Of horses, camels and extinct lineages

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After a rather long hiatus, and while we wait for the long anticipated final version of Narasimhan et al. (hopefully out very soon), here’s a quick post commenting on a few things that have been published lately.

 

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Fages et al. 2019

A follow up to their previous paper, briefly commented on a previous post, that brings some new information about the history of domestic horses, though far from clarifying things it makes everything less clear opening new questions. Here is their graphical abstract:

And the key findings regarding early history of domestication:

  • Two now-extinct horse lineages lived in Iberia and Siberia some 5,000 years ago
  • Iberian and Siberian horses contributed limited ancestry to modern domesticates

These newly found extinct lineages of early domestic horses add to the Botai ones, which didn’t go extinct but apparently went feral and survive in the form of Przewalski horses, as found in an even earlier paper (Gaunitz et al. 2018).

So let’s start to look at this puzzle and try to put a few pieces together. We have a horse lineage in Siberia living up until 5000 years ago that didn’t contribute any significant ancestry to the main (and for a long time the only) domestic lineage. Then we have another lineage further west, in Kazakhstan, that was domesticated c. 3500 BC but that also didn’t contribute much to main domestic horses. And finally we have a lineage in Iberia that we domesticated somewhere in the late Chalcolithic, and while it seems to have been used for a while as an early domestic horse in Europe it also ultimately went extinct without contributing much to the main domestic lineage.

A closer look at the data from this latter Iberian lineage brings us some additional interesting information: There is a sample from 2600 BC (note that this predates the arrival of R1b/steppe people) belonging to this domestic lineage (native to Iberia). But then another Iberian samples from 1900 BC (note that his is 500 years after the arrival of R1b/steppe Bell Beaker folk) is still of the same kind. Furthermore, a sample from Hungary c. 2100 BC shows some 12% admixture from this Iberian lineage (the rest of its makeup being from main domestic horses and another unknown lineage).

What this suggests is something rather surprising: R1b/steppe Bel Beakers don’t seem to have carried horses with them to Western Europe. Otherwise those would have largely replaced the local Iberian ones. Instead, it seems that Bell Beaker horses were those who they found in Iberia and might have traded with them all the way to Hungary. Indeed, this comes to reinforce the scarce evidence for the use of domestic horses in EBA steppe related cultures. Not much evidence in the Corded Ware Culture (for example, domestic horses only arrived to the east Baltic in the Iron Age, in spite of the area being occupied by early CWC population).

So where did domestic horses come from? That’s the min question right now. Traditionally, the Pontic-Caspian steppe has been the main candidate for it. However, the previous paper from this same team, based on climatic simulations and found remains, seemed to discard that area as suitable for horses at the time of probable domestication. Now this new study adds to that hypothesis by providing no evidence of the people coming from that area to Europe in the early 3rd mill. bringing their own domestic horses. Unfortunately, this study had 2 or 3 samples that could represent the Pontic-Caspian steppe wild horses, but they all yielded a very low amount of endogenous DNA to be included in any autosomal analysis. So that question remains open.

The thing is that the first good evidence of clear and extensive use of domestic horses of the main lineage comes from Sintashta, c. 2000 BC. So where did those horses came from? It’s unlikely that they were local, given the proximity with the Botai Culture area (and in west Siberia), where we know that very divergent lineages existed. To me it seems that they could have arrived there from anywhere. And it might not be that relevat after all. The place where the main domestic lineage originated might be rather unimportant, given that for all we know this domestication seems to have occurred quite later than first thought (closer to 2500 BC than to the previously suggested 3500 BC), and it may have been the Sintashta people the first ones who found a real use for them, no matter where they got them from. Whatever the case, it seems that the history of domestic horses is also turning out to be quite different from what was previously thought. Hopefully the next paper before the year’s end will shed some light in all of this.

 

Whole-genome sequencing of 128 camels across Asia provides insights into origin and migration of domestic Bactrian camels

Lian Ming et al. 2019 (preprint)

This one is a modern DNA study dealing with the domestication fo the Bactrian camel. Though I’m not sold on their idea that Bactrian camels were domesticated 10.000 year ago, the rest of the hypothesis looks good (as far as modern DNA can be informative). An image and a few excerpts summarise it well.

The origin of domestic dromedaries was recently revealed by world-wide sequencing of modern and ancient mitochondrial DNA (mtDNA), which suggested that they were at first domesticated in the southeast Arabian Peninsula [11]. However, the origin of domestic Bactrian camels is still a mystery. One intuitive possibility was the extant wild Bactrian camels were the progenitor of the domestic form, which were then dispersed from the Mongolian Plateau to west gradually [7, 12].

[…]

Another possible place of origin was Iran [1], where early skeletal remains of domestic Bactrain camels (around 2,500-3,000 BC) were discovered [14].

[…]

The wild Bactrian camels made also little contribution to the ancestry of domestic ones. Among the domestic Bactrian camels, those from Iran exhibited the largest genetic distance from others, and were the first population to separate in the phylogeny. Although evident admixture was observed between domestic Bactrian camels and dromedaries living around the Caspian Sea, the large genetic distance and basal position of Iranian Bactrian camels could not be explained by introgression alone. Taken together, our study favored the Iranian origin of domestic Bactrian camels, which were then immigrated eastward to Mongolia where the native wild Bactrian camels inhabited.

[…]

This scenario could well resolve the mystery why the wild and domestic Bactrian camels from the Mongolian Plateau have so large genetic distance.

[…]

Despite the insights gleaned from our data, it was important to note that the direct wild progenitor of domestic Bactrian camels were not found in Iran now, which may no longer exist.

[…]

In future work, sequencing of ancient genomes from camel fossils will add to the picture of their early domestication.

Not much to add, really. They looked with an extensive set of modern camel DNA at the two different scenarios proposed for domestication and concluded that their data favoured the Iranian one, in spite of wild camels no longer existing in Iran, contrary to Mongolia (where they exist but are very divergent from domestic ones, just like the horses).

We’ll wait for ancient DNA to either confirm or deny this.

 

The population history of northeastern Siberia since the Pleistocene

Sikora et al. 2019

I already commented quite extensively on the very interesting and well written paper when the preprint was out last year. Now it’s been finally published and hopefully the genomes will be made available (if they aren’t already). I was glad to see that the only problem I found with the preprint (their hypothesis about ANS surviving somewhere in Beringia and mixing with East Asian populations to form the Native American one, which seemed to me incompatible with the genetic data presented, due to Native Americans sharing more alleles with Malta and AfontovaGora3 than with the Yana samples) has been addressed in the final versions:

For both Ancient Palaeo-Siberians and Native Americans, ANS-related ancestry is more closely related to Mal’ta than to the Yana individuals (Extended Data Fig. 3f), which rejects the hypothesis that the Yana lineage contributed directly to later Ancient Palaeo-Siberians or Native American groups.

So unfortunately for them, these Yana population seems to have died out during the LGM, something not too surprising when such climatic event catches you in the Arctic.

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208 thoughts on “Of horses, camels and extinct lineages

  1. “I’m more intrigued by other claims that apparently Niraj Rai made in some interview about upcoming papers (hopefully before the end of the year), so let’s see what they have.” —- Yeah, there are two upcoming papers, one on different R1a clades in modern indian pops and the other one on analysis of horse remains dated to mature harappan .

  2. By the way, since the Italy papers are coming soon, what do you think the haplogroup situation will be?

    It’ll be the first instance of a clearly non-IE population living next to a clearly IE population, so the differences between the Etruscans and the Italics will be interesting.

    My prediction is that the Italics differ from the Etruscans in that they carry Bronze Age Near Eastern Y-DNA, the populations being otherwise broadly similar where they neighbour each other.

  3. @ Marko

    Yep it sounds pretty awesome with 12,000 years of samples; but still 1-2 months away (?)

    “Rome as a genetic melting pot: Population dynamics over 12,000 years

    Nearly 2000 years ago, Rome was the largest urban center of the ancient world and the capital of an empire with over 60 million inhabitants. Although Rome has long been a subject of archaeological and historical study, little is known about the genetic history of the Roman population. To fill this gap, we performed whole genome sequencing on 127 individuals from 29 sites in and around Rome, spanning the past 12,000 years. Using allele frequency and haplotype-based genetic analyses, we show that Italy underwent two major prehistoric ancestry shifts corresponding to the Neolithic transition to farming and the Bronze Age Steppe migration, both prior to the founding of the Roman Republic. As Rome expanded from a small city-state to an empire controlling the entire Mediterranean, the city became a melting pot of inhabitants from across the empire, harboring diverse ancestries from the Near East, Europe and North Africa. Furthermore, we find that gene flow between Rome and surrounding regions closely mirrors Rome’s geopolitical interactions. Interestingly, Rome’s population remains heterogeneous despite these major ancestry shifts through time. Our study provides a first look into the dynamic genetic history of Rome from before its founding, into the modern era.”

    It sounds like truly that the city of Rome became cosmopolitan; & hence the differences between non- IE & IEs in Italy will be a challenging riddle; as elsewhere ; which will mostly fall on a steppe /MNE cline

  4. @Rob

    I guess to be particularly relevant to question of IE origins Italic is simply too late. I was hoping for additional samples from Anatolia and also from the shaft graves, but I guess we won’t be seeing these anytime soon.

    I hope we also get some samples from southern Italy.

    Edit: from the abstract it sounds like the authors might not have done a proper autosomal analysis.

  5. Marko
    The data from the study looks fine. Yes more samples are needed; but I don’t think it’ll suggest that PIE came from Mesopotamia

  6. @Rob

    Do you still think the eastern Balkanic/western Anatolian area looks best for Indo-Hitttite? I can’t make much sense of the data we have thus far to be honest.

  7. Marko,
    It’s still difficult to clearly characterise the details because there were several to / fro movements in the Black Sea zone; at least 2 neolithic waves followed by 2 or 3 ‘waves’ back to Anatolia. However, broadly speaking I think there is evidence to suggest I-H emerging somehwere around there; with nuclear I.E. beginning to expand more readily c. 2500 BC from a locus further north

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