Reconstruction of the deep history of "Parent-Daughter" relationships among vertebrate paralogs

TL;DR

This study introduces a novel method combining phylogenetic and synteny data to reconstruct the deep evolutionary history of 'Parent-Daughter' relationships among vertebrate paralogs, revealing mutation patterns and lineage inheritance.

Contribution

It is the first to reconstruct the deep history of 'Parent-Daughter' relationships among paralogs across multiple whole genome duplication events in vertebrates.

Findings

Parent copies have fewer mutations than Daughter copies since divergence.

Parent copies tend to remain the 'Parent' in subsequent duplications.

The method integrates phylogenetic reconstruction with synteny evidence.

Abstract

Gene duplication is a major mechanism through which new genetic material is generated. Although numerous methods have been developed to differentiate the ortholog and paralogs, very few differentiate the "Parent-Daughter" relationship among paralogous pairs. As coined by the Mira et al, we refer the "Parent" copy as the paralogous copy that stays at the original genomic position of the "original copy" before the duplication event, while the "Daughter" copy occupies a new genomic locus. Here we present a novel method which combines the phylogenetic reconstruction of duplications at different evolutionary periods and the synteny evidence collected from the preserved homologous gene orders. We reconstructed for the first time a deep evolutionary history of "Parent-Daughter" relationships among genes that were descendants from 2 rounds of whole genome duplications (2R WGDs) at early vertebrates and were further duplicated in later ceancestors like early Mammalia and early Primates. Our analysis reveals that the "Parent" copy has significantly fewer accumulated mutations compared with the "Daughter" copy since their divergence after the duplication event. More strikingly, we found that the "Parent" copy in a duplication event continues to be the "Parent" of the younger successive duplication events which lead to "grand-daughters".