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Mutually exclusive AA substitution for monotocous and polytocous species
Amino acid substitution sites in multiple sequence alignments, which are mutually exclusive between monotocous and polytocous species that could assert molecular convergent evolution for the trait, are termed 'mutually exclusive AA substitutions' in this study.
We selected the orthologous gene sets which have undergone adaptive evolution that were also on the site of mutually exclusive AA substitution to identify convergent evolution by adaptive selection pressure for the monotocous or polytocous traits.
We investigated the monotocous specific and polytocous specific genes for expansion as it is possible that the trait was acquired by gene expansion.
We collected monotocous and polytocous specific orthologous gene sets by selecting genes that only existed in the monotocous species or the polytocous species.
After filtering, 10 monotocous specific orthologous gene sets and 12 polytocous specific orthologous gene sets were collected.
We explored genes which have evolved differently between monotocous and polytocous species in a number of different scopes, specific amino acid substitution with site-wise adaptive evolution, gene expansion and specific orthologous group.
Among the 6,409 orthologous gene sets of the 16 species, the genes that have an adapted site specific to monotocous species and are supported by a mutually exclusive monotocous amino acid substitution are shown in Figure 2.
The results of the parsimonious inference showed that the episodic adaptive evolution event supports the ancestral branches of the monotocous group.
Genes under expansion in the monotocous and polytocous species were identified from the 7,508 orthologous gene sets including in-paralogs of leaf species from the phylogenetic topology.
We found that the gene, EPHA4, has undergone expansion in monotocous species and this results is supported by previous findings.
However, if a portion of the current species were analyzed for gene expansion by grouping them under a common ancestor, such as part of the monotocous species (human, chimpanzee, orangutan, and macaque) or polytocous species (cow and dolphin), a higher number of orthologous gene could have been assessed.