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

Keywords

Smoothing, Biology, Divergence (linguistics), Statistics, Evolutionary biology

References

• Molecular Clock Calibrations and Metazoan Divergence DatesAntonio Serrano González — 1999
• Examining rates and patterns of nucleotide substitution in plantsSpencer V. Muse — 2004
• The causes of molecular evolutionGillespie, John H. — 1991
• A molecular timescale for vertebrate evolutionSudhir Kumar, Simon Hedges — 1998
• Paleontological data and molecular phylogenetic analysisAndrew B. Smith, D. Timothy J. Littlewood — 1994
• A generalized least-squares estimate for the origin of sporophytic self-incompatibility.Marcy K. Uyenoyama — 1995
• A compound poisson process for relaxing the molecular clock.John P. Huelsenbeck, Bret Larget, David L. Swofford — 2000
• A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate ConstancyMichael J. Sanderson — 1997
• Estimating divergence dates from molecular sequences.Andrew Rambaut, Lindell Bromham — 1998
• The molecular clock of HIV-1 unveiled through analysis of a known transmission history.Thomas Leitner, Jan Albert — 1999
• The general stochastic model of nucleotide substitution.Francisco Rodríguez, José Luis Tejera Oliver, Antonio Marín García — 1990
• Seed plant phylogeny inferred from all three plant genomes: monophyly of extant gymnosperms and origin of Gnetales from conifers.Shu‐Miaw Chaw, Christopher L. Parkinson, Yuchang Cheng — 2000
• Model Selection and InferenceSurekha Mudivarthy, Marepalli B. Rao — 2000
• Can fast early rates reconcile molecular dates with the Cambrian explosion?Lindell Bromham, Michael D. Hendy — 2000
• Estimation of primate speciation dates using local molecular clocks.Anne D. Yoder, Ziheng Yang — 2000
• Rates of DNA sequence evolution differ between taxonomic groups.Roy J. Britten — 1986
• Timing the ancestor of the HIV-1 pandemic strains.Bette Korber, Mark Muldoon, James Theiler — 2000
• Performance of a divergence time estimation method under a probabilistic model of rate evolution.Hirohisa Kishino, Jeffrey L. Thorne, William Bruno — 2001
• Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in HominoideaMasami Hasegawa, Hirohisa Kishino, Taka-aki Yano — 1989
• Fitting Discrete Probability Distributions to Evolutionary EventsThomas Uzzell, Kendall W. Corbin — 1971

Cited by

• Introduction and synthesis: Plant phylogeny and the origin of major biomes.Vicent Garés Timor — 2004
• Molecular dating when rates vary.George M. Lady, Anthony E. Bopp, Christopher Boyden Alt — 2005
• RATES OF MOLECULAR EVOLUTION IN BACTERIA ARE RELATIVELY CONSTANT DESPITE SPORE DORMANCYDavid M. Jaeger — 2007
• A Challenge to the Ancient Origin of SIVagm Based on African Green Monkey Mitochondrial GenomesLyman L. Johnson — 2007
• Caveats on the Use of Fossil Calibrations for Molecular Dating: A Comment on Near et al.昇 中垣, Dissa Bandara, Bandara D.B.P.H. Dissa — 2007
• Rates and Patterns in the Evolution of Snake-Like Body Form in Squamate Reptiles: Evidence for Repeated Re-Evolution of Lost Digits and Long-Term Persistence of Intermediate Body FormsАбрамов Сергей Иванович — 2008
• Distinguishing Coevolution from Covicariance in an Obligate Pollination Mutualism: Asynchronous Divergence in Joshua Tree and its Pollinators良和 中岡 — 2008
• Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for north American/Asian disjunctions.Rachel Rachel — 2008
• Relationship between Species Co-Occurrence and Rate of Morphological Change in Percina Darters (Percidae: Etheostomatinae)Katrin Gaßner, Heinz Ulrich Hoppe, Andreas Lingnau — 2009
• The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal dataLluı́s Cuatrecasas Arbós, Jordi Olivella Nadal — 2009
• Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points.María del Prado Escobar Bonilla — 2005
• Adaptive Radiation and Ecological Opportunity in Sulawesi and Philippine Fanged Frog (Limnonectes) CommunitiesEdward J. Schnee — 2011
• Evaluating fossil calibrations for dating phylogenies in light of rates of molecular evolution: a comparison of three approaches.Charles Amson — 2012
• An Expansion of Age Constraints for Microbial Clades that Lack a Conventional Fossil Record Using Phylogenomic DatingGeorge Britton, A. S. Islam, Yue Xuan — 2011
• Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales).Siti Nor Bayaah Ahmad, Azlina Shaikh Awadz, Normaziah Che Musa — 2012
• treePL: divergence time estimation using penalized likelihood for large phylogeniesStephen A. Smith, Brian C. O’Meara — 2012
• A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys.順弥 横田 — 2013
• Not only for egg yolk--functional and evolutionary insights from expression, selection, and structural analyses of Formica ant vitellogenins.みゆき 井戸 — 2014
• Molecular evolution and phylogenetics of caecilian amphibians (Gymnophiona)Diego Espinoza San Martín — 2006
• A global perspective on Campanulaceae: Biogeographic, genomic, and floral evolution.George Meredith — 2016

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