IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v159y2024icp108-124.html
   My bibliography  Save this article

Demographic inference for spatially heterogeneous populations using long shared haplotypes

Author

Listed:
  • Forien, Raphaël
  • Ringbauer, Harald
  • Coop, Graham

Abstract

We introduce a modified spatial Λ-Fleming–Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.

Suggested Citation

  • Forien, Raphaël & Ringbauer, Harald & Coop, Graham, 2024. "Demographic inference for spatially heterogeneous populations using long shared haplotypes," Theoretical Population Biology, Elsevier, vol. 159(C), pages 108-124.
    • Handle: RePEc:eee:thpobi:v:159:y:2024:i:c:p:108-124
    DOI: 10.1016/j.tpb.2024.03.002
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580924000285
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.tpb.2024.03.002?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Guindon, Stéphane & Guo, Hongbin & Welch, David, 2016. "Demographic inference under the coalescent in a spatial continuum," Theoretical Population Biology, Elsevier, vol. 111(C), pages 43-50.
    2. Stepfanie M Aguillon & John W Fitzpatrick & Reed Bowman & Stephan J Schoech & Andrew G Clark & Graham Coop & Nancy Chen, 2017. "Deconstructing isolation-by-distance: The genomic consequences of limited dispersal," PLOS Genetics, Public Library of Science, vol. 13(8), pages 1-27, August.
    3. 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.
    4. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7219), pages 274-274, November.
    5. Barton, N.H. & Etheridge, A.M. & Kelleher, J. & Véber, A., 2013. "Inference in two dimensions: Allele frequencies versus lengths of shared sequence blocks," Theoretical Population Biology, Elsevier, vol. 87(C), pages 105-119.
    6. 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.
    7. John Novembre & Toby Johnson & Katarzyna Bryc & Zoltán Kutalik & Adam R. Boyko & Adam Auton & Amit Indap & Karen S. King & Sven Bergmann & Matthew R. Nelson & Matthew Stephens & Carlos D. Bustamante, 2008. "Genes mirror geography within Europe," Nature, Nature, vol. 456(7218), pages 98-101, November.
    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. Guindon, Stéphane & Guo, Hongbin & Welch, David, 2016. "Demographic inference under the coalescent in a spatial continuum," Theoretical Population Biology, Elsevier, vol. 111(C), pages 43-50.
    2. Wirtz, Johannes & Guindon, Stéphane, 2024. "On the connections between the spatial Lambda–Fleming–Viot model and other processes for analysing geo-referenced genetic data," Theoretical Population Biology, Elsevier, vol. 158(C), pages 139-149.
    3. Jerome Kelleher & Alison M Etheridge & Gilean McVean, 2016. "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes," PLOS Computational Biology, Public Library of Science, vol. 12(5), pages 1-22, May.
    4. Marco Lopez-Cruz & Fernando M. Aguate & Jacob D. Washburn & Natalia Leon & Shawn M. Kaeppler & Dayane Cristina Lima & Ruijuan Tan & Addie Thompson & Laurence Willard Bretonne & Gustavo los Campos, 2023. "Leveraging data from the Genomes-to-Fields Initiative to investigate genotype-by-environment interactions in maize in North America," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Beatrix Eugster & Rafael Lalive & Andreas Steinhauer & Josef Zweimüller, 2011. "The Demand for Social Insurance: Does Culture Matter?," Economic Journal, Royal Economic Society, vol. 121(556), pages 413-448, November.
    6. Filippini, Massimo & Wekhof, Tobias, 2021. "The effect of culture on energy efficient vehicle ownership," Journal of Environmental Economics and Management, Elsevier, vol. 105(C).
    7. Andrey V Khrunin & Denis V Khokhrin & Irina N Filippova & Tõnu Esko & Mari Nelis & Natalia A Bebyakova & Natalia L Bolotova & Janis Klovins & Liene Nikitina-Zake & Karola Rehnström & Samuli Ripatti & , 2013. "A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-9, March.
    8. Diana Dunca & Sandesh Chopade & María Gordillo-Marañón & Aroon D. Hingorani & Karoline Kuchenbaecker & Chris Finan & Amand F. Schmidt, 2024. "Comparing the effects of CETP in East Asian and European ancestries: a Mendelian randomization study," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    9. Wenhan Chen & Yang Wu & Zhili Zheng & Ting Qi & Peter M. Visscher & Zhihong Zhu & Jian Yang, 2021. "Improved analyses of GWAS summary statistics by reducing data heterogeneity and errors," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    10. Pierre Luisi & Angelina García & Juan Manuel Berros & Josefina M B Motti & Darío A Demarchi & Emma Alfaro & Eliana Aquilano & Carina Argüelles & Sergio Avena & Graciela Bailliet & Julieta Beltramo & C, 2020. "Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina," PLOS ONE, Public Library of Science, vol. 15(7), pages 1-30, July.
    11. Brielin C Brown & Nicolas L Bray & Lior Pachter, 2018. "Expression reflects population structure," PLOS Genetics, Public Library of Science, vol. 14(12), pages 1-15, December.
    12. Gad Abraham & Michael Inouye, 2014. "Fast Principal Component Analysis of Large-Scale Genome-Wide Data," PLOS ONE, Public Library of Science, vol. 9(4), pages 1-5, April.
    13. Beatrix Brügger & Rafael Lalive & Josef Zweimüller, 2009. "Does Culture Affect Unemployment? Evidence from the Röstigraben," NRN working papers 2009-10, The Austrian Center for Labor Economics and the Analysis of the Welfare State, Johannes Kepler University Linz, Austria.
    14. Diana Chang & Alon Keinan, 2014. "Principal Component Analysis Characterizes Shared Pathogenetics from Genome-Wide Association Studies," PLOS Computational Biology, Public Library of Science, vol. 10(9), pages 1-14, September.
    15. Alejandro Ochoa & John D Storey, 2021. "Estimating FST and kinship for arbitrary population structures," PLOS Genetics, Public Library of Science, vol. 17(1), pages 1-36, January.
    16. Victor Ronda & Esben Agerbo & Dorthe Bleses & Preben Bo Mortensen & Anders Børglum & Ole Mors & Michael Rosholm & David M. Hougaard & Merete Nordentoft & Thomas Werge, 2022. "Family disadvantage, gender, and the returns to genetic human capital," Scandinavian Journal of Economics, Wiley Blackwell, vol. 124(2), pages 550-578, April.
    17. Feldman, Michael J., 2023. "Spiked singular values and vectors under extreme aspect ratios," Journal of Multivariate Analysis, Elsevier, vol. 196(C).
    18. Mateus H. Gouveia & Amy R. Bentley & Thiago P. Leal & Eduardo Tarazona-Santos & Carlos D. Bustamante & Adebowale A. Adeyemo & Charles N. Rotimi & Daniel Shriner, 2023. "Unappreciated subcontinental admixture in Europeans and European Americans and implications for genetic epidemiology studies," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    19. Nicola Barban & Elisabetta De Cao & Sonia Oreffice & Climent Quintana-Domeque, 2016. "Assortative Mating on Education: A Genetic Assessment," Working Papers 2016-034, Human Capital and Economic Opportunity Working Group.
    20. Bryc, Katarzyna & Bryc, Wlodek & Silverstein, Jack W., 2013. "Separation of the largest eigenvalues in eigenanalysis of genotype data from discrete subpopulations," Theoretical Population Biology, Elsevier, vol. 89(C), pages 34-43.

    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:eee:thpobi:v:159:y:2024:i:c:p:108-124. 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: Catherine Liu (email available below). General contact details of provider: https://www.sciencedirect.com/journal/theoretical-population-biology .

    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.