Investigation of ancestral alleles in the Bovinae subfamily v1

Abstract

In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele -AA), co-exist or be replaced by a mutated state (derived alleles -DA). Defining AA and DA at polymorphic sites is useful to test hypotheses regarding molecular evolutionary processes, including estimation of allelic age, formation of linkage disequilibrium patterns and selection signatures. In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily (gaur, yak, bison, wisent, gayal, and cattle) to the cattle reference genome (ARS.UCD-1.2). We then identified sequence variants in three outgroups, i.e. yak, bison and gayal-gaur-banteng. Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups resulting in ~32.4 million variants. Using nonoverlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0.1% (high count) and regions without any occurrence of AA (null count). As mutation occurs across autosome independently, high count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. Gene ontology terms were inferred for functionality of referred regions. For both cattle, high count regions were associated to basal lipid metabolism which is essential on surviving of various condition pressures. Mutated regions were associated to productive traits in taurine such as higher metabolism, cell development and behaviors. While for zebu, mutation appeared for adaptation to marginal environment showed mainly by function in immune response domain. Our findings suggest that retaining and losing AA in some genes or regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.