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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Online Access: | https://dx.doi.org/10.48550/arxiv.1905.07050 https://arxiv.org/abs/1905.07050 |
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ftdatacite:10.48550/arxiv.1905.07050 2023-05-15T17:14:03+02:00 NANUQ: A method for inferring species networks from gene trees under the coalescent model Allman, Elizabeth Banos, Hector Rhodes, John 2019 https://dx.doi.org/10.48550/arxiv.1905.07050 https://arxiv.org/abs/1905.07050 unknown arXiv arXiv.org perpetual, non-exclusive license http://arxiv.org/licenses/nonexclusive-distrib/1.0/ Populations and Evolution q-bio.PE Statistics Theory math.ST FOS Biological sciences FOS Mathematics 92B10, 92D15 Article CreativeWork article Preprint 2019 ftdatacite https://doi.org/10.48550/arxiv.1905.07050 2022-03-10T16:47:14Z 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 in 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. Article in Journal/Newspaper nanuq DataCite Metadata Store (German National Library of Science and Technology) |
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DataCite Metadata Store (German National Library of Science and Technology) |
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topic |
Populations and Evolution q-bio.PE Statistics Theory math.ST FOS Biological sciences FOS Mathematics 92B10, 92D15 |
spellingShingle |
Populations and Evolution q-bio.PE Statistics Theory math.ST FOS Biological sciences FOS Mathematics 92B10, 92D15 Allman, Elizabeth Banos, Hector Rhodes, John NANUQ: A method for inferring species networks from gene trees under the coalescent model |
topic_facet |
Populations and Evolution q-bio.PE Statistics Theory math.ST FOS Biological sciences FOS Mathematics 92B10, 92D15 |
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 in 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 |
Article in Journal/Newspaper |
author |
Allman, Elizabeth Banos, Hector Rhodes, John |
author_facet |
Allman, Elizabeth Banos, Hector Rhodes, John |
author_sort |
Allman, Elizabeth |
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 |
arXiv |
publishDate |
2019 |
url |
https://dx.doi.org/10.48550/arxiv.1905.07050 https://arxiv.org/abs/1905.07050 |
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nanuq |
genre_facet |
nanuq |
op_rights |
arXiv.org perpetual, non-exclusive license http://arxiv.org/licenses/nonexclusive-distrib/1.0/ |
op_doi |
https://doi.org/10.48550/arxiv.1905.07050 |
_version_ |
1766071306673979392 |