Genome diversity and signatures of natural selection in mainland Southeast Asia

[okarinaofsteiner]

Thought this warranted its own thread. https://www.nature.com/articles/s41586-025-08998-w https://doi.org/10.1038/s41586-025-08998-w

Abstract
Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

I don't have access to the paper itself, but I found a translated copy online that contains some of the key figures from the paper.
https://view.inews.qq.com/k/20250516A01M1F00




Figure 2. Population sampling distribution and composition of the Southeast Asian Genome Project Phase I SEA3K


Figure 3. Genetic structure and composition of the MSEA population
TBN = Tibetan, JPT = 1000 genomes Tokyo, CHB = 1000 genomes Beijing university students, CHS = 1000 genomes Hunan and Fujian Han Chinese, CDX = 1000 genomes Chinese Dai, VIKI = probably Kinh Vietnamese from Hanoi, PEL = 1000 genomes Peruvians, BEB = 1000 genomes Bangladeshis (note the shared dark blue component that’s maximized in CHS, CHB, CDX, JPT, and VIKI, this represents East Asian ancestry in Bengalis)


Figure 4. Natural selection signals and potential environmental adaptation phenotypes in the genomes of mainland Southeast Asian populations


Figure 5. Unique Denisovan introgression patterns in the MSEA population

[okarinaofsteiner]

Thought this warranted its own thread. https://www.nature.com/articles/s41586-025-08998-w https://doi.org/10.1038/s41586-025-08998-w

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Figure 4. Natural selection signals and potential environmental adaptation phenotypes in the genomes of mainland Southeast Asian populations

Google Translate of the Chinese captions:

Smaller body and shorter limbs
Common curly hair characteristics
Having a wider and flatter nose
Have a darker skin tone
Unique bitterness sensitivity
Anti-insect bites and anti-itching ability
Greater diversity of gut flora
Stronger anti-inflammatory activity
Earlier sexual maturity
Unique energy metabolism and fat storage capabilities
Immune resistance to tropical diseases
Stronger resistance to parasitic infections
Higher bone density

[ZZ131]

A new haplogroup K called K-ZS9385 has been added