Evolutionary history of the human multigene families reveals widespread gene duplications throughout the history of animals

Abstract

Background: The hypothesis that vertebrates have experienced two ancient, whole genome duplications (WGDs) is of central interest to evolutionary biology and has been implicated in evolution of developmental complexity. Three-way and Four-way paralogy regions in human and other vertebrate genomes are considered as vital evidence to support this hypothesis. Alternatively, it has been proposed that such paralogy regions are created by small-scale duplications that occurred at different intervals over the evolution of life. Results: To address this debate, the present study investigates the evolutionary history of multigene families with at least threefold representation on human chromosomes 1, 2, 8 and 20. Phylogenetic analysis and the tree topology comparisons classified the members of 36 multigene families into four distinct co-duplicated groups. Gene families falling within the same co-duplicated group might have duplicated together, whereas genes belong to different co-duplicated groups might have distinct evolutionary origins. Conclusion: Taken together with previous investigations, the current study yielded no proof in favor of WGDs hypothesis. Rather, it appears that the vertebrate genome evolved as a result of small-scale duplication events, that cover the entire span of the animals' history.

Context-dependent functional compensation between Ythdf m6A readers

“…of Ythdf protein (named Ythdf), vertebrates have three functional proteins (Figure S1b), probably 62 generated following duplication events (Pervaiz et al 2019). 63 64…”

Molecular evolutionary and structural analysis of human UCHL1 gene demonstrates the relevant role of intragenic epistasis in Parkinson’s disease and other neurological disorders

“…The putative orthologous protein sequences of human UCHL1 were retrieved from protein databases accessible at Ensemble [ 50 ] and National Center for Biotechnology Information [ 51 ] by using BLAST p bidirectional best hit approach [ 52 ]. Further confirmation of the common ancestry of the putative orthologs was obtained by clustering homologous proteins within phylogenetic trees [ 53 , 54 ]. Sequences whose position within a tree is in sharp conflict with the uncontested animal phylogeny are excluded from the analysis.…”

An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice

“…Although a lot of arguments seem now to be more in favor of the “2R hypothesis”, the question is still not completely resolved. Very recently, an investigation using phylogenetic approaches and tree topology comparisons of gene families containing at least three members and located on several human chromosomes led to the conclusion that small-scale duplication (SSD) events scattered on all the animal history were more likely to be involved in vertebrate genome evolution rather than WGD [ 29 ].…”