@article{BurleighBansalEulensteinetal.2011, author = {Burleigh, J. Gordon and Bansal, Mukul S. and Eulenstein, Oliver and Hartmann, Stefanie and Wehe, Andre and Vision, Todd J.}, title = {Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees}, series = {Systematic biology}, volume = {60}, journal = {Systematic biology}, number = {2}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1063-5157}, doi = {10.1093/sysbio/syq072}, pages = {117 -- 125}, year = {2011}, abstract = {Phylogenetic analyses using genome-scale data sets must confront incongruence among gene trees, which in plants is exacerbated by frequent gene duplications and losses. Gene tree parsimony (GTP) is a phylogenetic optimization criterion in which a species tree that minimizes the number of gene duplications induced among a set of gene trees is selected. The run time performance of previous implementations has limited its use on large-scale data sets. We used new software that incorporates recent algorithmic advances to examine the performance of GTP on a plant data set consisting of 18,896 gene trees containing 510,922 protein sequences from 136 plant taxa (giving a combined alignment length of >2.9 million characters). The relationships inferred from the GTP analysis were largely consistent with previous large-scale studies of backbone plant phylogeny and resolved some controversial nodes. The placement of taxa that were present in few gene trees generally varied the most among GTP bootstrap replicates. Excluding these taxa either before or after the GTP analysis revealed high levels of phylogenetic support across plants. The analyses supported magnoliids sister to a eudicot + monocot clade and did not support the eurosid I and II clades. This study presents a nuclear genomic perspective on the broad-scale phylogenic relationships among plants, and it demonstrates that nuclear genes with a history of duplication and loss can be phylogenetically informative for resolving the plant tree of life.}, language = {en} } @article{BonizzoniBourjeaChenetal.2011, author = {Bonizzoni, Mariangela and Bourjea, Jerome and Chen, Bin and Crain, B. J. and Cui, Liwang and Fiorentino, V. and Hartmann, Stefanie and Hendricks, S. and Ketmaier, Valerio and Ma, Xiaoguang and Muths, Delphine and Pavesi, Laura and Pfautsch, Simone and Rieger, M. A. and Santonastaso, T. and Sattabongkot, Jetsumon and Taron, C. H. and Taron, D. J. and Tiedemann, Ralph and Yan, Guiyun and Zheng, Bin and Zhong, Daibin}, title = {Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011}, series = {Molecular ecology resources}, volume = {11}, journal = {Molecular ecology resources}, number = {5}, publisher = {Wiley-Blackwell}, address = {Malden}, organization = {Mol Ecology Resources Primer Dev}, issn = {1755-098X}, doi = {10.1111/j.1755-0998.2011.03046.x}, pages = {935 -- 936}, year = {2011}, abstract = {This article documents the addition of 92 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anopheles minimus, An. sinensis, An. dirus, Calephelis mutica, Lutjanus kasmira, Murella muralis and Orchestia montagui. These loci were cross-tested on the following species: Calephelis arizonensi, Calephelis borealis, Calephelis nemesis, Calephelis virginiensis and Lutjanus bengalensis.}, language = {en} } @article{StruckPaulHilletal.2011, author = {Struck, Torsten H. and Paul, Christiane and Hill, Natascha and Hartmann, Stefanie and Hoesel, Christoph and Kube, Michael and Lieb, Bernhard and Meyer, Achim and Tiedemann, Ralph and Purschke, Guenter and Bleidorn, Christoph}, title = {Phylogenomic analyses unravel annelid evolution}, series = {Nature : the international weekly journal of science}, volume = {471}, journal = {Nature : the international weekly journal of science}, number = {7336}, publisher = {Nature Publ. Group}, address = {London}, issn = {0028-0836}, doi = {10.1038/nature09864}, pages = {95 -- U113}, year = {2011}, abstract = {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.}, language = {en} } @phdthesis{Hartmann2011, author = {Hartmann, Stefanie}, title = {Phylogenomics: comparative genome analysis ursing large-scale gene family data}, address = {Potsdam}, year = {2011}, language = {en} }