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… 
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1,738 Citations

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TLDR
It is shown that phylogenomic data can substantially advance the understanding of arthropod evolution and resolve several conflicts among existing hypotheses.
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.
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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.
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.
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.
Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology
TLDR
The last common animal ancestor may has been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.
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.
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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.
Putting Animals in their Place within a Context of Eukaryotic Innovations
TLDR
The current understanding of animal evolutionary relationships is reviewed, including which of the basal metazoan phyla (Porifera, Placozoa, Cnidaria, or Ctenophora) is basal-most, the branching order of the three major lineages of Arthropoda, the relationships within Lophotrochozoa, and the placement of several so-called minor groups such as Chaetognatha.
Animal Phylogeny and Its Evolutionary Implications
TLDR
There is far more homoplasy for all these characters than had previously been anticipated, even among many complex characters such as segmentation and nervous systems, which has important implications for the understanding of the evolution of development, morphology, genomes, and other characters.
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