Phylogenetic diversification of the globin gene superfamily in chordates

Abstract

Phylogenetic reconstructions provide a means of inferring the branching relationships among members of multigene families that have diversified via successive rounds of gene duplication and divergence. Such reconstructions can illuminate the pathways by which particular expression patterns and protein functions evolved. For example, phylogenetic analyses can reveal cases in which similar expression patterns or functional properties evolved independently in different lineages, either through convergence, parallelism, or evolutionary reversals. The purpose of this article is to provide a robust phylogenetic framework for interpreting experimental data and for generating hypotheses about the functional evolution of globin proteins in chordate animals. To do this, we present a consensus phylogeny of the chordate globin gene superfamily. We document the relative roles of gene duplication and whole-genome duplication in fueling the functional diversification of vertebrate globins, and we unravel patterns of shared ancestry among globin genes from representatives of the three chordate subphyla (Craniata, Urochordata, and Cephalochordata). Our results demonstrate the value of integrating phylogenetic analyses with genomic analyses of conserved synteny to infer the duplicative origins and evolutionary histories of globin genes. We also discuss a number of case studies that illustrate the importance of phylogenetic information when making inferences about the evolution of globin gene expression and protein function. Finally, we discuss why the globin gene superfamily presents special challenges for phylogenetic analysis, and we describe methodological approaches that can be used to meet those challenges.

Figure 1

Maximum likelihood phylogram describing relationships among globin genes from representative chordates: 11 jawed vertebrates (Gnathostomata), 3 jawless fishes (Cyclostomata), the sea squirt (Ciona intestinalis [Urochordata]) and amphioxus (Branchiostoma floridae [Cephalochordata]). Numbers above the nodes correspond to maximum likelihood bootstrap support values, and those below the nodes correspond to Bayesian posterior probabilities. The inset tree depicts the organismal phylogeny and the timing of two successive whole-genome duplications (the “1R” and “2R” duplications) in the stem lineage of vertebrates.

Figure 2

Graphical depiction of gene duplicates that are shared between the three globin-defined paralogons (Cygb, Mb, and Hb) and the “Gb⁻” paralogon in the human genome. There are seven 4:1 gene families that unite the 4th paralogon with the Cygb, Mb, and Hb paralogons, there are seven 3:1 gene families that unite the Gb⁻ paralogon with two of the three globin-defined paralogons, and there are four 2:1 gene families that unite the Gb⁻ paralogon with a single globin-defined paralogon. On each chromosome, annotated genes are depicted as grey bars. The “missing” globin gene on the Gb⁻ paralogon is denoted by an “X”. The shared paralogs are depicted in colinear arrays for display purposes only, as there is substantial variation in gene order among the four paralogons. For clarity of presentation, genes that are not shared between the Gb⁻ paralogon and any of the three globin-defined paralogons are not shown. In the human genome, the Gb⁻ paralogon on Chromosome 19 shares multiple gene duplicates with fragments of the Hb paralogon on Chromosomes 16 and 7.

Figure 3

Maximum likelihood phylogenies of representative 4:1 gene families that unite the Cygb, Mb, Hb, and Gb⁻ paralogons. Individual members of the CACNG, Grin2, KCNJ, and MYH gene families (panels A-D, respectively) are located on each of the four globin-defined paralogons (see Fig. 2 for their chromosomal locations in the human genome). As the tree topologies indicate, paralogous members of the same gene family always form a monophyletic group relative to the putative ortholog in non-vertebrate chordates (amphioxus or sea squirt). In each of the four maximum likelihood trees, bootstrap support values are shown for the node uniting all vertebrate-specific gene as a monophyletic group. These phylogenies (and those for many other globin-linked gene duplicates; Hoffmann et al. 2010a) are consistent with the genome-duplication hypothesis, and indicate that each of the gene families diversified prior to the divergence between tetrapods and teleost fish.

Figure 4

Cladogram describing phylogenetic relationships among chordate globins. The products of whole-genome duplications (the 1R and 2R duplications) are indicated in the clade of vertebrate-specific globins.