Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation

Abstract

Gene duplication has long been acknowledged by biologists as a major evolutionary force shaping genomic architectures and characteristics across the Tree of Life. Major research has been conducting on elucidating the fate of duplicated genes in a variety of organisms, as well as factors that affect a gene's duplicability--that is, the tendency of certain genes to retain more duplicates than others. In particular, two studies have looked at the correlation between gene duplicability and its degree in a protein-protein interaction network in yeast, mouse, and human, and another has looked at the correlation between gene duplicability and its complexity (length, number of domains, etc.) in yeast. In this paper, we extend these studies to six species, and two trends emerge. There is an increase in the duplicability-connectivity correlation that agrees with the increase in the genome size as well as the phylogenetic relationship of the species. Further, the duplicability-complexity correlation seems to be constant across the species. We argue that the observed correlations can be explained by neutral evolutionary forces acting on the genomic regions containing the genes. For the duplicability-connectivity correlation, we show through simulations that an increasing trend can be obtained by adjusting parameters to approximate genomic characteristics of the respective species. Our results call for more research into factors, adaptive and non-adaptive alike, that determine a gene's duplicability.

Figure 1. Duplicability-connectivity correlations vs. genome sizes and evolutionary relationship.

Spearman’s rank correlation coefficient () between gene duplicability and gene connectivity for six species: H. sapien (Hsap), M. musculus (Mmus), D. melanogaster (Dmel), C. elegans (Cele), S. cerevisiae (Scer), and E. coli (Ecol). The evolutionary relationship of the species is based in part on . Genome size (in Mbp) information for all species, except E. coli, were obtained from the Animal Genome Size Database and the Fungal Genome Database.

Figure 2. Duplicability-connectivity correlations in simulations.

Spearman’s rank correlation coefficient () between gene duplicability and gene connectivity for different settings under the subfunctionalization model (model Ib in [5]) and the neofunctionalization model (model IIc in [5]). The parameter values in each of the four settings are given in Table 2.