Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Nicolas Lartillot, Hervé Philippe

Abstract

Inferring the relationships among Bilateria has been an active and controversial research area since Haeckel. The lack of a sufficient number of phylogenetically reliable characters was the main limitation of traditional phylogenies based on morphology. With the advent of molecular data, this problem has been replaced by another one, statistical inconsistency, which stems from an erroneous interpretation of convergences induced by multiple changes. The analysis of alignments rich in both genes and species, combined with a probabilistic method (maximum likelihood or Bayesian) using sophisticated models of sequence evolution, should alleviate these two major limitations. We applied this approach to a dataset of 94 genes and 79 species using CAT, a previously developed model accounting for site-specific amino acid replacement patterns. The resulting tree is in good agreement with current knowledge: the monophyly of most major groups (e.g. Chordata, Arthropoda, Lophotrochozoa, Ecdysozoa, Protostomia) was recovered with high support. Two results are surprising and are discussed in an evo-devo framework: the sister-group relationship of Platyhelminthes and Annelida to the exclusion of Mollusca, contradicting the Neotrochozoa hypothes...Continue Reading

References

Feb 12, 1988·Science·K G FieldR A Raff
Jan 1, 1987·Cold Spring Harbor Symposia on Quantitative Biology·G J Olsen
Mar 1, 1965·Journal of Theoretical Biology·E Zuckerkandl, L Pauling
Sep 1, 1994·Nature·D Arendt, K Nübler-Jung
Jan 23, 1999·Current Opinion in Genetics & Development·H Philippe, J Laurent
Mar 27, 1999·Journal of Molecular Evolution·P G Foster, D A Hickey
May 1, 1999·Trends in Genetics : TIG·A AdoutteR de Rosa
Jun 16, 1999·Molecular Biology and Evolution·H Brinkmann, H Philippe
Apr 26, 2000·Proceedings of the National Academy of Sciences of the United States of America·A AdoutteR de Rosa
May 3, 2002·BMC Evolutionary Biology·Jaime E BlairS Blair Hedges
Aug 13, 2003·Bioinformatics·Fredrik Ronquist, John P Huelsenbeck
Jan 7, 2004·Genome Research·Yuri I WolfEugene V Koonin
Mar 12, 2004·Molecular Biology and Evolution·Nicolas Lartillot, Hervé Philippe
Jun 30, 2004·BMC Evolutionary Biology·Gangolf JobbKorbinian Strimmer
Oct 27, 2004·Systematic Biology·Peter G Foster
Feb 11, 2005·Molecular Biology and Evolution·Hervé PhilippeHenner Brinkmann
Apr 30, 2005·Nature Reviews. Genetics·Frédéric DelsucHervé Philippe
Aug 30, 2005·Systematic Biology·Dennis V Lavrov, B Franz Lang
Mar 25, 2006·Molecular Phylogenetics and Evolution·Yale Passamaneck, Kenneth M Halanych
Jun 10, 2006·Trends in Ecology & Evolution·Jeffrey L Boore
Aug 8, 2006·Current Biology : CB·David Q MatusMaximilian J Telford
Aug 8, 2006·Current Biology : CB·Ferdinand MarlétazYannick Le Parco
Aug 22, 2006·Trends in Ecology & Evolution·Hervé Philippe, Maximilian J Telford
Oct 3, 2006·Molecular Biology and Evolution·Denis BaurainHervé Philippe
Feb 10, 2007·BMC Evolutionary Biology·Nicolas LartillotHervé Philippe
Feb 15, 2007·Molecular Biology and Evolution·Igor B RogozinEugene V Koonin
May 24, 2007·Systematic Biology·Naiara Rodríguez-EzpeletaHervé Philippe
May 26, 2007·Molecular Biology and Evolution·Manuel IrimiaScott William Roy
Aug 9, 2007·PloS One·Hervé PhilippeJaume Baguñà

❮ Previous
Next ❯

Citations

Oct 15, 2013·Trends in Genetics : TIG·Arhat Abzhanov
Oct 21, 2010·Proceedings of the National Academy of Sciences of the United States of America·Alysha M HeimbergKevin J Peterson
Sep 8, 2011·Proceedings of the National Academy of Sciences of the United States of America·Lahcen I CampbellDavide Pisani
Jul 14, 2010·Genome Biology and Evolution·Omar Rota-StabelliDennis V Lavrov
Jan 15, 2013·Genome Biology and Evolution·Chung-Shien WuYa-Yi Huang
Oct 30, 2009·Molecular Biology and Evolution·Frida BelinkyDorothée Huchon
Apr 13, 2010·Molecular Biology and Evolution·Maximilian P NesnidalBernhard Hausdorf
Jun 11, 2010·Molecular Biology and Evolution·Karen MeusemannBernhard Misof
Jul 21, 2011·Molecular Biology and Evolution·Guifré TorruellaIñaki Ruiz-Trillo
Dec 3, 2011·Molecular Biology and Evolution·Romain Derelle, B Franz Lang
Aug 30, 2012·Molecular Biology and Evolution·Béatrice RoureHervé Philippe
Aug 13, 2010·Proceedings. Biological Sciences·Omar Rota-StabelliMaximilian J Telford
Feb 3, 2012·Proceedings. Biological Sciences·Fabien BurkiPatrick J Keeling
Aug 30, 2013·Proceedings. Biological Sciences·Matthew W BrownAndrew J Roger
Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Maximilian J Telford, D Timothy J Littlewood
Jan 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Maximilian J TelfordOmar Rota-Stabelli
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Nicolas Galtier, Vincent Daubin
Mar 28, 2013·BMC Bioinformatics·Thomas BigotGuy Perrière
Oct 7, 2008·BMC Bioinformatics·Celine ScornavaccaVincent Ranwez
Dec 4, 2010·BMC Evolutionary Biology·Fabien BurkiJan Pawlowski
Jan 18, 2011·BMC Evolutionary Biology·Béatrice Roure, Hervé Philippe
Jul 30, 2011·BMC Evolutionary Biology·Konstantin V GunbinNikolay A Kolchanov
Sep 19, 2008·BMC Evolutionary Biology·Ferdinand Marlétaz, Yannick Le Parco
Jun 6, 2008·Genome Biology·Ferdinand MarlétazYannick Le Parco
Mar 22, 2013·PloS One·Georg MayerPaul A Stevenson
Mar 29, 2014·Molecular Biology and Evolution·Rosa FernándezGonzalo Giribet
Aug 30, 2014·Molecular Biology and Evolution·Sónia C S AndradeGonzalo Giribet
Aug 16, 2014·Molecular Phylogenetics and Evolution·Janus BornerThorsten Burmester

❮ Previous
Next ❯

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.