Principles and Practice of

Phylogenetic Systematics

 

Lecture Notes

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  1.  Models

  2.  Species concepts

Harrison, R.G.  1998.  Linking evolutionary pattern and process: the relevance of species concepts for the study of speciation.  Pp. 19-31 in: Endless Forms: Species and Speciation.  D.J. Howard and S.T. Berlocher (eds.).  Oxford Univ. Press, New York.  [pdf]

Hull, D.L.  1997.  The ideal species concept -- and why we can't get it.  Pp. 357-380 in: Species: the Units of Biodiversity.  M.F. Claridge, H.A. Dawah, and M.R. Wilson (eds.). Chapman & Hall, London.  [pdf]

Mayden, R.L.  1977.  A hierarchy of species concepts: the denouement in the sage of the species problem.  Pp. 381-424 in: Species: the Units of Biodiversity.  M.F. Claridge, H.A. Dawah, and M.R. Wilson (eds.). Chapman & Hall, London.  [pdf]

Noor, M.A.F.  2002.  Is the biological species concept showing its age?  Trends in Ecology and Evolution 17:153-154.  [pdf]

Pigliucci, M.  2003.  Species as family resemblance concepts: the (dis-)solution of the species problem?  BioEssays 25:596-602.  [pdf]

Templeton, A.R.  1998.  Species and speciation: geography, population structure, ecology, and gene trees.  Pp. 32-43 in: Endless Forms: Species and Speciation.  D.J. Howard and S.T. Berlocher (eds.).  Oxford Univ. Press, New York.  [pdf]

Wiens, J.J.  2004.  What is speciation and how should we study it?  American Naturalist 163:914-923.  [pdf]

  3.  Characters and homology

Fristrup, K.M.  2001.  A history of character concepts in evolutionary biology.  Pp. 13-35 in: The Character Concept in Evolutionary Biology.  G.P. Wagner (ed.).  Academic Press, San Diego.  [pdf]

Hould, D.  2001.  Characters as the units of evolutionary change.  Pp. 109-140 in: The Character Concept in Evolutionary Biology.  G.P. Wagner (ed.).  Academic Press, San Diego.  [pdf]

Lauder, G.V.  1994.  Homology, form, and function.  Pp. 152-197 in: Homology: the Hierarchical Basis of Comparative Biology.  B.K. Hall (ed.).  Academic Press, San Diego.  [pdf]

    4.  Character coding

Poe, S. and J.J. Wiens.  2000.  Character selection and the methodology of morphological phylogenetics.  Pp. 20-36 in: Phylogenetic Analysis of Morphological Data.  J.J. Wiens (ed.).  Smithsonian Institution Press, Washington DC.  [pdf]

Stevens, P.F.. 1991.  Character states, morphological variation, and phylogenetic analysis: a review. Systematic Botany 16:553-583.  [pdf]

Wiens, J.J.  1995.  Polymorphic characters in phylogenetic systematics.  Systematic Biology 44:482-500.  [pdf]

    5.  History of phylogenetic methods (Adam Ferguson)

Edwards, A.W.F. and L.L. Cavalli-Sforza.  1964.  Reconstruction of evolutionary trees.  Pp. 67-76 in: Phenetic and Phylogenetic Classification.  V.H. Haywood and J. McNeill (eds.).  Systematics Association Publ. No. 6., London.  [pdf]

Felsenstein, J. 1982.  Numerical methods for inferring evolutionary trees. Quarterly Review of Biology57:379-404.  [pdf]

Felsenstein, J. 2001.  The troubled growth of statistical phylogenetics. Systematic Biology 50:465-467.  [pdf]

  6.  Trees and networks

de Queiroz, K. and D.A. Good.  1997.  Phenetic clustering in biology: a critique.  Quarterly Review of Biology 72:3-30.  [pdf]

Huelsenbeck, J.P. and B. Rannala.  1997.  Phylogenetic methods come of age: testing hypotheses in an evolutionary context.  Science 276:227-232.  [pdf]

Maddison, W.P., M.J. Donoghue, and D.R. Maddison.  1984.  Outgroup analysis and parsimony.  Systematic Biology 33:83-103.  [pdf]

Milinkovitch, M.C. and J. Lyons-Weiler.  1998.  Finding optimal ingroup topologies and convexities when the choice of outgroups is not obvious.  Molecular Phylogenetics and Evolution 9:348-357.  [pdf]

Steel, M. and D. Penny.  2000.  Parsimony, likelihood, and the role of models in molecular phylogenetics.  Molecular Biology and Evolution 17:839-850. [pdf]

Strauss, R.E.  1993.  Phylogenetics. Pp. 55-68 in: Advances in Computer Methods in Systematic Biology: Artificial Intelligence, Databases, Computer Vision.  R. Fortuner (ed.).  Johns Hopkins University Press, Baltimore.  [pdf]

  7. Ultrametric and additive trees

Brown, J.K.M.  1994.  Bootstrap hypothesis tests for evolutionary trees and other dendrograms.  Proceedings of the National Academy of Sciences 91:12293-12297.  [pdf]

Faith, D.P.  2001.  Distance methods and the approximation of most-parsimonious trees.  Systematic Zoology 34:312-325.  [pdf]

Farris, J.S.  1969.  On the cophenetic correlation coefficient.  Systematic Zoology 18:279-285.  [pdf]

Kim, J., F.J. Rohlf, and R.R. Sokal.  1993. The accuracy of phylogenetic estimation using the neighbor-joining method.  Evolution 47:471-486.  [pdf]

Lance, G.N. and W.T. Williams.  1967.  A general theory of classificatory sorting strategies.  I.  Hierarchical systems.  Computer Journal 9:373-380.  [pdf]

Rohlf, F.J.  1970.  Adaptive hierarchical clustering schemes.  Systematic Zoology 18:58-82.  [pdf]

  8.  Hybridization and reticulation (Peter Larsen)

Legendre, P. and V. Makarenkov.  2002.  Reconstruction of biogeographic and evolutionary networks using reticulograms.  Systematic Biology 51:199-216.  [pdf]

McDade, L.A.  1997.  Hybrids and phylogenetic systematics III.  Comparison with distance methods.  Systematic Botany 22:669-683.  [pdf]

Posada, D. and K.A. Crandall.  2001.  Intraspecific gene genealogies: trees grafting into networks.  Trends in Ecology and Evolution 16:37-45.  [pdf]

Reeves, P.A. and C.M. Richards.  2007.  Distinguishing terminal monophyletic groups from reticulate taxa: performance of phenetic, tree-based, and network procedures.  Systematic Biology 56:302-320.  [pdf]

  9.  Minimum-evolution trees

Adams, E.N.  1972.  Consensus techniques and the comparison of taxonomic trees.  Systematic Zoology 21:390-397.  [pdf]

Archie, J.W.  1989.  Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index.  Systematic Zoology 38:253-269.  [pdf]

Farris, J.S.  1970.  Methods for computing Wagner trees.  Systematic Zoology 18:83-92.  [pdf]

Fitch, W.M.  1971.  Toward defining the course of evolution: minimum change for a specific tree topology.  Systematic Zoology 20:406-416.  [pdf]

10.  Ancestral reconstruction (Jennifer Miller)

Clark, J.R., R.H. Ree, M.E. Alfaro, M.G. King, W.L. Wagner, and E.H. Roalson.  2008.  A comparative study in ancestral range reconstruction methods: retracing the uncertain histories of insular lineages.  Systematic Biology 57:693-707.  [pdf]

Cunningham, C.W., K.E. Omland, and T.H. Oakley.  1998.  Reconstructing ancestral character states: a critical reappraisal.  Trends in Ecology and Evolution 13:361-366. [pdf]

Losos, J.B.  1999.  Uncertainty in the reconstruction of ancestral character states and limitations on the use of phylogenetic comparative methods.  Animal Behaviour 58:1319-1324.  [pdf]

Omland, K.E.  1999.  The assumptions and challenges of ancestral state reconstructions.  Systematic Biology 48:604-611.  [pdf]

Pupko, T., I. Pe'er, M. Hasegawa, D. Graur, and N. Friedman.  2002.  A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: application to the evolution of five gene families.  Bioinformatics 18:1116-1123.  [pdf]

Swofford, D.L. and W.P. Maddison.  1987.  Reconstructing ancestral character states under Wagner parsimony.  Mathematical Biosciences 87:199-229.  [pdf]

Swofford, D.L. and W.P. Maddison.  1992.  Parsimony, character-state reconstructions, and evolutionary inferences. Pp. 186-223 in: Systematics, Historical Ecology, and North American Freshwater Fishes.  R.L. Mayden (ed.).  Stanford University Press, Stanford.  [pdf]

11.  Mapping continuous characters onto trees

12.  Maximum-likelihood trees

13.  Bayesian trees

14.  Analysis of tree shape (Lizette Siles-Mendoza)

Harcourt-Brown, K.G., P.N. Pearson, and M. Wilkinson.  2001. The imbalance of paleontological trees.  Paleobiology 27:188-204.  [pdf]

Huelsenbeck, J.P. and M. Kirkpatrick.  1996.  Do phylogenetic methods produce trees with biased shapes?  Evolution 50:1418-1424.  [pdf]

Mooers, A.O. and S.B. Heard.  1997.  Inferring evolutionary process from phylogenetic tree shape.  Quarterly Review of Biology 72:31-54.  [pdf]

von euler, F.  2001.  Selective extinction and rapid loss of evolutionary history in the bird fauna.  Proceedings of the Royal Society of London B 268:127-130.  [pdf]

15.  Taxon-sampling effects (Molly McDonough)

Hovenkamp, P.  2006.  Can taxon-sampling effects be minimized by using branch supports?  Cladistics 22:264-275.  [pdf]

Poe, S. and D.L. Swofford.  1999.  Taxon sampling revisited.  Nature 398:299-300.  [pdf]

Rosenberg, M.S. and S. Kumar.  2001.  Incomplete taxon sampling is not a problem for phylogenetic inference.  Proceedings of the National Academy of Science 98:10751-10756.  [pdf]

Zwickl, D.J. and D.M. Hillis.  2002.  Increased taxon sampling greatly reduces phylogenetic error.  Systmatic Biology 51:588-598.  [pdf]

16.  Combining data sets (Matt Muldin)

de Queiroz, A., M.J. Donoghue, and J. Kim.  1995.  Separate versus combined analysis of phylogenetic evidence.  Annual Review of Ecology and Systematics 26:657-681.  [pdf]

Kluge, A.G.  1989.  A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes).  Systematic Zoology 38:7-25.  [pdf]

Lecointre, G. and P. Deleporte.  2005.  Total evidence requires exclusion of phylogenetically misleading data.  Zoologica Scripta 34:101-117.  [pdf]

17.  Comparing trees (Juan Diaz)

Penny, D. and M.D. Hendy.  1985.  The use of tree comparison metrics.  Systematic Zoology 34:75-82.  [pdf]

Rohlf, F.J.  1974.  Methods of comparing classifications.  Annual Review of Ecology and Systematics 5:101-113.  [pdf]

Steel, M.A. and D. Penny.  1993.  Distributions of tree comparison metrics -- some new results.  Systematic Biology 42:126-141.  [pdf]

18.  Phylogeography concepts (Cody Thompson)

Arbogast, B.S. and G.J.Kenagy.  2001.  Comparative phylogeography as an integrative approach to historical biogeography.  Journal of Biogeography 28:819-825.  [pdf]

Avise, J.C., J. Arnold, R.M. Ball, E. Bermingham, T. Lamb, J.E. Neigel, C.A. Reeb, and N.C. Saunders.  1987.  Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics.  Annual Review of Ecology and Systematics 18:489-522.  [pdf]

Avise, J.C.  1998.  The history and purview of phylogeography: a personal reflection.  Molecular Ecology 7:371-379.  [pdf]

Avise, J.C.  2009.  Phylogeography: retrospect and prospect.  Journal of Biogeography 36:3–15.  [pdf]

In addition, the following book is a good resource:  Avise, J. C.  2000.  Phylogeography: The history and formation of species.  Harvard University Press, Cambridge, Massachusetts.

19.  Phylogeography methods (Stephen Roussos)

Barber, P.H., M.K. Moosa, and S.R. Palumbi.  2002. Rapid recovery of genetic diversity of stomatopod populations on Krakatau: temporal and spatial scales of marine larval dispersal.  Proceedings of the Royal Society of London B 269:1591-1597.  [pdf]

Hewitt, G.  2000.  The genetic legacy of the Quaternary ice ages.  Nature 405:907-913.  [pdf]

Knowles, L.L. and W.P. Maddison.  2002.  Statistical phylogeography.  Molecular Ecology 11:2623-2635.  [pdf]

Taberlet, P., L. Fumagalli, A.-G. Wust-Saucy, and J.-F. Cosson.  1998.  Comparative phylogeography and postglacial colonization routes in Europe.  Molecular Ecology 7:453-464.  [pdf]

Templeton, A.R.  2008.  Nested clade analysis: an extensively validated method for strong phylogeographic inference.  Molecular Ecology 17:1877-1880.  [pdf]

Waltari, E., R.J. Hijmans, A.T. Peterson, A. Nyari, S.L. Perkins, and R.P. Guralnick.  2007.  Locating Pleistocene refugia: comparing phylogeographic and
ecological niche model predictions. PLoS ONE 2(7): e563. doi:10.1371/journal.pone.0000563.  [pdf]

20.  Phylogenetic classification (Cebele Caio)

Cantino, P.D.  2004.  Classifying species versus naming clades.  Taxon 53:795-798.  [pdf]

Cantino, P.D. and K. de Queiroz.  2007.  PhyloCode: international code of phylogenetic nomenclature, version 4b. <http://www.ohio.edu/phylocode/>  [pdf]

Dayrat, B.  2005.  Advantages of naming species under the PhyloCode: An example of how a new species of Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) may be named.  Marine Biology Research 1:216-232.  [pdf]

de Queiroz, K.  2007.  Species concepts and species delimitation.  Systematic Biology 56:879-886.  [pdf]

de Queiroz, K. and J. Gauthier.  1992.  Phylogenetic taxonomy.  Annual Review of Ecology and Systematics 23:449-480.  [pdf]

21.  Sequence alignment (Miryam Venegas-Anaya)

Giribet, G. and W.C. Wheeler.  1999.  On gaps.  Molecular Phylogenetics and Evolution 13:132-143.  [pdf]

Löytynoja, A. and N. Goldman.  2008.  Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis.  Science 320:1632-1635.  [pdf]

Notredame, C.  2007.  Recent evolutions of multiple sequence alignment algorithms. PLoS Computational Biology 3(8): e123:1405-1408.  [pdf]

Phillips, A., D. Janies, and W. Wheeler.  2000.  Multiple sequence alignment in phylogenetic analysis.  Molecular Phylogenetics and Evolution 16:317-330.  [pdf]

Wheeler, W.C.  1995.  Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data.  Systematic Biology 44:321-331.  [pdf]

22.  Molecular markers (Faisal Anwarali)

Agarwal, M., N. Shrivastava, and H. Padh.  2008. Advances in molecular marker techniques and their applications in plant sciences.  Plant Cell Reports 27:617-631.  [pdf]

Ali, B.A., T.-H. Huang, D.-N. Qin, and X.-M. Wang.  2004.  A review of random amplified polymorphic DNA (RAPD) markers in fish research.  Reviews in Fish Biology and Fisheries 14:443-453.  [pdf]

Robinson, J.P. and S.A. Harris.  1999.  Amplified fragment length polymorphisms and microsatellites: a phylogenetic perspective. Chapter 12 in: Which DNA Marker for Which Purpose?  Final Compendium of the Research Project Development, optimisation and validation of molecular tools for assessment of biodiversity in forest trees.  E.M. Gillet (ed.).  European Union DGXII Biotechnology FW IV Research Programme.  [pdf]

Triest, L.  2008.  Molecular ecology and biogeography of mangrove trees: towards conceptual insights on gene flow and barriers: a review.  Aquatic Botany 89:138–154.  [pdf]

23.  Models of DNA, RNA, and protein evolution (Nicte Ordonez-Garza)

Lio, P. and N. Goldman.  1998.  Models of molecular evolution and phylogeny.  Genome Research 8:1233-1244.  [pdf]

Ren, F., H. Tanaka, and Z. Yang. 2005.  An empirical examination of the utility of codon-substitution models in phylogeny reconstruction. Systematic Biology 54:808-818.  [pdf]

Savill, N.J., D.C. Hoyle, and P.G Higgs.  2001.  RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.  Genetics 157:399-411.  [pdf]

Yang, Z., R. Nielsen, and M. Hasegawa.  1998.  Models of amino acid substitution and applications to mitochondrial protein evolution.  Molecular Biology and Evolution 15:1600-1611.  [pdf]

24.  Gene families and phylogenetics (Megan Corley)

Cotton, J.A. and R.D.M. Page.  2002.  Going nuclear: gene family evolution and vertebrate phylogeny reconciled.  Proceedings of the Royal Society of London B269:1555-1561.  [pdf]

Cotton, J.A. and R.D.M. Page.  2006.  The shape of human gene family phylogenies.  BMC Evolutionary Biology 6:66.1-66.8.  [pdf]

Demuth, J.P., T.D. Bie, J.E. Stajich, N. Cristianini, and M.W. Hahn.  2006.  The evolution of mammalian gene families.  PLoS ONE 1(1): e85.1-85.10.  [pdf]

Henikoff, S., E.A. greene, S. Pietrokovski, P. Bork, T.K. Attwood, and L. Hood.  1997. Gene families: the taxonomy of protein paralogs and chimeras.  Science 278:609-614.  [pdf]

Hoffmann, F.G., J.C. Opazo, and J.F. Storz.  2008.  New genes originated via multiple recombinational pathways in the β-globin gene family of rodents.  Molecular Biology and Evolution 25:2589-2600.  [pdf]

Liberles, D.A. and K. Dittmar.  2008.  Characterizing gene family evolution.  Biological Procedures Online 10(1):66-73.  [pdf]

25.  Gene trees and taxon trees (Ben Qin)

Cao, Y., J. Adachi, T. Yano, and M. Hasegawa.  1994.  Phylogenetic place of Guinea Pigs: no support of the rodent-polyphyly hypothesis from maximum-likelihood of multiple protein sequences.  Molecular Biology and Evolution 11:593-604.  [pdf]

Martignetti, J.A. and J. Brosius.  1993.  Neural BC1 RNA as an evolutionary marker: Guinea Pig remains a rodent.  Proceedings of the National Academy of Sciences 90:9698-9702.  [pdf]

Reyes, A., C. Gissi, G. Pesole, F.M. Catzeflis, and C. Saccone.  2000.  Where do rodents fit?  Evidence from the complete mitochondrial genome of Sciurus vulgarisMolecular Biology and Evolution 17:979-983. [pdf]

26.  Coalescence (Roxy Larsen)

Belfiore, N.M., L. Liu, and C. Moritz.  2008.  Multilocus phylogenetics of a rapid radiation in the genus Thomomys (Rodentia: Geomyidae).  Systematic Biology 57:294-310.  [pdf]

Carstens, B.C. and L.L. Knowles.  2007.  Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers.  Systematic Biology 56:400-411.  [pdf]

Fu, Y.-X. and W.-H. Li.  1999.  Coalescing into the 21st Century: an overview and prospects of coalescent theory.  Theoretical Population Biology 56:1-10.  [pdf]

Klingman, J.F.C.  2000.  Origins of the coalescent: 1974–1982.  Genetics 156:1461-1463.  [pdf]

Rosenberg, N.A. and M. Nordborg.  2002.  Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.  Nature Reviews Genetics 3:380-390.  [pdf]

Wakeley, J.  2009.  Coalescent Theory.  Roberts and Company Publ., Colorado.  432 p.

27.  Quantitative characters (Miguel Pinto)

Cardini, A. and S. Elton.  2008.  Does the skull carry a phylogenetic signal? Evolution and modularity in the guenons.  Biological Journal of the Linnean Society 93:813-834.  [pdf]

Felsenstein, J.  1988.  Phylogenies and quantitative characters.  Annual Review of Ecology and Systematics 19:445-471.  [pdf]

Goloboff, P.A., C.I. Mattoni, and A.S.Quinteros.  2006.  Continuous characters analyzed as such.  Cladistics 22:589-601.  [pdf]

Gonzalez-Jose, R. and I. Escapa.  2008.  Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution.  Nature 453:775-779.  [pdf]

Rae, T.C.  1998. The logical basis for the use of continuous characters in phylogenetic systematics.  Cladistics 14:221-228.  [pdf]

Scotland, R.W., R.G. Olmstead, and J.R. Bennett.  2003.  Phylogeny reconstruction: the role of morphology.  Systematic Biology 52:539-548.  [pdf]

Wiens, J.J.  2001.  Character analysis in morphological phylogenetics: problems and solutions.  Systematic Biology 50:689-699.  [pdf]

Wiens, J.J.  2004.  The role of morphological data in phylogeny reconstruction.  Systematic Biology 53:653-661.  [pdf]

28.  Character correlations (Zhongyi Xiao)

Alizadeh, A.A. et al.  2000.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.  Nature 403:503-511.  [pdf]

Cubo, J. and W. Arthur.  2001.  Patterns of correlated character evolution in flightless birds: a phylogenetic approach.  Evolutionary Ecology 14:693-702.  [pdf]

Huelsenbeck, J.P. and B. Rannala.  2003.  Detecting correlation between characters in a comparative analysis with uncertain phylogeny.  Evolution 57:1237-1247.  [pdf]

Maddison, W.P.  1990.  A method for testing the correlated evolution of two binary characters: are gains or losses concentrated on certain branches of a phylogenetic tree?  Evolution 44:539-557.  [pdf]

Maddison, W.P.  2000.  Testing character correlation using pairwise comparisons on a phylogeny.  Journal of Theoretical Biology 202:195-204.  [pdf]

29.  Phylogenetically independent contrasts (Liza Garcia)

Felsenstein, J.  1985.  Phylogenies and the comparative method.  American Naturalist 125:1-15.  [pdf]

Garland, T.  1992.  Rate tests for phenotypic evolution using phylogenetically independent contrasts.  American Naturalist 140:509-519.  [pdf]

Garland, T., A.W. Dickerman, C.M. Janis, and J.A. Jones.  1992.  Phylogenetic analysis of covariance by computer simulation.  Systematic Biology 42:265-292.  [pdf]

30.  Detecting adaptation (Sheri Westerman)

Baum, D.A. and A. Larson.  1991.  A phylogenetic methodology for studying character macroevolution.  Systematic Zoology 40:1-18.  [pdf]

Kornegay, J.R., J.W. Schilling, and A.C. Wilson.  1994. Molecular adaptation of a leaf-eating bird: stomach lysozyme of the Hoatzin.  Molecular Biology and Evolution 11:921-928.  [pdf]

Revell, L.J., M.A. Johnson, J.A. Schulte II, J.J. Kolbe, and J.B. Losos.  2007.  A phylogenetic test for adaptive convergence in rock-dwelling lizards.  Evolution 61:2898-2912.  [pdf]

Wiens, J.J., P.T. Chippindale, and D.M. Hillis.  2003.  When are phylogenetic analyses misled by convergence? A case study in Texas cave salamanders. Systematic Biology 52:501-514.  [pdf]

Zhang, J. and S. Kumar.  1997.  Detection of convergent and parallel evolution at the amino acid sequence level.  Molecular Biology and Evolution 14:527-536.  [pdf]

31.  Rates of evolution (Juliana Senawi)

Lenski, R.E.  2001.  Evolutionary rate.  Pp. 671-672 in: Encyclopedia of Genetics.  S. Brenner and J. Miller (eds.). Academic Press, San Diego.  [pdf]

Pereira, S.L. and A.J. Baker.  2006.  A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock.  Molecular Biology and Evolution 23:1731-1740.  [pdf]

Rambaut, A.  2000.  Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies.  Bioinformatics 16:395-399.  [pdf]

Reznick, D.N., F.H. Shaw, F.H. Rodd, and R.G. Shaw.  1997. Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata).  Science 275:1934-1937.  [pdf]

Sanderson, M.J.  2002. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach.  Molecular Biology and Evolution 19:101-109.  [pdf]

Smith, A.B., D. Pisani, J.A. Mackenzie-Dodds, B. Stockley, B.L. Webster, and D.T.J. Littlewood.  2006.  Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata).  Molecular Biology and Evolution 23:1832-1851. [pdf]

Thorne, J.L., H. Kishino, and I.S. Painter.  1998.  Estimating the rate of evolution of the rate of molecular evolution.  Molecular Biology and Evolution 15:1647-1657.  [pdf]

32.  Stratigraphy and phylogenetics (Juan Pablo Carrera)

Huelsenbeck, J.P. and B. Rannala.  2000.  Using stratigraphic information in phylogenetics.  Pp. 165-191 in: Phylogenetic Analysis of Morphological Data.  J.J. Wiens (ed.).  Smithsonian Institution Press, Washingtown.  [pdf]

Koutsoukos, E.A.M.  2005.  Stratigraphy: evolution of a concept. Pp. 3-19 in: Applied Stratigraphy.  E.A.M. Koutsoukos (ed.).  Springer, New York.  [pdf]

33.  Supertrees (Noe de la Sancha)

Purvis, A.  1995.  A composite estimate of primate phylogeny.  Philosophical Transactions of the Royal Society of London B 348:405-421.  [pdf]

Bininda-Emonds, O.R.P.  2003.  Novel versus unsupported clades: assessing the qualitative support for clades in MRP Supertrees.  Systematic Biology 52:839-848.  [pdf]

Bininda-Emonds, O.R.P., K.E. Jones, S.A. Price, R. Grenyer, M. Cardillo, M. Habib, A. Purvis, and J.L. Gittleman.  2003.  Supertrees are a necessary not-so-evil: a comment on Gatesy et al.  Systematic Biology 52:724-729.  [pdf]

Bininda-Emonds, O.R.P., M. Cardillo, K.E. Jones, R.D.E. PacPhee, R.M.D. Beck, R. Grenyer, S.A. Price, R.A. Vos, J.L. Gittleman, and A. Purvis.  2007.  The delayed rise of present-day mammals.  Nature 446:507-512.  [pdf]

34.  Tree of Life (Xi Chen)

Bininda-Emonds,O.R.P., J.L. Gittleman, and M.A. Steel.  2002.  The (super)tree of life: procedures, problems, and prospects.  Annual Review of Ecology and Systematics 33:265-289.  [pdf]

Doolittle, W.F.  1999.  Phylogenetic classification and the universal tree.  Science 284:2124-2128.  [pdf]

Maddison, D.R., K.-S. Schulz, and W.P. Maddison.  2007.  The Tree of Life project.  Zootaxa 1668:19-40.  [pdf]

Woese, C.R.  2000. Interpreting the universal phylogenetic tree.  Proceedings of the National Academy of Science 97:8392-8396.  [pdf]

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