolu sites. These have some connections with the steppic Andronovo (MeiJianjun and Shell 1999) and the more localized and slightly later Karasuk cultures (Jia et al. 2009).


[115] Ancient DNA of a Nomadic Population Provides Evidence of the Genetic Structure of the Royal Ancient Mongols

Li, Jiawei (School of Life Science, Jilin University), Ye Zhang (School of Life Science, Jilin University), Xiyan Wu (School of Life Science, Jilin University), Yongbin Zhao (College of Life Science, Jilin Normal University) and Hui Zhou (School of Life Science, Jilin University)

The genetic diversity of the ancient Mongols, especially the Gold family of Genghis Khan remains unclear. Gangga site was a nomadic site dated to the eighth to tenth centuries AD in the HulunBuir grassland, northeast China. This site belonged to the Shiwei population, believed to be the direct ancestors of the ancient Mongols. Nine graves at the Gangga site were excavated with log coffins, which were considered the characteristic burial custom of the royal ancient Mongols, included the Gold family of Genghis Khan. This suggests the Gangga people had a close relationship with the royal ancient Mongols. In this study, mitochondrial and Y-chromosome aDNA were extracted to analyze the genetic structure of the Shiwei population at the Gangga site. Haplogroups D, F, C, B, G, N9a were typed in the mtDNA. Haplogroup C-M130 was detected in Y-chromosome aDNA. Gangga people exhibited a high frequency of Haplogroup C-F3918 (belonging to C3*), indicating it may be the main Y-haplogroup in the Shiwei population. In addition, all Gangga males buried in log coffins exhibited C-F3918 suggesting that C-F3918 might be the characteristic Y-chromosome haplogroup of the royal ancient Mongols.


  1. The authors favored temporally distant Yamnaya as an ancestral proxy mostly for its lack of ultimately Anatolian-derived Early European Farmer ancestry (EEF), which was apparently a post-Poltavka arrival on the western steppe. EEF admixture is ubiquitous in published samples attributed to Andronovo and Sintashta but was argued by Unterländer et al. (2017) to be absent from their Scythians.
  2. As of the time of this post, there’s only one published ancient African genome: this 4.5ka Ethiopian sample. Also read erratum here.
  3. I’d sit up if we saw more of it. As things rest, it’s like a single find of central incisor shoveling in the Medieval Basque Country. (That’s the “classic” dental trait whose genetics we probably understand best — EDAR V370A is not its simple Mendelian determinant and it’s not always a reliable tag of East Eurasian/Native American ancestry.)
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