Syst. Biol. 48(2):233--253, 1999

Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics

P. K. Flook 1, S. Klee, and C. H. F. Rowell

Zoology Institute, University of Basel, 4051-Basel, Switzerland

1 Address correspondence to Dr. P.K. Flook, Zoologiches Institut, Rheinsprung 9, 4051-Basel, Switzerland

Abstract.---A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree, lacking several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets that identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis; comparative analysis of trees recovered from resampled data sets and the application of a randomization test. The results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, and we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the ML criteria is the most discriminating approach for the combined sequences. The results indicate that the caeliferan Pneumoroidea and Pamphagoidea (as previously suggested) are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.
[Combined analysis; insect phylogeny; molecular evolution; Orthoptera; ribosomal DNA.]

Syst. Biol. 48(2):254--285, 1999

Phylogenetic relationships and tempo of early diversification in Anolis lizards

Todd R. Jackman 1,3, Allan Larson 1, Kevin de Queiroz 2, and Jonathan B. Losos 1

1 Department of Biology, Washington University, St. Louis, Missouri 63130-4899, USA;
E-mail: (TRJ), (AL), (JBL)

2 National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;

Abstract.---We examine phylogenetic relationships among anoles using mitochondrial DNA sequences from the NADH dehydrogenase subunit 2 gene (ND2) and five transfer-RNA genes representing 1,455 alignable base positions and 866 phylogenetically informative characters (parsimony criterion). We also present 16 morphological characters for phylogenetic analysis. Our analyses yielded poorly-supported nodes deep in the anole tree but many well-supported nodes for more recent phylogenetic divergences. We test the hypothesis that the major clades of anoles form a hard polytomy and present a general statistical framework for testing hypothesis of simultaneous branching of lineages by using molecular sequence data. Our results suggest that rapid diversification early in the evolutionary history of anoles explains why numberous researchers have had difficulty reconstruction well-supported dichotomous phylogenetic trees for anoles.
[Anolis; mitochondrial DNA; parametric bootstrap; permutation test; phjylogeny; polytomy.]

Syst. Biol. 48(2):286--299, 1999

Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes

Ronald W. DeBry

Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA;

Abstract.---Aligned protein-coding genes from 19 completely sequenced mammalian mitochondrial genomes were examined by parsimony and maximum likelihood analyses. Particular attention is given to a comparison between gene-based and structure-based data partitions. Because actual structures are not known for most of the mitochondrially encoded proteins, three different surrogate partitioning schemes were examined, each based identity of the consensus amino acid at a specific homologous position. One of the amino-acid-based partitioning schemes gave the highest likelihood, but that scheme was based on concordance with a well-corroborated phylogeny from an earlier parsimony analysis. The gene-based partitioning scheme gave a significantly higher likelihood compared to the only structure-based scheme examined that could be generated without prior assumptions about the phylogeny. Two contrasting phylogenetic inferences were supported by the analyses. Both unpartitioned analyses and analyses in which all partitions were constrained to have identical patterns of branch lengths supported ((Artiodactyla, Cetacea) (Perissodactyla, Carnivora)), whereas all analyses with that constraint relaxed supported (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).
[Combined analysis; Mammalia; maximum likelihood; mitochondrial DNA; parsimony; process partitions.]

Syst. Biol. 48(2):300--316, 1999

Type I error and the power of the s-test: old lessons from a new, analytically justified statistical test for phylogenies

Marcos A. Antezana 1 and Richard R. Hudson

Department of Ecology and Evolutionary Ecology, University of California, Irvine, California 92717, USA;
E-mail: (MAA), (RRH)

1 Address correspondence to this author at the Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637-1573

Abstract.---We present a new procedure for assessing the statistical significance of the most likely unrooted dichotomous topology inferrable from four DNA sequences. The procedure calculates directly a P-value for the support given to this topology by the informative sites congruent with it, assuming the most likely star topology as the null hypothesis. Informative sites are crucial in the determination of the maximum likelihood dichotomous topology and are therefore an obvious target for a statistical test of phylogenies. Our P-value is the probability of producing through parallel substitutions on the branches of the star topology at least as much support as that given to the maximum likelihood dichotomous topology by the aforementioned informative sites, for any of the three possible dichotomous topologies. The degree of statistical significance is simply the complement of this P-value. Ours is therefore an a posteriori testing approach, in which no dichotomous topology is specified in advance. We implement the test for the case in which all sites behave identically and the substitution model has a single parameter. Under these conditions, the P-value can be easily calculated on the basis of the probabilities of change on the branches of the most likely star topology, because under these assumptions, each site can become informative independently from every other site; accordingly, the total number of informative sites of each kind is binomially distributed. We explore the testŐs type I error by applying it to data produced in star topologies having all branches equally long, or having two short and two long branches, and various degrees of homoplasy. The test is conservative but we demonstrate, by means of a discreteness correction and progressively assumption-free calculations of the P-values, that (1) the conservativeness is mostly due to the discrete nature of informative sites and (2) the P-values calculated empirically are moreover mostly quite accurate in absolute terms. Applying the test to data produced in dichotomous topologies with increasing internal branch length shows that, despite the testŐs "conservativeness," its power is much higher than that of the bootstrap, especially when the relevant informative sites are few.
[Analytical; bootstrap; continuity; discreteness; FisherŐs exact test; homoplasy; hypergeometric; informative sites; maximum likelihood; parallel changes; phylogeny; power; P-value; statistics; type I error]

Syst. Biol. 48(2):317--328, 1999

Effect of nonindependent substitution on phylogenetic accuracy

John P. Huelsenbeck 1 and Rasmus Nielsen 2

1 Department of Biology, University of Rochester, Rochester, New York 14627, USA;

2 Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA;

Abstract.---All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic properties of phylogenetic methods do not appear to change under a compound Poisson process of DNA substitution. Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process.
[Compound Poisson process; nonindependent substitution; phylogenetic accuracy.]

Syst. Biol. 48(2):329--351, 1999

Definitions in phylogenetic taxonomy: critique and rationale

Paul C. Sereno

Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th Street, Chicago, Illinois, USA;

Abstract.---A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the relationship between the trio of taxa at a branchpoint, in the face of local change in phylogenetic relationships or addition/deletion of taxa. Crown-total taxonomies use survivorship as a criterion for placement of node-stem triplets within a taxonomic hierarchy. Diversity, morphology, and tradition also constitute heuristic criteria for placement of node-stem triplets.
[Content; crown; definition; node; phylogeny; stability; stem; taxonomy.]

Syst. Biol. 48(2):352--364, 1999

Charles Darwin's views of classification in theory and practice

Kevin Padian

Department of Integrative Biology and Museum of Paleontology, 1101 VLSB, University of California, Berkeley, California 94720, USA;

Abstract.---It has long been argued that Charles Darwin was the founder of the school of "evolutionary taxonomy" of the Modern Synthesis and, accordingly, that he recognized genealogy and similarity as dual, synergistic criteria for classification. This view is based on three questionable interpretations: first, of isolated passages in the 13th chapter of the Origin of Species; second, of one phrase in a letter that Darwin wrote about the work of an author he had partly misunderstood; and third, of his taxonomic practice in the barnacle monographs, which only implicitly embody his philosophy of classification, if at all. These works, seen in fuller context and with the perspective of extensive correspondence, are consistent with the view that Darwin advocated only genealogy as the basis of classification, and that similarity was merely a tool for discovering evolutionary relationships. Darwin was neither a Mayrian taxonomist nor a cladist, and he did not approach systematic issues in the same terms that we do in the late 20th century.
[Cladistics; classification; Darwin; systematics.]

Syst. Biol. 48(2):365--379, 1999

Coding polymorphism for phylogeny reconstruction

D. J. Kornet 1,3 and Hubert Turner 2,4

1 Theoretical Biology, Institute of Evolutionary and Ecological Sciences, Leiden University, PO Box 9516, 2300 RA Leiden, The Netherlands;

2 Institute for Systematics and Population Biology, University of Amsterdam, PO Box 94766, 1090 GT Amsterdam, The Netherlands

3 Address correspondence to this author.

4 Present address: Theoretical Biology, Institute of Evolutionary and Ecological Sciences, Leiden University, PO Box 9516, 2300 RA Leiden, The Netherlands;

Abstract.---The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signal that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors.
[Coding methods; evolutionary novelty; fixation; polymorphism; reversals (hard, soft); start of character states (hard, soft)]

Syst. Biol. 48(2):380--395, 1999

Discriminating and locating character covariance: an application of permutation tail probability (PTP) analyses

Jinzhong Fu and Robert W. Murphy 1

Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ontario, Canada M5S 2C6 and Department of Zoology, University of Toronto, Toronto, Ontario, Canada M5S 2C6;
E-mail: (JF), (RWM)

1 Address correspondence to this author at the Centre for Biodiversity and Conservation Biology, Royal Ontario Museum.

Abstract.---The ability of permutation tail probability (PTP) analyses to discriminate between character covariance and noise is investigated with both hypothetical and published data sets. PTP is shown to be a powerful tool, not only for detecting character covariance, but also for locating that covariance on trees. PTP is especially useful for evaluating DNA sequence data that may have a high level of homoplasy. A three-step PTP procedure for locating covaried characters is presented.
[Character covariance; cladistic analysis; DNA sequence data; permutation tail probability; phylogeny; bootstrap; skewness.]