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ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE

Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower fre...

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Autores principales: ANÉ, CÉCILE, FOGG, JOHN, ALLMAN, ELIZABETH S., BAÑOS, HECTOR, RHODES, JOHN A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473666/
https://www.ncbi.nlm.nih.gov/pubmed/37662314
http://dx.doi.org/10.1101/2023.08.18.553582
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author ANÉ, CÉCILE
FOGG, JOHN
ALLMAN, ELIZABETH S.
BAÑOS, HECTOR
RHODES, JOHN A.
author_facet ANÉ, CÉCILE
FOGG, JOHN
ALLMAN, ELIZABETH S.
BAÑOS, HECTOR
RHODES, JOHN A.
author_sort ANÉ, CÉCILE
collection PubMed
description Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of 3(2)-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods.
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spelling pubmed-104736662023-09-02 ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE ANÉ, CÉCILE FOGG, JOHN ALLMAN, ELIZABETH S. BAÑOS, HECTOR RHODES, JOHN A. bioRxiv Article Reticulations in a phylogenetic network represent processes such as gene flow, admixture, recombination and hybrid speciation. Extending definitions from the tree setting, an anomalous network is one in which some unrooted tree topology displayed in the network appears in gene trees with a lower frequency than a tree not displayed in the network. We investigate anomalous networks under the Network Multispecies Coalescent Model with possible correlated inheritance at reticulations. Focusing on subsets of 4 taxa, we describe a new algorithm to calculate quartet concordance factors on networks of any level, faster than previous algorithms because of its focus on 4 taxa. We then study topological properties required for a 4-taxon network to be anomalous, uncovering the key role of 3(2)-cycles: cycles of 3 edges parent to a sister group of 2 taxa. Under the model of common inheritance, that is, when each gene tree coalesces within a species tree displayed in the network, we prove that 4-taxon networks are never anomalous. Under independent and various levels of correlated inheritance, we use simulations under realistic parameters to quantify the prevalence of anomalous 4-taxon networks, finding that truly anomalous networks are rare. At the same time, however, we find a significant fraction of networks close enough to the anomaly zone to appear anomalous, when considering the quartet concordance factors observed from a few hundred genes. These apparent anomalies may challenge network inference methods. Cold Spring Harbor Laboratory 2023-08-21 /pmc/articles/PMC10473666/ /pubmed/37662314 http://dx.doi.org/10.1101/2023.08.18.553582 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
ANÉ, CÉCILE
FOGG, JOHN
ALLMAN, ELIZABETH S.
BAÑOS, HECTOR
RHODES, JOHN A.
ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title_full ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title_fullStr ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title_full_unstemmed ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title_short ANOMALOUS NETWORKS UNDER THE MULTISPECIES COALESCENT: THEORY AND PREVALENCE
title_sort anomalous networks under the multispecies coalescent: theory and prevalence
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10473666/
https://www.ncbi.nlm.nih.gov/pubmed/37662314
http://dx.doi.org/10.1101/2023.08.18.553582
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