Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome

Abstract

-Despite growing evidence of rapid evolution in protein coding genes, the contribution of positive selection to intra-and interspecific differences in protein coding regions of the genome is unclear. We attempted to see if genes coding for secreted proteins and genes with narrow expression, specifically those preferentially expressed in the mammary gland, have diverged at a faster rate between domestic cattle (Bos taurus) and humans (Homo sapiens) than other genes and whether positive selection is responsible. Using a large data set, we identified groups of genes based on secretion and expression patterns and compared them for the rate of nonsynonymous (dN) and synonymous (dS) substitutions per site and the number of radical (Dr) and conservative (Dc) amino acid substitutions. We found evidence of rapid evolution in genes with narrow expression, especially for those expressed in the liver and mammary gland and for genes coding for secreted proteins. We compared common human polymorphism data with human-cattle divergence and found that genes with high evolutionary rates in human-cattle divergence also had a large number of common human polymorphisms. This argues against positive selection causing rapid divergence in these groups of genes. In most cases dN/dS ratios were lower in human-cattle divergence than in common human polymorphism presumably due to differences in the effectiveness of purifying selection between long-term divergence and short-term polymorphism.

Association of A‐FABP gene polymorphism and mRNA expression with intramuscular fat content (IMF) in Baicheng‐You chicken

“…Second, a positive correlation was observed in these tissues in the LM of WBYC. Homoplastically, a positive association was also observed between A-FABP gene mRNA and fat content in the muscle homogenate of pigs (Damon et al, 2006). In contrast, a significantly negative correlation was confirmed in the breast muscle of Jingxing chickens (Li, Zhao, Chen, Zheng, & Wen, 2009 its mRNA expression index, and the mechanism might be that high A-FABP gene mRNA expression induced a high lipolytic rate (Shi, Wang, Zhang, Leng, & Li, 2010), which was verified in A-FABP knockout mice (Smith, Thompson, Sanders, & Bernlohr, 2008).…”

Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

“…Thus, the dN/dS rate is high in the recent evolution of Domestic cattle, Mithan and Yak and remains high in polymorphisms in B. taurus . This finding also appears to be true for humans [ 12 ], who have gone through an ancient population bottleneck and a relatively recent population expansion, especially when low frequency polymorphisms are not removed.…”

“…This algorithm should be accurate as we detected no large bias for transitional to transversional substitutions amongst bovids in our study. Incorporating various lineages from the Bovinae subfamily in the test reduces the requirement of dN/dS ratios to be above one, which is an unrealistic test for selection [ 12 ].…”

“…Candidate genes were selected using a priori knowledge of the genes position in relation to suspected milk QTL, or evidence of higher than average rates of molecular evolution for pairwise comparisons between Bos taurus , Homo sapiens and Bos indicus [ 12 , 41 ]. In total 84 amplicons, which typically consisted of exonic and flanking noncoding regions, were sequenced from the following 15 genes: NRIP-1, PIT-1, ITGBP-5, 5-HT-1F, IGFBP-2, IGFBP-5, H-FABP, LACS3, 5-HT-6, GMEB-1, EGF, ERA, PRRP, PABPC-1 and MFGE8, in at least 1 individual from genomic DNA.…”

“…In this study genes that underlie putative QTL in Holstein for milk production traits from 20 centiMorgan (cM) regions on Bovine chromosomes 1, 2, 6, 9 and 26 were examined [ 9 - 11 ] and hence should give a representative look at a wide sample of genes from the cattle genome. Additional genes were examined from previous work on lactation-associated genes with high expression in the mammary gland and relatively rapid rates of evolution for pairwise comparisons between human and cattle [ 12 ]. These genes were mapped to regions of Bovine chromosomes 14 and 21 and did not underlie QTL.…”