Biología (plan 1997) 2022-1

Segundo Semestre, Sistemática I

¡Bienvenid@s a la clase de SISTEMÁTICA en el semestre 2022-1!

En el semestre 2022-1 las clases serán del 20 de septiembre de 2021 al 28 de enero 2022

En esta clase aprenderemos a interpretar y reconstruir filogenias de diferentes grupos biológicos, así como las métodologías utilizadas para contruir e interpretar otros tipos de árboles.

EL ENLACE E INFORMACIÓN PARA LA PRIMERA SESIÓN (21 DE SEPTIEMBRE, 2021) SE SE LES ENVIARÁ POR CORREO ELECTRÓNICO EL DÍA VIERNES 17 DE SEPTIEMBRE.

Profesores:

Dr. Alejandro Zaldívar Riverón

M. en C. Jovana Magdalena Jasso Martínez

Correos de Profesores:

azaldivar@ib.unam.mx, jovanajasso@ciencias.unam.mx

Las clases se llevarán a cabo a través de las plataformas Google Meet y Zoom

Las tareas, ejercicios se enviarán a través de la plataforma Google Classroom.

IMPORTANTE

A los alumnos y alumnas que se inscriban a este cruso, les pedimos de la manera más atenta que toda la comunicación con los profesores la hagan usando sus correos @ciencias.unam.mx o bien desde @gmail.com

Esto es importante para no tener inconvenientes al ingresar a las sesiones virtuales de la plataforma de Google Classroom.

Forma de Evaluación

1. Tres exámenes parciales ---------- 50%

2. Tareas y prácticas ------------------- 40%

3. Participación ---------------------------10%

TOTAL ------------------------------------------ 100%

Software a emplear en las prácticas:

- PAUP*

- IQtree

- PartitionFinder

- MrBayes: Bayesian Inference of Phylogeny

- BEAST: Bayesian Evolutionary Analysis Sampling Trees

- ClustalW2, MAFFT

- Mesquite

Introducción a servidores de análisis como:

Galaxy (https://usegalaxy.org/)

CIPRES (http://www.phylo.org/)

CRONOGRAMA (A – Alejandro; J – Jovana)

Literatura de referencia

Baum, D. A., Smith, S. D., & Donovan, S. S. (2005). The tree-thinking challenge. Science, 310(5750), 979-980.

Baum, D. A., & Offner, S. (2008). Phylogenics & tree-thinking. The American Biology Teacher, 70(4), 222-229.

Bleidorn, C. 2017. Phylogenomics: An Introduction. Springer, Cham, Suiza.

Cracraft, J. 1983. Species concepts and speciation analysis. In Current ornithology (pp. 159-187). Springer, Boston, MA, EEUU.

Chifman, J., y Kubatko, L. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics, 30(23): 3317-3324.

De Pinna, M.C. 1991. Concept and tests of homology in the cladistic paradigm. Cladistics 7: 367-394.

De Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation. Endless form: species and speciation, 57-75.

De Queiroz, K. (2007). Species concepts and species delimitation. Systematic biology, 56(6), 879-886.

Doyle, J.J. y J. I Davis. 1998. Homology in molecular phylogenetics: A parsimony perspective. En: D.E. Soltis, P.S. Soltis y J.J. Doyle. Molecular systematics of plants II. DNA sequencing. Kluwer Academic Publishers. Boston, EEUU. pp:101-131.

Drummond, A. J., y Bouckaert, R. R. 2015. Bayesian evolutionary analysis with BEAST. Cambridge University Press.

Farris. J.J. 1974. Formal definitions of paraphyly and polyphyly. Syst. Zool. 23: 548-554.

Felstenstein, J. 1973. Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Systematic Zoology, 22: 240-249.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of molecular evolution, 17(6): 368-376.

Felsenstein, J. 2004. Inferring phylogenies (Vol. 2). Sunderland, MA: Sinauer associates.

Edwards, S. V., Liu, L., y Pearl, D. K. 2007. High-resolution species trees without concatenation. Proceedings of the National Academy of Sciences, 104(14): 5936-5941.

García-Sandoval, R. (2014). Why some clades have low bootstrap frequencies and high Bayesian posterior probabilities. Israel Journal of Ecology & Evolution, 60(1), 41-44.

Giribet, G. (2016). New animal phylogeny: future challenges for animal phylogeny in the age of phylogenomics. Organisms Diversity & Evolution, 16(2), 419-426.

Grant, T. y A. Kluge. 2003. Data exploration in phylogenetic inference: scientific, heuristic or neither. Cladistics, 19: 379-418.

Hennig, W. 1968. Elementos de una Sistemática Filogenética. EUDEBA, Buenos Aires, Argentina.

Hall, B.K. 1994. Homology: The hierarchical basis of comparative biology (ed.). Academic Press, Nueva York, EEUU.

Hillis, D. M. 1987. Molecular versus morphological approaches to systematics. Annual review of Ecology and Systematics, 18(1): 23-42.

Holder, M., y Lewis, P. O. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nature reviews genetics, 4(4): 275.

Kingman, J. F. 1982. On the genealogy of large populations. Journal of applied probability, 19(A): 27-43.

Kluge, A.G. 2001. Parsimony with and without scientific justification. Cladistics, 17: 199-210.

Knowles, L. L., y Kubatko, L. S. (Eds.). 2011. Estimating species trees: practical and theoretical aspects. John Wiley and Sons, New York.

Lister, A. M., & Climate Change Research Group. (2011). Natural history collections as sources of long-term datasets. Trends in ecology & evolution, 26(4), 153-154.

Liu, L., y Pearl, D. K. 2007. Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology, 56(3): 504- 514.

Liu, L., Yu, L., Kubatko, L., Pearl, D. K., y Edwards, S. V. 2009. Coalescent methods for estimating phylogenetic trees. Molecular Phylogenetics and Evolution, 53(1): 320-328.

Maddison, W.P. M.J. Donoghue y D.R. Maddison. 1984. Outgroup analysis and parsimony. Syst. Zool. 33: 83-103.

Mayr, E. 1942. Systematics and the Origin of Species from the viewpoint of a zoologist. Columbia University Press.

Morrone, J. J. 2000. El lenguaje de la cladística. UNAM, Dirección General de Publicaciones y Fomento Editorial.

Morrone, J. J. (2013). Sistemática. Fundamentos, métodos, aplicaciones. Facultad de Ciencias, UNAM, Ciudad de México.

Nichols, R. (2001). Gene trees and species trees are not the same. Trends in Ecology & Evolution, 16(7), 358-364.

Nixon, K.C. y H. Ochoterena. 2000. Taxonomía tradicional, cladística y construcción de hipótesis filogenéticas. En: H.M. Hernández, A. García Aldrete, F. Alvarez y M. Ulloa (compiladores). Enfoques contemporáneos para el estudio de la biodiversidad. UNAM – Fondo de Cultura Económica, México D.F., México.

Patterson, C. 1982. Morphological characters and homology. En: K.A. Joysey y E. Friday (eds.). Problems of phylogenetic reconstruction. Systematic Association Special Volume 21, pp. 21-74. Academic Press, Londres, Inglaterra.7.

Popper, K.R. 1980. The logic of scientific discovery. Routledge, Londres, Inglaterra (tercera reimpresión del original de 1959).

Rocha, L. A., Aleixo, A., Allen, G., et al. 2014. Specimen collection: An essential tool. Science, 344(6186): 814-815.

Saitou, N. y M. Nei. 1987. The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 6: 514-525

Salemi, M., Vandamme, A. M., y Lemey, P. (Eds.). 2009. The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing. Cambridge University Press.

Siddall, M.E. 2001. Philosophy and phylogenetic inference: A comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Cladistics, 17: 395-399.

Sneath, P.H.A., y R.R. Sokal. 1973. Numerical taxonomy. W.H. Freeman, San Francisco.

Stevens, P.F. 1991. Character states, morphological variation, and phylogenetic analysis: review. Systematic Botany 16(3): 553-583.

Wakeley, J. 2009. Coalescent theory: an introduction. Harvard University Press.

Wiens, J.J. (ed.). 2000. Phylogenetic analysis of morphological data. Smithsonian Institution Press, Washington, EEUU.

Wiley, E.O., D. Siegel-Causey, D.R. Brooks y V.A. Funk. 1991. The Compleat Cladist.

Literatura adicional

A Primer of Phylogenetic Procedures. The University of Kansas, Museum of Natural History, Special Publication 19, Kansas.

Barrowclough, G. F., Cracraft, J., Klicka, J., & Zink, R. M. (2016). How many kinds of birds are there and why does it matter?. PLoS One, 11(11): e0166307.

Bergsten, J. 2005. A review of long-branch attraction. Cladistics, 21: 163-193.

Breinholt, J. W., Earl, C., Lemmon, A. R., Lemmon, E. M., Xiao, L., y Kawahara, A. Y. 2017. Resolving relationships among the megadiverse butterflies and moths with a novel pipeline for Anchored Phylogenomics. Systematic Biology, 67(1): 78-93.

Brumfield, R. T., Liu, L., Lum, D. E., y Edwards, S. V. 2008. Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data. Systematic Biology, 57(5): 719-731.

Bryant, D., Bouckaert, R., Felsenstein, J., Rosenberg, N. A., y RoyChoudhury, A. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular biology and evolution, 29(8): 1917-1932.

Camin, J.H. y R.R. Sokal, 1965. A method for deducing branching sequences in phylogeny. Evolution, 19: 311-326.

Carpenter, J. M. 1988. Choosing among multiple equally parsimonious cladograms. Cladistics, 7: 351-366.

Cracraft, J. 1989. Speciation and its ontology: the empirical consequences of alternative species concepts for understanding patterns and process of differentiation. Speciation and its Consequences, 28-59.

De Leat, J. 1997. A reconsideration of three-item analysis, the use of implied weights in cladistics, and a practical application in Gentianaceae. Tesis de doctorado, Universidad Católica de Lovaina, Bélgica.

De Queiroz, K. 1985. The ontogenetic method for determining character polarity and its relevance to phylogenetic systematics. Syst. Zool., 34: 280-299.

De Queiroz, K. 2007. Species concepts and species delimitation. Systematic biology, 56(6): 879-886.

Doyle, J.J. 1992. Gene trees and species trees: molecular systematics as one character taxonomy. Syst. Bot., 17(1): 144-163.

Efron, B., Halloran, E., y Holmes, S. 1996. Bootstrap confidence levels for phylogenetic trees. Proceedings of the National Academy of Sciences, 93(23:, 13429-13429.

Erixon P., B. Svennblad, T. Britton, et al. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol., 52: 665-673.

Farris, J.S. 1969. A succesive approximations approach to character weighting. Syst. Zool., 18: 374-385.

Farris, J. 1970. Methods for computing Wagner trees. Syst. Zool., 19: 83-92.

Farris, J.S. 1990. Phenetics in camouflage. Cladistics, 6: 91-100.

Farris, J.S. 1999. Likelihood and inconsistency. Cladistics, 15: 199-204.

Farris, J.S. 2000. Corroboration vs. “strongest evidence”. Cladistics, 16: 385-393.

Farris, J.S., V.A. Albert, M. Kallersjo, D. Lipscomb y A.G. Kluge. 1996. Parsimony jackknifing outperforms neighbour- joining. Cladistics, 12: 99-124.

Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4): 783-791.

Harrison, R. G., & Larson, E. L. (2014). Hybridization, introgression, and the nature of species boundaries. Journal of Heredity, 105(S1), 795-809.

Mayden, R. 1997. A hierarchy of species concepts: the denouement in the saga of the species problem. En M. F. Claridge, H. A. Dawah y M. R. Wilson (eds.) Species: The Units of Biodiversity. Chapman & Hall. pp. 381–423.

Fitch, W. M. 1971. Towards defining the course of evolution: Minimum change for a specific topology. Syst. Zool., 20: 406-416.

Goloboff, P.A. 1998. Principios básicos de cladística. Sociedad Argentina de Botánica, Buenos Aires, Argentina.

Goloboff, P. A. 1999. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics, 15(4): 415-428.

Goloboff, P. A. 2003. Parsimony, likelihood, and simplicity. Cladistics, 19: 91-103.

Goldman, N. 1989. Fewest variables coding method for multistate characters. Syst. Zool., 38: 79-85.

Chase, M.W., D.E. Soltis, R.G. Olmstead, et al. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard., 80: 528-580.

Guindon S. y O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52: 696-704.

Hennig, W. 1950. Grundzüge einer Theorie der Phylogenetiscen Systematik. Deutscher Zentralverlag, Berlin, Alemania.

Hennig, W. 1966. Phylogenetic Systematics. University of Illinois Press, Chicago, EEUU.

Hill, G. E. 2017. The mitonuclear compatibility species concept. The Auk, 134(2): 393-409.

Hillis, D. M., y Bull, J. J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic biology, 42(2): 182-192.

Hillis, D. M., C. Moritz, y B. K. Mable y Olmstead, R. G. (Eds.). 1996. Molecular systematics (Vol. 23). Sunderland, MA: Sinauer Associates.

Heled, J., y Drummond, A. J. 2009. Bayesian inference of species trees from multilocus data. Molecular biology and evolution, 27(3): 570-580.

Huelsenbeck, P., F. Ronquist y B. Hall. s.f. MrBayes: A program for the bayesian inference of phylogeny. Versión en Pdf disponible en http://morphbank.ebc.uu.se/mrbayes

Huelsenbeck J.P. y K.M. Lander. 2003. Frequent inconsistency of parsimony under a simple model of cladogenesis. Syst. Biol., 52: 641-648.

Humphries, C.J. 1988. Ontogeny and systematics. Museo de Historia Natural de Londres, Inglaterra.

Jarvis, E. D., Mirarab, S., Aberer, A. J., et al. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. Science, 346(6215): 1320-1331.

Kitching, I.J., P.L. Forey, C.J. Humphries y D.M. Williams. 1998. Cladistics: The Theory and Practice of Parsimony Analysis. The Systematic Association Publication 11. Oxford Science Publications, Oxford, Inglaterra.

Keller Pérez, R. A. 1998. Bases metodológicas del uso de grupo externo en análisis cladísticos. Tesis, Biólogo. Facultad de Ciencias, UNAM. México D.F., México.

Kluge, A. G. 1985. Ontogeny and phylogenetic systematics. Cladistics, 1: 13-27.

Kluge, A. G. y J. Wolf. 1993. Cladistics: What’s in a word?. Cladistics, 9: 183-199.

Knowles, L. L., y Carstens, B. C. 2007. Delimiting species without monophyletic gene trees. Systematic biology, 56(6): 887-895.

Knowles, L. L. 2009. Estimating species trees: methods of phylogenetic analysis when there is incongruence across genes. Systematic Biology, 58(5): 463-467.

Kubatko, L. S., y Degnan, J. H. 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Systematic Biology, 56(1): 17-24.

Leaché, A. D., Banbury, B. L., Felsenstein, J., De Oca, A. N. M., y Stamatakis, A. 2015. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Systematic biology, 64(6): 1032-1047.

Lemmon A.R. y E.C. Moriarty. 2004. The importance of proper model assumption in Bayesian phylogenetics. Syst. Biol., 53: 265-277.

Lipscomb, D. 1998. Basics of Cladistic Analysis. George Washington University, Washington DC. EUA.

Liu, L., Pearl, D. K., Brumfield, R. T., y Edwards, S. V. 2008. Estimating species trees using multiple‐allele DNA sequence data. Evolution 62(8): 2080-2091.

Mabee, P. M. 1989. An empirical rejection of the ontogenetic polarity criterion. Cladistics, 5: 409-416.

Maddison, W.P. 1993. Missing data versus missing characters in phylogenetic analysis. Syst. Biol., 42: 576-581.

Maddison, W. P., y Knowles, L. L. 2006. Inferring phylogeny despite incomplete lineage sorting. Systematic biology, 55(1): 21-30.

McCormack, J. E., Huang, H., y Knowles, L. L. 2009. Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design. Systematic biology, 58(5): 501-508.

McCormack, J. E., Faircloth, B. C., Crawford, N. G., Gowaty, P. A., Brumfield, R. T., y Glenn, T. C. 2012. Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis. Genome research, 22(4): 746-754.

McGuire, J. A., Witt, C. C., Remsen Jr, J. V., Corl, A., Rabosky, D. L., Altshuler, D. L., y Dudley, R. 2014. Molecular phylogenetics and the diversification of hummingbirds. Current Biology, 24(8): 10-916.

Minin V., Z. Abdo, P. Joyce, et al. 2003. Performance-based selection of likelihood models for phylogeny estimation. Syst. Biol., 52: 674-683.

Mirarab, S., Bayzid, M. S., Boussau, B., y Warnow, T. 2014. Statistical binning enables an accurate coalescent-based estimation of the avian tree. Science, 346(6215): 1250463.

Misof, B., Liu, S., Meusemann, K., Peters, et al. 2014. Phylogenomics resolves the timing and pattern of insect evolution. Science, 346(6210): 763-767.

Nixon, K.C. 1996. Paleobotany in Cladistics and Cladistics in paleobotany: enlightenment and uncertainty. Review of Palaeobotany and Palynology, 90: 361-373.

Nixon, K. C., y Wheeler, Q. D. 1990. An amplification of the phylogenetic species concept. Cladistics, 6(3): 211-223.

Nixon, K.C. 1999. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics, 15(4): 4407-414.

Nixon, K.C. y J.M. Carpenter. 1993. On outgoups. Cladistics, 9: 413-426.

Nixon, K.C. y J.M. Carpenter. 1996. On simultaneous analyses. Cladistics 12: 221-241.Nylander, J.A.A., F. Ronquist y J.P. Huelsenbeck, et al. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol., 53: 47-67.

Pimentel, R.A. y R. Riggins. 1987. The nature of cladistic data. Cladistics 3(3): 201-209.

Platnick, N. Paraphyletic and polyphyletic groups. Syst. Zool., 26: 195-200.

Pol, D. 2004. Empirical problems of the hierarchical likelihood ratio test for model selection. Syst. Biol., 53: 949-962.

Prum, R. O., Berv, J. S., Dornburg, A., Field, D. J., Townsend, J. P., Lemmon, E. M., y Lemmon, A. R. 2015. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature, 526(7574): 569.

Rabosky, D. L. 2014. Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees. PloS one, 9(2): e89543.

Rabosky, D. L., Santini, F., Eastman, J., Smith, S. A., Sidlauskas, B., Chang, J., y Alfaro, M. E. 2013. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nature communications, 4, 1958.

Rabosky, D. L., Chang, J., Title, P. O., et al. 2018. An inverse latitudinal gradient in speciation rate for marine fishes. Nature, 559(7714): 392.

Rice, K.A., M.J. Donoghue y R.G. Olmstead. 1997. Analyzing large data sets: rbcL 500 revised. Systematic Biology, 46: 554-563.

Roch, S., y Warnow, T. 2015. On the robustness to gene tree estimation error (or lack thereof) of coalescent-based species tree methods. Systematic Biology, 64(4), 663-676.

Schulmeister, S. 2004. Inconsistency of maximum parsimony revisited. Syst. Biol., 53: 521-528.

Schuh, R. T. 2000. Biological Systematics: Principles and Applications. Cornell University Press, Ithaca, NY, EUA.

Siddall, M.E. 1998. Success of parsimony in the four taxon case: long-branch repultion by likelihood in the Farris zone. Cladistics, 14: 209-220.

Siddall, M.E. y M.F. Whiting. 1999. Long branch abstractions. Cladistics, 15: 9-24.

Simmons, M. y H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol., 49(2): 369-381.

Simmons, M. P., H. Ochoterena y T. G. Carr. 2001. Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Syst. Biol., 50: 454-462.

Simmons, M.P. and M. Miya. 2004. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches. Mol. Phyl. Evol., 31: 351-362.

Simpson, G. G. 1944. Tempo and mode in evolution (No. 15). Columbia University Press.

Sokal, R.R., J.H. Camin, F.J. Rohlf y P.H.A. Sneath. 1965. Numerical taxonomy: Some points of view. Systematic Zoology, 14: 237-243.

Song, S., Liu, L., Edwards, S. V., y Wu, S. 2012. Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proceedings of the National Academy of Sciences, 109(37): 14942-14947.

Sosa, V. y E. de Luna. 1998. Morphometrics and character state recognition for cladistic analysis in the Bletia reflexa complex (Orchidaceae). Pl. Syst. Evol. 212: 185-213.

Strait, D.S., M.A. Moniz y P.T. Strait. 1996. Finite mixture coding: A new approach to coding continuous characters. Syst. Biol., 45: 67-78.

Strauch Jr., J.G. 1978. The phylogeny of the Charadriiformes: A new estimate using the method of character compatibility analysis. Transactions of the Zoological Society of London, 34: 263–345.

Swiderski, D.L., M.L. Zelditch y W. L. Fink. 1998. Why morphometrics is not special: Coding quantitative data for phylogenetic analysis. Syst. Biol.,47: 508-519.

Vaidya, G., Lepage, D., y Guralnick, R. 2018. The tempo and mode of the taxonomic correction process: How taxonomists have corrected and recorrected North American bird species over the last 127 years. PloS one, 13(4): e0195736.

Watrous I. E. & D. Wheeler. 1981. The outgroup comparison method of character analysis. Syst. Zool.,30: 1-11.

Wheeler, W. C. 1990. Nucleic acid sequence phylogeny and random outgroups. Cladistics, 6: 363-367.

Wheeler, Q., y Meier, R. (Eds.). 2000. Species concepts and phylogenetic theory: a debate. Columbia University Press.

Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., et al. 2014. Phylotranscriptomic analysis of the origin and early diversification of land plants. Proceedings of the National Academy of Sciences, 111(45): E4859-E4868.

Wiley, E. O. 1978. The evolutionary species concept reconsidered. Systematic zoology, 27(1), 17-26.

Yang Z.H. y A.D. Yoder. 2003. Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute- looking mouse lemur species. Syst. Biol., 52: 705-716.

Yang Z, y B. Rannala. 2005. Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol., 54: 455-470.

Zink, R. M., y Klicka, J. 2018. Species Concepts and Speciation Analysis. Ornithology: Foundation, Analysis, and Application, 39.