Human Y Chromosome Haplogroup L1-M22 Traces Neolithic Expansion in West Asia and Supports the Elamite and Dravidian Connection

Overview

Journal iScience

Publisher Cell Press

Date 2024 Jun 17

PMID 38883810

Authors

Ajai Kumar Pathak

Hovann Simonian

Ibrahim Abdel Aziz Ibrahim

Peter Hrechdakian

Doron M Behar

Qasim Ayub

Pakhrudin Arsanov

Ene Metspalu

Levon Yepiskoposyan

Siiri Rootsi

Phillip Endicott

Richard Villems

Hovhannes Sahakyan

Affiliations

Soon will be listed here.

Abstract

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.

References

Qamar R, Ayub Q, Mohyuddin A, Helgason A, Mazhar K, Mansoor A . Y-chromosomal DNA variation in Pakistan. Am J Hum Genet. 2002; 70(5):1107-24. PMC: 447589. DOI: 10.1086/339929. View

Suchard M, Lemey P, Baele G, Ayres D, Drummond A, Rambaut A . Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018; 4(1):vey016. PMC: 6007674. DOI: 10.1093/ve/vey016. View

Thangaraj K, Chaubey G, Singh V, Vanniarajan A, Thanseem I, Reddy A . In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India. BMC Genomics. 2006; 7:151. PMC: 1534032. DOI: 10.1186/1471-2164-7-151. View

Kivisild T, Bamshad M, Kaldma K, Metspalu M, Metspalu E, Reidla M . Deep common ancestry of indian and western-Eurasian mitochondrial DNA lineages. Curr Biol. 1999; 9(22):1331-4. DOI: 10.1016/s0960-9822(00)80057-3. View

Maier R, Flegontov P, Flegontova O, Isildak U, Changmai P, Reich D . On the limits of fitting complex models of population history to -statistics. Elife. 2023; 12. PMC: 10310323. DOI: 10.7554/eLife.85492. View

Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K . Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature. 2014; 513(7518):409-13. PMC: 4170574. DOI: 10.1038/nature13673. View

Pybus O, Suchard M, Lemey P, Bernardin F, Rambaut A, Crawford F . Unifying the spatial epidemiology and molecular evolution of emerging epidemics. Proc Natl Acad Sci U S A. 2012; 109(37):15066-71. PMC: 3443149. DOI: 10.1073/pnas.1206598109. View

Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S . Genetic origins of the Minoans and Mycenaeans. Nature. 2017; 548(7666):214-218. PMC: 5565772. DOI: 10.1038/nature23310. View

Rambaut A, Drummond A, Xie D, Baele G, Suchard M . Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7. Syst Biol. 2018; 67(5):901-904. PMC: 6101584. DOI: 10.1093/sysbio/syy032. View

10.

Reich D, Thangaraj K, Patterson N, Price A, Singh L . Reconstructing Indian population history. Nature. 2009; 461(7263):489-94. PMC: 2842210. DOI: 10.1038/nature08365. View

11.

Margaryan A, Lawson D, Sikora M, Racimo F, Rasmussen S, Moltke I . Population genomics of the Viking world. Nature. 2020; 585(7825):390-396. DOI: 10.1038/s41586-020-2688-8. View

12.

Kitchen A, Ehret C, Assefa S, Mulligan C . Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East. Proc Biol Sci. 2009; 276(1668):2703-10. PMC: 2839953. DOI: 10.1098/rspb.2009.0408. View

13.

Sudmant P, Rausch T, Gardner E, Handsaker R, Abyzov A, Huddleston J . An integrated map of structural variation in 2,504 human genomes. Nature. 2015; 526(7571):75-81. PMC: 4617611. DOI: 10.1038/nature15394. View

14.

Underhill P, Jin L, Lin A, Mehdi S, Jenkins T, Vollrath D . Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res. 1997; 7(10):996-1005. PMC: 310671. DOI: 10.1101/gr.7.10.996. View

15.

Li H, Durbin R . Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589-95. PMC: 2828108. DOI: 10.1093/bioinformatics/btp698. View

16.

Sengupta S, Zhivotovsky L, King R, Mehdi S, Edmonds C, Chow C . Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet. 2006; 78(2):202-21. PMC: 1380230. DOI: 10.1086/499411. View

17.

Karafet T, Mendez F, Meilerman M, Underhill P, Zegura S, Hammer M . New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res. 2008; 18(5):830-8. PMC: 2336805. DOI: 10.1101/gr.7172008. View

18.

Heled J, Drummond A . Bayesian inference of population size history from multiple loci. BMC Evol Biol. 2008; 8:289. PMC: 2636790. DOI: 10.1186/1471-2148-8-289. View

19.

McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A . The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20(9):1297-303. PMC: 2928508. DOI: 10.1101/gr.107524.110. View

20.

Ayres D, Darling A, Zwickl D, Beerli P, Holder M, Lewis P . BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics. Syst Biol. 2011; 61(1):170-3. PMC: 3243739. DOI: 10.1093/sysbio/syr100. View