Patterns of gene conversion in duplicated yeast histones suggest strong selection on a coadapted macromolecular complex

We find evidence for interlocus gene conversion in five duplicated histone genes from six yeast species. The sequences of these duplicated genes, surviving from the ancient genome duplication, show phylogenetic patterns inconsistent with the well-resolved orthology relationships inferred from a likelihood model of gene loss after the genome duplication. Instead, these paralogous genes are more closely related to each other than any is to its nearest ortholog. In addition to simulations supporting gene conversion, we also present evidence for elevated rates of radical amino acid substitutions along the branches implicated in the conversion events. As these patterns are similar to those seen in ribosomal proteins that have undergone gene conversion, we speculate that in cases where duplicated genes code for proteins that are a part of tightly interacting complexes, selection may favor the fixation of gene conversion events in order to maintain high protein identities between duplicated copies

Characterizing a Region of Bovine Chromosome 6 Associated with Three Cattle Coat Color Phenotypes

Coat color of mammals, especially mice, has been a valuable model for the study of adaptation, pleiotropy, and gene action and interactions. More recently, however, the characterization of coat color in livestock has begun to identify genes associated with and causing different coat color phenotypes. Color is an especially important attribute in livestock as it is often a required component of breed recognition and registration. There are also numerous point-of-sale marketing programs designed to offer economic premiums for certain colors. Pigmentation in purebred cattle typically follows a pattern of Mendelian inheritance, but crossbred cattle often produce colors that are atypical of purebred cows. The aim of this study was to characterize a region on bovine chromosome 6 previously associated with three cattle coat color phenotypes in a population of Nellore-Angus crossbred cattle: gray, reddening, and white spotting. Genome-wide association studies (GWAS) were performed for the gray and spotting phenotypes using high-density SNP genotypes, and the regions associated with all three phenotypes were fine mapped. GWAS identified the same genes associated with gray and spotting phenotypes found in previous studies—CORIN and KIT, respectively. Fine mapping revealed that the E+E+ genotype at MC1R coupled with a mutation within CORIN was coincident with the gray phenotype, although later findings suggest that these factors are necessary but not sufficient for gray. A missense variant in CHIC2 was identified in the whole-genome sequenced founders contributing to EDE+ red animals. Additionally, founder data indicated that KIT and the region associated with white spotting lies within a poorly assembled region of the bovine genome. Haplotype breed of origin also tends to influence all three phenotypes. Histological examinations of skin and hair revealed that gray coat color in this population results when white hair occurs atop dark-pigmented skin, and that lack of hair pigmentation is due to both melanocyte depletion and displacement