Literature DB >> 21252385

Biologically inspired phylogenetic models strongly outperform the no common mechanism model.

John P Huelsenbeck1, Michael E Alfaro, Marc A Suchard.   

Abstract

But Tuffley and Steel (1997) introduced a model called No Common Mechanism (NCM), in which characters may-but are not required to-vary their relative rates independently, both within and between branches. Because the independent variation is taken only as a possibility, not as a requirement, NCM would apply to almost any situation, and so may be accepted as realistic. This is useful because Tuffley and Steel also showed that maximum likelihood under NCM selects the same trees as does parsimony. With the realistic NCM in the background, then, most parsimonious trees have greatest power to explain available observations. -Farris (2008).

Mesh:

Year:  2011        PMID: 21252385      PMCID: PMC3038349          DOI: 10.1093/sysbio/syq089

Source DB:  PubMed          Journal:  Syst Biol        ISSN: 1063-5157            Impact factor:   15.683


  18 in total

1.  Inference of population structure using multilocus genotype data.

Authors:  J K Pritchard; M Stephens; P Donnelly
Journal:  Genetics       Date:  2000-06       Impact factor: 4.562

Review 2.  Are you my mother? Bayesian phylogenetic inference of recombination among putative parental strains.

Authors:  Janet S Sinsheimer; Marc A Suchard; Karin S Dorman; Fang Fang; Robert E Weiss
Journal:  Appl Bioinformatics       Date:  2003

3.  The akaike information criterion will not choose the no common mechanism model.

Authors:  Mark T Holder; Paul O Lewis; David L Swofford
Journal:  Syst Biol       Date:  2010-05-31       Impact factor: 15.683

4.  Sampling properties of DNA sequence data in phylogenetic analysis.

Authors:  M P Cummings; S P Otto; J Wakeley
Journal:  Mol Biol Evol       Date:  1995-09       Impact factor: 16.240

5.  Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.

Authors:  Z Yang
Journal:  Mol Biol Evol       Date:  1993-11       Impact factor: 16.240

6.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods.

Authors:  Z Yang
Journal:  J Mol Evol       Date:  1994-09       Impact factor: 2.395

7.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

Authors:  M Kimura
Journal:  J Mol Evol       Date:  1980-12       Impact factor: 2.395

8.  Disparate rates of molecular evolution in cospeciating hosts and parasites.

Authors:  M S Hafner; P D Sudman; F X Villablanca; T A Spradling; J W Demastes; S A Nadler
Journal:  Science       Date:  1994-08-19       Impact factor: 47.728

9.  Evolutionary trees from DNA sequences: a maximum likelihood approach.

Authors:  J Felsenstein
Journal:  J Mol Evol       Date:  1981       Impact factor: 2.395

10.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA.

Authors:  M Hasegawa; H Kishino; T Yano
Journal:  J Mol Evol       Date:  1985       Impact factor: 2.395

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  6 in total

1.  Modelling rate distributions using character compatibility: implications for morphological evolution among fossil invertebrates.

Authors:  Peter J Wagner
Journal:  Biol Lett       Date:  2011-07-27       Impact factor: 3.703

2.  Proving universal common ancestry with similar sequences.

Authors:  Leonardo de Oliveira Martins; David Posada
Journal:  Trends Evol Biol       Date:  2012-05-09

3.  Strepsiptera, phylogenomics and the long branch attraction problem.

Authors:  Bastien Boussau; Zaak Walton; Juan A Delgado; Francisco Collantes; Laura Beani; Isaac J Stewart; Sydney A Cameron; James B Whitfield; J Spencer Johnston; Peter W H Holland; Doris Bachtrog; Jeyaraney Kathirithamby; John P Huelsenbeck
Journal:  PLoS One       Date:  2014-10-01       Impact factor: 3.240

4.  The deep(er) roots of Eukaryotes and Akaryotes.

Authors:  Ajith Harish; David Morrison
Journal:  F1000Res       Date:  2020-02-13

5.  Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals.

Authors:  Tamaki Yuri; Rebecca T Kimball; John Harshman; Rauri C K Bowie; Michael J Braun; Jena L Chojnowski; Kin-Lan Han; Shannon J Hackett; Christopher J Huddleston; William S Moore; Sushma Reddy; Frederick H Sheldon; David W Steadman; Christopher C Witt; Edward L Braun
Journal:  Biology (Basel)       Date:  2013-03-13

6.  Integrated likelihood for phylogenomics under a no-common-mechanism model.

Authors:  Hunter Tidwell; Luay Nakhleh
Journal:  BMC Genomics       Date:  2020-04-16       Impact factor: 3.969

  6 in total

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