TY - JOUR A1 - Bleidorn, Christoph A1 - Hill, Natascha A1 - Erséus, Christer A1 - Tiedemann, Ralph T1 - On the role of character loss in orbiniid phylogeny (Annelida) : molecules vs. morphology N2 - Orbiniid phylogeny is matter of debate and incongruence between hypothesis based on molecules and morphology has been repeatedly reported. Moreover, the phylogenetic position of the "oligochaetoid polychaetes" of the taxon Questa varies between morphological and molecular cladistic analyses. Here, we present a nearly complete mitochondrial genome of Questa ersei. The mitochondrial gene order is roughly identical to known orbiniid taxa. Several translocations of tRNAs are unique to Orbiniidae and Questa when compared to other annelid mitochondrial genomes. Additionally, we assembled sequence data of six genes (18S, 16S, cox1, cox3, nad1, nad4) for a representative orbiniid taxon sampling and analysed all data in concatenation using Maximum Likelihood and Bayesian inference. For comparison with morphology we compiled a morphological data matrix for all taxa included in our molecular analyses. Our results strongly support a close relationship of Questa with orbiniids (sequence data, gene order, an 18 bp indel, morphology), and a position nested within orbiniids is recovered in our sequence based analyses. We demonstrate remarkable incongruence of most included morphological characters with the recovered best ML tree and suppose that repeated independent character loss might be an explanation. Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/10557903 U6 - https://doi.org/10.1016/j.ympev.2009.03.022 SN - 1055-7903 ER - TY - JOUR A1 - Bleidorn, Christoph A1 - Lanterbecq, Deborah A1 - Eeckhaut, Igor A1 - Tiedemann, Ralph T1 - A PCR survey of Hox genes in the myzostomid Myzostoma cirriferum N2 - Using degenerate primers, we were able to identify seven Hox genes for the myzostomid Myzostoma cirriferum. The recovered fragments belong to anterior class (Mci_lab, Mci_pb), central class (Mci_Dfd, Mci_Lox5, Mci_Antp, Mci_Lox4), and posterior class (Mci_Post2) paralog groups. Orthology assignment was verified by phylogenetic analyses and presence of diagnostic regions in the homeodomain as well as flanking regions. The presence of Lox5, Lox4, and Post2 supports the inclusion of Myzostomida within Lophotrochozoa. We found signature residues within flanking regions of Lox5, which are also found in annelids, but not in Platyhelminthes. As such the available Hox genes data of myzostomids support an annelid relationship. Y1 - 2009 UR - http://www.springerlink.com/content/100526 U6 - https://doi.org/10.1007/s00427-009-0282-z SN - 0949-944X ER - TY - JOUR A1 - Bleidorn, Christoph A1 - Podsiadlowski, Lars A1 - Bartolomaeus, Thomas T1 - The complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii (Annelida, Orbiniidae) : a novel gene order for Annelida and implications for annelid phylogeny N2 - Relationships of annelid subtaxa are controversially discussed and additional markers are necessarily needed to get further insights into their evolution. Due to their high content of information, mitochondrial genomes have been proven very useful in phylogenetic analyses. Whereas many complete mitochondrial genomes of arthropods are available, lophotrochozoan taxa are only scarcely represented and this is especially true for annelids. Here we present the complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii. The circular genome is 15,558 bp in size and contains the same 37 genes as found in most other metazoans. As in the case for all studied annelids all genes are transcribed from the same strand. Compared with the known data from other annelids at least five gene translocations must be hypothesized for O. latreillii. A comparison of the available data shows that gene translocations within Annelida seem to be less frequent than in molluscs, but more frequent as previously assumed. Phylogenetic analyses of mitochondrial DNA sequence data and amino acid data support an inclusion Of Sipuncula within Annelida and a closer relationship to orbiniids is recovered for this taxon. Y1 - 2006 UR - http://www.sciencedirect.com/science/journal/03781119 U6 - https://doi.org/10.1016/j.gene.2005.11.018 SN - 0378-1119 ER - TY - GEN A1 - Bleidorn, Christoph A1 - Podsiadlowski, Lars A1 - Zhong, Min A1 - Eeckhaut, Igor A1 - Hartmann, Stefanie A1 - Halanych, Kenneth M. A1 - Tiedemann, Ralph T1 - On the phylogenetic position of Myzostomida : can 77 genes get it wrong? N2 - Background: Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, hylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa. Results: Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data. Conclusion: We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 123 KW - Cirriferum myzostomida KW - Mitochondrial genomes KW - Transfer-rna KW - Data sets KW - Sequence Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44893 ER - TY - JOUR A1 - Hartmann, Stefanie A1 - Helm, Conrad A1 - Nickel, Birgit A1 - Meyer, Matthias A1 - Struck, Torsten H. A1 - Tiedemann, Ralph A1 - Selbig, Joachim A1 - Bleidorn, Christoph T1 - Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data JF - PLoS one N2 - Background: In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic ( or parasitic) protostomes that are either placed with annelids or flatworms. Methodology: Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony. Conclusions: Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic. Y1 - 2012 U6 - https://doi.org/10.1371/journal.pone.0029843 SN - 1932-6203 VL - 7 IS - 1 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Hausen, Harald A1 - Bleidorn, Christoph T1 - Significance of chaetal arrangement for maldanid systematics (Annelida : Maldanidae) JF - Scientia marina : international journal on marine sciences N2 - Maldanids are usually divided into several subfamilies: Euclymeninae, Lumbriclymeninae, Maldaninae, Nicomachinae, Rhodininae, Clymenurinae, Notoproctinae, and Boguinae. The taxonomy of maldanids and the delimination of these taxa are mainly based on head morphology, total number of segments, chaetal structure, shape of the pygidium, and position of the anus. The maldanid ingroup relationships, as well as the monophyly of the proposed subfamilies, have so far not been investigated. Pilgrim (1977) described a shift of the notopodial chaetal rows from a transverse direction in anterior chaetigers to a more longitudinal one in posterior chaetigers in Clymene torquata (Leidy, 1855) and Euclymene oerstedii (Claparede, 1863), both belonging to the Euclymeninae. We investigated several maldanid species to assess the usefulness of this character for maldanid systematics and used 3D-reconstruction techniques to reveal the complete geometry of the chaetal sacs. Our investigation shows that a shift is apparent in Euclymene, Axiothella, Johnstonia (all Euclymeninae) and Clymenura (Clymenurinae), but absent in species like Maldane sarsi (Malmgren, 1865), Metasychis disparidentata (Moore, 1904) (both Maldaninae) and Petaloproctus borealis Ardwisson, 1906 (Nicomachinae). The shift is not typical for sedentary polychaetes and is apomorphic within maldanid polychaetes. It thus argues for a close relationship between Euclymeninae and Clymenurinae. The investigation of further maldanid species of different subfamilies may shed additional light on maldanid systematics. KW - Annelida KW - Polychaeta KW - Maldanidae KW - systematics KW - chaetae KW - chaetal arrangement Y1 - 2006 SN - 0214-8358 VL - 70 SP - 75 EP - 79 PB - Institut de Ciències del Mar CY - Barcelona ER - TY - JOUR A1 - Hill, Natascha A1 - Leow, Alexander A1 - Bleidorn, Christoph A1 - Groth, Detlef A1 - Tiedemann, Ralph A1 - Selbig, Joachim A1 - Hartmann, Stefanie T1 - Analysis of phylogenetic signal in protostomial intron patterns using Mutual Information JF - Theory in biosciences N2 - Many deep evolutionary divergences still remain unresolved, such as those among major taxa of the Lophotrochozoa. As alternative phylogenetic markers, the intron-exon structure of eukaryotic genomes and the patterns of absence and presence of spliceosomal introns appear to be promising. However, given the potential homoplasy of intron presence, the phylogenetic analysis of this data using standard evolutionary approaches has remained a challenge. Here, we used Mutual Information (MI) to estimate the phylogeny of Protostomia using gene structure data, and we compared these results with those obtained with Dollo Parsimony. Using full genome sequences from nine Metazoa, we identified 447 groups of orthologous sequences with 21,732 introns in 4,870 unique intron positions. We determined the shared absence and presence of introns in the corresponding sequence alignments and have made this data available in "IntronBase", a web-accessible and downloadable SQLite database. Our results obtained using Dollo Parsimony are obviously misled through systematic errors that arise from multiple intron loss events, but extensive filtering of data improved the quality of the estimated phylogenies. Mutual Information, in contrast, performs better with larger datasets, but at the same time it requires a complete data set, which is difficult to obtain for orthologs from a large number of taxa. Nevertheless, Mutual Information-based distances proved to be useful in analyzing this kind of data, also because the estimation of MI-based distances is independent of evolutionary models and therefore no pre-definitions of ancestral and derived character states are necessary. KW - Mutual Information KW - Evolution KW - Gene structure Y1 - 2013 U6 - https://doi.org/10.1007/s12064-012-0173-0 SN - 1431-7613 VL - 132 IS - 2 SP - 93 EP - 104 PB - Springer CY - New York ER - TY - JOUR A1 - Kolora, Sree Rohit Raj A1 - Weigert, Anne A1 - Saffari, Amin A1 - Kehr, Stephanie A1 - Walter Costa, Maria Beatriz A1 - Spröer, Cathrin A1 - Indrischek, Henrike A1 - Chintalapati, Manjusha A1 - Lohse, Konrad A1 - Doose, Gero A1 - Overmann, Jörg A1 - Bunk, Boyke A1 - Bleidorn, Christoph A1 - Grimm-Seyfarth, Annegret A1 - Henle, Klaus A1 - Nowick, Katja A1 - Faria, Rui A1 - Stadler, Peter F. A1 - Schlegel, Martin T1 - Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation JF - GigaScience N2 - Background Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. Findings Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. Conclusion The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids. KW - sister species KW - PacBio and Illumina KW - de novo hybrid assembly KW - transcripts KW - noncoding RNA KW - zinc fingers KW - positive selection KW - UV response KW - inversions KW - gene flow Y1 - 2018 U6 - https://doi.org/10.1093/gigascience/giy160 SN - 2047-217X VL - 8 IS - 2 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Moodley, Yoshan A1 - Bruford, Michael W. A1 - Bleidorn, Christoph A1 - Wronski, Torsten A1 - Apio, Ann A1 - Plath, Martin T1 - Analysis of mitochondrial DNA data reveals non-monophyly in the bushbuck (Tragelaphus scriptus) complex Y1 - 2009 UR - http://www.sciencedirect.com/science/journal/16165047 U6 - https://doi.org/10.1016/j.mambio.2008.05.003 SN - 1616-5047 ER - TY - GEN A1 - Mwinyi, Adina A1 - Meyer, Achim A1 - Bleidorn, Christoph A1 - Lieb, Bernhard A1 - Bartolomaeus, Thomas A1 - Podsiadlowski, Lars T1 - Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida N2 - Background: Mitochondrial genomes are a valuable source of data for analysing phylogenetic relationships. Besides sequence information, mitochondrial gene order may add phylogenetically useful information, too. Sipuncula are unsegmented marine worms, traditionally placed in their own phylum. Recent molecular and morphological findings suggest a close affinity to the segmented Annelida. Results: The first complete mitochondrial genome of a member of Sipuncula, Sipunculus nudus, is presented. All 37 genes characteristic for metazoan mtDNA were detected and are encoded on the same strand. The mitochondrial gene order (protein-coding and ribosomal RNA genes) resembles that of annelids, but shows several derivations so far found only in Sipuncula. Sequence based phylogenetic analysis of mitochondrial protein-coding genes results in significant bootstrap support for Annelida sensu lato, combining Annelida together with Sipuncula, Echiura, Pogonophora and Myzostomida. Conclusion: The mitochondrial sequence data support a close relationship of Annelida and Sipuncula. Also the most parsimonious explanation of changes in gene order favours a derivation from the annelid gene order. These results complement findings from recent phylogenetic analyses of nuclear encoded genes as well as a report of a segmental neural patterning in Sipuncula. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - paper 124 KW - Transfer-rna genes; Phylogenetic analysis; Animal phylogeny; Control region; Sister Taxau Y1 - 2009 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-44916 ER -