The effect of functional compensation among duplicate genes can constrain their evolutionary divergence

Abstract

Gene duplicates have the inherent property of initially being functionally redundant. This means that they can compensate for the effect of deleterious variation occurring at one or more sister sites. Here, I present data bearing on evolutionary theory that illustrates the manner in which any functional adaptation in duplicate genes is markedly constrained because of the compensatory utility provided by a sustained genetic redundancy. Specifically, a two-locus epistatic model of paralogous genes was simulated to investigate the degree of purifying selection imposed, and whether this would serve to impede any possible biochemical innovation. Three population sizes were considered to see if, as expected, there was a significant difference in any selection for robustness. Interestingly, physical linkage between tandem duplicates was actually found to increase the probability of any neofunctionalization and the efficacy of selection, contrary to what is expected in the case of singleton genes. The results indicate that an evolutionary trade-off often exists between any functional change under either positive or relaxed selection and the need to compensate for failures due to degenerative mutations, thereby guaranteeing the reliability of protein production.

Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits

“…The average number of alleles per locus was 10.46 among the 532 accessions genotyped with 258 markers. The allele number per locus is higher than that reported by Garris et al 37 , Agrama et al 39 , and Vanniaraja et al 40 but lower than that reported by Borba et al 41 and Li et al 42 . The average PIC value in this study was 0.7042, which is the highest value among previous studies for rice populations 41 43 , with an exception of the PIC value of 0.71 reported by Li et al 42 and PIC value of 0.75 reported by Borba et al 44 .…”

“…To date, varying results have been reported for LD patterns by researchers in rice. Olsen et al 45 and Mather et al 46 reported LD decay occurring at an approximately 1 cM distance using DNA sequencing, whereas Dang et al 30 , Agrama et al 39 , and Vanniarajan et al 40 reported LD decay at 10–80 cM, 20–30 cM and 20–30 cM distances, respectively, using SSR markers. Compared with previous studies, the LD values for POP1-POP6 in the present study were similar to those reported by Vanniarajan et al 40 .…”

Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

“…It is expected that paralogs on different chromosomes would have more divergent regulation compared with paralogs from LGD events and theoretical models show that paralogs in close linkage will diverge in function (Bozorgmehr 2012). This is supported by evidence in several plant species, where WGD paralogs are associated with subfunctionalization through divergent expression, whereas higher rates of relaxed purifying selection and novel gene function (neofunctionalization) have been observed (Guan et al 2007; Carretero-Paulet and Fares 2012; Fares et al 2013).…”

Deubiquitinating enzyme USP20 is a positive regulator of claspin and suppresses the malignant characteristics of gastric cancer cells

“…A prior study revealed that the mutation of the pVHL gene is strongly associated with many kinds of tumors such as haemangioblastoma, phaeochromocytoma and clear-cell renal cell carcinoma (ccRCC) (19). Currently, a study found that the high frequency of the 3-bp deletion in the USP20 gene in Korean population, which mean a biased susceptibility of Korean individuals to certain cancer types, and the potential mechanisms of carcinogenesis caused by mutant USP20 are still unknown (20). Furthermore, searching public databases of the Sanger Cosmic and the Cancer Genome Atlas, frequent point mutations and deletions of USP20 are found to exist in a variety of malignancies (13).…”