Broad phylogenomic sampling improves resolution of the animal tree of life

@article{Dunn2008BroadPS,
  title={Broad phylogenomic sampling improves resolution of the animal tree of life},
  author={Casey W. Dunn and Andreas Hejnol and David Q. Matus and Kevin Pang and William E. Browne and Stephen A. Smith and Elaine C Seaver and Greg W. Rouse and Matthias Obst and Gregory D. Edgecombe and Martin Vinther S{\o}rensen and Steven H. D. Haddock and Andreas Schmidt‐Rhaesa and Akiko Okusu and Reinhardt M{\o}bjerg Kristensen and Ward C. Wheeler and Mark Q. Martindale and Gonzalo Giribet},
  journal={Nature},
  year={2008},
  volume={452},
  pages={745-749}
}
Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often… Expand
Assessing the root of bilaterian animals with scalable phylogenomic methods
  • A. Hejnol, M. Obst, +14 authors C. Dunn
  • Biology, Medicine
  • Proceedings of the Royal Society B: Biological Sciences
  • 2009
TLDR
New sequence data and methods strongly uphold previous suggestions that Acoelomorpha is sister clade to all other bilaterian animals, find diminishing evidence for the placement of the enigmatic Xenoturbella within Deuterostomia, and place Cycliophora with Entoprocta and EctoproCTa. Expand
A phylogenomic approach to resolve the arthropod tree of life.
TLDR
It is shown that phylogenomic data can substantially advance the understanding of arthropod evolution and resolve several conflicts among existing hypotheses. Expand
Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes
TLDR
Ribosomal RNA genes are considered a reliable source for the study of deep divergences in the metazoan tree, provided that the data are treated carefully and the LBA effect is minimized. Expand
Testing the new animal phylogeny: a phylum level molecular analysis of the animal kingdom.
TLDR
The data show strong support for the basic structure of the new animal phylogeny as well as for the Mandibulata including Myriapoda, and some resolution within the Lophotrochozoa is provided. Expand
Phylogeny of Animals: Genomes Have a Lot to Say
TLDR
This work has triggered several advances regarding metazoan relationships such as the reevaluation of chordate relationships and the re-positioning of some problematic minor phyla with improved accuracy, and raised new questions about the processes that underlie morphological evolution, as well as the future of molecular phylogenetics. Expand
Genomics and the animal tree of life: conflicts and future prospects
TLDR
This work discusses some of the major controversies and poorly resolved deep nodes still remain in the animal tree of life, and explores the meaning of total support in phylogenomic analyses, highlighting cases in which a data set can provide total support for contradictory nodes. Expand
Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data
TLDR
Based on the first phylogenomic approach including these three ambiguous polyneopteran orders, conclusive support for monophyletic Polyneoptera is provided, contesting the hypothesis of Zoraptera + Paraneoptera and Plecoptera + remaining Neoptera. Expand
Revisiting metazoan phylogeny with genomic sampling of all phyla
TLDR
The first attempt to investigate animal relationships using genome-scale data from all phyla is presented, and matrix construction with an eye towards testing specific relationships is explored, showing that Lophotrochozoa can be constructed in strongly conflicting ways using different taxon- and/or orthologue sets. Expand
Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships
TLDR
This work recovers monophyletic Porifera as the sister group to all other Metazoa and suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Expand
Evidence for sponges as sister to all other animals from partitioned phylogenomics with mixture models and recoding
TLDR
It is shown that incorporating site-heterogeneous mixture models and recoding into partitioned phylogenomics alleviates systematic errors that hamper commonly-applied phylogenetic models and improves model-fit that attenuates branching artefacts induced by systematic error. Expand
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