TY - JOUR A1 - Struck, Torsten H. A1 - Paul, Christiane A1 - Hill, Natascha A1 - Hartmann, Stefanie A1 - Hoesel, Christoph A1 - Kube, Michael A1 - Lieb, Bernhard A1 - Meyer, Achim A1 - Tiedemann, Ralph A1 - Purschke, Guenter A1 - Bleidorn, Christoph T1 - Phylogenomic analyses unravel annelid evolution JF - Nature : the international weekly journal of science N2 - Annelida, the ringed worms, is a highly diverse animal phylum that includes more than 15,000 described species and constitutes the dominant benthic macrofauna from the intertidal zone down to the deep sea. A robust annelid phylogeny would shape our understanding of animal body-plan evolution and shed light on the bilaterian ground pattern. Traditionally, Annelida has been split into two major groups: Clitellata (earthworms and leeches) and polychaetes (bristle worms), but recent evidence suggests that other taxa that were once considered to be separate phyla (Sipuncula, Echiura and Siboglinidae (also known as Pogonophora)) should be included in Annelida(1-4). However, the deep-level evolutionary relationships of Annelida are still poorly understood, and a robust reconstruction of annelid evolutionary history is needed. Here we show that phylogenomic analyses of 34 annelid taxa, using 47,953 amino acid positions, recovered a well-supported phylogeny with strong support for major splits. Our results recover chaetopterids, myzostomids and sipunculids in the basal part of the tree, although the position of Myzostomida remains uncertain owing to its long branch. The remaining taxa are split into two clades: Errantia (which includes the model annelid Platynereis), and Sedentaria (which includes Clitellata). Ancestral character trait reconstructions indicate that these clades show adaptation to either an errant or a sedentary lifestyle, with alteration of accompanying morphological traits such as peristaltic movement, parapodia and sensory perception. Finally, life history characters in Annelida seem to be phylogenetically informative. Y1 - 2011 U6 - https://doi.org/10.1038/nature09864 SN - 0028-0836 VL - 471 IS - 7336 SP - 95 EP - U113 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wronski, Torsten A1 - Wacher, Timothy A1 - Hammond, Robert L. A1 - Winney, Bruce A1 - Hundertmark, Kris J. A1 - Blacket, Mark J. A1 - Mohammed, Osama B. A1 - Flores, Benito A1 - Omer, Sawsan A. A1 - Macasero, William A1 - Plath, Martin A1 - Tiedemann, Ralph A1 - Bleidorn, Christoph T1 - Two reciprocally monophyletic mtDNA lineages elucidate the taxonomic status of Mountain gazelles (Gazella gazella) N2 - Mountain gazelles (Gazella gazella) rank among the most critically endangered mammals on the Arabian Peninsula. Past conservation efforts have been plagued by confusion about the phylogenetic relationship among various 'phenotypically discernable' populations, and even the question of species boundaries was far from being certain. This lack of knowledge has had a direct impact on conservation measures, especially ex situ breeding programmes, hampering the assignment of captive stocks to potential conservation units. Here, we provide a phylogenetic framework, based on the analysis of mtDNA sequences (360 bp cytochrome b and 213 bp Control Region) of 126 individuals collected from the wild throughout the Arabian Peninsula and from captive stocks. Our analyses revealed two reciprocally monophyletic genetic lineages within the presumed species Gazella gazella: one 'northern clade' on the Golan Heights (Israel/Syrian border) and one genetically diverse larger clade from the rest of the Arabian Peninsula including the Arava Valley (Negev, Israel). Applying the Strict Phylogenetic Species Concept (sensu Mishler & Theriot, 2000) allows assigning species status to these two major clades. Y1 - 2010 UR - http://www.informaworld.com/smpp/title~content=t913521959~db=all U6 - https://doi.org/10.1080/14772001003613192 SN - 1477-2000 ER - 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 - Sammler, Svenja A1 - Bleidorn, Christoph A1 - Tiedemann, Ralph T1 - Full mitochondrial genome sequences of two endemic Philippine hornbill species (Aves: Bucerotidae) provide evidence for pervasive mitochondrial DNA recombination JF - BMC genomics N2 - Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle". Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation. Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes. Y1 - 2011 U6 - https://doi.org/10.1186/1471-2164-12-35 SN - 1471-2164 VL - 12 IS - 2 PB - BioMed Central CY - London 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 - 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 - 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 - 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 - 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 -