Syst. Biol. 45(2):127--134, 1996

Confidence Intervals for the Divergence Time of Two Clades

Mike A. Steel 1, Alan C. Cooper 2, and David Penny 3

1 Department of Mathematics and Statistics, University of Canterbury,
Christchurch, New Zealand;
E-mail: m.steel@math.canterbury.ac.nz
2 National Zoological Park, Smithsonian Institution,
Washington, D.C. 20008, USA
3 School of Biological Sciences, Massey University,
Palmerston North, New Zealand

Abstract.---We describe a simple method for generating tighter confidence intervals for the date of divergence of two monophyletic groups of taxa. This technique exploits the variation that exists within each of two groups that have evolved separately from a common ancestor. We illustrate the method (plus a technique to test the molecular clock hypothesis) using sequence dissimilarity within the orders of ratites and of tinamous (small birds from South America commonly regarded as the closest relative to ratites).
[Aligned sequences; clades; divergence times; molecular clock; phylogeny.]


Syst. Biol. 45(2):135--150, 1996

Ontogeny and Individual Variation: Analysis of Patterned Covariance Matrices with Common Principal Components

Christian Peter Klingenberg 1, Beat E. Neuenschwander 2, and Bernard D. Flury 3

1 Department of Biological Sciences, University of Alberta,
Edmonton, Alberta T6G 2E9, Canada;
E-mail: cklingen@gpu.srv.ualberta.ca
2 Swiss Federal Office of Public Health, Division of Epidemiology,
Hess-Strasse 27E, 3097 Liebefeld, Switzerland;
E-mail: neuen@ispm.unibe.ch
3 Department of Mathematics, Rawles Hall, Indiana University,
Bloomington, Indiana 47405, USA;
E-mail: flury@ucs.indiana.edu

Abstract.---Morphometric data from longitudinal growth studies with multiple measurements made in several growth stages on the same specimens confront researchers with difficult statistical problems because traits are correlated both within and across stages. Here, we introduce a statistical model especially designed to deal with this complexity. The common principal component (CPC) model for dependent random vectors is based on the assumption that the same pattern underlies both variation within stages and covariation across stages. Thus, a single transformation, when applied to all stages, renders the resulting CPCs uncorrelated not only within but also across stages. Because of these simplifying assumptions, the CPC model greatly reduces the number of parameters to be estimated; it is thus an efficient tool for data reduction. This model is demonstrated using growth of the water strider Limnoporus canaliculatus. The CPCs can be interpreted as patterns of "size" variation and contrasts between parts that are common to all stages, although there are minor deviations from the model. The "size" CPC accounts for most variation in all instars and is therefore an effective measure of overall growth. Moreover, the CPC model clarifies the link between static and ontogenetic variation by including both levels in a joint analysis and can be used to study morphological integration and constraints on the evolution of ontogenies.
[Allometry; common principal components; Gerridae; growth; longitudinal data; multivariate morphometrics; size.]


Syst. Biol. 45(2):151--167, 1996

Temporal Congruence Revisited: Comparison of Mitochondrial DNA Sequence Divergence in Cospeciating Pocket Gophers and Their Chewing Lice

Roderic D. M. Page 1

Department of Zoology, University of Oxford,
South Parks Road, Oxford OX1 3PS, England

Abstract.---Molecular phylogenies can be used to test hypotheses of cospeciation between hosts and parasites by comparing both cladistic relationships and branch lengths. Molecular data can also help discriminate between competing reconstructions of the history of the host--parasite association. Methods for comparing sequence divergence in hosts and parasites are described and applied to data for pocket gophers and their chewing lice. The hypothesis of cospeciation between these two clades is strongly supported. The lengths of homologous branches in the gopher and louse phylogenies are positively correlated, but there is little support for the hypothesis that lice are evolving an order of magnitude faster than are their hosts.
[Cospeciation; component analysis; DNA sequences; molecular clock; phylogeny; rates of evolution; tree comparison; pocket gophers; chewing lice; Geomys; Orthogeomys; Pappogeomys; Thomomys; Geomydoecus; Thomomydoecus.]

1 Present address: Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland.
E-mail: r.page@bio.gla.ac.uk.
Syst. Biol. 45(2):168--173, 1996

How Many Taxa Must Be Sampled to Identify the Root Node of a Large Clade?

Michael J. Sanderson

Section of Evolution and Ecology, University of California,
Davis, California 95616, USA;
E-mail: mjsanderson@ucdavis.edu

Abstract.---The importance of choice of taxa in phylogenetic analysis has been explored mainly with reference to its effect on the accuracy of tree estimation. Taxon sampling can also introduce other kinds of errors. Even if the sampled topology agrees with the true topology, it may not include the true root node of a clade, a node that is of interest for many reasons. Using a simple Yule model for the diversification process, the probability of identifying this node is derived under random sampling of taxa. For large clades, the minimum sample size needed to be 95% confident of identifying the root node is approximately 40 and is independent of the size of the clade. If rates of diversification differ in the two sister groups descended from the root node, the minimum sample size needed increases markedly. If these two sister groups are so different in diversity that a Yule model would be rejected by conventional diversification tests, then the necessary sample size is an order of magnitude greater than when diversification is homogeneous.
[Diversification; phylogeny; branching; speciation; Yule model; taxon sampling.]


Syst. Biol. 45(2):174--189, 1996

Explicitness, Stability, and Universality in the Phylogenetic Definition and Usage of Taxon Names: A Case Study of the Phylogenetic Taxonomy of the Carnivora (Mammalia)

Harold N. Bryant

Provincial Museum of Alberta, 12845 102 Avenue,
Edmonton, Alberta T5N 0M6, Canada;
E-mail: hbryant@mcd.gov.ab.ca

Abstract.---In phylogenetic taxonomy, the clade denoted by a taxon name is determined by the phylogenetic definition of the name and by the phylogenetic context. The clade referred to by the phylogenetic definition of a taxon name depends on (1) the reference phylogeny, (2) the meanings of taxon names referred to in the definition, and (3) whether the name is defined as a node-, stem-, or apomorphy-based taxon. Ambiguity in the clade referred to by the definition results from (1) imprecise wording so that no single ancestor is specified, the clade identified by the definition changes with the extinction of taxa, or the definition is a tautology, (2) failure to specify a reference phylogeny, and (3) the lack of phylogenetic definitions of taxon names referred to in the definition. In phylogenetic taxonomy, phylogenetic pattern has the central role in determining the identity and attributes of the clades denoted by particular taxon names. Because phylogenetic definitions may associate taxon names with different clades on different cladograms, definitions may have to be emended with changes in our understanding of phylogeny to preserve the association between a taxon name and a particular clade. As phylogenetic hypotheses stabilize, so will the definitions and usage of taxon names. Conventions can promote universality in the formation, definition, and usage of taxon names in phylogenetic taxonomy. Ambiguity is reduced by using standard formats for node- and stem-based definitions and by citing authorities for the meaning of taxon names used in definitions. Reference to undefined taxon names in definitions can be avoided by referring instead to the species referred to that taxon in a standard taxonomic reference. Recommended usages of taxon names provide a mechanism for restricting the use of a name to a clade with a particular exclusive common ancestry. Continuity of usage should help to promote the acceptance of phylogenetic taxonomy by biologists. These issues are discussed within the context of the phylogenetic taxonomy of the Carnivora.
[Carnivora; nomenclatural stability; phylogenetic definition; phylogenetic taxonomy; taxon names; taxonomic conventions; taxonomic usage.]


Syst. Biol. 45(2):190--222, 1996

Phylogenetic Hypotheses of the Relationships of Arthropods to Precambrian and Cambrian Problematic Fossil Taxa

Benjamin M. Waggoner

Department of Integrative Biology, University of California,
Berkeley, California 94720, USA;
E-mail: bmw@uclink2.berkeley.edu

Abstract.---A number of Vendian (latest Precambrian) body fossils have traditionally been considered arthropods or arthropodlike organisms. Several Cambrian "weird wonders" have also been linked with the arthropods. However, these relationships are difficult to express in traditional Linnean systematics. I present a morphological cladistic analysis of seven Vendian "arthropodlike" taxa compared with 21 representative Cambrian arthropods, lobopods, and weird wonders. Four arthropods from the later Phanerozoic (a pycnogonid, a monuran, and the problematic Cheloniellon and Arthropleura), five extant tardigrades, two extant kinorhynchs, and an extant priapulid, myriapod, pycnogonid, and onychophoran are also included. Monophyly of the Arthropoda is supported, but the anomalocarids and their relatives (Anomalopoda) fall out very close to the base of the traditional Arthropoda and should be included within it. The relationships among arthropods with uniramous appendages are not well resolved, but the group does not appear to be monophyletic. The biramous arthropods do form a clade and are divided into a crustaceanomorph clade and an arachnomorph clade that includes the trilobites. Most Vendian arthropodlike fossils form two clades, the Vendiamorpha and the Sprigginidae, in the arthropod stem group. The Lobopoda is a monophyletic clade with three branches: tardigrades, onychophorans, and marine lobopods. An unranked taxonomic scheme is proposed for the major clades identified here. There is no compelling reason to accept the hypothesis that the Vendian organisms included here are not metazoans.
[Precambrian; Vendian; Ediacara fauna; Cambrian; problematica; arthropod; lobopod.]


Syst. Biol. 45(2):223--246, 1996

Testing Hypotheses of Chaetognath Origins: Long Branches Revealed by 18S Ribosomal DNA

Kenneth M. Halanych

Department of Zoology, University of Texas, Austin, Texas 78712, USA;
and
Department of Zoology and Entomology, University of Pretoria,
Pretoria 0002, South Africa

Abstract.---Many hypotheses regarding the phylogenetic position of the Chaetognatha (arrow worms) have been proposed; these organisms are problematic primarily because their morphology offers few unambiguous systematic characters that ally them with other taxa. Early researchers proposed a plethora of phylogenetic placements for the Chaetognatha, grouping them with such divergent taxa as acanthocephalans and mollusks, but more traditional hypotheses posit that chaetognaths are, in fact, deuterostomes. Recently, Telford and Holland (1993, Mol. Biol. Evol. 10:660--676) and Wada and Satoh (1994, Proc. Natl. Acad. Sci. USA 91:1801--1804) disputed the deuterostome affinities of chaetognaths based on 18S nuclear ribosomal RNA (rDNA) gene sequence data. By employing published 18S rDNA gene sequence data, I extended these previous analyses by testing specific hypotheses of chaetognath affinities to nematodes, mollusks, acanthocephalans, and deuterostomes. Both parsimony and neighbor-joining analyses supported the monophyly of a chaetognath--nematode clade. Faith's T-PTP test and winning-sites analyses were employed to discriminate among competing hypotheses. The possibility of long-branch attraction accounting for the chaetognath--nematode relationship was explored by analyzing alternative four-taxon trees. An evolutionary scenario for the origin of the chaetognath lineage from a vermiform benthic organism is presented.
[Chaetognatha; Nematoda; 18S rDNA; long branches; winning-sites test; phylogeny.]