The genetic structures of the Churu, Ede and Giarai unravelled by complete mitochondrial DNA

Huong Thao Dinh; Huu Dinh Tran; Thuy Duong Nguyen

doi:10.15625/2615-9023/18604

Author affiliations

Authors

Dinh Huong Thao Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam
Tran Huu Dinh Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam
Nguyen Thuy Duong Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Ha Noi, Vietnam

DOI:

https://doi.org/10.15625/2615-9023/18604

Keywords:

Churu, Ede, Giarai, mtDNA, Vietnam.

Abstract

Vietnam, a nation with a rich and complex history of migration and settlement, is home to 5 fundamental language families: Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), Sino-Tibetan (ST) and Hmong-Mien (HM). Among them is the Austronesian, a language family substantial in island Southeast Asia (ISEA) but marginal in mainland counterpart (MSEA), constituted five Vietnamese ethnolinguistic groups. Here, we analyzed the control region, and the complete mitochondrial DNA (mtDNA) of 121 individuals from 3 AN-speaking populations (Churu, Ede, and Giarai). To explore the molecular diversity, the sequences were aligned against the Reconstructed Sapiens Reference Sequence (RSRS). The quantification and distribution of nucleotide variations resulted in 6,369 variants in our dataset in which the control region and coding region retained 1,707 and 4,662 variants, respectively. Churu harbored the most diversity (54.6 ± 2.8 variants/person), followed by Giarai (52.2 ± 3.3 variants/person), and Ede (51.1 ± 5.3 variants/person). Both the control region and whole mtDNA were input to Haplogrep3 to call haplogroups, resulting in 47.11% of our samples having their haplogroup changed from 17 whole mtDNA lineages to 16 different control region lineages. The haplogroup profile derived from whole mtDNA included 31 unique clades, in which only B5a1d was shared among three groups, and 23/31 lineages were present exclusively in a single population. The haplogroup component of each minority also revealed that all 3 AN groups had the majority of their samples attributed to the macrohaplogroups M, B, and F, with the disparity fixed in their underlying sublineages. This study increased the knowledge wealth of the genetic characteristics of AN speakers in the region from a different analysis approach, and highlighted the contribution of variants in different complete mtDNA, providing insight to reconstruct a comprehensive genetic architecture of Vietnam.

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

Behar D. M., van Oven M., Rosset S., Metspalu M., Loogväli E.-L., Silva N. M., Kivisild T., Torroni A. & Villems R., 2012. A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root. The American Journal of Human Genetics, 90(4): 675–684.

Bodner M., Zimmermann B., Röck A., Kloss-Brandstätter A., Horst D., Horst B., Sengchanh S., Sanguansermsri T., Horst J., Krämer T., Schneider P. M. & Parson W., 2011. Southeast Asian diversity: First insights into the complex mtDNA structure of Laos. BMC Evolutionary Biology, 11(1): 49.

Delfin F., Min-Shan Ko A., Li M., Gunnarsdóttir E. D., Tabbada K. A., Salvador J. M., Calacal G. C., Sagum M. S., Datar F. A., Padilla S. G., De Ungria M. C. A. & Stoneking M., 2014. Complete mtDNA genomes of Filipino ethnolinguistic groups: A melting pot of recent and ancient lineages in the Asia-Pacific region. European Journal of Human Genetics, 22(2): 228–237.

Duong N. T., Macholdt E., Ton N. D., Arias L., Schröder R., Van Phong N., Thi Bich Thuy V., Ha N. H., Thi Thu Hue H., Thi Xuan N., Thi Phuong Oanh K., Hien L. T. T., Hoang N. H., Pakendorf B., Stoneking M. & Van Hai N., 2018. Complete human mtDNA genome sequences from Vietnam and the phylogeography of Mainland Southeast Asia. Scientific Reports, 8(1): 11651.

Eberhard D. M., Simons G. F., & Fennig C. D. (Eds.), 2023. Ethnologue: Languages of the World. (26^th ed.). SIL International. http://www.ethnologue.com.

General Statistic Office, 2019. Completed Results of the 2019 Vietnam Population and Housing Census (p. 840) [Population Census]. General Statistics Office. https://www.gso.gov.vn/wp-content/uploads/2019/12/Ket-qua-toan-bo-Tong-dieu-tra-dan-so-va-nha-o-2019.pdf

Katoh K. & Standley D. M., 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30(4): 772–780.

Kloss-Brandstätter A., Summerer M., Horst D., Horst B., Streiter G., Raschenberger J., Kronenberg F., Sanguansermsri T., Horst J. & Weissensteiner H., 2021. An in-depth analysis of the mitochondrial phylogenetic landscape of Cambodia. Scientific Reports, 11(1): 10816.

Ko A. M.-S., Chen C.-Y., Fu Q., Delfin F., Li M., Chiu H.-L., Stoneking M. & Ko Y.-C., 2014. Early Austronesians: Into and Out Of Taiwan. The American Journal of Human Genetics, 94(3): 426–436.

Kusuma P., Cox M. P., Pierron D., Razafindrazaka H., Brucato N., Tonasso L., Suryadi H. L., Letellier T., Sudoyo H. & Ricaut F.-X., 2015. Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations. BMC Genomics, 16(1): 191.

Kutanan W., Kampuansai J., Srikummool M., Kangwanpong D., Ghirotto S., Brunelli A. & Stoneking M., 2017. Complete mitochondrial genomes of Thai and Lao populations indicate an ancient origin of Austroasiatic groups and demic diffusion in the spread of Tai–Kadai languages. Human Genetics, 136(1): 85–98.

Liu D., Duong N. T., Ton N. D., Van Phong N., Pakendorf B., Van Hai N. & Stoneking M., 2020. Extensive Ethnolinguistic Diversity in Vietnam Reflects Multiple Sources of Genetic Diversity. Molecular Biology and Evolution, 37(9): 2503–2519.

Macholdt E., Arias L., Duong N. T., Ton N. D., Van Phong N., Schröder R., Pakendorf B., Van Hai N. & Stoneking M., 2020. The paternal and maternal genetic history of Vietnamese populations. European Journal of Human Genetics, 28(5): 636–645.

Maricic T., Whitten M. & Pääbo S., 2010. Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products. PLoS ONE, 5(11): e14004.

Matsumura H., Shinoda K., Shimanjuntak T., Oktaviana A. A., Noerwidi S., Octavianus Sofian H., Prastiningtyas D., Nguyen L. C., Kakuda T., Kanzawa-Kiriyama H., Adachi N., Hung H., Fan X., Wu X., Willis A. & Oxenham M. F., 2018. Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia. Plos one, 13(6): e0198689.

Nenadic O., Greenacre M., 2007. Correspondence Analysis in R, with Two- and Three-dimensional Graphics: The ca Package. Journal of Statistical Software, 20(3): 1–13.

Oksanen J., Simplson G. L., Blanchet F. G., Kindt R., Legendre P., Minchin P. R., O’Hara R. B., Solymos P., Stevens M. H. H, Szoecs E., Wagner H., Barbour M., Bedward M., Bolker B., Borcard D., Carvalho G., Chirico M., De Caceres M., Durand S., Evangelista H. B. A., FitzJohn R., Friendly M., Furneaux B., Hannigan G., Hill M. O., Lahti L., McGlinn D., Ouelette M-H., Cunha E. R., Smith T., Stier A., Braak C. J. F. T, Weedon J., 2022. Vegan: community ecology package, 2.6-2. R Foundation for Statistical Computing.

Peng M.-S., Quang H. H., Dang K. P., Trieu A. V., Wang H.-W., Yao Y.-G., Kong Q.-P. & Zhang Y.-P., 2010. Tracing the Austronesian Footprint in Mainland Southeast Asia: A Perspective from Mitochondrial DNA. Molecular Biology and Evolution, 27(10), 2417–2430.

Phương T. K., Lockhart B. M. & Vickery Michael (Eds.), 2011. Champa Revised. In The Cham of Vietnam: History, Society and Art (1–37). NUS Press.

Summerer M., Horst J., Erhart G., Weißensteiner H., Schönherr S., Pacher D., Forer L., Horst D., Manhart A., Horst B., Sanguansermsri T. & Kloss-Brandstätter A., 2014. Large-scale mitochondrial DNA analysis in Southeast Asia reveals evolutionary effects of cultural isolation in the multi-ethnic population of Myanmar. BMC Evolutionary Biology, 14(1): 17.

Tätte K., Metspalu E., Post H., Palencia-Madrid L., Luis J. R., Reidla M., Rea A., Tamm E., Moding E. J., de Pancorbo M. M., Garcia-Bertrand R., Metspalu M. & Herrera R. J., 2021. The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations. European Journal of Human Genetics, 29(7): 1092–1102.

Thao D. H., Dinh T. H., Mitsunaga S., Duy L. D., Phuong N. T., Anh N. P., Anh N. T., Duc B. M., Thi Thu Hue H., Ha N. H., Ton N. D., Hübner A., Pakendorf B., Stoneking M., Inoue I., Duong N. T., Hai N. V., 2024, Investigating demic versus cultural diffusion and sex bias in the spread of Austronesian languages in Vietnam, bioRxiv.

Trejaut J. A., Kivisild T., Loo J. H., Lee C. L., He C. L., Hsu C. J., Li Z. Y. & Lin M., 2005. Traces of Archaic Mitochondrial Lineages Persist in Austronesian-Speaking Formosan Populations. PLoS Biology, 3(8): e247.

Underhill P. A. & Kivisild T., 2007. Use of Y Chromosome and Mitochondrial DNA Population Structure in Tracing Human Migrations. Annual Review of Genetics, 41(1): 539–564.

van Oven M. & Kayser M., 2009. Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Human Mutation, 30(2): E386–E394.

Weissensteiner H., Pacher D., Kloss-Brandstätter A., Forer L., Specht G., Bandelt H.-J., Kronenberg F., Salas A. & Schönherr S., 2016. HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Research, 44(W1): W58–W63.

Zhang X., Qi X., Yang Z., Serey B., Sovannary T., Bunnath L., Seang Aun H., Samnom H., Zhang H., Lin Q., van Oven M., Shi H. & Su B., 2013. Analysis of mitochondrial genome diversity identifies new and ancient maternal lineages in Cambodian aborigines. Nature Communications, 4(1): 2599.