Genetic History of the South East Asian Negritos

 1.  Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture

Abstract

Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.

2.  Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

Abstract

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

3. Unveiling the Genetic History of the Maniq, a Primary Hunter-Gatherer Society 

Abstract

The Maniq of southern Thailand is one of the last remaining practicing hunter-gatherer communities in the world. However, our knowledge on their genetic origins and demographic history is still largely limited. We present here the genotype data covering ∼2.3 million single nucleotide polymorphisms of 11 unrelated Maniq individuals. Our analyses reveal the Maniq to be closely related to the Semang populations of Malaysia (Malay Negritos), who altogether carry an Andamanese-related ancestry linked to the ancient Hòabìnhian hunter-gatherers of Mainland Southeast Asia (MSEA). Moreover, the Maniq possess ∼35% East Asian-related ancestry, likely brought about by recent admixture with surrounding agriculturist communities in the region. In addition, the Maniq exhibit one of the highest levels of genetic differentiation found among living human populations, indicative of their small population size and historical practice of endogamy. Similar to other hunter-gatherer populations of MSEA, we also find the Maniq to possess low levels of Neanderthal ancestry and undetectable levels of Denisovan ancestry. Altogether, we reveal the Maniq to be a Semang group that experienced intense genetic drift and exhibits signs of ancient Hòabìnhian ancestry.

Negritos in Taiwan and the wider prehistory of Southeast Asia: new discovery from the Xiaoma Caves

 

Taiwan is known as the homeland of the Austronesian-speaking groups, yet other populations already had lived here since the Pleistocene. Conventional notions have postulated that the Palaeolithic hunter-gatherers were replaced or absorbed into the Neolithic Austronesian farming communities. Yet, some evidence has indicated that sparse numbers of non-Austronesian individuals continued to live in the remote mountains as late as the 1800s. The cranial morphometric study of human skeletal remains unearthed from the Xiaoma Caves in eastern Taiwan, for the first time, validates the prior existence of small stature hunter-gatherers 6000 years ago in the preceramic phase. This female individual shared remarkable cranial affinities and small stature characteristics with the Indigenous Southeast Asians, particularly the Negritos in northern Luzon. This study solves the several-hundred-years-old mysteries of ‘little black people’ legends in Formosan Austronesian tribes and brings insights into the broader prehistory of Southeast Asia.

Figure 10. The cranial profile of the Xiaoma female

The Xiaoma skeleton from the preceramic burial feature has revealed new insights into the ancient population structure of Taiwan and the larger regional picture in Southeast Asia. The apparent Negrito affiliation at Xiaoma nearly 6000 years ago conceivably could represent a direct descendance from the original Palaeolithic Changbinian population who had settled at the Baxian Caves of eastern Taiwan about 30,000 years ago, but equally the Negrito affiliation could represent a second or later wave of migration, still within the general ‘first layer’ of hunter-gatherer occupation of East/Southeast Asia.