Ancient Ainu mariners!

By Razib Khan | April 11, 2013 7:44 pm

Ainu man from 1870 (colorized)

Well, not really. But a new paper in PLOS GENETICS has a really weird speculation nested into the discussion of what seems a relatively banal paper on the phylogeography of South Americans. It’s a Y chromosomal survey of the populations of the New World, so it’s tracing the male lineage only. Because Amerindian populations likely went through at least one (more if you accept multiple migrations) bottleneck the variation on the Y chromosome is low. Ideally you’d be looking at tens of thousands of markers on the autosome, the non-sex inherited genome. But this group had a very good population coverage. Over 1,000 men from 50 tribal populations, with a focus on South America. Additionally, non-recombining markers are more manageable in terms of reconstructing demographic histories.

Here’s the frankly bizarre inference (it may still be right, but it’s still bizarre):

In view of the above, two scenarios for the introduction of C3* into Ecuador seem credible: (i) one or more late migratory waves that quickly passed North and Central America without leaving a trace of C3*, and (ii) long-distance contact with East Asia. As regards the second scenario, there appears to be at least some…In particular, the similarity of ceramic artifacts found in both regions led to the hypothesis of a trans-Pacific connection between the middle Jōmon culture of Kyushu (Japan) and the littoral Valdivia culture in Ecuador at 4400–3300 BC. In view of the close proximity of the spotty C3* cluster to the Valdivia site, which was considered at the time to represent the earliest pottery in the New World [40], it may well be that C3* was introduced into the northwest of South America from East Asia by sea, either along the American west coast or across the Pacific (with some help by major currents). Please note that they modeled the last common ancestors of the East Asian and South American C3* lineages, and it looks to be ~6,000 years before the present. But if I’m reading the results table right the intervals could push it as far as ~10,000 years before the present.

To me this looks like the Indian-admixture-into-Australians paper. Suggestive, but so strange that we should wait until our prior expectations are obviously wrong. Unfortunately I don’t see the raw data in the links, though perhaps if someone could find them they could post that in the comments. I would be curious to replicate the results at some point.

  • Patrick Wyman

    This is a fascinating result. Whether it ends up being the case or not – and I’d say it’s plausible, if not likely or probable – we’ll still learn something interesting about methodology and the sorting of particular lineages. It seems to me, though, that the more we learn about population history, the weirder it gets. The archaeological and written records are full of holes, and there are places for which we just have no data of any kind for decades, centuries, or millennia. There are far more recent population movements, such as the Visigoths in Aquitaine or the Burgundians around the same time, for which there’s absolute paucity of archaeological and inconclusive genetic evidence. Expecting population movements (even substantial ones) from thousands of years ago to be reflected in multiple lines of evidence may be less realistic than we might hope. With that said, more data of any kind would obviously be preferable.

  • Charles Nydorf

    Joseph Birdsell, the same mid-20th century anthropologist who proposed the Indians into Australia model as thought that American Indians had an Ainu component.

  • Karl Zimmerman

    Can someone tell me if anything new had been discovered regarding Ainu genetics? AFAIK genetic tests have found no components which are that unusual for a population on the boundary between East Asia and Siberia, but I don’t know if modern admixture studies have been done on them.

  • Julian Karadjov

    “Valdivia site, which was considered at the time to represent the earliest pottery in the New World [40]” – the oldest pottery in the Americas is ~2K years older, in the Lower Amazon region (Anna Roosevelt).

  • christopher_y

    A lot of skeletal analyses of the Kennewick burial have suggested Ainu affinities. I’m not sure if any genetic analysis has been published yet.

  • Iain Smith

    “Are there papers about DNA analyses of domesticated animals in Japan and South America that can prove early migration or contact?”

    Presence of the HTLV-1 virus in both Japan and South America also supports early contact.

    Furthermore, sub-types of HTLV-1 exist that are even more geographically limited. One specific subtype, ‘Cosmopolitan group A’, occurs only among native peoples in the Andes mountain area of northern Chile and in a sub-population of the Japanese. … Tajima’s group screened over 100 mummies, and was able to isolate viral DNA from one of them. Analysis of the viral sequence revealed that the Atacamanian people did indeed carry the same strain of HTLV-1 as modern-day Chilean and Japanese individuals.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at


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