Contribution of both positive selection and relaxation of selective constraints to degeneration of flyability during geese domestication

<div><p>Flyability is the most discrepant trait between modern-day geese and their wild ancestors, and the degeneration of flyability is a key marker of the successful domestication of wild geese. In light of the relatively short history of domestic geese, intense artificial selection is thought to play an important role in the degeneration of flyability. However, the underlying mechanism behind this phenomenon has seldom been investigated. In this study, we applied a molecular evolutionary approach to the evaluation of partial breeds of domestic geese in order to look for genes involved in the selection pressure toward degeneration of flyability. The haplotype networks, pairwise fixation index (<i>F</i>_<i>ST</i>) values, and analysis of molecular variance results all clearly illustrated a population variance between Landes geese and partial Chinese domestic geese. We also detected signatures of positive artificial selection in the <i>COX2</i> and <i>COX3</i> genes, and related selection in the <i>HBB</i> gene. Our results support the independent origins of partial European domestic geese and Chinese domestic geese. In addition, both positive artificial selection and the relaxation of functional constraints appeared to play important roles in the degeneration of flyability in domestic geese.</p></div

Haplotype networks of five genes across each population. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>HBA1</i>, (D) <i>HBA2</i>, and (E) <i>HBB</i>.

<p>Haplotype networks of five genes across each population. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>HBA1</i>, (D) <i>HBA2</i>, and (E) <i>HBB</i>.</p

Differentiated loci between partial Chinese domestic geese and Landes geese. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>HBA1</i>, (D) <i>HBA2</i>, and (E) <i>HBB</i>.

<p><i>F</i>_<i>ST</i>: locus-specific genetic divergence among populations. Heterozygosity: measure of heterozygosity per locus. Single-locus <i>F</i>_<i>ST</i> values are plotted against heterozygosity, with the red-filled circles representing loci significant at the 1% level, and blue-filled circles representing loci significant at the 5% level.</p

Matrix of pairwise <i>F</i>_<i>ST</i> for each gene across populations. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>HBA1</i>, (D) <i>HBA2</i>, and (E) <i>HBB</i>.

<p>Matrix of pairwise <i>F</i>_<i>ST</i> for each gene across populations. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>HBA1</i>, (D) <i>HBA2</i>, and (E) <i>HBB</i>.</p

Values of the Hudson-Kreitman-Aguade test for each gene across populations^a.

<p>Values of the Hudson-Kreitman-Aguade test for each gene across populations<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185328#t002fn001" target="_blank">^a</a>.</p

Molecular diversity indices of six gene fragments. (A) <i>COX2</i>, (B) <i>COX3</i>, (C) <i>EVC2P</i>, (D) <i>HBA1</i>, (E) <i>HBA2</i>, and (F) <i>HBB</i>.

<p>θ_<i>k</i>, average number of nucleotide differences; θ_<i>H</i>, haplotype diversity; θ_<i>S</i>, number of polymorphic sites; θ_π, nucleotide diversity.</p

Results of the hierarchical AMOVA for grouping hypothesis^a.

<p>Results of the hierarchical AMOVA for grouping hypothesis<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185328#t001fn001" target="_blank">^a</a>.</p