Guido Fritzsch

University of Leipzig , Leipzig, Saxony, Germany

Are you Guido Fritzsch?

Claim your profile

Publications (24)47.07 Total impact

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.
    Molecular Phylogenetics and Evolution 05/2013; · 4.07 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.
    Molecular Phylogenetics and Evolution 09/2012; · 4.07 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The genome architecture and amino acid sequences of six new complete mitochondrial genomes were determined from representatives of Hemichordata (1), Ophiuroidea (3), Echinoidea (1) and Holothuroidea (1) and were analysed together with previously known sequences. Phylogenetic analyses recovered three lineages within echinoderms, Crinoidea, Ophiuroidea and a group comprising Holothuroidea, Echinoidea, and Asteroidea. In contrast to previous analyses of mitochondrial genomes the increased data set recovered the classical echinoderm phylogeny of Eleutherozoa and Echinozoa in Maximum Likelihood and Bayesian analyses using hemichordate out-group representatives. However, an inconsistent ramification appeared with vertebrate out-groups and in Maximum Parsimony and Neighbour Joining reconstructions. The basal (consensus) gene orders of all three lineages could be derived from a hypothetical ancestral crinoid gene order by one single rearrangement in each lineage. The genome architecture was highly conserved in Echinoidea, whereas the highest gene order differences and large amounts of unassigned sequences (UAS) were detected in Ophiuroidea, supporting a higher evolutionary rate than in any other echinoderm lineage. The variability in gene order and UAS regions in ophiuroid genomes suggest dominating rearrangement mechanisms by duplication events.
    Molecular Phylogenetics and Evolution 02/2010; 56(1):201-11. · 4.07 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A comprehensive analysis of the mitochondrial gene orders of all previously published and two novel Antedon mediterranea (Crinoidea) and Ophiura albida (Ophiuroidea) complete echinoderm mitochondrial genomes shows that all major types of rearrangement operations are necessary to explain the evolution of mitochondrial genomes. In addition to protein coding genes we include all tRNA genes as well as the control region in our analysis. Surprisingly, 7 of the 16 genomes published in the GenBank database contain misannotations, mostly unannotated tRNAs and/or mistakes in the orientation of tRNAs, which we have corrected here. Although the gene orders of mt genomes appear very different, only 8 events are necessary to explain the evolutionary history of echinoderms with the exception of the ophiuroids. Only two of these rearrangements are inversions, while we identify three tandem-duplication-random-loss events and three transpositions.
    Molecular Phylogenetics and Evolution 06/2008; 47(2):855-64. · 4.07 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Xenoturbella bocki has recently been identified as one of the most basal deuterostomes, although an even more basal phylogenetic position cannot be ruled out. Here we report on a polymerase chain reaction survey of partial Hox homeobox sequences of X. bocki. Surprisingly, we did not find evidence for more than five Hox genes, one clear labial/PG1 ortholog, one posterior gene most similar to the PG9/10 genes of Ambulacraria, and three central group genes whose precise assignment to a specific paralog group remains open. We furthermore report on a re-evaluation of the available published evidence of Hox genes in other basal deuterostomes.
    Journal of Experimental Zoology Part B Molecular and Developmental Evolution 06/2008; 310(3):278-84. · 2.12 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of "tree quality". In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/ .
    Algorithms for Molecular Biology 01/2008; · 1.61 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The systematic assessment of rate variations across large datasets requires a systematic approach for summarizing results from individual tests. Often, this is performed by coarse-graining the phylogeny to consider rate variations at the level of sub-claded. In a phylo-geographic setting, however, one is often more interested in other partitions of the data, and in an exploratory mode a pre-specified subdivision of the data is often undesirable. We propose here to arrange rate variation data as the partially ordered set defined by the significant test results.
    01/2008;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: We present the web-based program CREx for heuristically determining pairwise rearrangement events in unichromosomal genomes. CREx considers transpositions, reverse transpositions, reversals and tandem-duplication-random-loss (TDRL) events. It supports the user in finding parsimonious rearrangement scenarios given a phylogenetic hypothesis. CREx is based on common intervals, which reflect genes that appear consecutively in several of the input gene orders. AVAILABILITY: CREx is freely available at http://pacosy.informatik.uni-leipzig.de/crex
    Bioinformatics 12/2007; 23(21):2957-8. · 5.47 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The phylogenetic position of Xenoturbella bocki has been a matter of controversy since its description in 1949. We sequenced a second complete mitochondrial genome of this species and performed phylogenetic analyses based on the amino acid sequences of all 13 mitochondrial protein-coding genes and on its gene order. Our results confirm the deuterostome relationship of Xenoturbella. However, in contrast to a recently published study (Bourlat et al. in Nature 444:85-88, 2006), our data analysis suggests a more basal branching of Xenoturbella within the deuterostomes, rather than a sister-group relationship to the Ambulacraria (Hemichordata and Echinodermata).
    Theory in Biosciences 09/2007; 126(1):35-42. · 0.93 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Chromist algae including the Heterokontophyta are supposed to have evolved monophyletically by secondary endosymbiosis from a eukaryotic host cell that engulfed a eukaryotic red alga. The red algal endosymbiont was then reduced to a secondary plastid surrounded by four enveloping membranes. On the basis of the amoeboid marine alga Synchroma grande gen. et spec. nov., the Synchromophyceae are described here as a new class of Heterokontophyta. Their taxonomic position is characterized by 18S rRNA and rbcL gene phylogenies, morphology, and pigment composition. The so far unique feature of the Synchromophyceae is the occurrence of conspicuous chloroplast complexes representing multiplastidic red secondary endosymbionts. In these remarkable secondary endosymbionts, several primary chloroplasts are aggregated in a common periplastidial compartment and are collectively enveloped by an additional outer membrane pair. The discovery of this novel plastid morphology is highly relevant for research on algal evolution and is discussed in terms of the postulated monophyletic origin of Chromista.
    Protist 08/2007; 158(3):277-93. · 4.14 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: For the first time the complete mitochondrial genome was sequenced for a member of Lacertidae. Lacerta viridis viridis was sequenced in order to compare the phylogenetic relationships of this family to other reptilian lineages. Using the long-polymerase chain reaction (long PCR) we characterized a mitochondrial genome, 17,156 bp long showing a typical vertebrate pattern with 13 protein coding genes, 22 transfer RNAs (tRNA), two ribosomal RNAs (rRNA) and one major noncoding region. The noncoding region of L. v. viridis was characterized by a conspicuous 35 bp tandem repeat at its 5' terminus. A phylogenetic study including all currently available squamate mitochondrial sequences demonstrates the position of Lacertidae within a monophyletic squamate group. We obtained a narrow relationship of Lacertidae to Scincidae, Iguanidae, Varanidae, Anguidae, and Cordylidae. Although, the internal relationships within this group yielded only a weak resolution and low bootstrap support, the revealed relationships were more congruent with morphological studies than with recent molecular analyses.
    Gene 06/2007; 394(1-2):69-77. · 2.20 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology. In this contribution we review the state of the art of "computational RNomics", i.e., the bioinformatics approaches to genome-wide RNA annotation. Instead of rehashing results from recently published surveys in detail, we focus here on the open problem in the field, namely (functional) annotation of the plethora of putative RNAs. A series of exploratory studies are used to provide non-trivial examples for the discussion of some of the difficulties.
    Journal of Experimental Zoology Part B Molecular and Developmental Evolution 02/2007; 308(1):1-25. · 2.12 Impact Factor
  • Source
    Guido Fritzsch, Martin Schlegel, Peter F Stadler
    [Show abstract] [Hide abstract]
    ABSTRACT: Mitochondrial genomes provide a valuable dataset for phylogenetic studies, in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence-based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combine pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements. We, furthermore, demonstrate that our approach is also applicable to the much larger genomes of chloroplasts.
    Journal of Theoretical Biology 07/2006; 240(4):511-20. · 2.35 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The systematic position of the rare Indian turtle Geoemyda silvatica Henderson is examined by a phylogenetic analysis of mtDNA sequence data (cytochrome-b gene) of most species of Geoemydidae. Geoemyda silvatica represents a basal and isolated taxon within Geoemydidae, definitely not a close relative of any species of Geoemyda or Heosemys, the genera in which G. silvatica has been placed in the past. Therefore, the new genus Vijayachelys is proposed for G. silvatica. Cranial morphology and some other osteological characters of Vijayachelys silvatica are described and illustrated. Differential diagnoses are given for the type species of Melanochelys and the respective type species of the superficially similar genera Geoemyda, Heosemys, and Leucocephalon. According to Bayesian analysis of mtDNA data, Melanochelys trijuga could be distantly related to V. silvatica, whereas the morphological similarity of the other species probably is the result of a similar mode of life. The discovery of the phylogenetically isolated position of V. silvatica highlights the importance of the Western Ghats as a biodiversity hotspot rich in higher-level endemics.
    Organisms Diversity & Evolution 01/2006; 6:151-162. · 3.37 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The systematic position of the rare Indian turtle Geoemyda silvatica Henderson is examined by a phylogenetic analysis of mtDNA sequence data (cytochrome-b gene) of most species of Geoemydidae. Geoemyda silvatica represents a basal and isolated taxon within Geoemydidae, definitely not a close relative of any species of Geoemyda or Heosemys, the genera in which G. silvatica has been placed in the past. Therefore, the new genus Vijayachelys is proposed for G. silvatica. Cranial morphology and some other osteological characters of Vijayachelys silvatica are described and illustrated. Differential diagnoses are given for the type species of Melanochelys and the respective type species of the superficially similar genera Geoemyda, Heosemys, and Leucocephalon. According to Bayesian analysis of mtDNA data, Melanochelys trijuga could be distantly related to V. silvatica, whereas the morphological similarity of the other species probably is the result of a similar mode of life. The discovery of the phylogenetically isolated position of V. silvatica highlights the importance of the Western Ghats as a biodiversity hotspot rich in higher-level endemics.
    Organisms Diversity & Evolution - ORG DIVERS EVOL. 01/2006; 6(3):254-254.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Mauremys leprosa, distributed in Iberia and North-west Africa, contains two major clades of mtDNA haplotypes. Clade A occurs in Portugal, Spain and Morocco north of the Atlas Mountains. Clade B occurs south of the Atlas Mountains in Morocco and north of the Atlas Mountains in eastern Algeria and Tunisia. However, we recorded a single individual containing a clade B haplotype in Morocco from north of the Atlas Mountains. This could indicate gene flow between both clades. The phylogenetically most distinct clade A haplotypes are confined to Morocco, suggesting both clades originated in North Africa. Extensive diversity within clade A in south-western Iberia argues for a glacial refuge located there. Other regions of the Iberian Peninsula, displaying distinctly lower haplotype diversities, were recolonized from within south-western Iberia. Most populations in Portugal, Spain and northern Morocco contain the most common clade A haplotype, indicating dispersal from the south-western Iberian refuge, gene flow across the Strait of Gibraltar, and reinvasion of Morocco by terrapins originating in south-western Iberia. This hypothesis is consistent with demographic analyses, suggesting rapid clade A population increase while clade B is represented by stationary, fragmented populations. We recommend the eight, morphologically weakly diagnosable, subspecies of M. leprosa be reduced to two, reflecting major mtDNA clades: Mauremys l. leprosa (Iberian Peninsula and northern Morocco) and M. l. saharica (southern Morocco, eastern Algeria and Tunisia). Peripheral populations could play an important role in evolution of M. leprosa because we found endemic haplotypes in populations along the northern and southern range borders. Previous investigations in another western Palearctic freshwater turtle (Emys orbicularis) discovered similar differentiation of peripheral populations, and phylogeographies of Emys orbicularis and Mauremys rivulata underline the barrier status of mountain chains, in contrast to sea straits, suggesting common patterns for western Palearctic freshwater turtles.
    Zoologica Scripta 12/2005; 35(1):97 - 108. · 2.79 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A plethora of new functions of non-coding RNAs (ncRNAs) have been discovered in past few years. In fact, RNA is emerging as the central player in cellular regulation, taking on active roles in multiple regulatory layers from transcription, RNA maturation, and RNA modification to translational regulation. Nevertheless, very little is known about the evolution of this "Modern RNA World" and its components. In this contribution, we attempt to provide at least a cursory overview of the diversity of ncRNAs and functional RNA motifs in non-translated regions of regular messenger RNAs (mRNAs) with an emphasis on evolutionary questions. This survey is complemented by an in-depth analysis of examples from different classes of RNAs focusing mostly on their evolution in the vertebrate lineage. We present a survey of Y RNA genes in vertebrates and study the molecular evolution of the U7 snRNA, the snoRNAs E1/U17, E2, and E3, the Y RNA family, the let-7 microRNA (miRNA) family, and the mRNA-like evf-1 gene. We furthermore discuss the statistical distribution of miRNAs in metazoans, which suggests an explosive increase in the miRNA repertoire in vertebrates. The analysis of the transcription of ncRNAs suggests that small RNAs in general are genetically mobile in the sense that their association with a hostgene (e.g. when transcribed from introns of a mRNA) can change on evolutionary time scales. The let-7 family demonstrates, that even the mode of transcription (as intron or as exon) can change among paralogous ncRNA.
    Theory in Biosciences 05/2005; 123(4):301-69. · 0.93 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Sequence data of the mitochondrial cytochrome b gene of stripe-necked terrapins (Mauremys leprosa) have been compared from localities north and south of the Atlas Mts . (Ceuta; Morocco) and from Donana National Park (Spain). A low maximum sequence divergence (approximately I %) corresponds to two major clades; one is re presented by localities to the north of the Atlas Mts. and in Dofiana National Park and the other by localities to the south of the Atlas Mts. Differentiation between populations north and south of the Atlas Mts. is much more pronounced than that found between samples from each side of the Strait of Gibraltar. These findings suggest that the Strait of Gibraltar is, in contrast to the Atlas Mts .. not a significant barrier to gene flow in s tripe -necked terrapins. The major c lades could reflect taxonomic segregation between populations north and south of the Atlas Mts . Sequences from Marrakech (corresponding to M. I. marokkensis), Ceuta, and the Donana National Park (M. Ieprosa) are only weakly differentiated. South of the Atlas Mts. we found no consistent differences between samples from catchment basins of the Oued Draa (M. I. vanmeerhaghei) and the Oued Noun (M. I. saharica). Our findings imply that taxonomic differentiation within M. leprosa is currently overestimated.
    Edgar Lehr. 01/2005;
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Barth, D. Bernhard, D. Fritzsch, G. & Fritz, U. (2004): The freshwater turtle genus Mauremys— a textbook example of an east–west disjunction or a taxonomic misconcept? —Zoologica Scripta, 33, 213–221.We compare 1036 bp of the mitochondrial cytochrome b gene (cyt b) from all six Mauremys species with 16 other taxa, representing both currently recognized subfamilies of the Geoemydidae (Geoemydinae and Batagurinae) to contribute a comprehensive dataset towards resolving the conflicting Mauremys taxonomy and phylogeography. Mauremys, a representative of the Geoemydinae, is thought to be an example of a taxon with an east–west disjunction due to Pleistocene glacial extinction, with species occurring in the western Palearctic and species in the eastern Palearctic and Oriental regions. Our results contradict this traditional zoogeographical scheme and the current taxonomy of the Geoemydidae. Mauremys is paraphyletic with respect to two East Asian genera belonging to the Batagurinae: Chinemys and Ocadia. Therefore, Mauremys, as currently understood, clearly represents a taxonomic misconcept. Mauremys+Chinemys+Ocadia contains four well supported clades, two of which —M. japonica+Chinemys+Ocadia and M. annamensis+M. mutica— are confined to eastern Asia. The other two —M. caspica+M. rivulata and M. leprosa— occur in the western Palearctic. Mauremys leprosa may represent an ancient lineage which differentiated before the split between the other western and eastern species occurred. The patchy distribution of the four clades is likely the result of several ancient radiations rather than of a Pleistocene extinction. The sister-group of Mauremys+Chinemys+Ocadia is Cuora, a morphologically highly specialized genus with a complicated shell hinging mechanism.
    Zoologica Scripta 04/2004; 33(3):213 - 221. · 2.79 Impact Factor
  • 01/2004;