Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
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Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference. / Vankan, Mezzalina; Ho, Simon Y. W.; Duchene Garzon, David Alejandro.
In: Systematic Biology, Vol. 71, No. 2, 2022, p. 490-500.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Evolutionary Rate Variation Among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference
AU - Vankan, Mezzalina
AU - Ho, Simon Y. W.
AU - Duchene Garzon, David Alejandro
PY - 2022
Y1 - 2022
N2 - 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 the 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.
AB - 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 the 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.
U2 - 10.1093/sysbio/syab051
DO - 10.1093/sysbio/syab051
M3 - Journal article
C2 - 34255084
VL - 71
SP - 490
EP - 500
JO - Systematic Biology
JF - Systematic Biology
SN - 1063-5157
IS - 2
ER -
ID: 327058506