Despite the title, some of the patterns and trends are very straight forward as figures 1A and 1B from the paper, below, illustrate:
There is a stark division between the populations to the west of the Wallace line, which line up along a mostly north to south axis along the far left side of the PCA analysis, and the populations to the east of the Wallace line which stretch in a west to east cline along the first principal component.
For the most part, the east of the Wallace line populations cluster with Austronesian populations on the second principal component. But, a pull driven by Austronesian admixture may be problematic, because individuals from the Papuan highland and coast with almost no Austronesian ancestry in ADMIXTURE are also found at that point on the second principal component. Oceania, however, looks more like Eastern Indonesia than it does like Melanesia.
Bernard, as translated from the French by Google, summarizes the ADMIXTURE analysis that was done as follows (emphasis added):
In the region there are two main components: a continental component in yellow and a Papuan component in violet. A third component often referred to as Austronesian appears in light blue from K=5. There is a clear difference between Western Indonesia which includes a high proportion of Austronesian ancestry and virtually no Papuan ancestry, and Eastern Indonesia which has little Austronesian ancestry and a high proportion of Papuan ancestry.
Basically, this suggests that while there were modern humans in Sumatra shortly after the Toba eruption, that there was a major migration by a genetically distinct population from mainland Southeast Asia, resulting in near total population replacement of what may have been a Papuan-like, Denisovan admixed population, around the time of the Last Glacial Maximum when low sea levels created a land bridge to the mainland, ca. 20,000 years ago.
This would have happened despite the fact that both populations would have been modern human hunter-gatherers, perhaps because the early Indonesians, protected from invaders by the sea, didn't need to master the art of war until it was too late to catch up with the men of the mainland who hadn't had that luxury.
This also corroborates other evidence that few mainland Asians are not the first wave of modern humans in the region.
Nias and Mentawai
The most "southerly" populations on the second principal component actually from small islands in western Indonesia, rather than up against the Wallace line. This is true despite the fact that they appear almost completely Austronesian, which is more "northerly" than these populations, in an ADMIXTURE analysis at K=5 to K=8 (after which they start to appear as distinct populations of their own).
These populations actually have more of the "Austronesian" component than populations from the Taiwanese point of origin of the Austronesians or populations form the Philippines that appear to be closer to the original Austronesians than modern indigenous Taiwanese populations, which suggests that something is backwards in how ADMIXTURE generated its populations.
In other words, only part of the "Austronesian" component in the ADMIXTURE analysis is probably actually Austronesian, and the balance is probably what is giving these populations their "southerly" pull on the second principal component in the PCA chart.
Baining, Nasioi and Vanuatu
Some of the Baining people. Note that, despite superficial appearances, the Baining people are no more closely related to Africans than people from China or England or Hawaii.
Even more surprising are the Baining people who live in the Baining mountains the esatern part of the island of New Britain off the coast of Papua New Guinea who appear to be a relict population with a distinct language small language family. According to Wikipedia:
They currently inhabit the Baining Mountains into where they are thought to have been driven by the Tolai tribes who migrated to the coastal areas in comparatively recent times. Another factor that might have influenced their migration inland was major volcanic activity that took place over centuries. (As recently as 1994, the nearby town of Rabaul was almost completely destroyed by two volcanoes, Tavurvur and Vulcan).
The Baining people (there are about 12,000 of them based upon the number of people who speak the five or six living Baining languages) are subsistence farmers with few animals who have been historically described as "the dullest people on Earth" for the very low levels of play, myths, festivals, religious traditions, or even interest in sex in their lives, and are compared to the early American "Puritans" in their lifestyle. They have one notable, somewhat all purpose ritual, a costumed fire-dance performed by young men which women and children do not participate in or watch. They are also notable for a very high level of adoption, about 36% of children, something promoted as "unnatural".
They do not justify their dances or their life choices with religion or symbolic meaning.[T]he Baining shun the bush, which they view as chaotic and dangerous, and they derogate play, especially that among children.According to Fajans, the Baining eschew everything that they see as “natural” and value activities and products that come from “work,” which they view as the opposite of play. Work, to them, is effort expended to overcome or resist the natural. To behave naturally is to them tantamount to behaving as an animal. The Baining say, “We are human because we work.” The tasks that make them human, in their view, are those of turning natural products (plants, animals, and babies) into human products (crops, livestock, and civilized human beings) through effortful work (cultivation, domestication, and disciplined childrearing).
The fifteen to nineteen languages of the general vicinity of the East Papuan area have some sub-groups with some similar pronouns, but many of these languages have almost no more similarity in vocabulary than would be expected from random chance, despite the fact that each is spoken by only a tiny number of people and many of the languages are spoken by people who live quite close to each other geographically and have done so for 35,000 years or so.
The Baining people are surprising, genetically, given their location, because they are very northerly indeed on the second principal component of the PCA chart, more so than the Han Chinese and Japanese, despite being also very Papuan on the first principal component. Similar, but much less strong impacts in that direction are seen on the adjacent island of Nasioi and in the near Oceanic island of Vanuatu, which probably derived from Baining admixture revealed in an ADMIXTURE analysis.
A naive explanation for the northerly anomaly would be that they arose during Japanese occupation. The effect seems very large for a fairly short duration event, but the base populations were small and there is no way to be sure how representative these samples are of these small populations. Cryptic maritime trade links to Japan or Northern China could also provide an explanation.
But, ADMIXTURE analysis strongly disfavors this interpretation. Even at K=3, Baining Island has none of the predominant component found in the Japanese and Han Chinese, so the recent admixture or trade linkage theory is pretty definitively shot down. A distinctive Baining component emerges at K=6 making up almost all of the ancestry from that island of the northern coast of Papua New Guinea, and present in lower proportions in neighboring Naisio and nearby Vanuatu, and even even lower proportions elsewhere in Oceania (i.e. Tonga, Samoa and Tahiti), where a distinct Oceanian variant of this component emerges at K=8.
The Clade based analysis below also shows the Baining people as sharing a clade with Papuans and in admixture at K=3 to K=5 they are almost indistinguishable from Papuans.
Thus, it seems likely that the divide between the Baining people and Papuans on the northern-southern second principal component, rather than being attributable to late Holocene admixture, probably has deep roots indeed. But, as a farming culture (presumably of indigenous Papuan crops as the Papuans were an independent Neolithic center), their ethnogenesis can't be much older than the Holocene (i.e. 10,000 years ago) either. It could be that the Baining people, given their small population and long standing isolation from the larger populations of Papuan New Guinea in the pre-Austronesian era (and apparently even after that development) have simply been more susceptible to genetic drift than people on Papua New Guinea itself who may have had low levels of bride or husband exchange sufficient to harmonize the genetic subpopulations somewhat, and that this is manifesting in what looks like a great northerly divergence on the second principal component in this study.
A Clade Based Analysis
While we know that a branching clade model is not a great description of the historical process by which Island Southeast Asia acquired its genetic diversity, the investigators did generate a clade based analysis with their data that captures the broad outlines of the conclusions reached by other means.