Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation

Molecular Biology and Evolution
J SullivanDavid L Swofford

Abstract

Almost all studies that estimate phylogenies from DNA sequence data under the maximum-likelihood (ML) criterion employ an approximate approach. Most commonly, model parameters are estimated on some initial phylogenetic estimate derived using a rapid method (neighbor-joining or parsimony). Parameters are then held constant during a tree search, and ideally, the procedure is repeated until convergence is achieved. However, the effectiveness of this approximation has not been formally assessed, in part because doing so requires computationally intensive, full-optimization analyses. Here, we report both indirect and direct evaluations of the effectiveness of successive approximations. We obtained an indirect evaluation by comparing the results of replicate runs on real data that use random trees to provide initial parameter estimates. For six real data sets taken from the literature, all replicate iterative searches converged to the same joint estimates of topology and model parameters, suggesting that the approximation is not starting-point dependent, as long as the heuristic searches of tree space are rigorous. We conducted a more direct assessment using simulations in which we compared the accuracy of phylogenies estimated using...Continue Reading

References

Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Jun 13, 1996·Nature·A M D'ErchiaU Arnason
Feb 1, 1996·Journal of Molecular Evolution·J SullivanC Simon
Feb 1, 1997·Journal of Molecular Evolution·F FratiD L Swofford
Dec 29, 1998·Molecular Biology and Evolution·R J Mason-GamerE A Kellogg
Dec 29, 1998·Molecular Biology and Evolution·J Mallatt, J Sullivan
Jan 27, 1999·Bioinformatics·D Posada, K A Crandall
Oct 8, 2003·Systematic Biology·Vladimir MininJack Sullivan
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
May 28, 2004·Molecular Biology and Evolution·Le Sy Vinh, Arndt Von Haeseler

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Citations

Jan 2, 2007·Revista iberoamericana de micología·Stephen W Peterson
Jul 10, 2010·Molecular Biology and Evolution·Jennifer Ripplinger, Jack Sullivan
Oct 15, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Mark T HolderChristophe Dessimoz
Aug 18, 2006·BMC Evolutionary Biology·Chunguang DuJoachim Messing
May 21, 2008·BMC Evolutionary Biology·Vera I D RosSteph B J Menken
Aug 7, 2009·BMC Evolutionary Biology·Georgia TsagkogeorgaFrédéric Delsuc
Apr 4, 2009·BMC Evolutionary Biology·Shani Blanga-KanfiDorothée Huchon
Mar 2, 2012·BMC Microbiology·Vera I D RosJohannes A J Breeuwer
May 4, 2010·Molecular Phylogenetics and Evolution·Jennifer RipplingerJack Sullivan
Feb 4, 2010·Molecular Phylogenetics and Evolution·Kin-Lan HanMichael J Braun
Oct 28, 2008·Molecular Phylogenetics and Evolution·Omar Torres-Carvajal, Kevin de Queiroz
Jul 2, 2008·Molecular Phylogenetics and Evolution·David C MarshallChris Simon
Jul 24, 2007·Molecular Phylogenetics and Evolution·Kathrin F Stanger-HallDavid M Hillis
May 1, 2007·Molecular Phylogenetics and Evolution·P LymberakisM Mylonas
Mar 27, 2007·Molecular Phylogenetics and Evolution·W Chris FunkDavid C Cannatella
Dec 26, 2006·Molecular Phylogenetics and Evolution·Tara L Fulton, Curtis Strobeck
Dec 30, 2006·Molecular Phylogenetics and Evolution·Carla Gutiérrez-RodríguezKevin de Queiroz
Feb 4, 2009·Evolution; International Journal of Organic Evolution·Panayiotis PafilisEfstratios D Valakos
Sep 27, 2007·Evolution; International Journal of Organic Evolution·Liam J RevellJonathan B Losos
Nov 25, 2006·The Journal of Eukaryotic Microbiology·Anders Jørgensen, Erik Sterud
Nov 1, 2006·Evolution & Development·Jonathan Q Richmond
Feb 28, 2008·Molecular Ecology·Jeffrey M GoodJack Sullivan

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