Natural selection drives the evolution of mitogenomes in Acrossocheilus

Abstract

The mitochondrial genome plays a crucial role in the balance of energy and heat production in organisms and, thus, may be under natural selection due to its potential role in adaptive divergence and speciation. Here, we studied natural selection on the mitogenome of Acrossocheilus (Cypriniformes: Cyprinidae), a genus of fish that inhabits a broad latitudinal distribution ranging from the tropics and subtropics through temperate regions. Specifically, we used 25 published mitogenome sequences of Acrossocheilus species to investigate phylogenetic relationships in this genus and detected signals of positive selection on 13 protein-coding, mitochondrial genes. We found that relaxed purifying selection and genetic drift were the predominant evolutionary forces acting on the analyzed mitogenomes. However, we also found evidence of diversifying selection on some codons, indicating episodes of positive selection. Additionally, we analyzed the mitogenomic data within an environmental modeling framework and found that the Ka/Ks ratio of ATP6 may correlated with a mean diurnal temperature range (p = 0.0449), while the Ka/Ks ratio of COX2 may correlated with precipitation during the driest month (p = 0.00761). These results suggest that the mitogenomes of Acrossocheilus species may be involved in evolutionary adaptations to different habitats. Based on this, we believe that our study provides a new insight into the role of the mitochondrial genome of Acrossocheilus species in adaptation to different environments. During our study, we also discovered several cases of paraphyly and polyphyly among accessions of species and their putative synonyms. Thus, our study suggests that a careful reassessment of the taxonomy of Acrossocheilus is using high-quality molecular data merited.

Fig 1. The Ka/Ks ratios of the 13 different mitochondrial genes in Acrossocheilus species.

Fig 2. Correlation analyses.

The dots denote the individual values for the 13 different mitochondrial genes in Acrossocheilus species and the line the best-fitted line. (A) Correlation between total number of mutations and length in bases of the genes. (B) Correlation between synonymous mutations and length in bases of the genes. (C) Correlation between nonsynonymous and synonymous mutations. (D) Correlation between nonsynonymous mutations and length in bases of the genes.

Fig 3. Maximum-likelihood tree of the Acrossocheilus genus based on 13 protein coding mitochondrial gene sequences.

Onychostoma barbatulum and O. barbatulum were used as outgroup. The different individuals are labeled at the tips. Numbers at the nodes denote the bootstrap values.