July 26, 2015

Paleoamericans galore

Two new papers in Nature and Science add to the debate on Native American origins. The first study (in Nature) detects that some Amazonians have a few percent ancestry from a group related to Australasians, which suggests that early native Americans were not homogeneous but came in two flavors: the main one found all over the Americans and the Australasian-related one. The second study (in Science) looks at ancient "Paleoamerican"-postulated populations and finds that they don't have any particular relationship to Australasians. Thus, whatever population brought the "Paleoamerican" admixture into the Amazon, it remains to be found.

Nature (2015) doi:10.1038/nature14895

Genetic evidence for two founding populations of the Americas 

Pontus Skoglund et al.

Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America1, 2, 3, 4. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia)5, 6, 7, 8. Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.


Science DOI: 10.1126/science.aab3884

Genomic evidence for the Pleistocene and recent population history of Native Americans

Maanasa Raghavan1,*, Matthias Steinrücken2,3,4,*, Kelley Harris5,*, Stephan Schiffels6,*, Simon Rasmussen7,*, Michael DeGiorgio8,*, Anders Albrechtsen9,*, Cristina Valdiosera1,10,*, María C. Ávila-Arcos1,11,*, Anna-Sapfo Malaspinas1* et al.

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.



Annie Mouse said...

A lot of information in these papers and I plan to spend some time chewing.

On first glance however it was curious to see European admixture in the 2 pre-Columbian mummies from Mexico.

terryt said...

"all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia".

The two papers are not irreconcilable if we consider that the isolation period in Beringia may not even have been as long as 8000 years. In that case the 'single migration wave' may have been considerably diverse as various populations had pushed north from several regions in Central and Eastern Eurasia.

Kristiina said...

In my opinion both papers detect the same signal but differ in their interpretation of the signal. Raghavan paper which rejects the Australasian palaeo-migration conclude the following:
”Nevertheless, a few tests do show significant differences between certain Native Americans in their affinity to Siberians, East Asians and Australo-Melanesians, and implicates admixture from a source which contained ancestry components related to present-day East Asians/Siberians and Australo-Melanesians.”

”Except for Karitiana (genome from (5) tested here) showing a weak affinity to the Papuan (genome from (38) tested here), none of the other Native Americans showed a Papuan-related signal in the tests using sampled reads (Fig. S11A). However, we still found a slightly stronger Papuan signal in the Aleut compared to the rest of the Native Americans (Fig. S11B). … Again, we could not reject the topologies (((Anzick-1, Karitiana), Papuan), Yoruba) (D=0.004) or topologies (((Anzick-1, Merged southern North American/South & Central Americans), Papuan), Yoruba) (D=0.002), where the merged southern North American/South & Central Americans are represented by the three Karitiana, one Yukpa, one Pima, one Aymara, one Huichol and one Mixe genomes.”

”Rejecting the test for the SNP chip genotype data for one Pericú and one Fuego-Patagonian could be interpreted as support for a two-wave migration. Yet, our interpretation is that this is rather the result of outgroup attraction.”

As for the craniometric data, it is noted that ”craniometric affinities of the Pericú male subsample with Australo-Melanesian populations indicate, in our view, convergence in terms of extreme dolichocephaly, probably as an effect of local adaptation/drift in a fairly isolated population.”

The Skoglund paper with the opposite conclusion notes that this [Australasian] signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.
If I understand the data of the Skoglund paper correctly, the Australasian signal is strongest in Amazonia and in the following populations: Karitiana, Surui, Xavante.
If, as the Raghavan paper says, it is only subsequent gene flow that resulted in some Native Americans sharing ancestry, more distantly, with Australo-Melanesians, I would expect that Clovis that was clearly ancestral to Amerinds and, in particular, to central and southern Amerinds should show this Australasian signature.
The debate goes on and more evidence is hopefully coming …
However and in addition to the above, the Raghavan paper includes a lot of interesting data and many migration trees that are worth a look.
Migration edges detected:
1. MA-1 > Amerinds
2. Europeans > Altai
3. MA-1 > Greenlanders
4. Amerinds > Yupik
5. Dai > Yoruba
6. Koryaks > Nivkhs
7. Sardinians > Buryats
8. Yupik > Koryak
9. Athabascan > Eskimos
10. Sardinians > Han/Dai
11. Europeans > Sakha

There are some new interesting migration edges. Geneflow from Amerinds to Yupik is evidence of backmigration from America to Siberia. Usually it is only highlighted that Eskimos stem from a recent migration from Asia, but, autosomally, they are 20-30% Northern Amerind which is confirmed by the migration edge from Athabascan to Eskimos. It is also interesting that while European geneflow to Altai is well-known, Buryats show geneflow from Sardinians to Siberia. The European geneflow that is visible in Sakha was also expected. The migration edge from Dai to Yoruba is interesting and offers several interpretations.

Ross said...

For the hypothetical Australasian ancestry, was there any Denisovan genetic material?

Kristiina said...

One more comment. When the Raghavan et al paper finds that the Paleoamerican-postulated populations (Pericúes from the Baja California peninsula, Fuego-Patagonian hunter-gatherers) don't have any particular relationship to Australasians, it should be noted that their analysis does not include any ancient Amazonian samples, while the other paper detects the Australasian signal specifically in the Amazonian Amerinds.

I look forward to seeing ancient genomes from hot climates to resolve this issue - as well as many other issues by the way - now that DNA from hot climates is said to be technically feasible.

eurologist said...

As to the Raghavan et al. paper, what a split time estimate of ~23kya really means is that there was some exchange between mongoloid NE Asians (established ~35-30kya?) and Beringians until LGM. We already knew that this exchange took place based on varying levels of mongoloid features within Native Americans and based on the significant (but varying) prevalence of the EDAR gene variant in them.

Apart from at least two documented waves of Inuit, it is good to see vindicated that the Athabaskans, or more generally Na-Dene speakers are different (deviating from the authors, I believe, from a slightly later coastal migration from the emerging Beringian islands and with a more clearly NE Asian (mongoloid) admixture and different languages). Of course, in addition, northern Athabaskans also have recent gene flow from Inuits.

"This additionally suggests that the Mal’ta-related admixture into the early Americans (4), representing ancestors of both Amerindians and Athabascans (Fig. 1 and fig. S5), occurred sometime after 23 KYA, following the Native American split from East Asians."

I find this hard to digest and hard to follow from the data and arguments provided. From both autosomal and uniparental markers, it makes much more sense that all the four groups (original NE Asians migrated from SC and SE Asia, EDAR-mutated NE Asians, W/C Siberians, and late north-migrating SE Asians) mixed before LGM.

German Dziebel said...

Discussed at http://anthropogenesis.kinshipstudies.org/2015/07/amerindians-are-even-more-genetically-diverse-and-older-than-we-thought/.

DocG said...

At last we see evidence of a genetic link between Melanesia and Amazonia. I've been puzzling over this for years, as there is abundant evidence of a truly ancient cultural connection, as exhibited not only in the musical distributions I've studied, but also many other cultural elements pertaining to initiation rites, gender relations, mythology, etc. For the musical evidence I'll direct you to Chapter Fifteen of my online book, Sounding the Depths: http://soundingthedepths.blogspot.com/2011/03/chapter-fifteen-upcoast-downcoast-from.html

For the cultural evidence generally, see the book "Gender in Amazonia and Melanesia," by Tuzin and Gregor.

Paul Setti said...

If they found Australoid lineages I wonder if they will find Denisovan admixture in a future study.

CleverPrimate said...

Was the Kenniwick genetic data include in either one of these studies?

Ryan said...

Paul/Ross - Interestingly enough, the populations that are the most Melanesian-like ancestry in this study also have the ones shown as having the least Denisovan ancestry in other studies. And the Melanesian-like ancestry is closed to the Onge, who have no Denisovan ancestry!

So either there were (at least) two Melanesian->Amerind admixture events, or there were (at least) two Denisovan->Modern human admixture events.

Unknown said...

A recent showing a common origin shared with Bering Strait "founder effects"/West Eurasian influences. It does not diminish the many waves in which groups followed one another to the New World (at least US North America)


shenandoah said...

More than just a couple of "flavors" of 'Native Americans'. And how is the term defined anyway? Pre-Columbian? Pre-Basque, pre-Viking, pre-Phoenician? Columbus did not discover America. He only rediscovered it for Spain.

NeilB said...

Dear Annie Mouse, although I read the abstracts/other information from the links above I could not find the details of pre-columbian European admixture for Mexican mummies you mention. Is it behind the paywall?Could you therefore give details? Regards NeilB

Unknown said...

"The migration edge from Dai to Yoruba is interesting and offers several interpretations.

what do you mean here precisely
Can you expound further

Fabbeyond Jefe said...

"The migration edge from Dai to Yoruba is interesting and offers several interpretations."

What do you mean here precisely
Can you expound further
Appreciate it in advance