Positive selection rather than relaxation of functional constraint drives the evolution of vision during chicken domestication

Abstract

As noted by Darwin, chickens have the greatest phenotypic diversity of all birds, but an interesting evolutionary difference between domestic chickens and their wild ancestor, the Red Junglefowl, is their comparatively weaker vision. Existing theories suggest that diminished visual prowess among domestic chickens reflect changes driven by the relaxation of functional constraints on vision, but the evidence identifying the underlying genetic mechanisms responsible for this change has not been definitively characterized. Here, a genome-wide analysis of the domestic chicken and Red Junglefowl genomes showed significant enrichment for positively selected genes involved in the development of vision. There were significant differences between domestic chickens and their wild ancestors regarding the level of mRNA expression for these genes in the retina. Numerous additional genes involved in the development of vision also showed significant differences in mRNA expression between domestic chickens and their wild ancestors, particularly for genes associated with phototransduction and photoreceptor development, such as RHO (rhodopsin), GUCA1A, PDE6B and NR2E3. Finally, we characterized the potential role of the VIT gene in vision, which experienced positive selection and downregulated expression in the retina of the village chicken. Overall, our results suggest that positive selection, rather than relaxation of purifying selection, contributed to the evolution of vision in domestic chickens. The progenitors of domestic chickens harboring weaker vision may have showed a reduced fear response and vigilance, making them easier to be unconsciously selected and/or domesticated.

Genetic Diversities and Differentially Selected Regions Between Shandong Indigenous Pig Breeds and Western Pig Breeds

“…Genomic data have provided new insights into plant domestication (Jiang et al, 2015;Han et al, 2016;Yang et al, 2018). In recent years, genomic data have been used to screen positive selection signals in dogs and chickens (Axelsson et al, 2013;Wang et al, 2016). However, to date, there has been little research on genetic relationships between local pig breeds in Shandong province and outside breeds involving large-scale analyses of genomic data.…”

A Comparison of Co-expression Networks in Silk Gland Reveals the Causes of Silk Yield Increase During Silkworm Domestication

“…Nucleotide polymorphism (π) and fixation index (Fst) of population differentiation were calculated using a sliding window analysis (Danecek et al, 2011). The window (π D /π w or π D -π w < 5% value of empirical distribution and Fst > 95% value of empirical distribution) is identified as the genomic regions harboring footprints of artificial selection in domestic silkworms (Xia et al, 2009;Qiu et al, 2015;Wang et al, 2016). The gene overlapped with a genomic region of artificial selection is identified as an artificial selection gene (Qiu et al, 2015;Wang et al, 2016).…”

Detecting Positive Selection in Populations Using Genetic Data

“…Searching for strong positive selection in the genomes of individuals of a natural population has been the focus of a multitude of studies over the past years [3,8,41,52,67,78,97,100,102]. The goals of these studies have been (1) to provide evidence of positive selection, (2) estimate the strength of selection, and (3) localize the targets of selection.…”