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Reading
List 8 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. 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; 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, 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], 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". 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. 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 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. April 18:
RETICULATION AND PHYLOGENETICS Arnold, M. L., C. M. Buckner and J. J. Robinson. 1991.
Pollen-mediated introgression and hybrid speciation in 1402. Arnold, M. L., J. J. Robinson, C. M. Buckner and B. D. Bennet. 1992. Pollen dispersal and interspecific
gene flow in 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.
67. *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.). 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. 72: 681-715. Gadgil and L. L. Cavalli-Sforza. 1995. Demographic history of 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- 163. 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. 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 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- 1700. **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.). Botanical Garden, 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.). 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
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