Evidence for relaxed selection of mitogenome in rapid-flow cyprinids

Hypoxia adaptation is developed in many fish species, which helped them to habitat most of water bodies. However, fishes living under high oxygen concentration may lose this feature. Rapid flows provide high level and stable dissolved oxygen, which facilitate organism's oxygen supply and energy production. Previous studies showed that fish species from rapid-flow habitats exhibited lower hypoxia tolerance compared with fish from intermediate- and slow-flow habitats. Mitochondrial genomes code 13 key components in oxidative phosphorylation pathway; these genes may be under relaxed selection in rapid-flow species.

The primary objectives of this study is to investigate the evolutionary patterns of the 13 mitochondrial OXPHOS genes among nine cyprinids from different water bodies and to test the hypotheses that mitochondrial OXPHOS genes may experience relaxed selection in rapid-flow habitats.

We classified nine cyprinid fish species into three groups based on their habitats: rapid-flow, intermediate-flow and slow-flow. To detect relaxed selections, we investigated the 13 protein-coding genes with codon evolution programs RELAX; to estimate evolutionary rates among the cyprinids, free-ratio model in Codeml program was applied; Branch-site models were applied to detect positive selection sites. The polymorphisms of homologous sites were evaluated with PROVEAN program and projected to 3D structure prediction of the proteins using SWISS-MODEL.

We found that nine out of the 13 genes are under relaxed selection in rapid-flow species. Furthermore, dN, dS and dN/dS are relatively increased when compared with those of intermediate-flow species. More amino acid polymorphic sites are presented in rapid-flow species than in intermediate- and slow-flow species. Furthermore, rapid-flow species had more deleterious substitutions than other groups. 3D structure prediction of these proteins and projection of the polymorphic sites indicated that these sites were randomly distributed, suggesting relaxed functional constraints of these proteins in rapid-flow species.

Our results suggest that mitochondrial genes are under relaxed selection in rapid-flow cyprinids.