For many genes, ray-finned fish (Actinopterygii) have two paralogous copies, where only one ortholog is present in tetrapods. The discovery of an additional, almost-complete set of Hox clusters in teleosts (zebrafish, pufferfish, medaka, and cichlid) but not in basal actinopterygian lineages ( Polypterus) led to the formulation of the fish-specific genome duplication hypothesis. The phylogenetic timing of this genome duplication during the evolution of ray-finned fish is unknown, since only a few species of basal fish lineages have been investigated so far. In this study, three nuclear genes ( fzd8, sox11, tyrosinase) were sequenced from sturgeons (Acipenseriformes), gars (Semionotiformes), bony tongues (Osteoglossomorpha), and a tenpounder (Elopomorpha). For these three genes, two copies have been described previously teleosts (e.g., zebrafish, pufferfish), but only one orthologous copy is found in tetrapods. Individual gene trees for these three genes and a concatenated dataset support the hypothesis that the fish-specific genome duplication event took place after the split of the Acipenseriformes and the Semionotiformes from the lineage leading to teleost fish but before the divergence of Osteoglossiformes. If these three genes were duplicated during the proposed fish-specific genome duplication event, then this event separates the species-poor early-branching lineages from the species-rich teleost lineage. The additional number of genes resulting from this event might have facilitated the evolutionary radiation and the phenotypic diversification of the teleost fish.

No abstract

The family Microhylidae has a large circumtropic distribution and contains about 400 species in a highly subdivided taxonomy. Relationships among its constituent taxa remained controversial due to homoplasy in morphological characters, resulting in conXicting phylogenetic hypotheses. A phylogeny based on four nuclear genes (rag-1, rag-2, tyrosinase, BDNF) and one mitochondrial gene (CO1) of representatives of all currently recognized subfamilies uncovers a basal polytomy between several subfamilial clades. A sister group relationship between the cophylines and scaphiophrynines is resolved with moderate support, which unites these endemic Malagasy taxa for the Wrst time. The American members of the subfamily Microhylinae are resolved to form a clade entirely separate from the Asian members of that subfamily. Otophryne is excluded from the subfamily Microhylinae, and resolved as a basal taxon. The placement of the Asian dyscophine Calluella nested within the Asian Microhyline clade rather than with the genus Dyscophus is corroborated by our data. Bayesian estimates of the divergence time of extant Microhylidae (47-90 Mya) and among the subclades within the family are discussed in frameworks of alternative possible biogeographic scenarios.

Phylogenetic relationships among major clades of anuran amphibians were studied using partial sequences of three nuclear protein coding genes, Rag-1, Rag-2, and rhodopsin in 26 frog species from 18 families. The concatenated nuclear data set comprised 2,616 nucleotides and was complemented by sequences of the mitochondrial 12S and 16S rRNA genes for analyses of evolutionary rates. Separate and combined analyses of the nuclear markers supported the monophyly of modern frogs (Neobatrachia), whereas they did not provide support for the monophyly of archaic frog lineages (Archaeobatrachia), contrary to previous studies based on mitochondrial data. The Neobatrachia contain two well supported clades that correspond to the subfamilies Ranoidea (Hyperoliidae, Mantellidae, Microhylidae, Ranidae, and Rhacophoridae) and Hyloidea (Bufonidae, Hylidae, Leptodactylidae, and Pseudidae). Two other families (Heleophrynidae and Sooglossidae) occupied basal positions and probably represent ancient relicts within the Neobatrachia, which had been less clearly indicated by previous mitochondrial analyses. Branch lengths of archaeobatrachians were consistently shorter in all separate analyses, and nonparametric rate smoothing indicated accelerated substitution rates in neobatrachians. However, relative rate tests confirmed this tendency only for mitochondrial genes. In contrast, nuclear gene sequences from our study and from an additional GenBank survey showed no clear phylogenetic trends in terms of differences in rates of molecular evolution. Maximum likelihood trees based on Rag-1 and using only one neobatrachian and one archaeobatrachian sequence, respectively, even had longer archaeobatrachian branches averaged over all pairwise comparisons. More data are necessary to understand the significance of a possibly general assignation of short branches to basal and species-poor taxa by tree-reconstruction algorithms.

BackgroundTeleost fish have seven paralogous clusters of Hox genes stemming from two complete genome duplications early in vertebrate evolution, and an additional genome duplication during the evolution of ray-finned fish, followed by the secondary loss of one cluster. Gene duplications on the one hand, and the evolution of regulatory sequences on the other, are thought to be among the most important mechanisms for the evolution of new gene functions. Cichlid fish, the largest family of vertebrates with about 2500 species, are famous examples of speciation and morphological diversity. Since this diversity could be based on regulatory changes, we chose to study the coding as well as putative regulatory regions of their Hox clusters within a comparative genomic framework.ResultsWe sequenced and characterized all seven Hox clusters of Astatotilapia burtoni, a haplochromine cichlid fish. Comparative analyses with data from other teleost fish such as zebrafish, two species of pufferfish, stickleback and medaka were performed. We traced losses of genes and microRNAs of Hox clusters, the medaka lineage seems to have lost more microRNAs than the other fish lineages. We found that each teleost genome studied so far has a unique set of Hox genes. The hoxb7a gene was lost independently several times during teleost evolution, the most recent event being within the radiation of East African cichlid fish. The conserved non-coding sequences (CNS) encompass a surprisingly large part of the clusters, especially in the HoxAa, HoxCa, and HoxDa clusters. Across all clusters, we observe a trend towards an increased content of CNS towards the anterior end.ConclusionThe gene content of Hox clusters in teleost fishes is more variable than expected, with each species studied so far having a different set. Although the highest loss rate of Hox genes occurred immediately after whole genome duplications, our analyses showed that gene loss continued and is still ongoing in all teleost lineages. Along with the gene content, the CNS content also varies across clusters. The excess of CNS at the anterior end of clusters could imply a stronger conservation of anterior expression patters than those towards more posterior areas of the embryo.