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Title: The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication
Authors: Katsura, Yukako  kyouindb  KAKEN_id
Nei, Masatoshi
Author's alias: 桂, 有加子
Keywords: phylogenetic trees
genome duplication
reliability
stability
reproducibility
diploidization
gene segregation
computer program RESTA
MHC class II α
and β
chain gene families
Issue Date: Feb-2020
Publisher: Oxford University Press (OUP)
Journal title: Genome Biology and Evolution
Volume: 12
Issue: 2
Start page: 3792
End page: 3796
Abstract: We previously introduced a numerical quantity called the stability (Ps) of an inferred tree and showed that for the tree to be reliable this stability as well as the reliability of the tree, which is usually computed as the bootstrap probability (Pb), must be high. However, if genome duplication occurs in a species, a gene family of the genome also duplicates, and for this reason alone some Ps values can be high in a tree of the duplicated gene families. In addition, the topology of the duplicated gene family can be similar to that of the original gene family if such gene families are identifiable. After genome duplication, however, the gene families are often partially deleted or partially duplicated, and the duplicated gene family may not show the same topology as that of the original family. It is therefore necessary to compute the similarity of the topologies of the duplicated and the original gene families. In this paper, we introduce another quantity called the reproducibility (Pr) for measuring the similarity of the two gene families. To show how to compute the Pr values, we first compute the Pb and Ps values for each of the MHC class II α and β chain gene families, which were apparently generated by genome duplication. We then compute the Pr values for the MHC class II α and β chain gene families. The Pr values for the α and β chain gene families are now low, and this suggests that the diploidization of gene segregation has occurred after the genome duplication. Currently higher animals, defined as animals with complex phenotypic characters, generally have a higher genome size, and this increase in genome size appears to have been caused by genome duplication and diploidization of gene segregation after genome duplication.
Rights: © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
URI: http://hdl.handle.net/2433/265337
DOI(Published Version): 10.1093/gbe/evz272
PubMed ID: 31950994
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