Tuesday, April 21, 2020

Samoan Population History

Oceania Maps – Freeworldmaps.net

A new study looked a modern genomes from a significant share of the entire population of Samoa (which has a total population of 246,000 people now), an Oceanian island in the Pacific Ocean, and inferred a great deal of past population history from the sample. 
A new study in Proceedings of the National Academy of Sciences analyzed the genomes of 1,197 individuals in Samoa and found that the effective population size of the first Samoans was small -- ranging from 700 to 3,400 people during the time period from approximately 3,000 to about 1,000 years ago. Starting about 1,000 years ago, population size rapidly increase to about 10,000 individuals, coinciding with increasing agricultural and socio-political complexity, but also with previously hypothesized contacts with other Oceanic peoples. 
This population history scenario for Samoa is consistent with the existing archaeological evidence of few, widely scattered and small-sized settlements in the first 2,000 years after Samoa's initial settlement. But it contrasts with archaeological population reconstructions of much larger population sizes for adjacent Pacific peoples in Tonga and Fiji during that first 1,500 to 2,000 years after initial discoveries around 3,000 years ago. . . . 
The new study also found that modern Samoans derive largely from the Austronesian lineage, including the aboriginal peoples of Taiwan, Island Southeast Asia, coastal New Guinea and other island groups of Oceania -- but share 24% of their ancestry with Papuans, the descendants of the people who settled Papua/New Guinea, an estimate markedly lower than found in neighboring Polynesian groups. 
The researchers also found strong evidence of population reduction coincident with outside contact from European-derived groups, presumably from infectious diseases new to Samoan immune systems and societal shocks from such epidemics. The whole genome sequence data from participants' DNA also enabled findings about some genetic diversification within Samoa that may be reflective of regional and local social processes. The genomic data also showed an increase in population size about 150 years ago.
This summary of the archaeology and history of Samoa 
is from the Supplemental Materials (Table S5).

It isn't entirely clear what happened around Y1K (i.e. 1000 CE) to fuel a sudden burst of population growth after two thousand years of modest populations, although the introduction of the kumara, a species of sweet potato native to South America that made it way from the Pacific coast of South America to Easter Island and eventually all of the way to New Zealand, possibly with other technologies from other islands in Polynesia, around this time, could be a plausible explanation. As Wikipedia explains at the link above in a well annotated account:
The origin and domestication of sweet potato occurred in either Central or South America. In Central America, domesticated sweet potatoes were present at least 5,000 years ago, with the origin of I. batatas possibly between the Yucatán Peninsula of Mexico and the mouth of the Orinoco River in Venezuela. The cultigen was most likely spread by local people to the Caribbean and South America by 2500 BCE. 
The sweet potato was grown in Polynesia before western exploration as the Ipomoea batatas, which is generally spread by vine cuttings rather than by seeds. Sweet potato has been radiocarbon-dated in the Cook Islands to 1400 CE. A common hypothesis is that a vine cutting was brought to central Polynesia by Polynesians who had traveled to South America and back, and spread from there across Polynesia to Easter Island, Hawaii and New Zealand. 
Pre-Columbian chicken bone ancient DNA from Chile suggests that the exchange of foodstuffs went in both directions. Pre-Columbian Polynesian contact with South America dates to sometime in the vicinity of 800 CE to 1200 CE, well in line with the Samoa demographic event.

The body text of the paper provides some further detail about this transition:
Since the ADMIXTURE analysis likely combined the expected Papuan ancestry in Samoans with the Samoan/Austronesian cluster, we used the D statistic to confirm the presence of Papuan ancestry in Samoans. The f4-ratio estimates of Papuan ancestry proportions indicate that Samoans have an average of 24.36% Papuan ancestry, similar to a smaller sampling of Samoan genomes. Furthermore, the Papuan ancestry is uniformly distributed among Samoans (SD = 0.04852), which could indicate that this admixture occurred prior to the peopling of Samoa. However, we cannot reject a scenario of multiple pulses of Papuan admixture with these data. We also find that this Papuan ancestry is correlated to Denisovan ancestry and not Neanderthal ancestry, which suggests that Denisovan ancestry was introduced to Samoans through Papuan admixture, as previously proposed. 
Samoans have less Papuan admixture (estimated through f4 ratio) than the other Polynesian (Tongans) and Polynesian outlier (Ontong_Java, RenBel, and Tikopia) populations in our dataset, which collectively have an average of 35.38% Papuan ancestry. Recent findings suggest that the second wave of Papuan admixture (50 to 80 generations ago, which is 1,500 to 2,400 y ago) into Remote Oceania occurred after Tonga and Samoa were founded by Lapita pottery populations. Therefore, it is likely that the magnitude of this pulse was not equal across the Lapita region of Remote Oceania. . . . 
Our estimates show that a greater period of growth began at about 30 to 35 generations ago (900 to 1,050 y ago), and the two islands’ Ne histories diverge while also increasing to over 10,000 individuals. This occurs during the same timeframe as the widespread appearance of surface architecture and landscape modification, much of it likely for agriculture, and is consistent with the presumed origins of complex chiefdoms. 
It is significant that Addison and Matisoo-Smith hypothesized a population migration into Samoa about 1,500 to 2,000 y ago (50 to 67 generations ago), possibly through the Micronesian Caroline Islands, that closely precedes the increase in Samoan Ne that we report here. Other important cultural changes are reported to have occurred around this time as well, including the loss of pottery 1,000 to 1,500 y ago (33 to 50 generations ago), the growth of Samoan settlements 500 to 1,000 y ago (17 to 33 generations ago), and the colonization of East Polynesia and the Polynesian outliers from Samoa and Tonga 800 to 1,000 y ago (27 to 33 generations ago). 
The divergence and increase in Ne that we identify might be due to the arrival of a new population in Samoa that admixed with and potentially replaced the initial founding population, although this would be an extreme hypothesis. In the case of a nonabsolute admixture, the IBDNe results would constitute a weighted average of these two populations. This case also implies that the potential incoming population was already admixed with Papuan individuals as the uniformity of the current distribution of Papuan ancestry proportion in Samoans implies a founder population with ∼25% Papuan and 75% Austronesian ancestry.

There are numerous questions posed by archaeological research about Samoa’s early history, which include a potential population replacement between 1,500 and 2,000 y ago. Our results use genetic data to enter this discussion of Samoan history, and support a potential population replacement by identifying the divergence of SAV and Upolu between 30 and 35 generations ago (900 to 1,050 y ago), and a subsequent period of growth. In addition, our results reflect a small growth period beginning at 100 generations ago (3,000 y ago) and then, a low Ne that persisted for about 70 generations (2,100 y) thereafter. This is consistent with archaeological findings supporting a Lapita founding event and a small early population size. However, if there was a complete population replacement, then the Ne history before 30 to 35 generations ago (900 to 1,050 y ago) represents the new incoming population’s history of that time period and not the history of the original Lapita population. Without ancient DNA evidence, we cannot definitively conclude that there was a population replacement or whether some other event caused the increase in population size that we detect. However, we can state that there was a clear demographic change 30 to 35 generations ago (900 to 1,050 y ago) that initiated a period of exponential growth after a long and severe bottleneck. Accordingly, a complete population replacement would be more difficult if there was an existing large population on Samoa before this point.
An infusion of migrants from islands in Oceania that admixed with native Samoans is suggested as a possibility, but the comparatively low proportion of Papuan admixture in Samoans relative to people on nearby islands which probably reached current levels before the Samoan demographic event suggests several plausible possibilities: (1) cultural diffusion of technologies rather than demic change was the main force behind the demic event, (2) the migrants were an atypical population in terms of Papuan admixture resulting in a Founder effect, or (3) the pre-demographic event Samoans had an even lower Papuan admixture level prior to the demographic event that diluted the Papuan admixture percentages which was then equalized through panmixia of the migrants with indigenous people after the demographic event. 

But, another data point suggests that the third option is probably the correct one, because we know from ancient DNA that Papuan ancestry arrived in not too distant Tonga and Vanuatu around 500 CE, which is before the demographic event in Samoa, but long after Samoa was settled, and before that time, Oceanians were purely Austronesian genetically. As I explained in an October 12, 2016 post at this blog (quoting someone else's summary of the process using a study that underestimated the percentage of Papuan ancestry in Tongans).
Polynesians are mostly descended from a population on Taiwan, represented today by Taiwanese aboriginals, and from a Melanesian population similar to New Guinea or the Solomon Islands. They’re about 25% Melanesian autosomally, 6% Melanesian in mtDNA, 65% Melanesian in Y-chromosomes. . . . 
Now they’ve looked at ancient DNA from Tonga and Vanuatu. The old samples don’t have any noticeable amount of Melanesian ancestry. So it was like this: the Lapita derived from Taiwan (thru the Philippines), settled Vanuatua and Tonga – then were conquered by some set of Melanesian men, who killed most of the local men and scooped up the women. Probably their sons extended the process, which resulted in a lower percentage of Melanesian ancestry while keeping the Y-chromosomes mostly Melanesian.  
After this conquest, the Polynesians expanded further east, and those later settlement (Tahiti, Marquesas, Hawaii, etc) all had that ~25% Melanesian component.  
From here.

I noted in that post that: "A rough look at the numbers fits that scenario, with perhaps 44% of the men and 6% of the women in the first generation of conquest being Melanesian, leaving 21% of the Y-DNA mix to come from descendants of the original men (just about half of the original percentage of Melanesian men)."

Together with the data above, we can infer that the ancestry of the modern Samoan population was not completely replaced and instead is derived about 31% from the original first wave Lapita migrants who arrived around 800 BCE, and about 69% of Polynesian migrants who arrived around 950 CE to 1100 CE. This may be an overestimate of the relative proportions of Samoan and non-Samoan ancestry at the time of the admixture event itself, however. 

It could be the some Papuan ancestry could have arrived through population exchange after the initial demographic event and even into modern times, which could help explain why the Samoan language and indigenous population were not overwhelmed and obliterated. It could also be that cultural diffusion spurred the demographic event, and that admixture from Tonga came just a little later, around its traditionally assumed historic date of about 1150 CE.

This possibility of an extended period of immigration into modern times is suggested by a comparison of ancestry percentages between regions within Samoa as show below in the following table from the Supplemental Materials:

We can also infer that the Samoans spoke a language close to the original Austronesian language of one of the indigenous populations of Taiwan albeit with drift over time, that the Melanesian men who arrived in Tonga and Vanuatu around 500 CE ended up adopting the Austronesian language of the people they conquered abandoning their own Papuan language, and that when they migrated to Samoa, the two Austronesian languages, separated by about 1300 years of language drift, either gave rise to the modern Samoan language, or one or the other of those languages became predominant. Linguistic data suggest that the original Samoan language was the linguistic parent language of modern Samoan, but that there were a significant number of Tongan loan words even in basic vocabulary that were integrated into the Samoan language at the time of the demographic transition:
Samoan is an analytic, isolating language and a member of the Austronesian family, and more specifically the Samoic branch of the Polynesian subphylum. It is closely related to other Polynesian languages with many shared cognate words such as aliʻi, ʻava, atua, tapu and numerals as well as in the name of gods in mythology
Linguists differ somewhat on the way they classify Samoan in relation to the other Polynesian languages. The "traditional" classification, based on shared innovations in grammar and vocabulary, places Samoan with Tokelauan, the Polynesian outlier languages and the languages of Eastern Polynesia, which include Rapanui, Māori, Tahitian and Hawaiian. Nuclear Polynesian and Tongic (the languages of Tonga and Niue) are the major subdivisions of Polynesian under this analysis. A revision by Marck reinterpreted the relationships among Samoan and the outlier languages. In 2008 an analysis, of basic vocabulary only, from the Austronesian Basic Vocabulary Database is contradictory in that while in part it suggests that Tongan and Samoan form a subgroup, the old subgroups Tongic and Nuclear Polynesian are still included in the classification search of the database itself.
See also here.

The linguistic data also favor a narrative of the demographic transition ca. 1000 CE in Samoa that is more peaceful than the bloody story of conquest that probably explains the demographic event that brought Papuan ancestry to Polynesia. Otherwise, Samoan would be unambiguously Tongan.

The paper is with its abstract are as follows:
Archaeological studies estimate the initial settlement of Samoa at 2,750 to 2,880 y ago and identify only limited settlement and human modification to the landscape until about 1,000 to 1,500 y ago. At this point, a complex history of migration is thought to have begun with the arrival of people sharing ancestry with Near Oceanic groups (i.e., Austronesian-speaking and Papuan-speaking groups), and was then followed by the arrival of non-Oceanic groups during European colonialism. However, the specifics of this peopling are not entirely clear from the archaeological and anthropological records, and is therefore a focus of continued debate. 
To shed additional light on the Samoan population history that this peopling reflects, we employ a population genetic approach to analyze 1,197 Samoan high-coverage whole genomes. We identify population splits between the major Samoan islands and detect asymmetrical gene flow to the capital city. We also find an extreme bottleneck until about 1,000 y ago, which is followed by distinct expansions across the islands and subsequent bottlenecks consistent with European colonization. These results provide for an increased understanding of Samoan population history and the dynamics that inform it, and also demonstrate how rapid demographic processes can shape modern genomes.
Daniel N. Harris, et al., "Evolutionary history of modern Samoans"Proceedings of the National Academy of Sciences, 201913157 (2020) DOI: 10.1073/pnas.1913157117 

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