Abstract
A phylogenetic tree can be used to illustrate the evolutionary relationship between a group of genes, especially duplicated genes, which are sources of genetic innovation and are often a hotspot of research. However, duplicated genes may have complex phylogenetic topologies due to changes in their evolutionary rates. Here, by constructing phylogenetic trees using different methods, we evaluated the phylogenetic relationships of duplicated genes produced by polyploidization in cotton. We found that at least 83.2% of phylogenetic trees did not conform the expected topology. Moreover, cotton homologous gene copy number has little effect on the topology of duplicated genes. Compared with their cacao orthologs, elevated evolutionary rates of cotton genes are responsible for distorted tree topology. Furthermore, as to both branch and site models, we inferred that positive natural selection during the divergence of fiber-development-related MYB genes was likely, and found that the reconstructed tree topology may often overestimate natural selection, as compared to the inference with the expected trees. Therefore, we emphasize the importance of borrowing precious information from gene collinearity in tree construction and evaluation, and have evidence to alert the citation of thousands of previous reports of adaptivity and functional innovation of duplicated genes.
Highlights
Molecular phylogeny describes evolutionary relationships among organisms or genes that they harbor through molecular biology technology (Yang and Rannala, 2012)
To understand the evolution of cotton’s duplicated genes, we involved cacao, the close relative of cotton, and grape, with a genome closely resembling that of the ancestral eudicot, to our experience in plant genomics analysis, in the present analysis
The cotton paralogs were likely produced by the decaploidization. 2123 cotton genes were involved in the above homologous groups, i.e., each group has an average 3.21 cotton paralogs
Summary
Molecular phylogeny describes evolutionary relationships among organisms or genes that they harbor through molecular biology technology (Yang and Rannala, 2012). It is an area of molecular evolution and has attracted wide attention in recent years, mainly because it is difficult to evaluate phylogenetic relationship by any other method in many cases (Zhang et al, 2018). If a phylogenetic tree is made up of multiple gene homologs from each and more species, often constructed to understand gene evolutionary trajectory or functional innovation, the tree could be much more complex and much diverted from the real tree, due to the above-mentioned reasons and more
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