New genes from old: asymmetric divergence of gene duplicates and the evolution of development

Abstract

One contribution of 17 to a theme issue 'Evodevo in the genomics era, and the origins of morphological diversity'. Gene duplications and gene losses have been frequent events in the evolution of animal genomes, with the balance between these two dynamic processes contributing to major differences in gene number between species. After gene duplication, it is common for both daughter genes to accumulate sequence change at approximately equal rates. In some cases, however, the accumulation of sequence change is highly uneven with one copy radically diverging from its paralogue. Such 'asymmetric evolution' seems commoner after tandem gene duplication than after whole-genome duplication, and can generate substantially novel genes. We describe examples of asymmetric evolution in duplicated homeobox genes of moths, molluscs and mammals, in each case generating new homeobox genes that were recruited to novel developmental roles. The prevalence of asymmetric divergence of gene duplicates has been underappreciated, in part, because the origin of highly divergent genes can be difficult to resolve using standard phylogenetic methods.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.

Alternative splicing and the evolution of phenotypic novelty

“…This has prompted comparisons between alternative splicing and gene duplication, widely recognized as a major source of phenotypic innovation [43][44][45]. The number of alternatively spliced isoforms per gene can decrease after a gene duplication event [46], suggesting that alternative splicing and gene duplication are to some extent equivalent mechanisms regulating transcript diversity.…”

Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era

“…The issue begins with articles about various aspects of genomics, with Holland et al [26] discussing gene duplication and Urrutia and co-workers [51] alternative splicing and their contributions to phenotypic innovation while Orlando and co-workers [47] outline the latest methodologies that allow analysis of fossil genomes. Tschopp & Tabin [25] consider the impact of genomics on the concept of deep homology.…”

“…Another class of genomic change that underlies morphological diversity is the creation of new genes by gene duplication. In this issue, Holland and co-workers argue that the importance of gene duplication as a mechanism for evolutionary change has been rather underplayed and give several examples from animal development where gene duplication followed by asymmetric divergence of the gene duplicates has created genes with new functions [26]. Duplication of individual genes or of the whole genome has occurred in both animal and plant evolution.…”

“…There is also growing interest in human evolution as novel tools become available to study it. In this issue, a detailed analysis of the human genome is described that has led to the discovery of a set of homeobox genes restricted to the genomes of placental mammals [26], whereas the article on ancient human genome sequences describes how these have already given fascinating insights into our ancestors and the origins of modern human populations [47]. Such studies, together with comparative genomics, hold out the promise of identifying the genetic basis for human-specific morphology (reviewed in [66]).…”

“…This conservation also suggested that evolutionary novelties arise by modification of pre-existing regulatory networks. It was also possible to begin to look at the phylogeny of developmental genes, bringing an entirely new perspective and providing a starting point for understanding the evolution of morphological differences (discussed in this issue by Holland et al [26]) and major transitions such as multicellularity (discussed in this issue by Babonis & Martindale [20]). …”