Abstract
BackgroundLong-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. Here we implement a pooled genome re-sequencing approach to investigate the consequences of 39 generations of bidirectional selection in White Leghorn chickens on a humoral immune trait: antibody response to sheep red blood cells.ResultsWe observed wide genome involvement in response to this selection regime. Many genomic regions were highly differentiated resulting from this experimental selection regime, an involvement of up to 20% of the chicken genome (208.8 Mb). While genetic drift has certainly contributed to this, we implement gene ontology, association analysis and population simulations to increase our confidence in candidate selective sweeps. Three strong candidate genes, MHC, SEMA5A and TGFBR2, are also presented.ConclusionsThe extensive genomic changes highlight the polygenic genetic architecture of antibody response in these chicken populations, which are derived from a common founder population, demonstrating the extent of standing immunogenetic variation available at the onset of selection.
Highlights
Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation
A general reduction in heterozygosity in these regions was observed relative to genome-wide heterozygosity in the selected lines
Our results suggest that not just that many loci play a role in sheep red blood cells (SRBC) antibody production, and that the founder population harbored substantial genetic variation upon which selection could act
Summary
Long-term selection experiments provide a powerful approach to gain empirical insights into adaptation, allowing researchers to uncover the targets of selection and infer their contributions to the mode and tempo of adaptation. The importance of de novo mutations and standing genetic variation to the mode and tempo of the adaptive process has been debated, as well as the importance of fixation for adaptation [1,2,3]. Interaction and competition between de novo mutations observed in experimental populations have provided valuable insights into the process of adaptation within microbial species [4,5,6]. The number of genes underlying an adaptive process often belies the complexity of the selective environment. For traits with a complex genetic basis, such as aging and courtship, experimental evolution studies in Drosophila
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