Literature DB >> 19324651

An examination of phylogenetic models of substitution rate variation among lineages.

Simon Y W Ho1.   

Abstract

Molecular evolutionary rates can show significant variation among lineages, complicating the task of estimating substitution rates and divergence times using phylogenetic methods. Accordingly, relaxed molecular clock models have been developed to accommodate such rate heterogeneity, but these often make the assumption of rate autocorrelation among lineages. In this paper, I examine the validity of this assumption.

Mesh：

Substances：

Year:  2009        PMID： 19324651      PMCID： PMC2679908          DOI： 10.1098/rsbl.2008.0729

Source DB:  PubMed          Journal:  Biol Lett        ISSN： 1744-9561            Impact factor:   3.703


  25 in total

1.  A compound poisson process for relaxing the molecular clock.

Authors:  J P Huelsenbeck; B Larget; D Swofford
Journal:  Genetics       Date:  2000-04       Impact factor: 4.562

2.  Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.

Authors:  Michael J Sanderson
Journal:  Mol Biol Evol       Date:  2002-01       Impact factor: 16.240

3.  Evolutionary rates and species diversity in flowering plants.

Authors:  T G Barraclough; V Savolainen
Journal:  Evolution       Date:  2001-04       Impact factor: 3.694

4.  Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny.

Authors:  Stéphane Aris-Brosou; Ziheng Yang
Journal:  Syst Biol       Date:  2002-10       Impact factor: 15.683

5.  Estimating absolute rates of synonymous and nonsynonymous nucleotide substitution in order to characterize natural selection and date species divergences.

Authors:  Tae-Kun Seo; Hirohisa Kishino; Jeffrey L Thorne
Journal:  Mol Biol Evol       Date:  2004-03-10       Impact factor: 16.240

6.  The rate of DNA evolution: effects of body size and temperature on the molecular clock.

Authors:  James F Gillooly; Andrew P Allen; Geoffrey B West; James H Brown
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-23       Impact factor: 11.205

7.  Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation.

Authors:  Simon Y W Ho; Matthew J Phillips; Alexei J Drummond; Alan Cooper
Journal:  Mol Biol Evol       Date:  2005-03-09       Impact factor: 16.240

8.  Rates of molecular evolution are linked to life history in flowering plants.

Authors:  Stephen A Smith; Michael J Donoghue
Journal:  Science       Date:  2008-10-03       Impact factor: 47.728

9.  Modeling the covarion hypothesis of nucleotide substitution.

Authors:  C Tuffley; M Steel
Journal:  Math Biosci       Date:  1998-01-01       Impact factor: 2.144

10.  Environmental energy and evolutionary rates in flowering plants.

Authors:  T Jonathan Davies; Vincent Savolainen; Mark W Chase; Justin Moat; Timothy G Barraclough
Journal:  Proc Biol Sci       Date:  2004-10-22       Impact factor: 5.349
View more
  29 in total

1.  New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI).

Authors:  Filipe O Costa; Gary R Carvalho
Journal:  Theory Biosci       Date:  2010-05-26       Impact factor: 1.919

2.  Advances in Time Estimation Methods for Molecular Data.

Authors:  Sudhir Kumar; S Blair Hedges
Journal:  Mol Biol Evol       Date:  2016-02-16       Impact factor: 16.240

3.  Introduction. Putting the 'bio' into bioinformatics.

Authors:  Lindell Bromham
Journal:  Biol Lett       Date:  2009-04-22       Impact factor: 3.703

4.  Estimating diversification rates: how useful are divergence times?

Authors:  Joel O Wertheim; Michael J Sanderson
Journal:  Evolution       Date:  2010-11-05       Impact factor: 3.694

5.  Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals.

Authors:  Fabia U Battistuzzi; Alan Filipski; S Blair Hedges; Sudhir Kumar
Journal:  Mol Biol Evol       Date:  2010-01-21       Impact factor: 16.240

6.  Estimating the timing of early eukaryotic diversification with multigene molecular clocks.

Authors:  Laura Wegener Parfrey; Daniel J G Lahr; Andrew H Knoll; Laura A Katz
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-02       Impact factor: 11.205

7.  Estimating divergence times in large molecular phylogenies.

Authors:  Koichiro Tamura; Fabia Ursula Battistuzzi; Paul Billing-Ross; Oscar Murillo; Alan Filipski; Sudhir Kumar
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-05       Impact factor: 11.205

8.  Life history influences rates of climatic niche evolution in flowering plants.

Authors:  Stephen A Smith; Jeremy M Beaulieu
Journal:  Proc Biol Sci       Date:  2009-09-23       Impact factor: 5.349

9.  Reassessing the temporal evolution of orchids with new fossils and a Bayesian relaxed clock, with implications for the diversification of the rare South American genus Hoffmannseggella (Orchidaceae: Epidendroideae).

Authors:  A Lovisa S Gustafsson; Christiano F Verola; Alexandre Antonelli
Journal:  BMC Evol Biol       Date:  2010-06-14       Impact factor: 3.260

10.  Estimating the phylogeny and divergence times of primates using a supermatrix approach.

Authors:  Helen J Chatterjee; Simon Y W Ho; Ian Barnes; Colin Groves
Journal:  BMC Evol Biol       Date:  2009-10-27       Impact factor: 3.260
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.