Bayesian inference of admixture graphs on Native American and Arctic populations

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Standard

Bayesian inference of admixture graphs on Native American and Arctic populations. / Nielsen, Svend V.; Vaughn, Andrew H.; Leppälä, Kalle; Landis, Michael J.; Mailund, Thomas; Nielsen, Rasmus.

In: PLOS Genetics, Vol. 19, No. 2, e1010410, 2023.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Nielsen, SV, Vaughn, AH, Leppälä, K, Landis, MJ, Mailund, T & Nielsen, R 2023, 'Bayesian inference of admixture graphs on Native American and Arctic populations', PLOS Genetics, vol. 19, no. 2, e1010410. https://doi.org/10.1371/journal.pgen.1010410

APA

Nielsen, S. V., Vaughn, A. H., Leppälä, K., Landis, M. J., Mailund, T., & Nielsen, R. (2023). Bayesian inference of admixture graphs on Native American and Arctic populations. PLOS Genetics, 19(2), [e1010410]. https://doi.org/10.1371/journal.pgen.1010410

Vancouver

Nielsen SV, Vaughn AH, Leppälä K, Landis MJ, Mailund T, Nielsen R. Bayesian inference of admixture graphs on Native American and Arctic populations. PLOS Genetics. 2023;19(2). e1010410. https://doi.org/10.1371/journal.pgen.1010410

Author

Nielsen, Svend V. ; Vaughn, Andrew H. ; Leppälä, Kalle ; Landis, Michael J. ; Mailund, Thomas ; Nielsen, Rasmus. / Bayesian inference of admixture graphs on Native American and Arctic populations. In: PLOS Genetics. 2023 ; Vol. 19, No. 2.

Bibtex

@article{e352fb82430b498ea24c5ce7fc6201c3,
title = "Bayesian inference of admixture graphs on Native American and Arctic populations",
abstract = "Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.",
author = "Nielsen, {Svend V.} and Vaughn, {Andrew H.} and Kalle Lepp{\"a}l{\"a} and Landis, {Michael J.} and Thomas Mailund and Rasmus Nielsen",
note = "Publisher Copyright: Copyright: {\textcopyright} 2023 Nielsen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.",
year = "2023",
doi = "10.1371/journal.pgen.1010410",
language = "English",
volume = "19",
journal = "P L o S Genetics",
issn = "1553-7390",
publisher = "Public Library of Science",
number = "2",

}

RIS

TY - JOUR

T1 - Bayesian inference of admixture graphs on Native American and Arctic populations

AU - Nielsen, Svend V.

AU - Vaughn, Andrew H.

AU - Leppälä, Kalle

AU - Landis, Michael J.

AU - Mailund, Thomas

AU - Nielsen, Rasmus

N1 - Publisher Copyright: Copyright: © 2023 Nielsen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2023

Y1 - 2023

N2 - Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.

AB - Admixture graphs are mathematical structures that describe the ancestry of populations in terms of divergence and merging (admixing) of ancestral populations as a graph. An admixture graph consists of a graph topology, branch lengths, and admixture proportions. The branch lengths and admixture proportions can be estimated using numerous numerical optimization methods, but inferring the topology involves a combinatorial search for which no polynomial algorithm is known. In this paper, we present a reversible jump MCMC algorithm for sampling high-probability admixture graphs and show that this approach works well both as a heuristic search for a single best-fitting graph and for summarizing shared features extracted from posterior samples of graphs. We apply the method to 11 Native American and Siberian populations and exploit the shared structure of high-probability graphs to characterize the relationship between Saqqaq, Inuit, Koryaks, and Athabascans. Our analyses show that the Saqqaq is not a good proxy for the previously identified gene flow from Arctic people into the Na-Dene speaking Athabascans.

U2 - 10.1371/journal.pgen.1010410

DO - 10.1371/journal.pgen.1010410

M3 - Journal article

C2 - 36780565

AN - SCOPUS:85148003685

VL - 19

JO - P L o S Genetics

JF - P L o S Genetics

SN - 1553-7390

IS - 2

M1 - e1010410

ER -

ID: 337577983