Abstract
This chapter reviews Hennigian, maximum likelihood, and Bayesian approaches to quantitative phylogenetic analysis and discusses their strengths and weaknesses and protocols for assessing the relative robustness of one’s results. Hennigian approaches are justified by the Darwinian concepts of phylogenetic conservatism and the cohesion of homologies, embodied in Hennig’s Auxiliary Principle, and applied using outgroup comparisons. They use parsimony as an epistemological tool. Maximum likelihood and Bayesian likelihood approaches are based on an ontological use of parsimony, choosing the simplest model possible to explain the data. All methods identify the same core of unambiguous data in any given data set, producing highly similar results. Disagreements most often stem from insufficient numbers of unambiguous characters in one or more of the data types. If analyses based on different types of data or using different methods of phylogeny reconstruction, or some combination of both, do not produce the same results, more data are needed. New developments in the application of phylogenetic methods in paleoanthropology have resulted in major advances in the understanding of morphological character development, modes of speciation, and the recent evolutionary history of the human species.
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References
Adams E (1972) Consensus techniques and the comparison of taxonomic trees. Syst Zool 21:390–397
Antón SC (2003) Natural history of Homo erectus. Yearb Phys Anthropol 46:126–170
Barnard GA, Bayes T (1958) Studies in the history of probability and statistics: IX. Thomas Bayes’s essay towards solving a problem in the doctrine of chances. Biometrika 45:293–315
Begun DR, Ward CV, Rose MD (eds) (1997) Function, phylogeny and fossils: Miocene hominoid evolution and adaptations. Plenum Press, New York, pp 389–415
Bremer K (1988) The limits of amino-acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795–803
Brillouin L (1962) Science and information theory, 2nd edn. Academic, New York
Brooks DR (1981) Classifications as languages of empirical comparative biology. In: Funk VA, Brooks DR (eds) Advances in cladistics: proceedings of the first meeting of the Willi Hennig Society. New York Botanical Garden, New York, pp 61–70
Brooks DR, McLennan DA (2002) The nature of diversity. Chicago University Press, Chicago
Brooks DR, O’Grady RT, Wiley EO (1986) A measure of the information content of phylogenetic trees, and its use as an optimality criterion. Syst Zool 35:571–581
Camin JH, Sokal RR (1965) A method for deducing branching sequences in phylogeny. Evolution 19:311–326
Cardini A, Elton S (2008) Does the skull carry a phylogenetic signal? Evolution and modularity in the guenons. Biol J Linn Soc 93:813–834
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution 21:550–570
Charlesworth MJ (1956) Aristotle’s razor. Philos Stud 6:105–112
Collard M, Wood B (2000) How reliable are human phylogenetic hypotheses? Proc Natl Acad Sci USA 97:5003–5006
Collard M, Wood B (2001) How reliable are current estimates of fossil catarrhine phylogeny? An assessment using extant great apes and old world monkeys. In: de Bonis L, Koufos G, Andrews P (eds) Phylogeny of the neogene hominoid primates of Eurasia. Cambridge University Press, Cambridge, pp 118–150
Collard M, Wood B (2007) Hominin homoiology: an assessment of the impact of phenotypic plasticity on phylogenetic analyses of humans and their fossil relatives. J Hum Evol 52:573–584
Colless DH (1966) A note on Wilson’s consistency test for phylogenetic hypotheses. Syst Zool 15:358–359
Darwin C (1859) On the origin of species. John Murray, London
Darwin C (1872) On the origin of species, 6th edn. John Murray, London
de Queiroz K, Poe S (2001) Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl R. Popper’s writings on corroboration. Syst Biol 50:305–321
de Queiroz K, Poe S (2003) Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper’s degree of corroboration. Syst Biol 52:352–367
Edwards AWF (1972) Likelihood. Cambridge University Press, Cambridge
Edwards AWF (1996) The origin and early development of the method of minimum evolution for the reconstruction of phylogenetic trees. Syst Biol 45:79–91
Edwards AWF, Cavalli-Sforza LL (1963) The reconstruction of evolution. Ann Hum Genet 27:105–106
Engelmann GF, Wiley EO (1977) The place of ancestor-descendant relationships in phylogeny reconstruction. Syst Zool 26:1–11
Farris JS (1970) Methods of computing Wagner trees. Syst Zool 19:83–92
Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668
Farris JS (1973) A probability model for inferring evolutionary trees. Syst Zool 22:250–256
Farris JS (1979) The information content of the phylogenetic system. Syst Zool 28:483–519
Farris JS (1983) The logical basis of phylogenetic analysis. In: Platnick NI, Funk VA (eds) Advances in cladistics, vol 2. Columbia University Press, New York
Farris JS (1989) The retention index and rescaled consistency index. Cladistics 5:417–419
Farris JS, Kluge AG, Eckardt MJ (1970) A numerical approach to phylogenetic systematics. Syst Zool 19:172–191
Farris JS, Albert VA, Källersjö M, Lipscomb D, Kluge AG (1996) Parsimony jackknifing outperforms neighbour-joining. Cladistics 12:99–124
Felsenstein J (1968) Statistical inference and the estimation of phylogenies. Ph.D. thesis, University of Chicago
Felsenstein J (1973) Maximum likelihood and minimum steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22:240–249
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (1983) Parsimony in systematics: biological and statistical issues. Ann Rev Ecol Syst 14:313–333
Felsenstein J (1985a) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Felsenstein J (1985b) Statistical inference and the estimation of phylogenies. Ph.D. dissertation, University of Chicago, Chicago
Felsenstein J (2004) Inferring phylogenies. Sinauer Associates, Sunderland
Fisher RA (1922) On the mathematical foundations of theoretical statistics. Phil Trans R Soc Lond Ser A 222:309–368
Fleagle JG, Gilbert CC, Baden AL (2010) Primate cranial diversity. Am J Phys Anthropol 142:565–578
Gatlin L (1975) Information theory and the living system. Columbia University Press, New York
Gilbert CC (2011) Phylogenetic analysis of the African papionin basicranium using 3-D geometric morphometrics: the need for improved methods to account for allometric effects. Am J Phys Anthropol 144:60–71
Gissi C, Reyes A, Pesole G, Saccone C (2000) Lineage-specific evolutionary rate in mammalian mtDNA. Mol Biol Evol 17:1022–1031
Goldman N (1990) Maximum likelihood inference of phylogenetic trees, with special reference to a poisson process model of DNA substitution and to parsimony analysis. Syst Zool 39:345–361
Goloboff PA (2003) Parsimony, likelihood and simplicity. Cladistics 19:91–103
Gómez Robles A, Polly PD (2012) Morphological integration in the hominin dentition: evolutionary, developmental, and functional factors. Evolution 66:1024–1043
Goswami A (2006) Morphological integration in the carnivoran skull. Evolution 60:169–183
Goswami A, Polly PD (2010) The influence of modularity on cranial morphological disparity in Carnivora and Primates (Mammalia). PLoS ONE 5:e9517
Green RE, Krause J, Ptak S, Briggs A, Ronan M, Simons J, Du L, Egholm M, Rothberg J, Paunovic M, Pääbo S (2006) Analysis of one million base pairs of Neanderthal DNA. Nature 444:330–336
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W et al (2010) A draft sequence of the Neandertal genome. Science 328:710–722
Grehan JR, Schwartz JH (2009) Evolution of the second orangutan: phylogeny and biogeography of hominid origins. J Biogeogr 36:1823–1844
Groves C (1978) Phylogenetic and population systematics of the mangabeys (Primates: Cercopithecoidea). Primates 19:1–34
Harper CW Jr (1979) A Bayesian probability view of phylogenetic systematics. Syst Zool 28:547–553
Hastings WK (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57:97–109
Hawks J (2004) How much can cladistics tell us about early hominid relationships? Am J Phys Anthropol 125:207–219
Hendy MD, Penny D (1982) Branch and bound algorithms to determine minimal evolutionary trees. Math Biosci 59:277–290
Hennig W (1950) Grundzüge einer theorie der phylogenetischen systematik. Deutscher Zentralverlag, Berlin
Hennig W (1966) Phylogenetic systematics. Illinois University Press, Urbana
Hillis DM, Bull JJ, White ME, Badgett MR, Molineaux IJ (1992) Experimental phylogenetics: generation of a known phylogen. Science 255:589–592
Hillis DM, Bull JJ, White ME, Badgett MR, Molineaux IJ (1993) Experimental approaches to phylogenetic analysis. Syst Biol 42:90–92
Hillis DM, Huelsenbeck JP, Swofford DL (1994) Hobgloblin of phylogenetics? Science 369:363–364
Huelsenbeck JP (1997) Is the Felsenstein zone a fly trap? Syst Biol 46:69–74
Huelsenbeck JP, Crandall KA (1997) Phylogeny estimation and hypothesis testing using maximum likelihood. Ann Rev Ecol Syst 28:437–466
Huelsenbeck JP, Hillis DM (1993) Success of phylogenetic methods in the four-taxon case. Syst Biol 42:247–264
Huelsenbeck JP, Nielsen R (1999) Effect of nonindependent substitution on phylogenetic accuracy. Syst Biol 48:317–328
Huelsenbeck JP, Rannala B (1997a) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227–232
Huelsenbeck JP, Rannala B (1997b) Maximum likelihood of phylogenies using stratigraphic data. Paleobiology 23:174–180
Huelsenbeck JP, Ronquist B, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314
Huelsenbeck JP, Larget B, Miller RE, Ronquist F (2002) Potential applications and pitfalls of Bayesian inference in phylogeny. Syst Biol 51:673–688
Jaynes ET (1957a) Information theory and statistical mechanics I. Phys Rev 106:620
Jaynes ET (1957b) Information theory and statistical mechanics II. Phys Rev 108:171
Kelchner SA, Thomas MA (2007) Model use in phylogenetics: nine key questions. Trends Ecol Evol 22:87–94
Kimbel W, Lockwood C, Ward C, Leakey M, Rak Y, Johanson D (2006) Was Australopithecus anamensis ancestral to A. afarensis? A case of anagenesis in the hominin fossil record. J Hum Evol 51:134–152
Kluge AG (1990) Species as historical individuals. Biol Philos 5:417–431
Kluge AG (1991) Boine snake phylogeny and research cycles. Misc Publ Mus Zool Univ Mich 178:1–58
Kluge AG (1997) Testability and the refutation and corroboration of cladistic hypotheses. Cladistics 13:81–96
Kluge AG (1999) The science of phylogenetic systematics: explanation, prediction, and test. Cladistics 15:429–436
Kluge AG (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
Kluge AG (2003) On the deduction of species relationships: a précis. Cladistics 19:233–239
Kluge AG, Farris JS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32
Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature: 1–4
Kullbach S (1951) Information theory and statistics. Wiley, New York
Lehtonen S, Sääksjärvi IE, Ruokolainen K, Tuomisto H (2010) Who is the closest extant cousin of humans? Total-evidence approach to hominid phylogenetics via simultaneous optimization. J Biogeogr 38:805–808
Lehtonen S, Tuomisto H, Sääksjärvi IE, Ruokolainen K (2012) On cladistics and human–ape relationships. J Biogeogr 39:1743–1748
Lewis GN (1930) The principle of identity and the exclusion of quantum states. Phys Rev 36:1144–1153
Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Syst Biol 50:913–925
Li S (1996) Phylogenetic tree construction using Markov Chain Monte Carlo. Ph.D. dissertation, Ohio State University, Columbus
Lieberman D (1999) Homology and hominid phylogeny: problems and potential solutions. Evol Anthropol 7:142–151
Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605–612
Lundberg JG (1972) Wagner networks and ancestors. Syst Zool 18:1–32
Maddison WP, Donoghue MJ, Maddison DR (1984) Outgroup analysis and parsimony. Syst Zool 33:83–103
Mau B (1996) Bayesian phylogenetic inference via Markov chain Monte Carlo Methods. Ph.D. dissertation, University of Wisconsin, Madison (abstract)
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21:1087–1092
Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prufer K et al (2012) A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–226
Mitchell PC (1901) On the intestinal tract of birds. Trans Linn Soc Lond Zool 8:173–275
Mitchell PC (1905) On the intestinal tract of mammals. Trans Zool Soc Lond 17:437–536
Mitchell A, Mitter C, Regier JC (2000) More taxa or more characters revisited: combining data from nuclear protein coding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst Biol 49:202–224
Neyman J (1974) Molecular studies: a source of novel statistical problems. In: Gupta SS, Yackel J (eds) Statistical decision theory and related topics. Academic, New York, pp 1–27
Nunn CL (2011) The comparative approach in evolutionary anthropology and biology. University of Chicago Press, Chicago
O’Leary MA, Gatesy J (2008) Impact of increased character sampling on the phylogeny of Cetartiodactyla (Mammalia): combined analysis including fossils. Cladistics 24:397–442
Pagel MD (1992) A method for the analysis of comparative data. J Theor Biol 156:431–442
Pagel M, Meade A, Barker D (2004) Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673–684
Penny D, Hendy MD, Steel MA (1992) Progress with methods for constructing evolutionary trees. Trends Ecol Evol 7:73–79
Popper KR (1968) The logic of scientific discovery. Harper and Row, New York
Popper KR (1997) The demarcation between science and metaphysics. In: Schilpp PA (ed) The philosophy of Rudolph Carnap. Open Court, La Salle, pp 183–226
Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics 14:817–818
Prim RC (1957) Shortest connection networks and some generalizations. Bell Syst Tech J 36:1389–1401
Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U et al (2010) Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060
Reich D, Patterson N, Kircher M, Delfin F, Nandineni MR, Pugach I, Ko AM-S, Ko Y-C, Jinam TA et al (2011) Denisova admixture and the first modern human dispersals into Southeast Asia and Oceania. Am J Hum Genet 89:516–528
Rindal E, Brower AVZ (2011) Do model-based phylogenetic analyses perform better than parsimony? A test with empirical data. Cladistics 27:331–334
Rodriguez F, Oliver JL, Marin A, Medina JR (1990) The general stochastic model of nucleotide substitution. J Theor Biol 142:485–501
Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:796–804
Ronquist F (2004) Bayesian inference of character evolution. Trends Ecol Evol 19:475–481
Rose KD, Chester SGB, Dunn RH, Boyer DM, Bloch JI (2011) New fossils of the oldest North American euprimate Teilhardina brandti (Omomyidae) from the Paleocene–Eocene thermal maximum. Am J Phys Anthropol 146:281–305
Shannon C (1948) A mathematical theory of communication. Bell Syst Tech J 27:379–423
Siddall ME, Kluge AG (1997) Probabilism and phylogenetic inference. Cladistics 13:313–336
Slice DE (2005) Modern morphometrics in physical anthropology. Springer, New York
Slice DE (2007) Geometric morphometrics. Ann Rev Anthropol 36:261–281
Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. W.H. Freeman, San Francisco
Sober E (1988) Reconstructing the past. Parsimony, evolution, and inference. MIT Press, Cambridge
Sokal RR, Sneath PHA (1963) Numerical taxonomy. W.H. Freeman, San Francisco
Steel M, Penny D (2000) Parsimony, likelihood, and the role of models in molecular phylogenetics. Mol Biol Evol 17:839–850
Steel MA, Hendy MD, Penny D (1993) Parsimony can be consistent! Syst Biol 42:581–587
Strait DS (2013) Human systematics. In: Begun DR (ed) A companion to paleoanthropology. Wiley, Chichester, pp 37–54
Strait D, Grine F (2004) Inferring hominoid and early hominid phylogeny using craniodental characters: the role of fossil taxa. J Hum Evol 47:399–452
Strait DS, Grine FE, Moniz MA (1997) A reappraisal of early hominid phylogeny. J Hum Evol 23:17–82
Strasser E, Delson E (1987) Cladistic analysis of cercopithecoid relationships. J Hum Evol 16:81–99
Swofford DL (1998) Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland
Swofford DL, Maddison WP (1987) Reconstructing ancestral character states under Wagner parsimony. Math Biosci 87:199–229
Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics, 2nd edn. Sinauer Associates, Sunderland, pp 407–514
Tribus M, McIrvine MC (1971) Energy and information. Sci Am 225:179–188
von Cramon-Taubadel N (2009) Revisiting the homoiology hypothesis: the impact of phenotypic plasticity on the reconstruction of human population history from craniometric data. J Hum Evol 57:179–190
von Cramon-Taubadel N, Smith HF (2012) The relative congruence of cranial and genetic estimates of hominoid taxon relationships: implications for the reconstruction of hominin phylogeny. J Hum Evol 62:640–653
Wagner WH Jr (1952) The fern genus Diellia: structure, affinities, and taxonomy. Univ Calif Publ Bot 26:1–212
Wagner WH Jr (1961) Problems in the classification of ferns. In: Recent advances in botany. From lectures and symposia presented to the IX International Botanical Congress, Montreal, 1959. University of Toronto Press, Toronto, pp 841–844
Wagner WH Jr (1969) The construction of a classification. In: Systematic biology. National Academy of Science USA, Publication 1692, pp 67–90
Wagner WH Jr (1980) Origin and philosophy of the groundplan-divergence method of cladistics. Syst Bot 5:173–193
Wagner PJ (1998) A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa. Paleobiology 24:430–449
Watrous LE, Wheeler QD (1981) The outgroup comparison method of character analysis. Syst Zool 30:1–11
Wenzel JW, Carpenter JM (1994) Comparing methods: adaptive traits and tests of adaptation. In: Eggleton P, Vane-Wright RI (eds) Phylogenetics and ecology. Academic, London, pp 79–101
Wenzel JW, Siddall ME (1999) Noise. Cladistics 15:51–64
Wiens JJ (2009) Paleontology, genomics, and combined-data phylogenetics: can molecular data improve phylogeny estimation for fossil taxa? Syst Biol 58:87–99
Wiens JJ, Kuczynski CA, Townsend T, Reeder TW, Mulcahy DG, Sites JW (2010) Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa. Syst Biol 59:674–688
Wiley EO (1975) Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Syst Zool 24:233–243
Wiley EO (1981) Phylogenetics: the theory and practice of phylogenetic systematics. Wiley, New York
Wiley EO, Lieberman BS (2011) Phylogenetics: the theory and practice of phylogenetic systematics, 2nd edn. Wiley-Blackwell, Hoboken
Wiley EO, Siegel-Causey DJ, Brooks DR, Funk VA (1991) The compleat cladist: a primer of phylogenetic procedures. Mus Nat Hist Univ Kansas Spec Publ 19:1–158
Wiley DF, Amenta N, Alcantara DA, Ghosh D, Kil YJ, Delson E, Harcourt-Smith W, Rohlf FJ, St John K, Hamman B (2005) Evolutionary morphing. Proc IEEE Vis 2005:431–438
Wilson EO (1965) A consistency test for phylogenies based on contemporaneous species. Syst Zool 14:214–220
Wilson EO (1967) The validity of the “consistency test” for phylogenetic hypotheses. Syst Zool 16:104
Yang Z (1994) Statistical properties of the maximum likelihood method of phylogenetic estimation and comparison with distance matrix methods. Syst Biol 43:329–342
Yang Z (1996) Phylogenetic analysis using parsimony and likelihood methods. J Mol Evol 42:294–307
Yang Z, Bielawski JP (2000) Statistical methods for detecting molecular adaptation. Trends Ecol Evol 15:496–503
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Folinsbee, K.E., Evans, D.C., Fröbisch, J., Brooks, D.R., Tsuji, L.A. (2015). Quantitative Approaches to Phylogenetics. In: Henke, W., Tattersall, I. (eds) Handbook of Paleoanthropology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39979-4_5
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