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Tuesday, January 11, 2022

Population genetics is a state of mind

Years of blogging about population genetics has seriously eroded my faith in the peer review process.

During the past decade I've witnessed an inordinate amount of crap published in basically all of the major science journals. Often the work is misguided in some way, sometimes even quite strange, and occasionally outright wrong.

Back in 2014, a team of scientists from the UK published a paper in Science emphatically titled A Genetic Atlas of Human Admixture History. These people were Garrett Hellenthal, George B. J. Busby, Gavin Band, James F. Wilson, Cristian Capelli, Daniel Falush, and Simon Myers. See here.

The thing that really sticks out for me in this paper is Figure 3, which shows the present-day Polish population as largely a mixture between Northern European- and Turkish-related ancestries. Incredibly, the Turkish-related ratio appears to be about 25% and dated to 438 CE.

This is not just inexplicable, but utterly wrong. It's a result that is impossible to reproduce with any standard population genetics methods.

In fact, in terms of deep ancient ancestry, present-day Poles are very similar to present-day Scandinavians, and even to Viking Age, Iron Age and Bronze Age Scandinavians. This is easy to demonstrate, for instance, with f4-statistics, in part based on samples from the Hellenthal et al. paper.

Chimp Yamnaya_Samara Swedish_modern Polish_modern -0.000311 -1.574
Chimp Yamnaya_Samara Ollsjo_Bronze_Age Polish_modern -0.000044 -0.152
Chimp Yamnaya_Samara Sealand_Iron_Age Polish_modern -0.000072 -0.293
Chimp Yamnaya_Samara Sealand_Viking_Age Polish_modern 0.000078 0.525
Chimp Yamnaya_Samara Gotland_Viking_Age Polish_modern -0.000141 -1.322

Chimp Barcin_N Swedish_modern Polish_modern -0.000318 -1.662
Chimp Barcin_N Ollsjo_Bronze_Age Polish_modern 0.000216 0.798
Chimp Barcin_N Sealand_Iron_Age Polish_modern -0.000023 -0.104
Chimp Barcin_N Sealand_Viking_Age Polish_modern -0.000186 -1.310
Chimp Barcin_N Gotland_Viking_Age Polish_modern 0.000083 0.788

Chimp Karelia_HG Swedish_modern Polish_modern -0.000134 -0.540
Chimp Karelia_HG Ollsjo_Bronze_Age Polish_modern 0.000056 0.162
Chimp Karelia_HG Sealand_Iron_Age Polish_modern 0.000047 0.153
Chimp Karelia_HG Sealand_Viking_Age Polish_modern 0.000424 2.241
Chimp Karelia_HG Gotland_Viking_Age Polish_modern 0.000134 0.959

Simply put, if Poles have ~25% ancestry from a Turkish-related source, then so do Swedes, Norwegians and basically all other Northern Europeans going back hundreds and even thousands of years. This is obviously not the case, and it's also not what Hellenthal et al. claimed anyway.

A year later, a team of scientists that again included Garrett Hellenthal, George B. J. Busby, James F. Wilson, Cristian Capelli and Simon Myers, published another, similar paper in Current Biology. And guess what? This paper also claimed that present-day Poles had Turkish-related ancestry, but this time dating to a somewhat later period. See Busby et al. 2015 Figure 4.C here.

I've got most of the samples from that paper, so I can analyze them myself, and I think I know what the problem is. Basically, the Turks are mixed. So what appears to have happened is that Busby et al. got things backwards.

Below are three plots from a Principal Component Analysis (PCA) largely based on data from Busby et al., featuring samples from England, Germany, Norway, Poland and Turkey. The first plot is based on dimensions 1 and 2, the second plot on dimensions 1 and 3, and the third plot on dimensions 1 and 4. The relevant data file is available here.

Note that the Europeans are more or less symmetrically related to the Turks, which means none of these European populations has significantly more Turkish-related ancestry than the others. Indeed, it's the Turks who show more variation in the first (horizontal) dimension, suggesting that they might have variable levels of European ancestry.

I chose the aforementioned papers to make my point here because they made quite an impression on me. In other words, they really pissed me off.

For the sake of completeness, I'm now going to try and get in touch with the authors and ask them how on earth they managed to make these Poles Turkish-related, and also why they never corrected their mistake.

See also...

Don't believe everything you read in peer reviewed papers

Thursday, December 23, 2021

When did Celtic languages arrive in Britain?

A new paper at Nature by Patterson et al. argues that Celtic languages spread into Britain during the Bronze Age rather than the Iron Age [LINK]. This argument is based on the observation that there was a large-scale shift in deep ancestry proportions in Britain during the Bronze Age.

In particular, the ratio of Early European Farmer (EEF) ancestry increased significantly in what is now England during the Late Bronze Age (LBA). On the other hand, the English Iron Age was a much more stable period in this context.

I don't have any strong opinions about the spread of Celtic languages into Britain, and Patterson et al. might well be correct, but their argument is potentially flawed because:

- significant population shifts need not result in any noticeable changes in ancient ancestry proportions

- ancient ancestry proportions can shift without significant migrations from afar due to cryptic population substructures

- large-scale population shifts need not result in langage shifts, especially if they're gradual

- small-scale population shifts can result in language shifts, especially if they're sudden.

Indeed, when I plot some of the key ancient samples from the paper in my ultra fine scale Principal Component Analyses (PCA) of Northern and Western Europe, it appears that it's only the Early Iron Age (EIA) population from England that overlaps significantly with a roughly contemporaneous group from nearby Celtic-speaking continental Europe. The relevant PCA data are available here and here, respectively.

See also...

Celtic vs Germanic Europe

Avalon vs Valhalla revisited

R1a vs R1b in third millennium BCE central Europe

Tuesday, November 9, 2021

Crazy stuff

I'm hoping that 2022 is the year when this problem is finally straightened out. Over to you David Reich, Nick Patterson, Iosif Lazaridis, David Anthony, Wolfgang Haak, Johannes Krause and colleagues.
See also...

An early Iranian, obviously

The Hajji Firuz fiasco

A Mycenaean and an Iron Age Iranian walk into a bar...

Wednesday, October 27, 2021

Local origins of the earliest Tarim Basin mummies (Zhang et al. 2021)

Over at Nature at this LINK. It's nice to see yet another huge surprise courtesy of ancient DNA. Please note that most of the ancients from this paper are already in the Global25 datasheets. Here's the abstract:

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious 1. Here we present genomic data from 5 individuals dating to around 3000–2800 bc from the Dzungarian Basin and 13 individuals dating to around 2100–1700 bc from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early–Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo 1,2 or to have originated among the Bactria–Margiana Archaeological Complex 3 or Inner Asian Mountain Corridor cultures 4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

Zhang, F., Ning, C., Scott, A. et al. The genomic origins of the Bronze Age Tarim Basin mummies. Nature (2021).

See also...

How the Shirenzigou nomads became Proto-Tocharians

Wednesday, October 20, 2021

Modern domestic horses came from the Eastern European steppe

Over at Nature at this LINK. I'm getting the impression that geneticists and the editors at Nature are really crap at geography. Obviously, this paper argues that modern domestic horses came from the Pontic-Caspian steppe, which is located very firmly in Eastern Europe. But, inexplicably, instead of actually saying this, the authors came up with the much more ambiguous term Western Eurasian steppes, and even put that in the title. I wonder why? Here's the paper abstract:

Domestication of horses fundamentally transformed long-range mobility and warfare 1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling 2,3,4 at Botai, Central Asia around 3500 bc3. Other longstanding candidate regions for horse domestication, such as Iberia 5 and Anatolia 6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes [my note: they actually mean the Pontic-Caspian steppe, which is located in Eastern Europe], especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 bc, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association 7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe [my note: the Yamnaya culture was located in Europe] around 3000 bc 8,9 driving the spread of Indo-European languages 10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium bc Sintashta culture 11,12.

Librado, P., Khan, N., Fages, A. et al. The origins and spread of domestic horses from the Western Eurasian steppes. Nature (2021).

Update: I emailed one of the lead authors, Ludovic Orlando, asking him for a comment. Here it is:

Thanks for your interest in our research. We indeed struggled finding the term that would be most appropriate and this was discussed with our coauthors. The Pontic-Caspian steppe would seem the most obvious choice but my understanding is that this would include a large region, stretching from the most north-western side of the Black sea to the foothills of the Urals. This is larger than the signature recovered in our data. My understanding is that the Eastern European steppes would also stretch more northernly than the region that we narrowed down. Eastern European steppes was also not immediately clear, even for European scholars such as myself. Therefore, it did not seem that there were any terms that were ready-made for truly qualifying our findings. We thus went for Western Eurasian steppes in the main title, and sticked to more precise locations such as the Don-Volga region in the main text. I guess that this is one of those cases where the activities of past herders did not exactly follow some geographic terms that would only be defined thousands of years later.

However, the Pontic-Caspian steppe and the Eastern European steppe are in fact terms that describe the western end of the Eurasian steppe. So they should be totally interchangeable with the term Western Eurasian steppes. Except, at least to me, they seem less ambiguous.

Ergo, the Eastern European steppe can't be more northerly than the Western Eurasian steppes, because it's the same thing. Moreover, the Pontic-Caspian steppe can't stretch further west than the Western Eurasian steppes, because, again, it's the same thing.

Indeed, the land north of the Eastern European/Western Eurasian steppes is called the forest steppe.

See also...

Friday, October 15, 2021

Coming soon?

This ISBA9 abstract seems to be highly relevant to the ultimate origins of the Yamnaya and Corded Ware peoples. Emphasis is mine:

Genomic signals of continuity and admixture in the Caucasus

Ghalichi Ayshin et al.

Situated between the Black and Caspian Sea, the Caucasus is a key geographic region that connects the Near East and the Eurasian Steppe, with a great ecological diversity of ecotones and landscapes rich in natural resources. A recent archaeogenetic study has shown that the genetically diverse Eneolithic and Bronze Age groups of the steppe and mountains correspond to eco-geographic zones in the Caucasus. However, the formation, interactions and population dynamics warrant further investigation. In this study we explore new genome-wide data of 68 individuals from 20 archaeological cultures across the Caucasus mountains, the piedmont and the steppe extending our temporal transect to 6000 years, doubling the number of available genomes from the region. We present the first genomic data from a Mesolithic individual (6100 calBCE) from the Northwest Caucasus that shows Eastern hunter-gatherer ancestry, Neolithic individuals from Georgia, as well as new data from genetically unexplored regions/cultures in the northeastern highlands and the dry steppe. We observe a degree of genetic continuity through time within the main mountain and steppe genetic groups, but also identify various episodes of gene flow between these and the neighboring regions. In the Late Eneolithic period, we find evidence of admixture from the south into the steppe groups, detectable through the presence of Anatolian_Neolithic-like ancestry. During the Bronze Age, we found in Steppe Maykop individuals a genetic link to West Siberian hunter-gatherers, a component that is absent from Yamnaya, North Caucasus and Catacomb groups, but reappears in Bronze Age individuals associated with the Lola culture.

I'm not quite sure what it's saying though. Is the Mesolithc individual from the Northwest Caucasus actually an Eastern European hunter-gatherer, or, as I'm expecting, a mixture between Caucasus and Eastern European hunter-gatherers? If the latter, then it's game over for the Out-of-Iran and Out-of-Armenia Indo-European hypotheses that have been so popular among academics in recent years.

The authors also mention the spread of Anatolian-related ancestry into the Eastern European steppe during the Late Eneolithic. They're probably referring to the phenomenon that gave rise to the so called Steppe Maykop outliers. The ISBA9 abstract PDF book is freely available here.

See also...

Understanding the Eneolithic steppe

Ancient DNA vs Ex Oriente Lux

A note on Steppe Maykop

Monday, September 27, 2021

The genetic origin and legacy of the Etruscans (Posth et al. 2021)

Over at Science Advances at ths LINK. I'll take a closer look at this issue after I get the relevant genotype data. Anyone got the link? Here's the paper abstract:

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

Citation: C. Posth, V. Zaro, M. A. Spyrou, S. Vai, G. A. Gnecchi-Ruscone, A. Modi, A. Peltzer, A. Mötsch, K. Nägele, &. J. Vågene, E. A. Nelson, R. Radzevičiūtė, C. Freund, L. M. Bondioli, L. Cappuccini, H. Frenzel, E. Pacciani, F. Boschin, G. Capecchi, I. Martini, A. Moroni, S. Ricci, A. Sperduti, M. A. Turchetti, A. Riga, M. Zavattaro, A. Zifferero, H. O. Heyne, E. Fernández-Domínguez, G. J. Kroonen, M. McCormick, W. Haak, M. Lari, G. Barbujani, L. Bondioli, K. I. Bos, D. Caramelli, J. Krause, The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect. Sci. Adv. 7, eabi7673 (2021).

See also...

Etruscans, Latins, Romans and others

Friday, September 17, 2021

Lizard Gorge

I was hiking through one of my favorite wilderness areas the other day. I call this place Lizard Gorge because it's full of monitor lizards that strut around like they own it.

Just a few minutes into my hike I noticed some birds going crazy atop a massive, hollow tree. They were calling loudly as if a predator was near, and, sure enough, when I peered into this tree I saw two monitors tearing apart the carcass of a large animal.

It was a gory but fascinating sight. Unfortunately, the stench made it difficult to bear, so I decided to move on.

As I backed away I was attacked by a swarm of insects. Initially, in my panic, I thought they were spiders, but on closer inspection they turned out to be gigantic ants.

I was bitten on the hand, arm and neck. It hurt like hell. The bite on the neck was especially painful. Were these ants venomous? Was I at risk of a dangerous allergic reaction? I didn't know, so I ran, seemingly for my life.

After a few minutes, however, the pain went away. I sat down beside a creek, looked all around for ants, and had a cool drink (from my hydration pack, not the creek). Despite my ordeal, it was an awesome hike, and I managed to get some great pics. Enjoy!

See also...

Eagle country

Wednesday, September 15, 2021

Yamnaya people drank horse milk (Wilkin et al. 2021)

Over at Nature at this LINK. I'm guessing the claim that Yamnaya pastoralists lived in Scandinavia is a huge typo. Obviously, the authors are referring to the people of the Corded Ware culture (CWC). From the paper:

During the Early Bronze Age, populations of the western Eurasian steppe expanded across an immense area of northern Eurasia. Combined archaeological and genetic evidence supports widespread Early Bronze Age population movements out of the Pontic–Caspian steppe that resulted in gene flow across vast distances, linking populations of Yamnaya pastoralists in Scandinavia with pastoral populations (known as the Afanasievo) far to the east in the Altai Mountains1,2 and Mongolia3. Although some models hold that this expansion was the outcome of a newly mobile pastoral economy characterized by horse traction, bulk wagon transport4,5,6 and regular dietary dependence on meat and milk5, hard evidence for these economic features has not been found. Here we draw on proteomic analysis of dental calculus from individuals from the western Eurasian steppe to demonstrate a major transition in dairying at the start of the Bronze Age. The rapid onset of ubiquitous dairying at a point in time when steppe populations are known to have begun dispersing offers critical insight into a key catalyst of steppe mobility. The identification of horse milk proteins also indicates horse domestication by the Early Bronze Age, which provides support for its role in steppe dispersals. Our results point to a potential epicentre for horse domestication in the Pontic–Caspian steppe by the third millennium bc, and offer strong support for the notion that the novel exploitation of secondary animal products was a key driver of the expansions of Eurasian steppe pastoralists by the Early Bronze Age.

Wilkin, S., Ventresca Miller, A., Fernandes, R. et al. Dairying enabled Early Bronze Age Yamnaya steppe expansions. Nature (2021).

See also...

On the origin of the Corded Ware people

Saturday, September 4, 2021

The genomic formation of modern Balkan peoples (Olalde et al. 2021 preprint)

Over at bioRxiv at this LINK. This preprint deals with some very complex issues, so I can't say much about it until I have a good look at the relevant genotype data. However, for now, my impression is that the authors have oversimplified the genetic origins of most Balkan peoples.

For instance, they model the present-day Greek population as a two way mixture between ancient Greeks from a Greek colony in Iberia and present-day Mordovians. The Mordovians are basically a proxy for the Slavs who moved into the Balkans during the Medieval period.

However, the problem is that, strictly speaking, this isn't a historically plausible model, because Mordovians are actually a Uralic-speaking group from the Volga region with significant Siberian ancestry. Needless to say, it's extremely unlikely that anyone like them had an appreciable impact on the present-day Greek gene pool.

So instead I'd like to see the authors try three-way and four-way models with ancients from Mycenae, Anatolia and some places (well to the west of the Volga River) likely to have been inhabited by early Slavs.

Feel free to let me know what you think about this preprint in the comments below. Here's the abstract:

The Roman Empire expanded through the Mediterranean shores and brought human mobility and cosmopolitanism across this inland sea to an unprecedented scale. However, if this was also common at the Empire frontiers remains undetermined. The Balkans and Danube River were of strategic importance for the Romans acting as an East-West connection and as a defense line against “barbarian” tribes. We generated genome-wide data from 70 ancient individuals from present-day Serbia dated to the first millennium CE; including Viminacium, capital of Moesia Superior province. Our analyses reveal large scale-movements from Anatolia during Imperial rule, similar to the pattern observed in Rome, and cases of individual mobility from as far as East Africa. Between ∼250-500 CE, we detect gene-flow from Central/Northern Europe harboring admixtures of Iron Age steppe groups. Tenth-century CE individuals harbored North-Eastern European-related ancestry likely associated to Slavic-speakers, which contributed >20% of the ancestry of today’s Balkan people.

Olalde et al., Cosmopolitanism at the Roman Danubian Frontier, Slavic Migrations, and the Genomic Formation of Modern Balkan Peoples, bioRxiv, posted August 31, 2021, doi:

See also...

A Greek tragedy