@article{BleidornPodsiadlowskiBartolomaeus2006,
  author    = {Bleidorn, Christoph and Podsiadlowski, Lars and Bartolomaeus, Thomas},
  title     = {The complete mitochondrial genome of the orbiniid polychaete Orbinia latreillii (Annelida, Orbiniidae) : a novel gene order for Annelida and implications for annelid phylogeny},
  issn      = {0378-1119},
  doi       = {10.1016/j.gene.2005.11.018},
  year      = {2006},
  abstract  = {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.},
  language  = {en}
}
@misc{MwinyiMeyerBleidornetal.2009,
  author    = {Mwinyi, Adina and Meyer, Achim and Bleidorn, Christoph and Lieb, Bernhard and Bartolomaeus, Thomas and Podsiadlowski, Lars},
  title     = {Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44916},
  year      = {2009},
  abstract  = {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.},
  language  = {en}
}
@misc{BleidornPodsiadlowskiZhongetal.2009,
  author    = {Bleidorn, Christoph and Podsiadlowski, Lars and Zhong, Min and Eeckhaut, Igor and Hartmann, Stefanie and Halanych, Kenneth M. and Tiedemann, Ralph},
  title     = {On the phylogenetic position of Myzostomida : can 77 genes get it wrong?},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-44893},
  year      = {2009},
  abstract  = {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.},
  language  = {en}
}