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Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference

Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help...

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Autores principales: Vankan, Mezzalina, Ho, Simon Y W, Duchêne, David A
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830059/
https://www.ncbi.nlm.nih.gov/pubmed/34255084
http://dx.doi.org/10.1093/sysbio/syab051
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author Vankan, Mezzalina
Ho, Simon Y W
Duchêne, David A
author_facet Vankan, Mezzalina
Ho, Simon Y W
Duchêne, David A
author_sort Vankan, Mezzalina
collection PubMed
description Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.]
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spelling pubmed-88300592022-02-11 Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference Vankan, Mezzalina Ho, Simon Y W Duchêne, David A Syst Biol Points of View Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.] Oxford University Press 2021-07-13 /pmc/articles/PMC8830059/ /pubmed/34255084 http://dx.doi.org/10.1093/sysbio/syab051 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of the Society of Systematic Biologists. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Points of View
Vankan, Mezzalina
Ho, Simon Y W
Duchêne, David A
Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title_full Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title_fullStr Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title_full_unstemmed Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title_short Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
title_sort evolutionary rate variation among lineages in gene trees has a negative impact on species-tree inference
topic Points of View
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8830059/
https://www.ncbi.nlm.nih.gov/pubmed/34255084
http://dx.doi.org/10.1093/sysbio/syab051
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