Dataset Information

The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication.

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 ? and ? chain gene families, which were apparently generated by genome duplication. We then compute the Pr values for the MHC class II ? and ? chain gene families. The Pr values for the ? and ? 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.

SUBMITTER: Katsura Y

PROVIDER: S-EPMC7012300 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication.

Katsura Yukako Y Nei Masatoshi M

Genome biology and evolution 20200201 2

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 duplicat ...[more]

PMID: 31950994

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Project description:Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.].

Dataset Information

The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication.

Publications

The Reproducibility of an Inferred Tree and the Diploidization of Gene Segregation after Genome Duplication.

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