Phylogenomic analyses of KCNA gene clusters in vertebrates: why do gene clusters stay intact?

<p>Abstract</p> <p>Background</p> <p>Gene clusters are of interest for the understanding of genome evolution since they provide insight in large-scale duplications events as well as patterns of individual gene losses. Vertebrates tend to have multiple copies of gene clusters that typically are only single clusters or are not present at all in genomes of invertebrates. We investigated the genomic architecture and conserved non-coding sequences of vertebrate <it>KCNA </it>gene clusters. <it>KCNA </it>genes encode shaker-related voltage-gated potassium channels and are arranged in two three-gene clusters in tetrapods. Teleost fish are found to possess four clusters. The two tetrapod <it>KNCA </it>clusters are of approximately the same age as the <it>Hox </it>gene clusters that arose through duplications early in vertebrate evolution. For some genes, their conserved retention and arrangement in clusters are thought to be related to regulatory elements in the intergenic regions, which might prevent rearrangements and gene loss. Interestingly, this hypothesis does not appear to apply to the <it>KCNA </it>clusters, as too few conserved putative regulatory elements are retained.</p> <p>Results</p> <p>We obtained <it>KCNA </it>coding sequences from basal ray-finned fishes (sturgeon, gar, bowfin) and confirmed that the duplication of these genes is specific to teleosts and therefore consistent with the fish-specific genome duplication (FSGD). Phylogenetic analyses of the genes suggest a basal position of the only intron containing <it>KCNA </it>gene in vertebrates (<it>KCNA7</it>). Sistergroup relationships of <it>KCNA1/2 </it>and <it>KCNA3/6 </it>support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of <it>KCNA </it>clusters in vertebrates and found that there are only a few conserved sequences shared between tetrapods and teleosts or between paralogous clusters. The orthologous teleost clusters, however, show sequence conservation in these regions.</p> <p>Conclusion</p> <p>The lack of overall conserved sequences in intergenic regions suggests that there are either other processes than regulatory evolution leading to cluster conservation or that the ancestral regulatory relationships among genes in <it>KCNA </it>clusters have been changed together with their regulatory sites.</p

Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates

BACKGROUND: Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution. RESULTS: We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found. CONCLUSION: The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function

Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

BACKGROUND: The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. RESULTS: We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. CONCLUSION: There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular - but possibly clusters of genes more generally - might be linked to the presence of promoter, enhancer or inhibitor motifs that serve to regulate more than just one gene. Therefore, deletions, inversions or relocations of individual genes could destroy the regulation of the clustered genes in this region. The existence of such a regulation network might explain the evolutionary conservation of gene order and orientation over the course of hundreds of millions of years of vertebrate evolution. Another possible explanation for the highly conserved gene order might be the existence of a regulator not located immediately next to its corresponding gene but further away since a relocation or inversion would possibly interrupt this interaction. Different ParaHox clusters were found to have experienced differential gene loss in teleosts. Yet the complete set of these homeobox genes was maintained, albeit distributed over almost twice the number of chromosomes. Selection due to dosage effects and/or stoichiometric disturbance might act more strongly to maintain a modal number of homeobox genes (and possibly transcription factors more generally) per genome, yet permit the accumulation of other (non regulatory) genes associated with these homeobox gene clusters

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

<p>Abstract</p> <p>Background</p> <p>Teleost 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.</p> <p>Results</p> <p>We sequenced and characterized all seven Hox clusters of <it>Astatotilapia burtoni</it>, 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 <it>hoxb7a </it>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.</p> <p>Conclusion</p> <p>The 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.</p

Hox clusters as models for vertebrate genome evolution

The surprising variation in the number of Hox clusters and the genomic architecture within vertebrate lineages, especially within the ray-finned fish, reflects a history of duplications and subsequent lineage-specific gene loss. Recent research on the evolution of conserved non-coding sequences (CNS) in Hox clusters promises to reveal interesting results for functional and phenotypic diversification

Tsingymantis antitra Glaw, Hoegg & Vences, 2006, sp. nov.

Tsingymantis antitra sp. nov. Holotype. ZSM 304 / 2004 (fieldnumber FGZC 589), collected on 27 February 2004 below the "Point de Vue Petit Tsingy", 12 ° 57 ' 25 ''S, 49 °07'06''E, 117 m alt, Ankarana Special Reserve, northern Madagascar, by F. Glaw, M. Puente & R. D. Randrianiaina. Paratypes. ZFMK 84436 (originally ZSM 305 / 2004), same data as holotype; ZSM 769 / 2003 (fieldnumber FG/MV 2002 -0577), cleared and stained specimen, collected on 12 February 2003, below "Campement des Anglais" (now called Campement Anilotra), Ankarana Special Reserve, northern Madagascar, by F. Glaw, R. D. Randrianiaina & A. Razafimanantsoa; UADBA 24766 (fieldnumber FGZC 531), collected on 25 February 2004 close to the "Grotte des Chauve-souris", 12 ° 57 'S, 49 °07'E, ca. 50 m alt, Ankarana Special Reserve, northern Madagascar, by F. Glaw, M. Puente & R. D. Randrianiaina. Diagnosis. A large species of mantellid frogs representing an isolated and basal lineage within the family, based on a molecular analysis of mitochondrial and nuclear genes (Fig. 3). Differs from all other mantellid genera and subgenera as outlined in the diagnosis of the genus Tsingymantis. It differs from all other large mantelline and laliostomine species that reach a SVL of more than 60 mm as follows: From Mantidactylus mocquardi, M. grandidieri, M. guttulatus, M. ambohimitombi, Boehmantis microtympanum, and Aglyptodactylus madagascariensis by largely connected lateral metatarsalia (versus separated), from Aglyptodactylus laticeps and Laliostoma labrosum by distinctly enlarged tips of fingers and toes, by the presence of a complete circummarginal groove on pads of fingers and toes, and by having the first finger shorter than the second. Description of the holotype. Adult female (with oocytes in the body cavity), in good state of preservation but with a midventral slit. SVL 67.1 mm, for further measurements see table 1. Body slender; head wider than body; snout approximately rounded in dorsal and lateral views, nostrils directed laterally, protuberant, much nearer to tip of snout than to eye; canthus rostralis distinct, straight; loreal region concave; tympanum very distinct, rounded, 76 % of eye diameter; supratympanic fold distinct, curved; tongue was ovoid and bifid posteriorly (part of the tongue was removed as DNA sample); vomerine teeth present in two groups, maxillary teeth present; choanae relatively rounded. Arms slender, subarticular tubercles single; fingers without webbing; relative length of fingers 1 <2 <4 <3; finger disks distinctly enlarged; nuptial pads absent. Hind limbs slender; tibiotarsal articulation reaches the eye when the hind limb is adpressed along the body; lateral metatarsalia largely connected; inner metatarsal tubercle distinct, outer metatarsal tubercle absent; webbing formula (according to Blommers-Schlösser 1979) between toes 1 (1), 2 i (1), 2 e(0.5), 3 i (1.5), 3 e(1), 4 i (2.5), 4 e(2), 5 (1); relative length of toes 1 <2 <3 <5 <4. Skin on the upper surface smooth, without folds or ridges. No distinct enlarged tubercles in the cloacal region; ventral skin smooth, finely granular on the shanks. No femoral glands. Colouration of the holotype. After 1.5 years in preservative, back blackish with indistinct dark brown reticulations and a few small greyish spots above the insertion of the left arm. Upper surfaces of arms and legs dark brown with indistinct black markings. Flanks lighter brown than back, although there is no distinct colour border between flanks and back. Tympanum light brown in periphery, darker brown in center. Ventrally dirty cream-whitish on belly, with fine indistinct mottling. Throat brown, chest and ventral surfaces of arms light brown, ventral surface of hindlegs yellowish in the center becoming darker brown to periphery. Ventral side of lower leg and tarsus dark brown, foot and webbing brown. The dorsal ground colour in life was brown with violet shade and with olive green spots (Fig. 1). The iris was silvery-grey with a brownish horizontal streak and a bluish iris periphery. The ventral surface was pinkish to brown (Fig. 2). Variation (see table 1 for measurements). The ZFMK and ZSM paratypes are very similar to the holotype in size and morphology. The colouration of ZFMK 84436 is generally similar to that of the holotype, but sligthly lighter, that of ZSM 769 / 2003 (assessed before clearing and staining) distinctly lighter, especially on the ventral side. All three specimens have pigmented oocytes in the body cavity although they are relatively small in size and numbers. The UADBA paratype is similar to the other specimens in size and colour, but was not available for detailed studies. Osteological features. A number of skeletal characters known to be relevant in mantellid systematics were assessed on the cleared and stained paratype ZSM 769 / 2003. Maxillary and vomerine teeth present. Omosternum forked, the greatest space between the arms being about two times the width of one arm, sternum unforked, bony part of sternum longer than that of omosternum. Hyoid with a distinct anterolateral and a small posterolateral process. Intercalary element present between ultimate and penultimate phalanges of all fingers and toes. Terminal phalanges distinctly Y-shaped, with rather broad and posteriorly serrated arms. Three free distal tarsals, the third tarsal being small. Etymology. The specific name is derived from the Malagasy word " antitra " (meaning old) and refers to the presumed old age of the Tsingymantis lineage. The name is considered as an invariable noun standing in apposition to the genus name. Habitat and natural history. The Ankarana reserve consists mainly of bizarre, eroded tsingy limestone formations and moderately dry forest areas. It is crossed by four rivers and includes more than 100 km inventorized subterraneous passages and caves. The climate of Ankarana is "dry tropical" with a long dry season between May and December. The wettest months are January, February, and March. There are about 86–92 rainy days per year. The hottest month is March (36.2°C) and the coldest month is June (13.5°C) (http://www.parcs-madagascar.com/ankarana/index.htm, as of 20 August 2005). All four specimens of Tsingymantis antitra were exclusively found at night and associated with tsingy formations. ZSM 769 / 2003 was found along a small brook, whereas the other three specimens were not found associated with open waters (although not far from dry riverbeds). UADBA 24766 was sitting on the ground close to the entrance of a big cave. The two other specimens were found on the top of the tsingy limestone and in a cave of ca. 1 m depth in tsingy, respectively, both close to a dry riverbed. A further individual was photographed along a brook (Paul Freed, pers. comm.). However, it remains unclear if the species is mainly distributed along streams or widespread in the tsingy formations of Ankarana. No unidentified frog calls were heard during the surveys and only small oocytes were found in the collected females, indicating that they were reproductively quiescent when collected. The period and mode of reproduction remain entirely unknown and at current no indications of cave breeding are known. ZSM 769 / 2003 had remains of a large orthopteran in the stomach. Distribution and conservation status. Tsingymantis antitra is only known from the Ankarana Special Reserve in northern Madagascar which has a total surface of 182 km 2 (Hawkins et al. 1990). The types of Tsingymantis antitra are from two areas in the Ankarana reserve, around the "Petit Tsingy" and around the "Campment des Anglais". The specimen photographed by P. Freed was discovered in a third area close to the "Campement des Americains" (now called "Campement d'Andrafiabe") in the west of the reserve, indicating that the species has a wider distribution in the central part of Ankarana. Connecting these three localities to a triangle allows to estimate the known extent of occurrence (see http://www.redlist.org/info/categories_criteria 2001 for definition) for this species as much smaller than 100 km 2 (this approach was also used to calculate the extent of occurrence of the other Malagasy amphibian species by the Global Amphibian Assessment, see Andreone et al. 2005). The actual range is certainly larger, but since the tsingy-dependent fauna and flora of Ankarana includes many presumed local endemics (e.g., the snake Alluaudina mocquardi) it appears likely that T. antitra is endemic to this reserve as well although it cannot be excluded that the species also occurs in other remote tsingy formations (e. g. Tsingy de Namoroka or Tsingy de Bemaraha) or other karstic areas (e. g. Analamera reserve). Due to its small assumed extent of occurrence (<182 km 2), its very small known extent of occurrence (<100 km 2), its very small known area of occupancy (<10 km 2), its apparent rareness (only four specimens have been found), and the fact that it represents a very ancient relict lineage we consider Tsingymantis antitra as "endangered" although its habitat currently seems to be relatively well protected. Molecular phylogenetic relationships. The tree shown in Fig. 3 includes for the first time representatives of all known lineages (genera, subgenera, and species groups) of mantellid frogs. Bayesian analysis of the molecular data yielded a tree (Fig. 3) with high support for most nodes. Especially the deeper nodes received much higher support than in the tree shown in Glaw & Vences (2006) which was obtained from less a complete data matrix. Maximum Bayesian support (100 %) was found for all genera as defined in Glaw & Vences (2006), and for many subgenera and species groups. The included species of the Mantellinae (to the exclusion of Tsingymantis) were highly supported as monophyletic group as well, with 100 % Bayesian and 99 % bootstrap support, and the same values were obtained for the species of the Boophinae. However, the relationships between the major mantellid lineages were not significantly resolved. The analysis placed Tsingymantis sister to the Mantellinae, and the Laliostominae (Aglyptodactylus and Laliostoma) sister to the Tsingymantis / Mantellinae clade. The Boophinae (genus Boophis) occupied the most basal position. However, none of these groupings received Bayesian support of 95 % or higher, or bootstrap support of 70 % or higher, and the molecular data can therefore merely seen as weak indication of possible relationships among the major mantellid lineages. In any case, Tsingymantis has a very isolated position.Published as part of Glaw, Frank, Hoegg, Simone & Vences, Miguel, 2006, Discovery of a new basal relict lineage of Madagascan frogs and its implications for mantellid evolution, pp. 27-43 in Zootaxa 1334 on pages 31-36, DOI: 10.5281/zenodo.17427

Tsingymantis Glaw, Hoegg & Vences, 2006, gen. nov.

Tsingymantis gen. nov. Type species and only included species. Tsingymantis antitra sp. nov. Etymology. Derived from "tsingy", the Malagasy word for eroded karstic limestone formations and the Greek word mantis = treefrog (see Vences et al. 1999 for the derivation of mantis). The genus name refers to the habitat, the tsingy formations of Ankarana. The gender of this genus is masculine. Diagnosis. Large-sized species (female snout-vent length 66–67 mm) with a large tympanum (66–76 % of eye diameter), toe 5> 3, males unknown. Relatively little webbing between toes. No webbing between fingers. Lateral metatarsalia largely connected. Inner metatarsal tubercle very distinct, outer metatarsal tubercle absent. Finger tips strongly enlarged. Finger and toe pads with a complete circummarginal groove. First finger slightly shorter than second finger. Tibiotarsal articulation reaches the eye when the hind limb is adpressed along the body. Femoral glands not recognizable in females from external view. Tibial glands absent. Tongue bifid. For osteological characters see below. Habits terrestrial in tsingy formations. Activity nocturnal. Eggs pigmented (verified by dissection). Tsingymantis gen. nov. does not show closer overall similarity to any other mantellid genus or species. Despite the absence of data on males, sexual dimorphism, and reproductive mode, there are still sufficient external characters to distinguish Tsingymantis from all other mantellid genera: Tsingymantis differs from the genus Boophis by a forked omosternum, largely connected metatarsalia, less webbing between toes and by general dissimilarity with any Boophis species; from Aglyptodactylus and Laliostoma by distinctly enlarged tips of fingers and toes, by the presence of a complete circummarginal groove on pads of fingers and toes, and by having the first finger shorter than the second; from Mantella (SVL 18–31 mm) and Wakea (SVL 11–16 mm) by much larger size, presence of maxillary teeth, and distinctly enlarged terminal finger disks; from Boehmantis and Mantidactylus sensu Glaw & Vences (2006), including the subgenera Brygoomantis, Chonomantis, Hylobatrachus, Maitsomantis, Mantidactylus, and Ochthomantis, by largely connected metatarsalia and in addition from most of these species by the absence of femoral glands in females and by less developed webbing between toes; from Blommersia (SVL 15–27 mm, tympanum/eye 35–55 %) by much larger size and larger relative tympanum size; from all Guibemantis (tympanum/eye up to 64 %) by larger relative tympanum size, furthermore from the subgenus Guibemantis by largely connected metatarsalia and less webbing between the toes, and from the subgenus Pandanusicola (SVL 22–38 mm) by much larger size and very different habits; from Spinomantis (SVL 22–60 mm, tympanum/eye 33–60 %) by larger body size and larger relative tympanum size; and from all Gephyromantis (SVL 20–50 mm, tympanum/eye 30–67 %), including the subgenera Duboimantis, Gephyromantis, Laurentomantis, Phylacomantis, and Vatomantis by larger size and a relatively larger tympanum. In addition, Tsingymantis differs from most mantelline species by the following characters: bony part of the sternum longer than that of the omosternum, outer metatarsal tubercle absent, and toe 5 clearly longer than toe 3 (see Glaw & Vences 1994: 122–125). Tsingymantis is the only clade in the subfamily Mantellinae that is unknown from the rain forest areas (including the central high plateau) of Madagascar (where almost all mantelline species occur, except Mantella expectata, M. viridis, and Gephyromantis corvus) and is only known from a very seasonal and moderately dry habitat. Justification. All hitherto known mantellid clades, including 164 described and many undescribed species, can all clearly be assigned to one of the three subfamilies Mantellinae, Laliostominae, or Boophinae based on their sequences of mitochondrial and nuclear genes, and strongly supported by high bootstrap values (see below and unpublished data). A clear attribution of all mantellid lineages to one of these three subfamilies is also possible based solely on morphological data (see Glaw & Vences 2006). In contrast, the phylogenetic position of Tsingymantis antitra gen. nov. sp. nov. is not significantly resolved by the molecular (Fig. 3) and morphological data although a basal sister group relationships to all other mantellines is indicated by the available overall evidence, and we propose preliminary inclusion of the new genus in the subfamily Mantellinae. Regarding this highly isolated position, the justification of the new genus is evident, but the possibility that future studies will reveal that Tsingymantis represents a fourth major lineage (subfamily) of the Mantellidae cannot be ruled out at present.Published as part of Glaw, Frank, Hoegg, Simone & Vences, Miguel, 2006, Discovery of a new basal relict lineage of Madagascan frogs and its implications for mantellid evolution, pp. 27-43 in Zootaxa 1334 on pages 30-31, DOI: 10.5281/zenodo.17427

Phylogeny and comparative substitution rates of frogs inferredfrom sequences of three nuclear genes

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

Phylogenetic Timing of the Fish-Specific Genome Duplication Correlates with the Diversification of Teleost Fish

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 rayfinned 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 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 rayfinned 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

A previously unrecognized radiation of ranid frogs in Southern Africa revealed by nuclear and mitochondrial DNA sequences

In sub-Saharan Africa, amphibians are represented by a large number of endemic frog genera and species of incompletely clarified phylogenetic relationships. This applies especially to African frogs of the family Ranidae. We provide a molecular phylogenetic hypothesis for ranids, including 11 of the 12 African endemic genera. Analysis of nuclear (rag-1, rag-2, and rhodopsin genes) and mitochondrial markers (12S and 16S ribosomal RNA genes) provide evidence for an endemic clade of African genera of high morphological and ecological diversity thus far assigned to up to five diVerent subfamilies: Afrana, Cacosternum, Natalobatrachus, Pyxicephalus, Strongylopus, and Tomopterna. This clade has its highest species diversity in southern Africa, suggesting a possible biogeographic connection with the Cape Floral Region. Bayesian estimates of divergence times place the initial diversification of the southern African ranid clade at »62 85 million years ago, concurrent with the onset of the radiation of Afrotherian mammals. These and other African ranids (Conraua, Petropedetes, Phrynobatrachus, and Ptychadena) are placed basally within the Ranoidae with respect to the Eurasian groups, which suggests an African origin for this whole epifamily