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Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies.
| dc.creator | Revell, Liam J. | spa |
| dc.creator | Harmon, Luke J. | spa |
| dc.creator | Glor, Richard E. | spa |
| dc.date.accessioned | 2020-08-19T14:41:11Z | |
| dc.date.available | 2020-08-19T14:41:11Z | |
| dc.date.created | 2005-12-01 | spa |
| dc.description | Las inferencias macroevolucionarias a partir de filogenias moleculares son cada vez más comunes (ver Harvey et al., 1996; Mooers y Heard, 1997; Pagel, 1999; Barraclough y Nee, 2001). Muchos métodos en los que se invocan filogenias para la inferencia histórica asumen que una filogenia molecular es una representación sin errores de la historia filogenética subyacente de los taxones incluidos (pero ver Lutzoni et al., 2001; Huelsenbeck et al., 2000; Huelsenbeck y Rannala, 2003 ). Sin embargo, las filogenias moleculares son estimaciones de esta historia basadas en un modelo particular de evolución; así, hay algo de Wagner, G. P. 1989b. El origen de los caracteres morfológicos y la base biológica de la homología. Evolución 43: 1157-1171. Wagner, G. P. y P. F. Stadler. 2003. Cuasi-independencia, homología y unidad de tipo: una teoría topológica de caracteres. J. Theor. Biol. 220: 505–527. Wheeler, W. C. 1996. Optimización de alineación: ¿El final de la alineación de múltiples secuencias en filogenia? Cladística 12: 1-10. Wheeler, W. C. y D. S. Gladstein. 1994. MALIGN: Un programa de alineación de secuencias múltiples. J. Hered. 85: 417–418. Wheeler, W. C. y R. L. Honeycutt. 1988. Diferencia de secuencia apareada en ARN ribosomales: implicaciones evolutivas y filogenéticas. Mol. Biol. Evol. 5: 90–96. Wiley, E. O. 1978. | spa |
| dc.description.abstract | Macroevolutionary inferences from molecular phylogenies are becoming increasingly common (see Harvey et al., 1996; Mooers and Heard, 1997; Pagel, 1999; Barraclough and Nee, 2001). Many methods in which phylogenies are invoked for historical inference assume that a molecular phylogeny is an errorless representation of the underlying phylogenetic history of the included taxa (but see Lutzoni et al., 2001; Huelsenbeck et al., 2000; Huelsenbeck and Rannala, 2003). However, molecular phylogenies are estimates of this history based on a particular model of evolution; thus, there is some Wagner, G. P. 1989b. The origin of morphological characters and the biological basis of homology. Evolution 43:1157–1171. Wagner, G. P., and P. F. Stadler. 2003. Quasi-independence, homology and the unity of type: A topological theory of characters. J. Theor. Biol. 220:505–527. Wheeler, W. C. 1996. Optimization alignment: The end of multiple sequence alignment in phylogenetics? Cladistics 12:1–10. Wheeler, W. C., and D. S. Gladstein. 1994. MALIGN: A multiple sequence alignment program. J. Hered. 85:417–418. Wheeler, W. C., and R. L. Honeycutt. 1988. Paired sequence difference in ribosomal RNAs: Evolutionary and phylogenetic implications. Mol. Biol. Evol. 5:90–96. Wiley, E. O. 1978. The evolutionary species concept reconsidered. Syst. Zool. 27:88–92. Wiley, E. O. 1980. Phylogenetic systematics and vicariance biogeography. Syst. Bot. 5:194–220. Wiley, E. O. 1981. Phylogenetics. John Wiley and Sons, New York. Wilkinson, 1995. A comparison of two methods of character construction. Cladistics 11:297–308. Won, H., and S. S. Renner. 2003. Horizontal gene transfer from flowering plants to Gnetum. Proc. Natl. Acad. Sci. USA 100:10824– 10829. Zhang, J. 2003. Evolution by gene duplication: an update. Trends Ecol. Evol. 18:292–298. Zimmer, E. A., S. L. Martin, S. M. Beverely, Y. W. Kan, and A. C. Wilson. 1980. Rapid duplication and loss of genes coding for the ? chains of hemoglobin. Proc. Natl. Acad. Sci. USA 77:2158–2162. Zouine, M., Q. Sculo, and B. Labedan. 2002. Correct assignment of homology is crucial when genomics meets molecular evolution. Comp. Funct. Genomics 3:488–493. First submitted 29 July 2004; reviews returned 2 February 2005; final acceptance 7 June 2005 Associate Editor: Allan Baker error associated with their estimation (Huelsenbeck and Kirkpatrick, 1996). Here we explore the effects of a particular type of error in phylogenetic branch-length estimation, that caused by assuming an underparameterized model of molecular evolution, on the ? -statistic of Pybus and Harvey (2000), a statistic that tests for changes in the rate of diversification through time. Although we restrict our attention to the estimation of diversification rates, our findings are germane to any macroevolutionary inferences relying on the accurate estimation of phylogenetic branch lengths such as molecular dating (e.g., Downloaded from https://academic.oup.com/sysbio/article/54/6/973/1631776 by guest on 07 August 2020 974 SYSTEMATIC BIOLOGY VOL. 54 Welch and Bromham, 2005) and probabilistic methods for ancestral state reconstruction (e.g., Ronquist, 2004). In phylogenetic analyses, models of molecular evolution are often used to estimate branch lengths so that distances separating species on the reconstructed phylogeny are proportional to the time since the species shared a common ancestor multiplied by the substitution rate on the branches separating the taxa (Felsenstein, 2004). When recovering these branch lengths, models of nucleotide substitution are necessary to correct for the effect of superimposed substitutions as genetic differences between taxa accrue. Such models vary from simple to complex. The simplest model, the Jukes and Cantor (1969) model, assumes that all types of nucleotide substitutions are equiprobable, that all sites share a common substitution rate, and that base frequencies are equal. If these assumptions are violated, distances calculated using a Jukes-Cantor correction will likely be underestimates of the actual extent of evolutionary divergence, with misestimation particularly severe for branches connecting more divergent sequences (Yang et al., 1994; Lemmon and Moriarty, 2004). More sophisticated models allow rate heterogeneity across sites (Uzzell and Corbin, 1971; Jin and Nei, 1990), incorporate invariant sites (Hasegawa, 1987), or allow specific types of substitutions to occur at different rates (Kimura, 1980; Lanave et al., 1984; Felsenstein, 2004). The most heavily parameterized model commonly used in phylogenetic studies (the general time reversible model with invariant sites and -distributed rate heterogeneity, GTR + I + : Uzzell and Corbin, 1971; Jin and Nei, 1990; Rodr´?guez et al., 1990) requires the specification of 10 parameters (Felsenstein, 2004). | spa |
| dc.format.mimetype | application/pdf | |
| dc.identifier.doi | https://doi.org/10.1080/10635150500354647 | |
| dc.identifier.issn | ISSN: 1063-5157 | |
| dc.identifier.uri | https://repository.urosario.edu.co/handle/10336/27160 | |
| dc.language.iso | eng | spa |
| dc.publisher | Society of Systematic Biologists | spa |
| dc.relation.citationEndPage | 983 | |
| dc.relation.citationIssue | No. 6 | |
| dc.relation.citationStartPage | 973 | |
| dc.relation.citationTitle | Systematic Biology, Systematic Zoology | |
| dc.relation.citationVolume | Vol. 54 | |
| dc.relation.ispartof | Systematic Biology, Systematic Zoology, ISSN:1063-5157, Vol.54, No.6 (2005);pp.973-983 | spa |
| dc.relation.uri | https://watermark.silverchair.com/54-6-973.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAqkwggKlBgkqhkiG9w0BBwagggKWMIICkgIBADCCAosGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMUyTeAoVXFju4twNaAgEQgIICXLJnhfnRzgUsMxCtv2vDk3DfKnI3mZ5rAHgvUuUTX2aYd8mmqAteHc6bo4M_XmUFQImOqHXACMqs4uTwHwaGBJ6kqKIHB7NDt1Bq9LClZaan | spa |
| dc.rights.accesRights | info:eu-repo/semantics/openAccess | |
| dc.rights.acceso | Abierto (Texto Completo) | spa |
| dc.source | Systematic Biology, Systematic Zoology | spa |
| dc.source.instname | instname:Universidad del Rosario | |
| dc.source.reponame | reponame:Repositorio Institucional EdocUR | |
| dc.subject | Tasas de diversificación | spa |
| dc.subject | Filogenias moleculares | spa |
| dc.subject | Inferencia macroevolucionaria | spa |
| dc.subject | Prueba de simulación para el efecto de la infraparametrización | spa |
| dc.subject.keyword | Diversification Rates | spa |
| dc.subject.keyword | Molecular Phylogenies | spa |
| dc.subject.keyword | Macroevolutionary inference | spa |
| dc.subject.keyword | Simulation Test for Effect of Underparameterization | spa |
| dc.title | Underparameterized model of sequence evolution leads to bias in the estimation of diversification rates from molecular phylogenies. | spa |
| dc.title.TranslatedTitle | El modelo de parametrización de la evolución de la secuencia con parámetros insuficientes conduce al sesgo en la estimación de las tasas de diversificación de las filogenias moleculares | spa |
| dc.type | article | eng |
| dc.type.hasVersion | info:eu-repo/semantics/publishedVersion | |
| dc.type.spa | Artículo | spa |
