Tuesday, March 30, 2021

"Paleo-Asian" Ancestry In The Amazon Is Widespread In South America And Looks Comparatively Recent

The "Paleo-Asian" signal originally seen in only a couple of mostly isolated tribes deep in the source waters of the Amazon. This could have been explained as an outlier attributable to a single or couple of nuclear families at the vanguard of the Pacific route expansion (and was hard to explain any other way). New data largely rules out this hypothesis.

The authors of a new paper have with more careful examination been seen all over the place in South America. They propose an origin in the Asian source population for Pacific route migrants to the Americas in the Founding area that was absent in the portion of the Founding population that ended up in North America and Central America.

The screaming loud problem with the hypothesis that this is associated with the Founding population of the Americas is that there is material and large interpopulation and intrapopulation variability in the signal, in populations spread across South America. 

Inter-population variability could be plausible for populations in isolated Amazonian tribes, or groups with strong endogamy norms. But immense intra-population variability simply should not survive for 14,000 years (about 500 generations). The law of averages catches up with that kind of variability surprisingly quickly in the case of traits that are ancestry informative but not distinguishable as a visible phenotype without extreme population structure, which a trait spread across myriad different pre-Columbian cultures simply couldn't maintain.

Instead, the wide variability and wide geographic range points to a source of this genetic component in much more recent mariners, certainly no older than the arrival of the Paleo-Eskimo ancestors of the Na-Dene in Alaska (ca. 4500 years ago), but more likely (since this ancestry is not seen anywhere outside South America) via Polynesian mariners in the last 1500 years or less (about 30 generations or less), where solid evidence already shows sign of some slight recent admixture of South Americans into Polynesian gene pools nearest to South America, and where evidence from remains of flora and fauna native to the Americas in Polynesia and native to Polynesia on the Pacific Coast has established that some limited pre-Columbian maritime trade via the Pacific Ocean had to have taken place in about that time frame. The likely epicenter from which the admixture radiates also coincides with one of the most likely loci of South American source admixture into Polynesians ca. 1200 CE.

It is disappointing that the paper doesn't have analysis addressing this glaring and obvious issue, despite all of its sophistication in other respects.

Some thin admixture of Polynesians (the average amount of admixture from the Paleo-Asian source is on the order of 2% with wide variation plus and minus in individuals where it is present, also suggesting a minimum date of admixture of 150-180 years ago, i.e. prior to 1840-1870 CE in five or six generations, although potentially much older than that) with high levels of Papuan admixture (some Papuan admixture is present in all Polynesians) into South American societies in these much more recent time periods (but not in modern times, in order to allow for dispersal of this ancestry throughout South America and to insure that it isn't more distinctively modern in character, e.g. ruling out a source from recent Japanese migrants to Peru) could produce the observed scatter. 

It isn't obvious why this signal isn't more obviously Polynesian. And this lack of clear Polynesian genetic affinity could point to some other explanation that is still in a time frame much more recent than the Founding era of the Americas. But whatever the explanation is, it just can't have a 14,000 years old source. 

Ideally, it ought to be possible to better estimate the time frame of this admixture with linkage disequilibrium analysis, but the data may be too thin and the source population too ill defined to make that feasible. Statistical modeling of the possible variation by Monte Carlo methods with the data in this paper alone ought to be sufficient to make a decent estimate that would be much younger than what is proposed. A good benchmark that is well studied over a time scale, that is a bit shorter but on the same order of magnitude, is the population genetic history of Quebec.

Fig. 1. Relative patterns of genetic affinity of Australasians among Native American groups. (A) Maximum Z values per population interpolated with the inverse distance weighting method. (B) Distribution of all estimated Z values (y axis) for each “Z” population (x axis) as violin and box plots. In B, the black dots represent outliers, and the red dashed lines indicate the Z-value thresholds of Z = −3 and Z = 3.

The paper and its abstract are as follows:

Different models have been proposed to elucidate the origins of the founding populations of America, along with the number of migratory waves and routes used by these first explorers. Settlements, both along the Pacific coast and on land, have been evidenced in genetic and archeological studies. However, the number of migratory waves and the origin of immigrants are still controversial topics. 
Here, we show the Australasian genetic signal is present in the Pacific coast region, indicating a more widespread signal distribution within South America and implicating an ancient contact between Pacific and Amazonian dwellers. 
We demonstrate that the Australasian population contribution was introduced in South America through the Pacific coastal route before the formation of the Amazonian branch, likely in the ancient coastal Pacific/Amazonian population. 
In addition, we detected a significant amount of interpopulation and intrapopulation variation in this genetic signal in South America. This study elucidates the genetic relationships of different ancestral components in the initial settlement of South America and proposes that the migratory route used by migrants who carried the Australasian ancestry led to the absence of this signal in the populations of Central and North America.

Marcos Araújo Castro e Silva, et al., "Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry" 118 (14) PNAS e2025739118 (April 6, 2021) https://doi.org/10.1073/pnas.2025739118 (Hat Tip to DDeden in the comments). Supplemental materials here. Data here.

As the body text explains:

A signal of genetic affinity between present-day and ancient natives from South America and present-day indigenous groups of South Asia, Australia, and Melanesia has been previously reported. This Australasian−Native American connection persists as one of the most intriguing and poorly understood events in human history. 
The controversial Australasian population genetic component (i.e., “Ypikuéra population” or “Y population” component) was identified exclusively in the present-day Amazonian populations suggesting at least two different founding waves leading to the formation of the people of this region. 
The first wave was inferred to be composed of direct descendants of the Beringian standstill population, and a second wave was formed by an admixed population of Beringian and southeast Asian ancestors that reached Beringia more recently. Both these populations would have settled and admixed in the Amazon region.

The contribution of an unsampled population to the autochthonous gene pool is thought to have led to the origin of the Australasian shared ancestry. In this sense, the Y population would be part of the first colonizing groups of the American continent. However, data from ancient South American samples indicated a weak Y signal around 10,000 yBP. This evidence indicates that, rather than a second wave entering South America from southeast Asia, the Y ancestry might be traced back to common ancestors of Native Americans, who lived in northeast Asia. 
Furthermore, a new line of evidence indicates that the first American clades split in East Asia, not in Beringia, which makes the gene flow of the Y ancestry from the ancestral East Asian groups even more likely. 
However, the paucity of the signal among present-day and ancient groups, along with the endemic and apparently random pattern of detection, has raised the possibility that it could be a false-positive detection, likely due to the strong genetic drift effects experienced by the Amazonian populations (and other indigenous South Americans). However, it might be the other way around, a scenario in which the signal went below the significance level in some populations, due to the high drift effects they experienced (i.e., false negatives).

We explored our dataset, which is currently the most comprehensive set of genomic data from South American populations (383 individuals; 438,443 markers), to shed light on this question. 
. . .

Our results showed that the Australasian genetic signal, previously described as exclusive to Amazonian groups, was also identified in the Pacific coastal population, pointing to a more widespread signal distribution within South America, and possibly implicating an ancient contact between Pacific and Amazonian dwellers. In addition, a significant amount of interpopulation and intrapopulation variation of this genetic signal was detected.

To test the existence of this excess allele sharing, we calculated the D(Mbuti, Australasian; Y, Z) statistic for every pair of Y and Z indigenous groups or individuals in our dataset, where “Australasian” is also iterated over the Australasian groups, namely Australian (and Australian.DG), Melanesian, Onge (i.e., ONG.SG), and Papuan. In the tests between groups, signal detection was reproduced in Karitiana and Suruí (Amazonia), but it was also observed in Chotuna (Mochica descendants from the Pacific coast), Guaraní Kaiowá (central west Brazil), and Xavánte (Central Brazilian Plateau)
When we used the maximum unrelated set of individuals, the signal lost significance level in Karitiana, Suruí, and Guaraní Kaiowá . However, the signal was still evident in the Pacific coast population and in the central Brazilian natives. 
. . . 
the loss of signal significance upon the shift from the complete set to the maximum unrelated set of samples was caused by the exclusion of specific individuals with higher levels of allele sharing with Australasians rather than by the removal of a bias caused by the relatedness among the tested samples in the first place. . . . .

This provides strong evidence that a significant variability of this signal exists not only at an interpopulation level but also between individuals from the same populations. These results suggest that the intrapopulation variability of this signal is not rare and is observed in several groups (Apalai, Guaraní Nãndeva, Karitiana, Munduruku, Parakanã, and Xavánte). Most significant tests detected this excess signal in Tupí-speaking individuals, but the signal was also detected in individuals from every major linguistic group and, at the same time, presented a widespread geographic distribution within South America. Conversely, a considerable number of samples were inferred to have a deficit of allele sharing with Australasians. 
Strikingly, the individual PAR137 (Parakanã) presented an extremely high proportion of significant tests (31.64%), indicating a relative deficit. This individual is not an outlier neither in the principal component analysis of the Native American samples, nor regarding its missingness rate, nor in a multidimensional scaling (MDS) of pairwise genetic distances between samples in the unrelated and unadmixed subset. Besides, the distribution of Y-population ancestry among present-day indigenous groups of South America showed no relationship with ethnolinguistic diversity or geographic location. 
. . .

Different migration routes to the South American region have been previously proposed and evidenced. Archeological and genetic data demonstrated that both routes, Pacific coastal and inland, were likely used by the first migrants. 
Our models point to an ancient genetic affinity between the Pacific coast and Amazonian populations that could be explained by the presence of Y ancestry in both geographic regions. 
In addition, this shared ancestry seems to precede the separation of the Pacific and Amazon branches, showing an entry through the west coast, followed by successive events of genetic drift in the Brazilian populations. This genetic evidence for the presence of Y ancestry on the South American Pacific coast indicates that this ancestry likely reached this region through the Pacific coastal route, and therefore could explain absence of this genetic component in the populations of North and Central America studied so far.
Previous Posts At This Blog

The following previous posts at this blog discuss the Paleo-Asian ancestry in the Americas issue or issues of pre-Columbian contact with Oceania and Asia, at least in passing:


james said...

Sarmiento's History of the Incas says the Incans claimed that Tupac Inca had sailed west and brought back "black people, gold, a chair of brass, and a skin and jaw bone of a horse" after a voyage of about a year.

Would such a long voyage have been attempted, especially with such a high-ranking prince, if there hadn't been earlier stories of contact?

andrew said...

Key point:

"The Inca Empire was preceded by two large-scale empires in the Andes: the Tiwanaku (c. 300–1100 AD), based around Lake Titicaca and the Wari or Huari (c. 600–1100 AD) centered near the city of Ayacucho. The Wari occupied the Cuzco area for about 400 years. Thus, many of the characteristics of the Inca Empire derived from earlier multi-ethnic and expansive Andean cultures." Inca Empire founded in 1438 CE. Columbus is 1492 CE. "Spanish conquistadors led by Francisco Pizarro and his brothers explored south from what is today Panama, reaching Inca territory by 1526." They return and defeat the Inca Empire in 1532.The last vestiges of the Inca Empire fall in 1572.

Then, "After the fall of the Inca Empire many aspects of Inca culture were systematically destroyed, including their sophisticated farming system, known as the vertical archipelago model of agriculture. Spanish colonial officials used the Inca mita corvée labor system for colonial aims, sometimes brutally. One member of each family was forced to work in the gold and silver mines, the foremost of which was the titanic silver mine at Potosí. When a family member died, which would usually happen within a year or two, the family was required to send a replacement. The effects of smallpox on the Inca empire were even more devastating. Beginning in Colombia, smallpox spread rapidly before the Spanish invaders first arrived in the empire. The spread was probably aided by the efficient Inca road system. Smallpox was only the first epidemic. Other diseases, including a probable Typhus outbreak in 1546, influenza and smallpox together in 1558, smallpox again in 1589, diphtheria in 1614, and measles in 1618, all ravaged the Inca people."

See https://en.wikipedia.org/wiki/Inca_Empire

So, anything in the Inca era or either of its two successive antecedent empires is in a time frame along the lines of what I'm suggesting rather than in the Founding era. The evidence of low level pre-Columbian contact with Oceanians and possibly even Asians is mounting, and explains to South American outlier genes better.

DDeden said...

I wonder if this signal has been detected in ancient Yahgan (Chile) or Pirahã (Amazon) genomes, they both made and used only bark canoes, were culturally isolated, and thought unusually primitive technologically.

Ryan said...

I find it very unlikely that any maritime contacts reshaped the genome of the deep Amazon. More likely to me would be some kind of pre-existing within-South America structure collapsing. Collapsing structure has been the story of the Holocene after all has it not? Why not in SA too?

andrew said...

There is virtually no plausible way to get the magnitude of intra-population variability seen over 500 generations in any kind of South American structure collapse over this wide of a geographic range in many distinct culturally and genetically distinguishable subpopulations. Yet without modern DNA tests there is no way to know who has this component and who doesn't and it doesn't appear to have any selective fitness enhancing component. There was a lost Neolithic society in the Amazon ca. 0 CE to 1000 CE that could have been involved in the dispersal of these genes. But the genes had to get there first and would have been homogenized by 0 CE or within that Neolithic community after 1000-ish years. See https://dispatchesfromturtleisland.blogspot.com/2012/01/picture-of-lost-civilization-in-amazon.html

In contrast, if you have maritime contacts ca. 1200 BCE, this provides 28 generations for sporadic instances of admixed individuals produced by the maritime contract to disperse via sporadic spouse exchange between populations in the Amazon which have quite low base populations which means that a very small number of spouse exchange events (on the order of 1-2 over the entire time period) would be necessary to produce the observed distribution. The more distant populations may have only had this ancestry component ingress into some of their communities only in the last century or so, affording the component many centuries to spread by sporadic gene exchange between communities that is consistent with the way that forest dwelling indigenous tribes admix with each other (there are faint hints that the interpopulation variability increases as you get more distant from Columbia).

The most plausible route is along the coast of Columbia, up a river draining into the Gulf of Mexico to its the South American highlands source, and then back down tributaries to the Amazon river which have their headwaters a day or so's hike away from the headwaters of the rivers going into the Gulf of Mexico, because this is where the signal was first detected and is strongest among Amazonian populations. Subsequent dispersal could be via riverine travel along the Amazon and its tributaries.

Ryan said...

"There was a lost Neolithic society in the Amazon ca. 0 CE to 1000 CE that could have been involved in the dispersal of these genes. But the genes had to get there first and would have been homogenized by 0 CE or within that Neolithic community after 1000-ish years. See"

That's what I'm suggesting. Maybe something Jomon-like persisting on the fringes from an early expansion along the coasts or the like that gets amplified by said culture.

"In contrast, if you have maritime contacts ca. 1200 BCE"

I assume you mean 1200 CE?

I have a hard time believing said maritime contacts on the Pacific Coast had a greater impact on Amazonians than European colonialism has to date.

I think a smaller demographic impact from a larger number of initial Pacific Islander-related culture is more plausible than handfuls of seafarers sporadically venturing up a massive river system for no apparent reason.

One would also expect a wider distribution of Polynesian-derived chickens in the Amazon, no? Instead they're confined to coastal populations of the Pacific.

Ryan said...

Like, the pre-Columbian population of Brazil was what? 4 mil? 5 mil?

2% of 4,000,000 is 80,000. How does that big of an influx get to the Amazon?

andrew said...

"I assume you mean 1200 CE?" I did.

"I have a hard time believing said maritime contacts on the Pacific Coast had a greater impact on Amazonians than European colonialism has to date."

It didn't. The Paleo-Asian component is a sporadic 2% at best. The vast majority of Native South Americans are much more heavily admixed than that. This simple was pruned to include only "pure blooded" Native South Americans, however (more than 99%).

"Like, the pre-Columbian population of Brazil was what? 4 mil? 5 mil?

2% of 4,000,000 is 80,000. How does that big of an influx get to the Amazon?"

For the Amazonian interior I think that the number is in the several hundreds of thousands. And, since it is sporadic, you are really talking about 2% admixture into perhaps half or a third of that population or less. It isn't that huge of an influx.

Seriously, while I don't have a great sense of the initial Paleo-Asian founding population, it just can't be all that big, and the episode of admixture would have to be pretty short because of the lack of uniparental traces. If you have sustained population expansion or a sustained source, the uniparental markers will stick. The fewer the generations with admixture, the more likely they are to go. If you have primarily bride exchange, you don't get Y-DNA haplogroup sharing (we don't see any old Y-DNA O in South Americans), and the dilution of mtDNA in subsequent generations can purge that haplogroups if the effective population is stable or declining and the raw numbers in the initial generations are low (we also don't see Polynesian mtDNA in South Americans, although admixture filters in past methodologies could influence that).