IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-61661-w.html
   My bibliography  Save this article

Resolving out of Africa event for Papua New Guinean population using neural network

Author

Listed:
  • Mayukh Mondal

    (Christian-Albrechts-Universität zu Kiel
    University of Tartu)

  • Mathilde André

    (University of Tartu
    University of Tartu
    University of)

  • Ajai K. Pathak

    (University of Tartu
    KU Leuven)

  • Nicolas Brucato

    (Université Toulouse 3—Paul Sabatier (UT3))

  • François-Xavier Ricaut

    (Université Toulouse 3—Paul Sabatier (UT3))

  • Mait Metspalu

    (University of Tartu)

  • Anders Eriksson

    (University of Tartu)

Abstract

The demographic history of the Papua New Guinean (PNG) population is a subject of interest due to its early settlement in New Guinea, its relative isolation and substantial Denisovan ancestry. Previous research suggested an admixture with an early diverged out of African population. This study re-examines the PNG population using newly published samples. Our findings demonstrate that the observed shifts in Relative Cross Coalescent Rate (RCCR) curves are driven by strong bottleneck and slower population growth rate of the PNG population, rather than the contributions from an earlier out of Africa population. Although a small contribution from the early out of Africa population cannot be ruled out, it is no longer needed to explain the observed results. Our analysis positions them as a sister group to other East Asian populations. This study provides insights on the PNG population and highlights the impact of population-specific demography on interpreting RCCR curves.

Suggested Citation

  • Mayukh Mondal & Mathilde André & Ajai K. Pathak & Nicolas Brucato & François-Xavier Ricaut & Mait Metspalu & Anders Eriksson, 2025. "Resolving out of Africa event for Papua New Guinean population using neural network," Nature Communications, Nature, vol. 16(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61661-w
    DOI: 10.1038/s41467-025-61661-w
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-61661-w
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-61661-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. repec:plo:pgen00:1000695 is not listed on IDEAS
    2. Mayukh Mondal & Jaume Bertranpetit & Oscar Lao, 2019. "Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    3. Aaron P. Ragsdale & Timothy D. Weaver & Elizabeth G. Atkinson & Eileen G. Hoal & Marlo Möller & Brenna M. Henn & Simon Gravel, 2023. "Publisher Correction: A weakly structured stem for human origins in Africa," Nature, Nature, vol. 620(7972), pages 11-11, August.
    4. Olivier Delaneau & Jean-François Zagury & Matthew R. Robinson & Jonathan L. Marchini & Emmanouil T. Dermitzakis, 2019. "Accurate, scalable and integrative haplotype estimation," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    5. Luca Pagani & Daniel John Lawson & Evelyn Jagoda & Alexander Mörseburg & Anders Eriksson & Mario Mitt & Florian Clemente & Georgi Hudjashov & Michael DeGiorgio & Lauri Saag & Jeffrey D. Wall & Alexia , 2016. "Genomic analyses inform on migration events during the peopling of Eurasia," Nature, Nature, vol. 538(7624), pages 238-242, October.
    6. Heng Li & Richard Durbin, 2011. "Inference of human population history from individual whole-genome sequences," Nature, Nature, vol. 475(7357), pages 493-496, July.
    7. Wu Liu & María Martinón-Torres & Yan-jun Cai & Song Xing & Hao-wen Tong & Shu-wen Pei & Mark Jan Sier & Xiao-hong Wu & R. Lawrence Edwards & Hai Cheng & Yi-yuan Li & Xiong-xin Yang & José María Bermúd, 2015. "The earliest unequivocally modern humans in southern China," Nature, Nature, vol. 526(7575), pages 696-699, October.
    8. Jeremy Choin & Javier Mendoza-Revilla & Lara R. Arauna & Sebastian Cuadros-Espinoza & Olivier Cassar & Maximilian Larena & Albert Min-Shan Ko & Christine Harmant & Romain Laurent & Paul Verdu & Guilla, 2021. "Genomic insights into population history and biological adaptation in Oceania," Nature, Nature, vol. 592(7855), pages 583-589, April.
    9. Aaron P. Ragsdale & Timothy D. Weaver & Elizabeth G. Atkinson & Eileen G. Hoal & Marlo Möller & Brenna M. Henn & Simon Gravel, 2023. "A weakly structured stem for human origins in Africa," Nature, Nature, vol. 617(7962), pages 755-763, May.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Kai Yuan & Xumin Ni & Chang Liu & Yuwen Pan & Lian Deng & Rui Zhang & Yang Gao & Xueling Ge & Jiaojiao Liu & Xixian Ma & Haiyi Lou & Taoyang Wu & Shuhua Xu, 2021. "Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Oded Galor & Marc Klemp & Daniel C. Wainstock, 2023. "The Impact of the Prehistoric Out of Africa Migration on Cultural Diversity," NBER Working Papers 31274, National Bureau of Economic Research, Inc.
    3. Galor, Oded & Klemp, Marc & Wainstock, Daniel Crisóstomo, 2024. "Roots of Cultural Diversity," IZA Discussion Papers 17481, Institute of Labor Economics (IZA).
    4. Cecilia Padilla-Iglesias & Javier Blanco-Portillo & Bogdan Pricop & Alexander G. Ioannidis & Balthasar Bickel & Andrea Manica & Lucio Vinicius & Andrea Bamberg Migliano, 2024. "Deep history of cultural and linguistic evolution among Central African hunter-gatherers," Nature Human Behaviour, Nature, vol. 8(7), pages 1263-1275, July.
    5. Filipe Duarte Santos & Tim O’Riordan & Miguel Rocha de Sousa & Jiesper Strandsbjerg Tristan Pedersen, 2023. "The Six Critical Determinants That May Act as Human Sustainability Boundaries on Climate Change Action," Sustainability, MDPI, vol. 16(1), pages 1-20, December.
    6. Sarah E. Freidline & Kira E. Westaway & Renaud Joannes-Boyau & Philippe Duringer & Jean-Luc Ponche & Mike W. Morley & Vito C. Hernandez & Meghan S. McAllister-Hayward & Hugh McColl & Clément Zanolli &, 2023. "Early presence of Homo sapiens in Southeast Asia by 86–68 kyr at Tam Pà Ling, Northern Laos," Nature Communications, Nature, vol. 14(1), pages 1-21, December.
    7. Mathilde André & Nicolas Brucato & Georgi Hudjasov & Vasili Pankratov & Danat Yermakovich & Francesco Montinaro & Rita Kreevan & Jason Kariwiga & John Muke & Anne Boland & Jean-François Deleuze & Vinc, 2024. "Positive selection in the genomes of two Papua New Guinean populations at distinct altitude levels," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    8. Heng Du & Lei Zhou & Zhen Liu & Yue Zhuo & Meilin Zhang & Qianqian Huang & Shiyu Lu & Kai Xing & Li Jiang & Jian-Feng Liu, 2024. "The 1000 Chinese Indigenous Pig Genomes Project provides insights into the genomic architecture of pigs," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    9. Ya-Mei Ding & Xiao-Xu Pang & Yu Cao & Wei-Ping Zhang & Susanne S. Renner & Da-Yong Zhang & Wei-Ning Bai, 2023. "Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    10. Romain Fournier & Zoi Tsangalidou & David Reich & Pier Francesco Palamara, 2023. "Haplotype-based inference of recent effective population size in modern and ancient DNA samples," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. Katherine A. Kentistou & Brandon E. M. Lim & Lena R. Kaisinger & Valgerdur Steinthorsdottir & Luke N. Sharp & Kashyap A. Patel & Vinicius Tragante & Gareth Hawkes & Eugene J. Gardner & Thorhildur Olaf, 2025. "Rare variant associations with birth weight identify genes involved in adipose tissue regulation, placental function and insulin-like growth factor signalling," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    12. Frédérik Saltré & Joël Chadœuf & Thomas Higham & Monty Ochocki & Sebastián Block & Ellyse Bunney & Bastien Llamas & Corey J. A. Bradshaw, 2024. "Environmental conditions associated with initial northern expansion of anatomically modern humans," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    13. Saedis Saevarsdottir & Kristbjörg Bjarnadottir & Thorsteinn Markusson & Jonas Berglund & Thorunn A. Olafsdottir & Gisli H. Halldorsson & Gudrun Rutsdottir & Kristbjorg Gunnarsdottir & Asgeir Orn Arnth, 2024. "Start codon variant in LAG3 is associated with decreased LAG-3 expression and increased risk of autoimmune thyroid disease," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    14. Guangping Huang & Lingyun Song & Xin Du & Xin Huang & Fuwen Wei, 2023. "Evolutionary genomics of camouflage innovation in the orchid mantis," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    15. Legried, Brandon & Terhorst, Jonathan, 2022. "Rates of convergence in the two-island and isolation-with-migration models," Theoretical Population Biology, Elsevier, vol. 147(C), pages 16-27.
    16. Jörn Bethune & April Kleppe & Søren Besenbacher, 2022. "A method to build extended sequence context models of point mutations and indels," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    17. Carmi, Shai & Wilton, Peter R. & Wakeley, John & Pe’er, Itsik, 2014. "A renewal theory approach to IBD sharing," Theoretical Population Biology, Elsevier, vol. 97(C), pages 35-48.
    18. Kyuto Sonehara & Yoshitaka Yano & Tatsuhiko Naito & Shinobu Goto & Hiroyuki Yoshihara & Takahiro Otani & Fumiko Ozawa & Tamao Kitaori & Koichi Matsuda & Takashi Nishiyama & Yukinori Okada & Mayumi Sug, 2024. "Common and rare genetic variants predisposing females to unexplained recurrent pregnancy loss," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    19. Aoki, Kenichi & Wakano, Joe Yuichiro, 2022. "Hominin forager technology, food sharing, and diet breadth," Theoretical Population Biology, Elsevier, vol. 144(C), pages 37-48.
    20. Megan C. Lancaster & Hung-Hsin Chen & M. Benjamin Shoemaker & Matthew R. Fleming & Teresa L. Strickland & James T. Baker & Grahame F. Evans & Hannah G. Polikowsky & David C. Samuels & Chad D. Huff & D, 2024. "Detection of distant relatedness in biobanks to identify undiagnosed cases of Mendelian disease as applied to Long QT syndrome," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-61661-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.