Diana Lipscomb

PARSIMONY JACKKNIFING OUTPERFORMS NEIGHBOR-JOINING

Abstract— Because they are designed to produced just one tree, neighbor‐joining programs can obscure ambiguities in data. Ambiguities can be uncovered by resampling, but existing neighbor‐joining programs may give misleading bootstrap frequencies because they do not suppress zero‐length branches and/or are sensitive to the order of terminals in the data. A new procedure, parsimony jackknifing, overcomes these problems while running hundreds of times faster than existing programs for neighbor‐joining bootstrapping. For analysis of large matrices, parsimony jackknifing is hundreds of thousands of times faster than extensive branch‐swapping, yet is better able to screen out poorly‐supported groups.

The intellectual content of taxonomy: a comment on DNA taxonomy

1 Tautz, D. et al. (2002) DNA points the way ahead in taxonomy. Nature 418, 479 2 Tautz, D. et al. (2003) A plea for DNA taxonomy. Trends Ecol. Evol. 18 DOI: 10.1016/S0169-5347(02)00041-1 3 Minelli, A. (2003) The status of taxonomic literature. Trends Ecol. Evol. 18 DOI: 10.1016/S0169-5347(02)00051-4 4 Knapp, S. et al. (2002) Taxonomy needs evolution, not revolution. Nature 419, 559 5 Godfray, H.C.J. (2002) Challenges for taxonomy. Nature 417, 17–19 6 Mallet, J. (2003) Taxonomy: renaissance or Tower of Babel? DOI: 10.1016/S0169-5347(02)00061-7 7 Lipscomb, D. et al. (2003) The intellectual content of taxonomy: a comment on DNA taxonomy. DOI: 10.1016/S0169-5347(02)00060-5

PARSIMONY, HOMOLOGY AND THE ANALYSIS OF MULTISTATE CHARACTERS

Abstract— The order of states in a transformation series describes an internested set of synapomorphies. States adjacent to each other in the transformation series thus share a degree of homology not found in the other states. Whether the level of homology is relatively apomorphic is determined by rooting the order with outgroup comparison. The analysis of state order is a homology problem and is solved with a two‐step process using similarity and congruence with other characters as criteria. Other methods that have been proposed (e.g. transformation series analysis, non‐additive analysis, morphocline analysis, ontogenetic analysis) fail to apply both similarity and congruence, and thus cannot be used independently for determining character state order.

Phylogenetic analyses of the fungi based on large rDNA data sets.

Two data sets of fungal small subunit (SSU) rDNA sequences, one from the Ribosomal Da- tabase Project (RDP) with 485 sequences, and the other from the rRNA WWW Server (RNA-S) with 785 sequences, have been analyzed to estimate group sup- port and to compare tree topologies resulting from independently aligned, large data sets of largely the same sequences. The analyses were conducted by us- ing a parsimony jackknifing computer program to search rapidly for supported groups in combination with branch swapping and random addition sequenc- es. The results show that gross topology is very simi- lar. The major differences were with the Ascomycetes, which were not recovered in the RDP tree, and with the Holobasidiomycetes, which were not recovered in the RNA-S tree. Both data sets identify and support many well known fungal groups such as the Gloma- les, Saccharomycetes, Dikaryomycetes, Basidiomy- cetes, Uredinomycetes, Ustilaginomycetes, Euasco- mycetes, Leotiomyceta, Sordariomycetes and the Chaetothyriomycetes. No support was found for some previously proposed groups, including the Chy- tridiomycetes, Taphrinomycotina, Pezizomycotina through Pezizales, Hymenomycetes, Tremellomyce- tes, Leotiomycetes and the Dothideomycetes. The analysis contradicted some other previously proposed groups, among them the Zygomycota, Zygomycetes, Lecanoromycetes and the Sordariomycetidae. Trans- version parsimony performed on the same data sets

Systematic, stratigraphic, and paleoenvironmental contexts of first-appearing Hipparion in the Vienna Basin, Austria

ABSTRACT The tridactyl horse Hipparion (s.l.) has long attracted the attention of paleontologists and geologists alike for its potential use as a stratigraphic and paleoenvironmental index. A central dogma surrounding this horses record is that it first occurred abruptly and instantaneously throughout the Old World ca. 12.5 Ma, heralding a general late Miocene environmental shift from forest to savanna ecosystems. We present data on the oldest known Central European hipparions, “Hipparion” primigenium (s.s.), that bear on these issues. Our analysis of the local Vienna Basin stratigraphie sequence and Paratethys geochronology suggests that hipparions first provincial occurrence was ca. 11.0–11.5 Ma. We falsify the hypotheses of an Old World “Hipparion Datum” and the purported initial association of this horse with savanna habitats. An explicit cladistic analysis of “Hipparion” primigenium (s.s.), its North American sister taxon Cormohipparion occidentale, and several Old World primitive hipparions (“Grou...

Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes

Sequences of the small subunit (SSU) ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most‐parsimonious trees, and finding them all may be impossible using convential phylogenetic methods. To examine the reliability of the number and relationships of eukaryotic kingdoms proposed by previous analyses of the SSU, we calculated trees from aligned sequences from eukaryotes in the Ribosomal Database Project using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups. Two separate analyses were carried out: an analysis in which all bases were equally weighted, and one in which transversions only were used. The parsimony jackknife procedure was able to efficiently find trees in which most major groups of eukaryotes were supported and in which some evolutionary hypotheses proposed by previous workers were tested. The relationships of these major groups to each other were largely unresolved, indicating that the SSU data, as represented in this database, is insufficient for answering questions about these deep branches. Interestingly, the analysis of transitions differs from the results of the entire data set, primarily being less resolved. This indicates that transversional mutations are important contributors to the resolved structure of the tree.

The misleading effects of composite taxa in supermatrices

With the amount of available sequence data rapidly increasing, supermatrices are at the forefront of systematic studies. As an alternative to supertrees, supermatrices utilize a total evidence approach where different genes and other lines of data are merged into a single data matrix, which is then analyzed in an attempt to obtain the phylogeny that best explains the data. However, questions may arise when combining data sets in which one or more taxa do not have sequences available for each individual gene. Two possible solutions to this situation are to either leave all taxa separate and code unavailable sequences as missing, or to combine taxa at a level for which monophyly is assumed a priori. By reanalyzing the previous work of, we show that combining taxa may yield misleading results, i.e., hypotheses of relationships that are not supported by the underlying data.

PARSIMONY AND THE CHOICE BETWEEN DIFFERENT TRANSFORMATIONS FOR THE SAME CHARACTER SET

Abstract— When phylogeneticists choose among alternative hypotheses, they choose the one that requires the fewest ad hoc assumptions, i.e. the one that is the most parsimonious. For some systematists, choosing among alternative transformation series for the same set of taxa is equivalent to attaining trees with shorter length and minimal homoplasy. Homoplasy is shown to be composed of hierarchical discordance and scattering, which are recognized and described for the first time. Neither the consistency nor retention indices can be used in assessing different theories of multistate character transformation because both are affected by the shape of the transformation series rather than the character state distribution on a tree. Fits of transformations to a tree are better assessed by comparing the transformation to the cladogram character and the nearest neighbor network. Nearest neighbor networks are graphical representations of the nearest neighbor matrix. Transformations with the closest greatest number of matches between cladogram characters and the least complexity in the nearest neighbor network are preferred. These transformations are shown to make the fewest number of ad hoc statements and hence to be the most parsimonious. A means for obtaining cladogram characters and nearest neighbor matrices using a widely distributed microcomputer program is presented.

Stephanopogon, a Phylogenetically Important "Ciliate," Shown by Ultrastructural Studies to Be a Flagellate

A benthic marine protist (Stephanopogon) with a homokaryotic nucleus has long been considered to be a gymnostome ciliate. It has been important in hypotheses concerning the origin of ciliates, the evolution and origin of the dual nuclear apparatus of contemporary species of the Ciliophora, and the origin of the multicellular Eumetazoa. Ultrastructural observations reveal that the organism should be reclassified as a flagellate, despite its superficial resemblance to ciliates.

A SIMPLE TEST: EVALUATING EXPLANATIONS FOR THE RELATIVE SIMPLICITY OF THE EDWARDSIIDAE (CNIDARIA: ANTHOZOA)

Abstract Many members of the cnidarian subclass Zoantharia (sea anemones, corals, and their allies) pass through a larval stage with eight complete mesenteries and without posterior musculature. This larva is usually transient, developing into an adult with 12 or more mesenteries. The adults of one family of sea anemones, the Edwardsiidae, bear the larval number and arrangement of mesenteries and lack the pedal disc seen in other sea anemones. The morphology of the Edwardsiidae has been interpreted in a number of ways: (1) the Edwardsiidae are the most basal extant zoantharian, having diverged before the evolution of additional mesenteries and basal musculature; (2) they are relatively advanced sea anemones that have secondarily simplified because they burrow in sand or mud rather than attaching to a hard substrate; or (3) edwardsiids are derived anemones that have retained a juvenile morphology through paedomorphosis. Phylogenetic analyses of small subunit ribosomal gene sequences reveal that the Edwardsiidae are derived zoantharians, nested within sea anemones. None of the proposed explanations fully explain the edwardsiids body plan; edwardsiid anatomy is a mosaic of retained primitive and derived features. The results of the present study provide insight into zoantharian phylogeny and illustrate how phylogenetic tests can be used to study the evolution of cnidarian body plans.