Molecular Mechanisms of the Convergent Adaptation of Bathypelagic and Abyssopelagic Fishes

Abstract

Harsh environments provide opportunities to study how different species adapt, at the molecular level, to similar environmental stressors. High hydrostatic pressure, low temperature, and absence of sunlight in the deep-sea environment are challenging conditions for gene expression, cell morphology and vision. Adaptation of fish to this environment appears independently in at least 22 orders of fish, but it remains uncertain whether these adaptations represent convergent evolution. In this study, we performed comparative genomic analysis of 80 fish species to determine genetic evidences for adaptations to the deep-sea environment. The 80 fishes were divided into six groups according to their order. Positive selection and convergent evolutionary analysis were performed and functional enrichment analysis of candidate genes was performed. Positively selected genes (pik3ca, pik3cg, vcl and sphk2) were identified to be associated with the cytoskeletal response to mechanical forces and gene expression. Consistent signs of molecular convergence genes (grk1, ednrb, and nox1) in dark vision, skin color, and bone rarefaction were revealed. Functional assays of Grk1 showed that the convergent sites improved dark vision in deep-sea fish. By identifying candidate genes and functional profiles potentially involved in cold, dark, and high-pressure responses, the results of this study further enrich the understanding of fish adaptations to deep-sea environments.

Keywords: GRK1; bathypelagic and abyssopelagic fishes; convergent evolution; positive selection.

Fig. 1.

Phylogenetic relationships of six groups of fishes. The bars on the right represent the depth range inhabited by the fish.

Fig. 2.

Results of positive selection analysis were presented. (A) Using Beryciformes as an example, positively selected genes were calculated by labeling branches A, B, C, and D respectively. (B) Positively selected genes statistic of six groups. The left bar graph shows the number of positively selected genes in each group, and the upper bar graph shows the number of statistical units, which are shown by dots and lines. (C) In the KEGG functional enrichment pathway diagram of positively selected genes, the bubble size represents -log₁₀^P-value, and the color represents the enrichment fold, which is the ratio of the probability of actual enrichment to the probability of random enrichment. See supplementary table 4, Supplementary Material online for abbreviations of species names.

Fig. 3.

(A) The positively selected site of Vcl. (B) STRING shows Vcl, Pik3ca, and Pik3cg interacting through Ras, Paxillin, and Actin. (C) The positively selected site of Pik3ca. (D) The positively selected site of Pik3cg. (E) The positively selected sites of Sphk2. (F) Venn diagram of gene distribution at three positively selected sites of Sphk2. The color of the square in front of the name of a species represents the maximum depth at which the species occurs. Consensus (50%) represents a consensus sequence at 50% conservation. The consensus sequence greater than 50% of the threshold is uppercase, and the consensus sequence less than 50% is lowercase. The histogram represents the conservation of each site in all species of the six orders.

Fig. 4.

Results of convergent evolutionary analysis were presented. (A) Using Beryciformes as an example, the A, B and C, D branches were labeled, and the gene convergence of the two branches was calculated. (B) Statistics of convergent genes per two branches. The left bar graph shows the number of convergence genes in each two branches, and the upper bar graph shows the number of statistical units, which are illustrated by dots and lines. (C) In the KEGG functional enrichment pathway diagram of convergence genes, the bubble size represents -log₁₀^P-value, and the color represents enrichment fold, which is the ratio of the probability of actual enrichment to the probability of random enrichment. See supplementary table 4 for abbreviations of species names.

Fig. 5.

(A) Convergence site of Nox1. (B) Convergence site of Ednrb. (C) Convergence sites of Grk1. Two convergence sites are located in RGS and S_TKc domain respectively. RGS: Regulator of G protein signaling domain; S_TKc: Serine/Threonine protein kinases, catalytic domain; S_TK_X: Extension to Ser/Thr-type protein kinases. (D) Kinase activities of zebrafish Grk1, zebrafish G144N Grk1, zebrafish Q152R Grk1, and zebrafish N402S Grk1 and all three sites were mutated Grk1. The error bars are the 95% confidence interval. The color of the square in front of the name of a species represents the maximum depth that the species inhabits. Consensus (50%) represents a consensus sequence at 50% conservation. The consensus sequence greater than 50% of the threshold is uppercase, and the consensus sequence less than 50% is lowercase. The histogram represents the conservation of each site in all species of six orders.

Fig. 6.

(A) Schematic diagram of a rod, and Grk1 phosphorylates rhodopsin in the rod out segments. Light activates Rho, and the chromophore changes from 11-cis-retinal to all-trans-retinal. Activated Rho (Rho*) binds Gt to hydrolyze cGMP to GMP, reducing the concentration of cGMP in rod cytoplasm and closing the cGMP gated channel. To terminate the phototransduction, Rho* is phosphorylated by Grk1 and the subsequent binding of Arr. (B) Schematic showing a cell responding to mechanical force. The actin cell skeleton is connected to the ECM and Vcl, and the focal adhesion is formed. The focal adhesion can regulate cellular shape and motility. Focal adhesion kinase is responsible for the binding of integrin-associated protein, such as paxillin and Scr. Scr can activate the expression of downstream genes through the PI3K signaling pathway. Rho, rhodopsin; Gt, transducing; Arr, arrestin; ECM, extracellular matrix.