NANUQ: a method for inferring species networks from gene trees under the coalescent model
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and nu...
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ftpubmed:oai:pubmedcentral.nih.gov:6896299 2023-05-15T17:14:03+02:00 NANUQ: a method for inferring species networks from gene trees under the coalescent model Allman, Elizabeth S. Baños, Hector Rhodes, John A. 2019-12-06 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896299/ https://doi.org/10.1186/s13015-019-0159-2 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896299/ http://dx.doi.org/10.1186/s13015-019-0159-2 © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. CC0 PDM CC-BY Research Text 2019 ftpubmed https://doi.org/10.1186/s13015-019-0159-2 2019-12-15T01:41:50Z Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters. We propose a new algorithm for statistical inference of a level-1 species network under this model, from data consisting of gene tree topologies, and provide the theoretical justification for it. The algorithm is based on an analysis of quartets displayed on gene trees, combining several statistical hypothesis tests with combinatorial ideas such as a quartet-based intertaxon distance appropriate to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph. Text nanuq PubMed Central (PMC) Algorithms for Molecular Biology 14 1 |
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Research Allman, Elizabeth S. Baños, Hector Rhodes, John A. NANUQ: a method for inferring species networks from gene trees under the coalescent model |
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Research |
description |
Species networks generalize the notion of species trees to allow for hybridization or other lateral gene transfer. Under the network multispecies coalescent model, individual gene trees arising from a network can have any topology, but arise with frequencies dependent on the network structure and numerical parameters. We propose a new algorithm for statistical inference of a level-1 species network under this model, from data consisting of gene tree topologies, and provide the theoretical justification for it. The algorithm is based on an analysis of quartets displayed on gene trees, combining several statistical hypothesis tests with combinatorial ideas such as a quartet-based intertaxon distance appropriate to networks, the NeighborNet algorithm for circular split systems, and the Circular Network algorithm for constructing a splits graph. |
format |
Text |
author |
Allman, Elizabeth S. Baños, Hector Rhodes, John A. |
author_facet |
Allman, Elizabeth S. Baños, Hector Rhodes, John A. |
author_sort |
Allman, Elizabeth S. |
title |
NANUQ: a method for inferring species networks from gene trees under the coalescent model |
title_short |
NANUQ: a method for inferring species networks from gene trees under the coalescent model |
title_full |
NANUQ: a method for inferring species networks from gene trees under the coalescent model |
title_fullStr |
NANUQ: a method for inferring species networks from gene trees under the coalescent model |
title_full_unstemmed |
NANUQ: a method for inferring species networks from gene trees under the coalescent model |
title_sort |
nanuq: a method for inferring species networks from gene trees under the coalescent model |
publisher |
BioMed Central |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896299/ https://doi.org/10.1186/s13015-019-0159-2 |
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nanuq |
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nanuq |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896299/ http://dx.doi.org/10.1186/s13015-019-0159-2 |
op_rights |
© The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
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CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s13015-019-0159-2 |
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