Simone Hoegg

University of Konstanz

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Axel Meyer

University of Konstanz

Miguel Vences

Technische Universität Braunschweig

Henner Brinkmann

Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures

Dirk Steinke

University of Guelph

Frank Glaw

Bavarian State Collection of Zoology

Arie van der Meijden

Universidade do Porto

Steven F. Perry

University of Ottawa

P Borst

Bethesda University

Jeroen Raes

Rega Institute for Medical Research

Matthew J. Kourakis

University of California, Santa Barbara

Cooperative Institutions

Pasadena City College

Bethesda University

Science Oxford

Universidad de Salamanca

Seattle University

United States Department of Justice

University of Cambridge

Advisory Board Company (United States)

University of San Francisco

Yale University

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Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins

Molecular Phylogenetics and Evolution (2007)

Arie van der Meijden Miguel Vences Simone Hoegg Renaud Boistel Alan Channing

Subfamily

Sister group

10.1016/j.ympev.2007.02.008

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Citations (147)

Editorial board and contents

Trends in Genetics (2005)

Simone Hoegg Axel Meyer Sharyl L. Wong Lan Zhang Frederick P. Roth

Editorial board

10.1016/s0168-9525(05)00176-9

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Citations (0)

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

Molecular Phylogenetics and Evolution (2005)

Arie van der Meijden Miguel Vences Simone Hoegg Axel Meyer

Endemism

10.1016/j.ympev.2005.05.001

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Citations (88)

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

BMC Genomics (2007)

Simone Hoegg Jeffrey L. Boore Jennifer V. Kuehl Axel Meyer

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.We 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.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.

Cichlid

Lineage (genetic)

10.1186/1471-2164-8-317

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Citations (86)

Hox clusters as models for vertebrate genome evolution

Trends in Genetics (2005)

Simone Hoegg Axel Meyer

Lineage (genetic)

10.1016/j.tig.2005.06.004

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Citations (193)

Discovery of a new basal relict lineage of Madagascan frogs and its implications for mantellid evolution

Zootaxa (2006)

Frank Glaw Simone Hoegg Miguel Vences

Frogs of the subfamily Mantellinae (Amphibia: Anura: Mantellidae) are a species-rich and diverse lineage endemic to the Madagascan region. The major synapomorphy of this clade is a derived reproductive mode including an unusual mating behaviour (loss of strong mating amplexus, egg deposition outside of water) and associated morphological adaptations (evolution of femoral glands, loss of nuptial pads). However, the evolutionary steps towards this unique character complex remain obscure. We here describe a recently discovered new frog, Tsingymantis antitra gen. nov., sp. nov. from the moderately dry karstic massif Tsingy de Ankarana in northern Madagascar. The new species is not referable to any existing genus or species groups. A phylogenetic analysis, based on DNA sequences of four mitochondrial genes (12S and 16S rRNA, tRNAVal, cytochrome b) and one nuclear gene (rhodopsin) placed Tsingymantis without significant support as sister taxon of the Mantellinae which was found to be a well-defined monophyletic group (100% Bayesian and 99% bootstrap support). The position of Tsingymantis as the most basal clade of the Mantellinae is in agreement with several morphological and osteological characters, suggesting that this subfamily including Tsingymantis may be a monophyletic group whereas the Boophinae could represent the most basal clade of the Mantellidae. We therefore include Tsingymantis in the Mantellinae in a preliminary way, pending further study. In contrast to the large majority of recent mantellid species which are adapted to humid rainforests, the most basal clades of the three subfamilies show adaptations to relatively dry conditions, indicating that the climate during the early radiation of mantellids (probably in the Eocene) may have been drier than in recent times.

Monophyly

Synapomorphy

Lineage (genetic)

Sister group

Subfamily

10.11646/zootaxa.1334.1.2

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Citations (52)

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

BMC Evolutionary Biology (2007)

Simone Hoegg Axel Meyer

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 KCNA gene clusters. KCNA 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 KNCA clusters are of approximately the same age as the Hox 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 KCNA clusters, as too few conserved putative regulatory elements are retained.We obtained KCNA 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 KCNA gene in vertebrates (KCNA7). Sistergroup relationships of KCNA1/2 and KCNA3/6 support that a large-scale duplication gave rise to the two clusters found in the genome of tetrapods. We analyzed the intergenic regions of KCNA 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.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 KCNA clusters have been changed together with their regulatory sites.

Concerted evolution

Intergenic region

Gene cluster

10.1186/1471-2148-7-139

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Citations (26)

Discovery of a new basal relict lineage of Madagascan frogs and its implications for mantellid evolution

Zenodo (CERN European Organization for Nuclear Research) (2006)

Frank Glaw Simone Hoegg Miguel Vences

Lineage (genetic)

Basal (medicine)

10.5281/zenodo.174270

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Citations (0)

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

BMC Genomics (2007)

Nicol Siegel Simone Hoegg Walter Salzburger Ingo Braasch Axel Meyer

Abstract 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.

Synteny

Gene cluster

Lineage (genetic)

Comparative Genomics

10.1186/1471-2164-8-312

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Citations (50)

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

BMC Biology (2006)

Dirk Steinke Simone Hoegg Henner Brinkmann Axel Meyer

Abstract 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.

Deuterostome

Lineage (genetic)

Chordate

Functional divergence

10.1186/1741-7007-4-16

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Citations (115)