TY  - JOUR
A1  - Burleigh, J. Gordon
A1  - Bansal, Mukul S.
A1  - Eulenstein, Oliver
A1  - Hartmann, Stefanie
A1  - Wehe, Andre
A1  - Vision, Todd J.
T1  - Genome-Scale Phylogenetics inferring the plant tree of life from 18,896 gene trees
JF  - Systematic biology
N2  - 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.
KW  - Gene tree-species tree reconciliation
KW  - gene tree parsimony
KW  - plant phylogeny
KW  - phylogenomics
Y1  - 2011
U6  - https://doi.org/10.1093/sysbio/syq072
SN  - 1063-5157
VL  - 60
IS  - 2
SP  - 117
EP  - 125
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
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  - Bonizzoni, Mariangela
A1  - Bourjea, Jerome
A1  - Chen, Bin
A1  - Crain, B. J.
A1  - Cui, Liwang
A1  - Fiorentino, V.
A1  - Hartmann, Stefanie
A1  - Hendricks, S.
A1  - Ketmaier, Valerio
A1  - Ma, Xiaoguang
A1  - Muths, Delphine
A1  - Pavesi, Laura
A1  - Pfautsch, Simone
A1  - Rieger, M. A.
A1  - Santonastaso, T.
A1  - Sattabongkot, Jetsumon
A1  - Taron, C. H.
A1  - Taron, D. J.
A1  - Tiedemann, Ralph
A1  - Yan, Guiyun
A1  - Zheng, Bin
A1  - Zhong, Daibin
T1  - Permanent genetic resources added to molecular ecology resources database 1 April 2011-31 May 2011
JF  - Molecular ecology resources
N2  - 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.
Y1  - 2011
U6  - https://doi.org/10.1111/j.1755-0998.2011.03046.x
SN  - 1755-098X
VL  - 11
IS  - 5
SP  - 935
EP  - 936
PB  - Wiley-Blackwell
CY  - Malden
ER  - 
TY  - THES
A1  - Hartmann, Stefanie
T1  - Phylogenomics: comparative genome analysis ursing large-scale gene family data
Y1  - 2011
CY  - Potsdam
ER  -