Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth

Abstract

Understanding the genetic basis of adaptation is one of the main enigmas of evolutionary biology. Among vertebrates, hemoglobin has been well documented as a key trait for adaptation to different environments. Here, we investigate the role of hemoglobins in adaptation to ocean depth in the diverse teleost order Gadiformes, with species distributed at a wide range of depths varying in temperature, hydrostatic pressure and oxygen levels. Using genomic data we characterized the full hemoglobin (Hb) gene repertoire for subset of species within this lineage. We discovered a correlation between expanded numbers of Hb genes and ocean depth, with the highest numbers in species occupying shallower, epipelagic regions. Moreover, we demonstrate that the Hb genes have functionally diverged through diversifying selection. Our results suggest that the more variable environment in shallower water has led to selection for a larger Hb gene repertoire and that Hbs have a key role in adaptive processes in marine environments.

Figure 1

The repertoire of hemoglobin genes in the Gadiformes. The number of Hbs in 27 species of Gadiformes, as well as three outgroup species from Stylephoriformes, Zeiformes and Percopsiformes, are mapped onto a time-calibrated molecular phylogeny. This phylogeny is part of a larger teleost phylogeny presented in ref. . α- and β-globin genes are indicated by boxes. Some species have more than one copy of a gene, which is indicated by a number. αx and βx refer to α- and β genes that are not 1:1 orthologs to the gadiform Hb genes. The ancestral Hb copy number with the highest likelihood is indicated at nodes where there has been an evolutionary change, as well as any ambiguity (Supplementary Fig. 1). Time is given in million years. Fish illustrations drawn by Geir Holm are reprinted with permission from ref. .

Figure 2

Phylogenetic relationships of α-globin genes. ML phylogeny of α-globin genes from 36 species of teleosts, and western clawed frog (Xenopus tropicalis) as the outgroup species. Numbers on nodes show bootstrap values and Bayesian posterior probabilities where topology is concordant, -- denotes support lower than 50/0.50. Sequences are colored according to timing of expression^, ; embryonic (red), adult (blue), embryonic and adult (purple) and unknown (black). For each gadiform α-globin gene the phylogenetic tree is shown separately. Some branches are shortened for convenience, which is indicated by gaps.

Figure 3

Phylogenetic relationships among β-globin genes. ML phylogeny of β-globin genes from 36 species of teleosts, and western clawed frog (Xenopus tropicalis) as the outgroup species. Numbers on nodes show bootstrap values and Bayesian posterior probabilities where topology is concordant, -- denotes support lower than 50/0.50. Sequences are colored according to timing of expression^, ; embryonic (red), adult (blue) and unknown (black). For each gadiform β-globin gene the phylogenetic tree is shown separately. Lineage specific duplications of β2 are indicated by red stars. Some branches are shortened for convenience, indicated by gaps.

Figure 4

Sites under diversifying selection at the surface of hemoglobin tetramers. In silico models of the hemoglobin tetramers, based on sequences from Atlantic cod (Gadus morhua). α sequences are highlighted in pink, and β sequences in orange, with respective gene names shown. Three different tests (indicated by symbols according to the key) were used to test for diversifying selection; REL, FEL and SLAC, respectively. Arrows point to sites under diversifying selection, which are also highlighted in green.