Deep genomic-scale analyses of the metazoa reject Coelomata: evidence from single- and multigene families analyzed under a supertree and supermatrix paradigm.

Genome Biology and Evolution
Thérèse A Holton, Davide Pisani

Abstract

Solving the phylogeny of the animals with bilateral symmetry has proven difficult. Morphological studies have suggested a variety of alternative hypotheses, of which, Hyman's Coelomata hypothesis has become the most established. Studies based on 18S rRNA have failed to endorse Coelomata, supporting instead the rearrangement of the protostomes into two new clades: the Lophotrochozoa (including, e.g., the molluscs and the annelids) and the Ecdysozoa (including the Panarthropoda and most pseudocoelomates, such as the nematodes and priapulids). Support for this new animal phylogeny has been attained from expressed sequence tag studies, although these generally have a limited gene sampling. In contrast, deep genomic-scale analyses have often supported Coelomata. However, these studies are problematic due to their limited taxonomic sampling, which could exacerbate tree reconstruction artifacts. Here, we address both of these sampling limitations; we study the effect of long-branch attraction (LBA) in deep genomic-scale analyses and provide convincing evidence, using both single- and multigene families, that Coelomata is an artifact. We show that optimal outgroup selection is key in avoiding LBA and identify the use of inadequate outg...Continue Reading

References

Mar 1, 1992·Molecular Phylogenetics and Evolution·M A Ragan
Sep 8, 1998·Molecular Biology and Evolution·M RobinsonD Mouchiroud
Jun 16, 1999·Molecular Biology and Evolution·H Brinkmann, H Philippe
Jun 12, 2001·Molecular Phylogenetics and Evolution·P D OlsonJ Mariaux
Aug 30, 2001·Proceedings of the National Academy of Sciences of the United States of America·M S Rosenberg, S Kumar
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Apr 12, 2002·Systematic Biology·Davide Pisani, Mark Wilkinson
May 3, 2002·BMC Evolutionary Biology·Jaime E BlairS Blair Hedges
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Jan 7, 2004·Genome Research·Yuri I WolfEugene V Koonin
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Sep 18, 2004·Bioinformatics·C J Creevey, J O McInerney
Dec 24, 2004·Proceedings. Biological Sciences·Christopher J CreeveyJames O McInerney
Feb 11, 2005·Molecular Biology and Evolution·Hervé PhilippeHenner Brinkmann
Mar 5, 2005·Molecular Biology and Evolution·Antonis Rokas, Sean B Carroll
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
May 17, 2005·Genome Biology·Hernán Dopazo, Joaquín Dopazo
Feb 24, 2006·Trends in Genetics : TIG·Olivier JeffroyHervé Philippe
Nov 24, 2006·BMC Evolutionary Biology·David A FitzpatrickGeraldine Butler
May 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch
May 17, 2007·Molecular Biology and Evolution·Davide PisaniJames O McInerney
May 26, 2007·Molecular Biology and Evolution·Manuel IrimiaScott William Roy
Aug 9, 2007·PloS One·Hervé PhilippeJaume Baguñà
Sep 26, 2007·Molecular Biology and Evolution·Jie ZhengTeresa M Przytycka
Oct 9, 2007·Molecular Biology and Evolution·Igor B RogozinEugene V Koonin
Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Maximilian J TelfordOmar Rota-Stabelli
Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nicolas Lartillot, Hervé Philippe
Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Kevin J PetersonDavide Pisani
Feb 19, 2008·Molecular Biology and Evolution·Scott William Roy, Manuel Irimia
Mar 28, 2008·Trends in Ecology & Evolution·James O McInerneyDavide Pisani
May 14, 2008·Bioinformatics·André WeheOliver Eulenstein

❮ Previous
Next ❯

Citations

May 22, 2013·Amino Acids·Katrina M Kutchko, Jessica Siltberg-Liberles
Dec 19, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Natascha HillStefanie Hartmann
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lahcen I CampbellDavide Pisani
Nov 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Roberto FeudaDavide Pisani
Aug 11, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Eyal Cohen, Benny Chor
Aug 30, 2011·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jul 3, 2013·Molecular Biology and Evolution·Claire C MorganMary J O'Connell
Mar 28, 2013·BMC Bioinformatics·Thomas BigotGuy Perrière
Jul 30, 2011·BMC Evolutionary Biology·Konstantin V GunbinNikolay A Kolchanov
Jan 26, 2012·PloS One·Stefanie HartmannChristoph Bleidorn
Jun 14, 2014·BMC Bioinformatics·Wasiu A AkanniDavide Pisani
Dec 20, 2013·Systematic Biology·Thérèse A HoltonDavide Pisani
Oct 5, 2014·Systematic Biology·Leonardo De Oliveira MartinsDavid Posada
Sep 10, 2013·Molecular Phylogenetics and Evolution·Bernd SchierwaterLars Podsiadlowski
Dec 2, 2015·Proceedings of the National Academy of Sciences of the United States of America·Davide PisaniGert Wörheide
Mar 19, 2011·Trends in Genetics : TIG·Maximilian J Telford, Richard R Copley
Sep 12, 2015·Royal Society Open Science·Wasiu A AkanniDavide Pisani
Dec 30, 2014·Systematic Biology·Ruchi ChaudharyDavid Fernández-Baca
Oct 30, 2012·Systematic Biology·Cody E Hinchliff, Eric H Roalson
Mar 28, 2012·Current Opinion in HIV and AIDS·Mick Bailey
Oct 13, 2021·Current Biology : CB·Erik TihelkaDavide Pisani

❮ Previous
Next ❯

Software Mentioned

CLANN
PERL
Phylobayes
PRANK
MrBayes
PHYML
Modelgenerator
MulTrees
Consense
Coelomata

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.