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Reading List 8
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.


April 11, 13: Phylogenetic Trees VI & VII: Measures of support, tree comparisons, total evidence


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


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


Archie, J. W. 1989. A randomization test for phylogenetic information in systematic data. Syst. Zool. 38: 239-252.


Barrett M, Donoghue MJ, and Sober E (1991) Against consensus. Syst. Zool. 40:486-493.


Bremer K (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evol. 42:795-803.


Bremer, K. 1990. Combinable component consensus. Cladistics 6:369-372.


Bremer, K. 1994. Branch support and tree stability. Cladistics 10(3):295-304


Brower, A. V. Z., R. DeSalle and A. Vogler. 1996. Gene trees, species trees, and systematics: a cladistic perspective. Ann. Rev. Ecol. Syst. 27: 423-450.


Bryant, D. 2003. A classification of consensus methods for phylogenetics. in Janowitz, M., Lapointe, F.J., McMorris, F., Mirkin, B. Robers, F. (eds.) Bioconsensus. DIMACS-AMS. 163-184.


Bull, J. J., J. P. Huelsenbeck, C. W. Cunningham, D. L. Swofford and P. J. Waddell. 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42: 384-397.


Cameron, S. A. and P. Mardulyn. 2001. Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera: Apinae). Systematic Biology 50: 194-214.


Cannon, C. H. and P. S. Manos. 2001. Combining and comparing morphometirc shape datya with a molecular phylogeny: the case of fruit type evolution in Bornean Lithocarpus (Fagaceae). Systematic Biology 50: 860-880.


Chavarria, G. and J. M. Carpenter. 1994. "Total evidence" and the evolution of highly social bees. Cladistics 10: 229-258.


Chippendale, P. T. and J. J. Wiens. 1994. Weighting, partitioning, and combining characters in phylogenetic analysis. Syst. Biol. 43: 278-287.


Coddington, J. and Scharff, N. 1994. Problems with zero-length branches. Cladistics 10(4): 415-423.


** de Queiroz, A., M. J. Donoghue and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Ann. Rev. Ecol. Syst. 26: 657-681.


DeBry, R. W. 2001. Improving interpretation of the decay index for DNA sequence data. Systematic Biology 50: 742-752.


DeBry, R. W. and R. G. Olmstead. 2000. A simulation study of reduced tree-search effort in bootstrap resampling analysis. Systematic Biology 49: 171-179.


Donoghue MJ, Olmstead RG, Smith JF, and Palmer JD (1992) Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Missouri Bot. Gard. 79:333-345.


Farris, J. S. 1989a. The retention index and homoplasy excess. Systematic Zoology 38:406-407.


Farris, J. S. 1989b. The retention index and the rescaled consistency index. Cladistics 5:417-419.


Farris J.S., Kallersjo, M., Kluge, A.G. and Bult, C. 1994. Testing significance of incongruence. Cladistics 10(3): 315-319


Farris, J. S., M. Kallersjo, and J. E. De Laet. 2001. Branch Lengths Do Not Indicate Support-Even in Maximum Likelihood. Cladistics 17: 298-299.


** Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.


Flook, P. K., S. Klee, and C. H. F. Rowell. 1999. Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics. Systematic Biology 48: 233-253.


Flores-Villela, O., K. M. Kjer, M. Benabib, and J. W. Sites Jr. 2000. Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phyrnosomatidae). Systematic Biology 49: 713-739.


Gatesy, J. 2000. Linked branch support and tree stability. Systematic Biology 49: 800-808.


Gatesy, J. and P. Arctander. 2000. Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes. Systematic Biology 49: 515-538.


Goldman, N., J. P. Anderson, and A. G. Rodrigo. 2000. Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49: 652-670.


Goloboff P (1991) Homoplasy and the choice among cladograms. Cladistics 7:215-232.


Grandcolas, P., P.-L. Deleporte, L. Desutter-Grandcolas, C. Daugeron. 2001. Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis. Cladistics 17: 104-110.


Graham LE, Delwiche CF, and Mishler BD (1991) Phylogenetic connections between the "green algae" and the "bryophytes". Advances in Bryology 4:213-244.


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


Huelsenbeck, J. P. 1991. Tree-length distribution skewness: an indicator of phylogenetic information. Syst. Zool. 40: 257-270.


Huelsenbeck, J.P. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44(1):17-48.


Huelsenbeck, J. P. and J. J. Bull. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45: 92-98.


* Huelsenbeck, J. P., J. J. Bull and C. W. Cunningham. 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11: 152-158.


Joy, T. and J. E. Conn. 2001. Molecular and morphological phylogenetic analysis of an insular radiation of Pacific black flies. Systematic Biology 50: 18-38.


Källersjö M, Farris JS, Kluge AG, and Bult C (1992) Skewness and permutation. Cladistics 8:275-287.


Kennedy, Martyn; Holland, Barbara R.; Gray, Russell D., et al. Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Systematic Biology 54 (4) : 620-633 AUG 2005


Kjer, K. M., R. J. Blahnik, and R. W. Holzenthal. 2001. Phylogeny fo Trichoptera (caddisflies): characterization of signal and noise within multiple data sets. Systematic Biology 50: 758-780.


Klassen GJ, Mooi RD, and Locke A (1991) Consistency indices and random data. Syst. Zool. 40:446-457.


Kluge AJ (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.


Kress, W. J., L. M. Price, W. J. Hahn, and E. A. Zimmer. 2001. Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence. Systematic Biology 50: 926-944.


Lee, M. S. Y. 2000. Tree robustness and clade significance. Systematic Biology 49: 829-836


Levaseur, C. and F.-J. Lapointe. 2001. War and peace in phylogenetics: a rejoinder on total evidence and consensus. Systematic Biology 50: 881-891.


McCracken, K. G., J. Harshman, D. A. McClellan, and A. D. Afton. 1999. Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks. Systematic Biology 48: 683-714.


McLennan, D. A. and M. Y. Mattern. 2001. The Phylogeny of the Gasterosteidae: Combining Behavioral and Morphological Data Sets. Cladistics 17: 11-27.


Mishler BD, Donoghue MJ, and Albert VA (1991) The decay index as a measure of relative robustness within a cladogram [abstract]. Hennig X [Annual meeting of the Willi Hennig Society], Toronto, Ontario.


Mishler, B. D., L. A. Lewis, M. A. Buchheim, K. S. Renzaglia, D. J. Garbary, C. F. Delwiche, F. W. Zechman, T. S. Kantz and R. L. Chapman. 1994. Phylogenetic relationships of the "green algae" and "bryophytes". Ann. MO Bot. Gard. 81: 451-483.


Miyamoto MM (1985) Consensus cladograms and general classifications. Cladistics 1:186-189.


Miyamoto, M.M. and M.W. Fitch. 1995. Testing species phylogenies and phylogenetic methods with congruence. Syst. Biol. 41(1): 64-76.


Mort, M. E., P. S. Soltis, D. E. Soltis, and M. L. Mabry. 2000. Comparison of methods for estimating internal support on phylogenetic trees. Systematic Biology 49: 160-171.


Nee, Sean. Extinct meets extant: simple models in paleontology and molecular phylogenetics. Paleobiology 30 (2) : 172-178 Spring 2004


Penny, D. and M. D. Hendy. 1985. The use of tree comparison metrics. Syst. Zool. 34: 75-82.


Poe S, Chubb AL. Birds in a bush: Five genes indicate explosive evolution of avian orders . EVOLUTION 58 (2): 404-415 FEB 2004


Quicke, D. L. J. and R. Belshaw. 1999. Incongruence between morphological data sets: an example from the evolution of endoparisitism among parasitic wasps (Hymenoptera: Braconidae). Systematic Biology 48:


Rohlf, F. J. 1982. Consensus indices for comparing classifications. Mathematical Biosciences 59:131-144.


Sanderson MJ, and Donoghue MJ (1989) Patterns of variation in levels of homoplasy. Evol. 43:1781-1795.


** Sanderson, M.J. 1995. Objections to boostraping phylogenies: a critique. Syst. Biol. 44(3):299-320.


Sanderson, M. J., and M. Wojciechowski. 2000. Improved bootstrap confidence limits in large scale phylogenies, with an example from neo-astragalus (Leguminoseae). Systematic Biology 49: 671-685.


Sharkey, M. J. and J. W. Leathers. 2001. Majority Does Not Rule: The Trouble with Majority-Rule Consensus Trees. Cladistics: 282-284.


Sorensen MV, Sterrer W, Giribet G. Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphology . CLADISTICS 22 (1): 32-58 FEB 2006


Steel, M., A. W. M. Dress, and S. Bocker. 2000. Simple but fundamental limitations on supertree and consensus tree methods. Systematic Biology 49: 363-368.


Sullivan, J. and D. L. Swofford. 2001. Should we use model-based methods for phylogenetic inference when we know that assumptions about among site rate variation and nucleotide substitution pattern are violated? Systematic Biology 50: 723-729.


Summral, C. D., C. A. Brochu, and J. W. Merck Jr. 2001. Global lability, regional resolution, and majority rule consensus bias. Paleobiology 27: 254-261.


Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pp. 295-333 in M. M. Miyamoto &J. Cracraft (ed.), Phylogenetic analysis of DNA sequences. Oxford University Press, New York.


Weiblen, G. D. 2001. Phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus based on mitochondrial DNA sequences and morphology. Systematic Biology 50: 243-267.


Wiens, J. J. and B. D. Hollingsworth. 2000. War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Systematic Biology 49: 143-159.


Wilkinson, M. 1994. Common cladistic information and its consensus representation: reduced Adams and reduced cladistic trees and profiles. Syst. Biol. 43: 343-368.


Wilkinson, M. and J. L. Thorley. 2001. Efficiency of strict consensus trees. Systematic Biology 50: 610-612.


Wilkinson, M., J. L. Thorley, and P. Upchurch. 2000. A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses. Systematic Biology 49: 754-776.


Wood, S.W. 1994. Monophyly and comparisons between trees. Cladistics: 10(4):339-346.


Yolder, A. D., J. A. Irwin, and B. A. Payseur. 2001. Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology 50: 408-424.


Zandler, R. H. 2001. A conditional probability of reconstruction measure for internal cladogram branches. Systematic Biology 50: 425-437.




Arnold, M. L., C. M. Buckner and J. J. Robinson. 1991. Pollen-mediated introgression

and hybrid speciation in Louisiana irises. Proc. Nat. Acad. Sci., U.S.A 88: 1398-



Arnold, M. L., J. J. Robinson, C. M. Buckner and B. D. Bennet. 1992. Pollen dispersal

and interspecific gene flow in Louisiana irises. Heredity 68: 399-404.


Avise, J. C. 1989. Gene trees and organismal histories: a phylogenetic approach to

population biology. Evol. 43: 1192-1208.


Avise, J. C. and R. M. Ball. 1990. Principles of geneological concordance in species

concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology 7: 45-



*Baum, D. 1992. Phylogenetic species concepts. Trends Ecol. Evol. 7: 1-2.


Baum, D. A., and K. L. Shaw. 1995. Genealogical perspectives on the species problem.

Pages 289-303 in Experimental and molecular approaches to plant biosystematics.

Monographs in systematics, Volume 53 (P. C. Hoch and A. G., Stevenson, eds.). Missouri Botanical Garden, St, Louis.


Carstens BC, Brunsfeld SJ, Demboski JR, et al. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: Hypothesis testing within a comparative phylogeographic framework. EVOLUTION 59 (8): 1639-1652 AUG 2005


Crandall, K. A. 1994. Intraspecific cladogram estimation: accuracy at higher levels of

divergence. Syst. Biol. 43: 222-235.


Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character

taxomony. Syst. Bot. 17: 144-163.


Funk, V. A. 1985. Phylogenetic patterns and hybridization. Ann. Missouri Bot. Gard.

72: 681-715.


Gadgil and L. L. Cavalli-Sforza. 1995. Demographic history of India and mtDNA sequence diversity. Am. J. Hum. Genet. 56: 979-992.


Goodman, M., J. Czelusniak, G. W. Moore, A. E. Romero-Herrera, and G. Matsuda.

1979. Fitting the gene lineage into its species lineage, a parsimony strategy

illustrated by cladograms constructed from globin sequences. Syst. Zool. 28: 132-



Heads M. Dating nodes on molecular phylogenies: a critique of molecular biogeography. CLADISTICS 21 (1): 62-78 FEB 2005


Heiser, C. B. 1973. Introgression re-examined. Bot. Rev. 39: 347-366.


*Hudson, R. R. 1991. Gene genealogies and the coalescent process. Oxford Surveys in

Evolutionary Biology 7: 1-44.


Hudson, R. R., M. Slatkin and W. P. Maddison. 1992. Estimation of levels of gene flow

from DNA sequence data. Genetics 132: 583-589.


James JK, Abbott RJ. Recent, allopatric, homoploid hybrid speciation: The origin of Senecio squalidus (Asteraceae) in the British Isles from a hybrid zone on Mount Etna, Sicily. EVOLUTION 59 (12): 2533-2547 DEC 2005


Kidwell, M. G. 1993. Lateral transfer in natural populations of eukaryotes. Annu. Rev.

Genet. 27: 235-256.


Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536.


Mason-Gamer, Roberta J. Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Systematic Biology 53 (1) : 25-37 February 2004


McDade, L. 1990. Hybrids and phylogenetic systematics. I. Patterns of character

expression in hybrids and their implications for cladistic analysis. Evol. 44: 1685-



**McDade, L. A. 1992. Hybrids and phylogenetic systematics II. The impact of hybrids

on cladistic analysis. Evol. 46: 1329-1346.


McDade, L. A. 1995. Hybridization and phylogenetics. in Experimental and molecular

approaches to plant biosystematics (Hoch, P. C. and A. G. Stephenson, ed.). Missouri

Botanical Garden, St. Louis.


McDade, L A. 1997. Hybrids and phylogenetic systematics III. Comparison with distance

methods. Systematic Botany, v.22, n.4, (1997): 669-683.


Mountain, J. L., J. M. Hebert, S. Bhattacharyya, P. A. Underhill, C. Ottolenghi, M.


Nason, J. D., N. C. Ellstrand and M. I. Arnold. 1992. Patterns of hybridization and

introgression in populations of oaks, manzanitas, and irises. Am. J. Bot. 79: 101-111.


Nieto, F.G., A.J. Fuertes, and J.A. Rossello. 2001. Can extensive reticulation and

concerted evolution result in a cladistically structured mmolecular data set?

Cladistics. 17(4):301-312.


Ree RH. Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. EVOLUTION 59 (2): 257-265 FEB 2005


Rieseberg, L. H. 1991. Homoploid reticulate evolution in Helianthus (Asteraceae):

evidence from ribosomal genes. Amer. J. Bot 78: 1218-1237.


Rieseberg, L. H., R. Carter and S. Zona. 1990. Molecular tests of the hypothesized

hybrid origin of two diploid Helianthus species (Asteraceae). Evol. 44: 1498-1511.


Schlefer, E. K., M. A. Romano, S. I. Guttman and S. B. Ruth. 1986. Effects of twenty

years of hybridization in a disturbed habitat on Hyla cinerea and Hyla gratiosa. J. of

Herpetology 20: 210-221.


Skala, Z. and Zrzavy J. 1994. Phylogenetic reticulations and cladistics - discussion of

methodological concepts. Cladistics 10(3): 305-313.


Slatkin, M. and W. Maddison. 1989. A cladistic measure of gene flow inferred from the

phylogenies of alleles. Genetics 123: 603-613.


Slatkin, M. and W. Maddison. 1990. Detecting isolation by distance using phylogenies

of genes. Genetics 126: 249-260.


Vrana, P. and W. Wheeler. 1992. Individual organisms as terminal entities: laying the

species problem to rest. Cladistics 8: 67-72.


Wagner, W. H. 1983. Reticulistics: the recognition of hybrids and their role in cladistics

and classification. Pages 63-79 in Advances in Cladistics, Volume 2 (Platnick, N. I.

and V. A. Funk, ed.). Columbia University Press, New York.


Williams ST, Reid DG. Speciation and diversity on tropical rocky shores: A global phylogeny of snails of the genus Echinolittorina. EVOLUTION 58 (10): 2227-2251 OCT 2004


Woodruff, D. S. and S. J. Gould. 1987. Fifty years of interspecific hybridization:

genetics and morphometrics of a controlled experiment on the land snail Cerion in the

Florida Keys. Evol. 41: 1022-1043.