Ayta Negritos: Highest Levels of Denisovan DNA

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Ayta Negritos: Highest Levels of Denisovan DNA Aug 25, 2021 4:45:43 GMT

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Results
Distinct Population Stratification across the Philippines Reveals Multiple Ancestral Sources.
Investigation by principal component analysis (PCA) demonstrates that all Philippine ethnic groups cluster together with Asia-Pacific populations in a global comparison (Fig. 1B and SI Appendix, Fig. S1 B and C). While Negritos form a distinctive cline that aligns between Papuans and non-Negritos, Cordillerans interestingly lie to the edge that defines the East Asian cluster on principal component (PC) 1, even more extreme than Native American groups and Oceanian groups (Fig. 1B). There is a clear dichotomy between Negritos and non-Negritos, indicating the deep divergence between Basal East Asian ancestry best represented by Cordillerans and Basal Australasian ancestry represented by Negrito-AustraloPapuans (Fig. 1B and SI Appendix, Fig. S1 B and C). Looking into the fine-scale analysis of Asia-Pacific populations, non-Negritos clearly separate into groups either affiliated with Cordillerans or with Mainland Southeast Asia (MSEA) ethnic groups (such as Htin and Mlabri, or Malay non-Negritos) (SI Appendix, Fig. S1 D–G).

Further analyses reveal distinct genetic structure among Philippine Negrito groups, as will be described later, and stratification among non-Negrito groups, exemplified by Cordillerans, Mangyans, Manobos, and Sama Dilaut groups (Fig. 1 C and D). These observations are consistent with inferred ancestry components (SI Appendix, Fig. S2 B–D). Briefly, stratification commences with a dichotomy between AustraloPapuan-related Negritos vs. non-Negritos, subsequent clustering of non-Negritos into Cordilleran vs. MSEA-affiliated populations, and stratification of Negritos into Ayta and Agta groups and non-Negritos into Cordilleran, Mangyan, Manobo, and Sama-related populations.

Philippine Negritos Exhibit Deep Divergences.
Given the geographical barriers and the likely long history of isolation between populations, some degree of differentiation is expected among Negrito groups. For instance, PCA restricted to Negrito groups reveals a gradient between Central Luzon Negrito groups and Southern Negrito groups (PC1), and an east-to-west clustering of Negritos in the northern Philippines along PC2 (SI Appendix, Fig. S4A). The Northern Negritos additionally exhibit deep population structure, separating into three clusters: Central Luzon Negritos (all Ayta Negritos), Southeastern Luzon Negritos (Agta groups of Bicol region and Quezon province), and Northeast Luzon Negritos (Agta, Atta, and Arta Negritos of Cagayan region) (SI Appendix, Fig. S4B).

Negritos of the northern Philippines are an outgroup to both Australians and Papuans (Fig. 2A and SI Appendix, Figs. S4 D, E, G–I and S5D). Using a coalescent-based split-time estimation approach and assuming a population divergence model (12, 13), we estimate the ancestors of Negritos of the northern Philippines to have diverged ∼46 kya (95% CI: 45.5 to 46.8 kya) from a common ancestral Australasian population (Basal Sunda). The divergence likely happened in the old continental landmass of Sundaland, prior to the Australian-Papuan divergence ∼25 kya (95% CI: 24.7 to 26.7 kya), possibly as a consequence of migration into Luzon to become present-day Negritos of the northern Philippines (SI Appendix, Figs. S4J and S5D).

Fig. 2.
Inferred admixture graph models for Australasians and East Asians. Inferred admixture graph models based on a combination of qpGraph and f statistical analyses presented in SI Appendix, Figs. S4–S8. (A) Topology of Australasian cluster indicating pulses of Denisovan introgression events, and estimation of divergence time between Philippine Negritos and AustraloPapuans. (B) Topology of the East Asian cluster showing relationships between Cordillerans, Manobo, Sama, and mainland Asian ethnic groups with inferred admixture events and divergence dates. See main text for divergence time confidence intervals.

In contrast to the north, the AustraloPapuan-like genetic signal is distinctively higher in Southern Negritos (e.g., Mamanwa) than in other Negrito groups (Fig. 2A and SI Appendix, Fig. S4 K–M). The Mamanwa Negritos also appear as an outgroup to Papuans and Australians (SI Appendix, section 4.3), indicating that the ancestral Mamanwa is an offshoot group of Basal Oceanian that diverged ∼37 kya (95% CI: 36.2 to 38.7 kya), by which entered Mindanao Island, likely via the Sulu Archipelago, prior to the Australian-Papuan divergence (Fig. 2A and SI Appendix, Figs. S4J and S5D). However, an alternative model where Southern Negritos form a clade with Northern Negritos is not rejected (SI Appendix, section 4.3 and Fig. S5G). Given this, we are unable to exclude a scenario where a common ancestral Negrito population entered the Philippines exclusively through a single port of entry, either via Palawan or via the Sulu archipelago, and subsequently diverged within the Philippines to become the Northern and Southern Negritos.

Both Northern and Southern Negritos subsequently admixed with Cordilleran-related populations, and, interestingly, Southern Negritos received an additional gene flow from Papuan-related populations after Australian-Papuan divergence (SI Appendix, Fig. S5 D and G). This previously unappreciated northwest gene flow of Papuan-related ancestry had its greatest impact on eastern Indonesia, as well as ethnic groups of the southeastern Philippines, such as Sangil and Blaan (SI Appendix, section 4.5).

Ancestral Manobos and Ancestral Sama Entered the Southern Philippines Earlier Than the Expansion of Cordilleran-Related Populations.
The ethnic groups of the southern Philippines exhibit a ubiquitous ancestry that is non–AustraloPapuan-related and which is generally absent among non-Negrito groups of the northern Philippines. This unique genetic signature, heretofore designated as “Manobo ancestry,” is highest among inland Manobo groups of Mindanao Island (SI Appendix, Fig. S6A). When we masked Cordilleran and Southern Negrito ancestry and retained only the Manobo ancestry, the Manobo component became more apparent among other ethnic groups of Mindanao (SI Appendix, Fig. S6B). In addition to Manobo ancestry, another distinct ancestry was identified in the southwestern Philippines. This genetic signal is highest among Sama sea nomads of the Sulu Archipelago and is designated as “Sama ancestry” (SI Appendix, Fig. S6G). When we mask all other ancestries and retain only Sama ancestry, the Sama component becomes more evident among ethnic groups of Zamboanga Peninsula, Palawan, Basilan, Sulu, and Tawi-Tawi islands, even among populations who do not self-identify as Sama or speak a Sama-related language (SI Appendix, Fig. S6H).

Ethnic groups with high Sama ancestry exhibit significantly higher genetic affiliation with Austroasiatic-speaking ethnic groups of MSEA, such as Mlabri and Htin, relative to the least admixed Manobo group, Manobo Ata (SI Appendix, Figs. S6K and S7 A–D, J, and K). This Htin/Mlabri-related genetic signal is not only found in Sama Dilaut and inland Sama groups, but also in Palawanic and Zamboanga peninsula ethnic groups of the southwestern Philippines. These findings are consistent with previous observations where a Htin/Mlabri-related genetic signal was detected among ethnic groups of western Indonesia (10). In our analysis, we find that this genetic signal also extends beyond western Indonesia and into the southwestern Philippines.

Both Manobo and Sama genetic ancestries diverge from a common East Asian ancestral gene pool (∼15 kya [95% CI: 14.8 to 15.4 kya]) earlier than the estimated divergence between the indigenous peoples of Taiwan and Cordillerans (Fig. 2B and SI Appendix, Fig. S7E). Surprisingly, both of these ancestries (Manobo and Sama) diverged from the common East Asian branch before Han, Dai, and Kinh split from Amis, Atayal, or Cordillerans (Fig. 2B and SI Appendix, Figs. S6 E, F, and L). Hence, our findings indicate that Ancestral Manobo and Ancestral Sama, together with other Htin/Mlabri-related ethnic groups, form a branch that diverged from Basal East Asians ∼15 kya even before the expansion of Han, Dai, Japanese, Kinh, Amis, and Atayal (Fig. 2B and SI Appendix, Figs. S6 E, F, and L and S7E).

Sama forms a clade with Htin relative to Manobo Ata (SI Appendix, Fig. S7 A–D and sections 5.5 and 5.6). The common ancestor of Sama and Htin/Mlabri populations was estimated to have diverged from Ancestral Manobo ∼12 kya (95% CI: 11.4 to 12.6 kya). Given the geographic distribution of the Htin/Mlabri-related genetic signal today, their ancestors likely expanded into western Indonesia and the southwestern Philippines, via Sundaland, before the expansion of Cordilleran-related populations (14). Interestingly, the above estimated divergences (15 kya and 12 kya) coincide with the major geological changes in ISEA, inferred from reconstructions of Sundaland at the end of the Last Glacial Period (SI Appendix, Fig. S3 E and F). Accordingly, climate-driven changes in ISEA may have prompted postglacial movements and isolation of populations, which led to the differentiation of ethnic groups in the region.

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Ayta Negritos: Highest Levels of Denisovan DNA Aug 25, 2021 20:34:56 GMT

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Cordillerans Represent the Least Admixed Basal East Asian Group in a Worldwide Set of Populations.
Cordilleran ethnic groups reside in the only landlocked region of the Philippines, across the Cordilleran mountain range in north-central Luzon. Historically, Cordillerans were known to resist direct colonization and Christianization by the Spanish and hence were able to retain many of their distinct cultural practices (15). This geographic and cultural isolation may have played a role in the high linguistic diversity of the region and the low levels of genetic admixture displayed by some groups. In addition to the previously reported Kankanaey (16), and following admixture and combination of f3 admixture and f4 statistical analyses, we found Bontoc, Balangao, Tuwali, Ayangan, Kalanguya, and Ibaloi as being among the least admixed populations bearing Basal East Asian ancestry (SI Appendix, Figs. S2 B–D and S8 A–C and section 6.1).

The homogenous ancestry among Cordillerans observed in all our Admixture analysis could be explained by the presence of strong genetic drift. However, a previous analysis (11) and our investigation on the number and tract length of runs of homozygosity do not support a recent bottleneck or extensive inbreeding among Cordillerans (SI Appendix, Fig. S1 H–J and section 3.8). Moreover, formal tests using f3 admixture and f4 statistics provide direct evidence that Central Cordillerans retained to be the only ethnic groups within the Philippines who did not receive gene flow from Negritos (SI Appendix, Fig. S8 A–C). This is unexpected, given the series of migrations and periods of colonization in the surrounding area of the Cordillera region and the documented records of trade and historical interactions with Negrito and non-Negrito groups of Luzon (17). All other ethnic groups in the Asia-Pacific region are admixed with Andaman, Papuan, Negrito, Htin/Mlabri, or northern East Asian (nEA)-related genetic ancestries (SI Appendix, Figs. S2 B–D and S9 D, E, and J and section 6.1). Hence, we find Cordilleran groups to consistently define the axis of PC1 in world PCA, in polar opposite to the African Khoe-San ethnic groups at the other extreme, even after we control for sample-size differences between regional groups (Fig. 1B and SI Appendix, section 6.1 and Fig. S1 B and C).

Cordillerans, and not Amis or Atayal of Taiwan, serve as the best modern-day surrogate for the least admixed genetic signal for the expansion of AN-speaking populations (11). Both Amis and Atayal exhibit admixture with genetic components resembling Htin/Mlabri-related (or “Austroasiatic-related”) and nEA-related (SI Appendix, Figs. S8 D and F–H and S9 D, E, and J). Additionally, all Philippine ethnic groups share more alleles with Cordillerans than with Amis or Atayal (SI Appendix, Table S7H). Moreover, Cordillerans, aside from Amis and Atayal, share the most alleles with Malaysians, Indonesians, and Oceanians, and even among ancient individuals from peninsular Malaysia and Oceanian Lapita (SI Appendix, Tables S7 J–M and Fig. S8 I and J (16)).

The 8,000-y-Old Liangdao-2 Woman Anchors the Migration of Cordilleran-Related Populations from Mainland Asia to the Philippines.
The two individuals from Liangdao of the Matsu archipelago in the Taiwan Strait (SI Appendix, Table S8A) share the highest levels of genetic drift with Cordillerans, Amis, Atayal, and ancient individuals from the northern Philippines, Malaysia, Taiwan, and Lapita (SI Appendix, Fig. S9 F–I). Given the location of Liangdao, close to mainland China (26 km and 167 km from Taiwan), the ∼7,000- to 8,000-y-old Liangdao-2 individual represents the oldest link of “Cordilleran” ancestry to mainland Asia. As expected, both Liangdao-1 and Liangdao-2 did not display admixture with Basal Sunda ancestry (SI Appendix, Table S8S). Both Liangdao-1 and Liangdao-2 exhibit clear evidence of shared ancestry/admixture with nEA, similar to present-day and ancient populations/individuals of mainland East Asia and Taiwan ((18) (SI Appendix, Figs. S9 D, E, and J)). This is consistent with the recent analysis of ancient individuals from East Asia, which revealed gene flow between populations across various points of time (18⇓–20) and showed that there is some genetic affiliation between nEAs and southern East Asians, including Liangdao individuals (19).

Present-day Cordillerans, however, do not display this nEA ancestry component (SI Appendix, Figs. S2 B–D and S9 D, E, and J and Tables S8 V and X), thereby providing a minimum bound for the divergence between Cordilleran-related groups and ethnic groups of mainland East Asia and Taiwan at ∼8,000 B.P. This finding, taken together with the earliest archaeological evidence of Neolithic assemblages dated to ∼3 to 4 kya in the northern Philippines (21), suggests that the earliest Cordillerans were, like other groups in coastal East Asia at this time (22), complex hunter-gatherers rather than settled agriculturists. The nEA ancestry must have arrived later, originating from the coastal China/Taiwan area and dispersing into Batanes Islands and coastal regions of Luzon (SI Appendix, Table S8X). If the presence of nEA ancestry is indeed a genetic signal for the spread of agriculture, its general absence among Cordillerans suggests that the Neolithic transition among these groups was a consequence of cultural, rather than demic, diffusion.

The Holocene Migrations and the Disentangling of Language and the Neolithic Package.
Two contrasting models have been forwarded for the Holocene migrations into the Philippines. One is the out-of-Taiwan hypothesis, which espouses a unidirectional, north-to-south spread of the Neolithic package by ocean navigators from Taiwan, bringing with them the AN languages, red-slipped pottery, and cereal agriculture (23). On the other hand is the out-of-Sundaland hypothesis, a complex south-to-north movement of population groups into the Philippines since the early Holocene, preceded by a maritime trading network, and by population dispersals from Sundaland following a climate change-driven inundation of previously habitable lands (24, 25).

Our analyses indicate that, after Negrito, Manobo, and Sama-like northward migrations, gene flow of Cordilleran-related ancestry from the Southern China/Taiwan area into the Philippines may have occurred in multiple pulses after ∼10 kya. This may explain the inferred (genetic) divergence between Amis and central Cordillerans being younger than the divergence between Cordillerans and various groups of the central and northern Philippines (SI Appendix, Figs S7E and S8 K–R). Furthermore, we do not observe a north-to-south gradient of chronology for Negrito/Papuan–Cordilleran admixture (SI Appendix, Fig. S8U and Table S7Q), which would be expected in a simplistic and stepwise unidirectional movement of Cordilleran-related ancestry from Luzon to Mindanao. On the contrary, the oldest dates for Negrito/Papuan–Cordilleran admixture are scattered throughout the archipelago, indicating a complex nonuniform movement of populations from a putative South China/Taiwan source area into the Philippines.

Despite the series of migrations from diverse genetic ancestries, the linguistic landscape of the Philippines is remarkably less diverse, in view of the fact that all Philippine ethnic groups speak a language that falls within the Malayo-Polynesian (MP) branch of the AN language family ((26), SI Appendix, section 8). One possible explanation for the linguistic-genetic dissonance is the dominant influence of migratory AN-speaking populations who precipitated widespread linguistic replacement throughout the archipelago and beyond. It may have not been complete replacement as some words may have been retained from the original non-AN language. For instance, some Negrito groups speak languages that potentially contain certain lexical elements that are not completely accounted for by any other AN etymologies (27). Likewise, Land Dayak AN-speakers of Borneo have some evidence of retained Austroasiatic lexical items in their language (28, 29).

The various lines of genetic and archeological evidence suggest that farming was not linked to the initial arrival of Cordilleran-related populations in the Philippines. In addition to the presence of an nEA ancestral component in ∼8,000-y-old Liangdao individuals, but not in Cordillerans, the divergence between Cordillerans and Amis/Atayal (8.4 kya [95% CI: 8.1 to 8.8 kya] and 8.9 kya [95% CI: 8.3 to 9.5 kya]) predates the arrival of agriculture into Taiwan and the Philippines. The divergence time is even older (∼17 kya [95% CI: 9.5 to 25 kya]) when we use publicly available genome sequence data and apply the Two-Two-outgroup (TTo) method (30), based on computing sample configurations in a population divergence model. Furthermore, archeological evidence indicates that communities in coastal South China and north Vietnam from 7 to 5 kya were fishermen and hunter-gatherers, and not farmers (22), and that paddy field rice agriculture was only established in southern China and ISEA late in the Holocene, around 2 to 3 kya (31). This is consistent with the recent comprehensive phylogenetic analysis of Oryza japonica where it was shown that rice entered ISEA only after 2.5 kya, indicating that rice agriculture in the Philippines likely commenced more recently (32). Moreover, the latter study does not provide support for derivation of Philippine and Indonesian rice varieties from Taiwan, nor does it provide strong support for a predominant out-of-Taiwan dispersal of rice.

Hence, the impetus for migration of Cordilleran-related groups may have been catalyzed by, instead of farming, a climate change-driven geological change in the ancient landmass between Taiwan and southern China, which resulted in the gradual submergence of the coastal plain from 12 to 7 kya (SI Appendix, Fig. S3G). This is around the time of an estimated drop in the effective population size of Cordillerans (SI Appendix, Fig. S8 S and T) and fits with the dates of divergence among Cordilleran-related populations and Amis/Atayal (SI Appendix, Fig. S8 Q and R). Thus, our findings, accompanied by previously argued lines of evidence (22, 33), do not lend support to a unitary model of farming–language–people dispersal in the context of Philippine and ISEA prehistory.

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Ayta Negritos: Highest Levels of Denisovan DNA Aug 25, 2021 22:07:44 GMT

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Evidence of Recent South Asian and Spanish Admixture into Some Philippine Ethnic Groups.
From ∼2 kya until precolonial times, cultural communities in ISEA actively participated in the region-wide Indian Ocean Trading Network (34). Along this long-distance transoceanic exchange route lie two sequential Hindu-Buddhist kingdoms, Srivijaya and Majapahit, which have ruled over a wide geographic area covering coastal MSEA, western Indonesia, Malaysia, and as far as Sulu Archipelago of the Philippines. The demographic impact of this extensive multilateral trade is evident today in lowlander Malays and some ethnic groups of Indonesia, provided by their detectable South Asian genetic signal (11, 35, 36). In addition to Javanese, Balinese, and Sumatran Indonesians, the seafaring Sama-related populations Kotabaru Bajo and Derawan Bajo also exhibit detectable levels of South Asian ancestry (37). Thus, though it is not unexpected, this report shows that Sama Dilaut sea nomads of Sulu Archipelago and Sama coastal dwellers of Zamboanga Peninsula exhibit evidence of gene flow from South Asians (SI Appendix, Table S6M).

The Philippines was a Spanish Colony for 333 y from 1565 until 1898. However, we only observe significant population-level signals of European admixture in some urbanized lowlanders, Bicolanos, and Spanish Creole-speaking Chavacanos (SI Appendix, Table S7Y). Some individuals from Bolinao, Cebuano, Ibaloi, Itabayaten, Ilocano, Ivatan, Kapampangan, Pangasinan, and Yogad groups also presented low levels of European admixture (SI Appendix, Table S7Y). This admixture is estimated to have taken place 100 to 450 y ago, which falls within the Spanish Colonial Period (SI Appendix, Table S7Z). In contrast to several other Spanish-colonized regions, Philippine demography appears to have remained largely unaffected by admixture with Europeans.

Summary
The nuanced demographic history of the Philippines described here does not fit exclusively with the basic models of either the out-of-Taiwan or out-of-Sundaland hypothesis. In summary, we demonstrate that the Philippines were populated by at least five major waves of ancient human migrations for the past ∼50,000 y (Fig. 3 A–D). The first two are characterized by the entry after ∼46 kya of Paleolithic hunter-gatherer groups, linked genetically to the Basal Australasian branch of modern humans. Of these, an earlier Negrito group entered the northern Philippines, likely via Palawan and Mindoro islands, and a subsequent branch (Basal Oceanians) (Figs. 2A and 3A), represented by the Mamanwa, entered the southern Philippines via Sulu Archipelago. In addition, it is likely that Denisovans or other related archaic humans were already present in the Philippines upon entry of Negritos, resulting in an independent and localized archaic admixture event (1, 3, 38). The archaic introgression signal remains evident until today, given the detectable levels of Denisovan ancestry among the Negrito ethnic groups (3, 38). Moreover, in contrast to European demographic history, where the original hunter-gatherer genetic ancestry, together with their foraging practices, was largely replaced and/or diluted due to subsequent migrations (39), the Negrito ancestry in the Philippines is still largely present until today. This is accompanied by, as observed in some groups until today, a practice of a hunter-gathering mode of subsistence.

Fig. 3.
Model for Philippine demographic history. Suggested models for the five major migration events into the Philippines, (A) starting with entry of Northern Negritos and Southern Negritos into the Philippines from Sundaland, (B and C) followed by south-to-north movement of Manobo-related and Sama-related populations during the end of Last Glacial Period, and (D) culminating with the Holocene expansion of Cordilleran-related populations.

Following Negritos is a sequential ancestral “Manobo”-like and ancestral “Sama”-like gene flow into the Philippines after ∼15 kya, which occurred likely via a southern route, at a time of major geological changes in ISEA at the end of the Last Glacial Period (Figs. 2B and 3 B and C). Thereafter or concurrently, there was a westward expansion of Papuan-related populations who had left a genetic legacy among the ethnic groups of the southeastern Philippines. Lastly, prior to the minor effects of South Asian gene flow into Sama ethnic groups and recent European admixture with some urbanized lowlanders (SI Appendix, sections 4.5, 5.7, and 6.7), the most recent major migration event was the movement of Cordilleran-related groups from the South China-Taiwan greater area into the Philippines as early as ∼8 to 10 kya (Figs. 2B and 3D). The expansion likely happened in pulses whereby ancient seafaring groups brought with them an enduring legacy of linguistic dominance resonant in present-day populations of the Philippines and beyond, characterized by the spread of AN languages.

We find no genetic evidence for an association between currently established dates for the arrival and expansion of paddy field rice agriculture (∼2 to 3 kya) (31, 32) and the demographic movement of people from the South China-Taiwan greater area into the Philippines. Given the genetic makeup of the Liangdao-2 woman and other ancient Taiwanese and southern East Asian individuals (18) who all present some nEA ancestry, the most parsimonious explanation is that Cordillerans entered the Philippines prior to the nEA gene flow. This observation sets a boundary for the date of arrival of Cordillerans in the Philippines, at least ∼7 to 8 kya or earlier, indicating that early Cordillerans in the Philippines were mobile hunter-gatherers. All other Cordilleran-like groups eventually admixed with local populations at various points in time, as seen from the complex admixture among Philippine groups. Accordingly, this places the Cordillerans in a unique position in human demographic history, being revealed as the least admixed descendants of Basal East Asians.

Supporting Information

www.pnas.org/content/pnas/suppl/2021/03/17/2026132118.DCSupplemental/pnas.2026132118.sapp.pdf

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Ayta Negritos: Highest Levels of Denisovan DNA Aug 26, 2021 6:48:38 GMT

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Post by Admin on Aug 26, 2021 6:48:38 GMT

A woman buried 7,200 years ago in what is now Indonesia belonged to a previously unknown human lineage that doesn't exist anymore, a new genetic analysis reveals.

The ancient woman's genome also revealed that she is a distant relative of present-day Aboriginal Australians and Melanesians, or the Indigenous people on the islands of New Guinea and the western Pacific whose ancestors were the first humans to reach Oceania, the researchers found.

Like the Aboriginal Australians and New Guineans, the woman had a significant proportion of DNA from an archaic human species known as the Denisovans, the researchers found. That's in sharp contrast with other ancient hunter-gatherers from Southeast Asia, such as in Laos and Malaysia, who do not have much Denisovan ancestry, said study co-leader Cosimo Posth, a professor at the Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen in Germany.

These genetic discoveries suggest that Indonesia and the surrounding islands, an area known as Wallacea, was "indeed the meeting point for the major admixture [mating] event between Denisovans and modern humans on their initial journey to Oceania," Posth told Live Science in an email.

Researchers have long been interested in Wallacea. It's estimated that ancient humans traveled through Wallacea at least 50,000 years ago (possibly even before 65,000 years ago) before they reached Australia and its surrounding islands.

Researchers found the mysterious woman's burial in Leang Panninge cave on the Indonesian island of Sulawesi in 2015. "This was an exciting discovery, as it was the first time a relatively complete set of human skeletal remains had been found in association with artifacts of the 'Toalean' culture, enigmatic hunter-gatherers who inhabited the southwestern peninsula of Sulawesi between around 8,000 to 1,500 years ago," study co-lead researcher Adam Brumm, a professor of archaeology at Griffith University in Australia, told Live Science in an email.

To learn more about this woman — who died at about age 18, an anatomical analysis revealed — the researchers studied her ancient DNA, which was still preserved in her inner ear bone. "This is a major technological achievement, as we all know ancient DNA does not preserve well in tropical regions," said Serena Tucci, an assistant professor of anthropology at Yale University and principal investigator of the Human Evolutionary Genomics lab there, who was not involved in the new study. "Only a few years ago we didn't even imagine this could be feasible."

The analysis marked the first time researchers have studied an ancient human genome in Wallacea, the researchers added.

The woman's genome showed that she was equally related to present-day Aboriginal Australians and Papuans, Posth said. "However, her particular lineage split off from these populations at an early point of time," Brumm noted.

Moreover, this woman's lineage doesn't appear to exist today, making it a "previously unknown divergent human lineage," the researchers wrote in the study. In other words, this ancient Toalean woman has a genome "that is unlike that of any modern people or groups that are known from the ancient past," Brumm said.

As such, the researchers found no evidence that the modern people of Sulawesi descend from the Toalean hunter-gatherers, at least based on the genome of this woman.

Perhaps this Toalean woman carried a local ancestry from ancient people who lived on Sulawesi before Australia and its surrounding islands were populated, the researchers said.

In all, the study is "very exciting and fascinating," Tucci told Live Science in an email.

"We are learning that there was a previously unknown population that migrated throughout this region, probably at about the same time as the ancestors of present day populations in Papua or Australia," she said. Even though this woman's lineage disappeared, "all these populations did coexist until relatively recently, which opens up to lots of questions about population interactions from a genetic but also from a cultural perspective," Tucci said.

The study was published online Wednesday (Aug. 25) in the journal Nature.

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Ayta Negritos: Highest Levels of Denisovan DNA Aug 26, 2021 20:04:53 GMT

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Genome of a middle Holocene hunter-gatherer from Wallacea
Selina Carlhoff, Akin Duli, […]Adam Brumm
Nature volume 596, 543–547 (2021)

Abstract
Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

Main
Modern humans crossed through Wallacea (Fig. 1a) to Sahul5,6,7,8 at least 50 thousand years ago (kya)9, and possibly by up to 65 kya10. Presently, however, the earliest archaeological evidence for our species in Wallacea dates to at least 45.5 kya for figurative art in Sulawesi11, and 47–43 kyr cal BP for a behavioural shift at Liang Bua (Flores, Indonesia)12. The oldest Homo sapiens skeletal remains date to 13 kya13. The route modern humans used to enter Sahul is not known14. Demographic models infer a population split between the ancestors of Oceanian and Eurasian groups approximately 58 kya, whereas Papuan and Aboriginal Australian groups separated around 37 kya5. Within this time interval, modern humans admixed multiple times with groups related to Denisovans15,16,17,18,19,20,21,22,23, and potentially other unknown hominins24,25. The genetic ancestry of the two Hòabìnhian-associated foragers from Pha Faen and Gua Cha1 shows the highest similarity to modern Andamanese peoples. These ancient and present-day peoples lack substantial amounts of Denisovan-related ancestry, suggesting that the Hòabìnhian-associated and Onge-related lineage diverged before the main archaic human introgression events1. Current Wallacean individuals carry larger proportions of Denisovan-related ancestry, but at substantially lower frequencies than is the case in Papuan and Indigenous Australian individuals20. This is probably due to admixture with the East Asian Neolithic farmers (‘Austronesian peoples’) who arrived in Wallacea around 4 kya20,26.

Fig. 1: Study site location.

a, Sulawesi and Wallacea. The red rectangle indicates the region shown in b. b, Leang Panninge. The dotted line indicates Toalean site distribution.