Comparative phylogenomic analyses of teleost fish Hox gene clusters: lessons from the cichlid fish Astatotilapia burtoni: comment

Abstract

A reanalysis of the sequences reported by Hoegg et al has highlighted the presence of a putative HoxC1a gene in Astatotilapia burtoni. We discuss the evolutionary history of the HoxC1a gene in the teleost fish lineages and suggest that HoxC1a gene was lost twice independently in the Neoteleosts. This comment points out that combining several gene-finding methods and a Hox-dedicated program can improve the identification of Hox genes.

Figure 1

Phylogenetic tree of Paralogous group 1 in selected vertebrates. Phylogenetic tree reconstructions were conducted with homeodomain sequences as in [2]. The represented tree is obtained by bayesian inference (BI) using MrBayes [11] [12]. Rooting is arbitrary. The first numbers above the internal branches are posterior probabilities obtained by BI. The second numbers correspond to bootstrap values produced by the program PHYML of maximum-likelihood (ML) tree reconstruction [13]. Only statistical support values > 50 for at least one of the methods used (ML or BI) are shown. Marginal probabilities at each internal branches were taken as a measure of statistical support. All the alignements and the trees are available upon request. Abbreviations: LATME: Latimeria menadoensis, BRARE: Danio rerio, ASTBU: Astatotilapia burtoni, GASAC: Gasterosteus aculeatus, fox: Fundulus heteroclitus, ORYLA: Oryzia latipes.

Figure 2

Overview of HoxC1a content in teleost species and gene loss events mapped on a phylogeny. HoxC1a genes are depicted with stars. Dashed lines indicate that corresponding species were not reported in [1] and their position in the phylogeny is hypothetic.