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Title: “Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error
Abstract The evolutionary histories of individual loci in a genome can be estimated independently, but this approach is error-prone due to the limited amount of sequence data available for each gene, which has led to the development of a diverse array of gene tree error correction methods which reduce the distance to the species tree. We investigate the performance of two representatives of these methods: TRACTION and TreeFix. We found that gene tree error correction frequently increases the level of error in gene tree topologies by “correcting” them to be closer to the species tree, even when the true gene and species trees are discordant. We confirm that full Bayesian inference of the gene trees under the multispecies coalescent model is more accurate than independent inference. Future gene tree correction approaches and methods should incorporate an adequately realistic model of evolution instead of relying on oversimplified heuristics.  more » « less
Award ID(s):
2030604
NSF-PAR ID:
10463337
Author(s) / Creator(s):
; ;
Editor(s):
Holland, Barbara
Date Published:
Journal Name:
Genome Biology and Evolution
Volume:
15
Issue:
6
ISSN:
1759-6653
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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    Availability and implementation

    QuCo is available on https://github.com/maryamrabiee/quco.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
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