Syst. Biol. 44(4):457-473, 1995

Cladistic Biogeography of Plants in Australia and New Guinea: Congruent Pattern Reveals Two Endemic Tropical Tracks

Michael D. Crisp 1, 4, H. Peter Linder 2, and Peter H. Weston 3

1 Division of Botany and Zoology, Australian National University,
Canberra, Australian Capital Territory 0200, Australia
2 Department of Botany, University of Cape Town,
Rondebosch 7700, South Africa
3 Royal Botanic Gardens, Mrs. Macquaries Road,
Sydney, New South Wales 2000, Australia
4 E-mail: mike.crisp@anu.edu.au

Abstract.---Although congruence among multiple taxa is accepted as the basis of the cladistic approach to biogeography, seldom has congruence been tested for patterns within continents. Moreover, contiguous land areas are subject to confounding factors that might lead to incongruence, and areas of endemism are difficult to define. Most previous studies have analyzed single taxa and therefore could not test for congruence. Here, we report the first cladistic biogeographic analysis of multiple plant taxa (11 angiosperm groups) within continental Australasia. We have used Page's (1994, Syst. Biol. 43:58--77) new mapping method implemented in his program COMPONENT 2.0, minimizing the optimality criterion "leaves added," which is the number of terminal branches that need to be added to reconcile all input cladograms with the general area cladogram. A randomization test showed significant congruence, and a jackknife test indicated which parts of the general area pattern are robust. Conflicting patterns shown by widespread species may have been influenced by recent range expansions. At least two independent histories are postulated for taxa endemic to the tropics. One appears as a close relationship between the monsoon tropical areas, including southern New Guinea, and the other is a track (a group of areas with a common history) of successive differentiation along the east and south coasts. The Australian wet tropics (the Atherton area), although geographically proximate to the monsoon tropics, are part of the east coast track. Tasmania shows a very early vicariance from the rest of the continent, and the central arid areas appear related to adjacent coastal areas rather than to each other (contra Cracraft, 1991, Aust. Syst. Bot. 4:211--227). The postulated exchange of taxa with southeast Asia following late Miocene contact was not tested because of a lack of suitable taxon cladograms.
[Cladistic biogeography; congruence; tree mapping; Australia; New Guinea; angiosperms; tropics.]


Syst. Biol. 44(4):474--481, 1995

Calculating the Probability Distributions of Ancestral States Reconstructed by Parsimony on Phylogenetic Trees

Wayne P. Maddison

Department of Ecology and Evolutionary Biology, University of Arizona,
Tucson, Arizona 85721, USA

Abstract.---Parsimony methods are often used to map a character's evolution on a phylogenetic tree by reconstructing the ancestral states at interior nodes of the tree. Although the statistical behavior of methods for reconstructing trees has been studied using stochastic models of evolution, there is little comparable work on methods for reconstructing character evolution. If a discrete character were to begin with an ancestral state at the root of a phylogenetic tree and evolve with specified probabilities of change on the branches of the tree, then the terminal taxa would receive one of many possible distributions of character states. These states in terminal taxa are the data used by parsimony methods in reconstructing character evolution on trees. Given a stochastic model of character evolution that specifies probabilities of change on the branches of a known phylogenetic tree, it is possible to calculate the probabilities of various ancestral state reconstructions at each node in the tree. Exact calculations for these probabilities are presented here. They can be used, for example, to calculate the probability that ancestral states would be reconstructed accurately.
[Phylogeny; character evolution; ancestral states; parsimony; mapping characters; probability distribution; accuracy.]


Syst. Biol. 44(4):482--500, 1995

Polymorphic Characters in Phylogenetic Systematics

John J. Wiens 1,2

Department of Zoology and Texas Memorial Museum, University of Texas,
Austin, Texas 78712-1064, USA

1 Present address: Section of Amphibians and Reptiles,
Carnegie Museum of Natural History, Pittsburgh, Pennsylvania 15213, USA.
2 E-mail: jwiens@mail.utexas.edu

Abstract.---The use of discrete, intraspecifically variable characters in parsimony analysis is reviewed. Seven data sets (two from morphology and five from allozymes) were analyzed to (1) compare different methods for treating polymorphic characters, (2) test for phylogenetic information in polymorphic characters, and (3) determine if there is a relationship between homoplasy and intraspecific variability. The performance of eight methods was compared using five criteria (number of characters treated as informative, number of shortest trees, phylogenetic signal, number of nodes supported by bootstrapping, and sensitivity to reduced sample size). Approaches that incorporate explicit frequency information perform best overall for all the criteria, although the "majority" method ties for best for the bootstrapping criterion. Levels of phylogenetic information in the polymorphic characters differ greatly among data sets and methods. Polymorphic characters in most data sets contained significant phylogenetic structure using most methods, but only one, the frequency method, extracts significant signal from the polymorphic characters in all seven data sets. Fixed characters appear to contain more signal than polymorphic characters, and homoplasy is significantly and positively correlated with intraspecific variability. This study supports the traditional view that polymorphic characters are less reliable in inferring phylogeny but does not necessarily support their exclusion. Systematists working with morphological data often do not report intraspecific variation, the frequencies of different traits, or how polymorphic characters are screened and analyzed; this situation should change.
[Polymorphic characters; character coding; character selection; character weighting; homoplasy; allozymes; morphology.]


Syst. Biol. 44(4):501--514, 1995

Coping with Abundant Missing Entries in Phylogenetic Inference Using Parsimony

Mark Wilkinson 1

School of Biological Sciences, University of Bristol,
Bristol BS8 1UG, England
1 E-mail: mark.wilkinson@bris.ac.uk

Abstract.---When cladistic data sets include taxa with abundant missing entries, parsimony analysis may yield multiple equally optimal trees and necessitate the use of consensus methods to summarize relationships that are common to the multiple trees. Determination of those relationships that are common to the equally parsimonious trees and are thus unambiguously supported by the parsimonious interpretation of the data may not be possible using consensus methods that are widely employed by systematists. Thus, missing data may have an obfuscatory effect upon phylogenetic relationships. This problem can be ameliorated or overcome by adopting a strategy of safe taxonomic reduction. In this approach, taxa that can have no effect upon the relationships inferred for other taxa but that may increase the numbers of equally most-parsimonious trees are identified. Eliminating such taxa through the application of a series of safe deletion rules may reduce the number of equally most-parsimonious trees and thereby facilitate the consensus representation of unambiguous relationships supported by the data. The methods are illustrated by reanalysis of cladistic data for the Saurischia.
[Phylogeny; parsimony; underdetermination; equivalence; safe taxonomic reduction; consensus; Saurischia.]


Syst. Biol. 44(4):515--532, 1995

Phylogenetic Relationships and Orthogenetic Evolution of Coat Color Among Tamarins (Genus Saguinus)

Susan C. Jacobs 1,2, Allan Larson 1, and James M. Cheverud 2
1 Department of Biology, Washington University,
St. Louis, Missouri 63130, USA
2 Department of Anatomy and Neurobiology,
Washington University School of Medicine,
St. Louis, Missouri 63110, USA

Abstract.---Orthogenetic evolutionary patterns may appear within taxa as a result of developmental constraints on the expression of genetic variation. Metachromism is a theory of variation in mammalian coat color that predicts an orthogenetic evolutionary pattern. This theory was based in part on studies of interspecific and geographic variation in the coat colors of New World monkeys. We tested the theory of metachromism in tamarins (Saguinus) using phylogenetic information derived from mitochondrial DNA sequences. Parsimony analysis of mitochondrial DNA sequences from the D-loop and cytochrome b genes supports recognition of Saguinus as a monophyletic genus composed of two major clades. Coat colors for 16 chromogenetic regions of the tamarin coat were examined using the molecular phylogeny to test predictions of the metachromatic theory. Our results support the hypothesis of an orthogenetic evolutionary pattern for coat color in tamarins.
[Orthogenesis; phylogeny; coat colors; Saguinus; tamarins, mitochondrial DNA.]


Syst. Biol. 44(4):533--547, 1995

Performance of the Maximum Likelihood, Neighbor Joining, and Maximum Parsimony Methods When Sequence Sites are Not Independent

Michael Schoeniger 1,3 and Arndt von Haeseler 2,4
1 Theoretical Chemistry, Tech. University Munich,
Lichtenbergstrasse 4, D-85747 Garching, Germany
2 Institute for Zoology, University of Munich,
P.O. Box 202136, D-80021 Munich, Germany
3 E-mail: schoeniger@theochem.tu-muenchen.de
4 E-mail: arndt@zi.biologie.uni-muenchen.de

Abstract.---The Felsenstein zone of various tree reconstruction methods for a four-species tree was evaluated for two models of sequence evolution. The first model assumes correlated sequence sites, as suggested by Schoeniger and von Haeseler (1994, Mol. Phylogenet. Evol. 3:240--247), thereby preserving the nonoverlapping doublet correlations (e.g., within base-paired nucleotides of stem regions of ribosomal RNA). The second model was proposed by Hasegawa, Kishino, and Yano (1985, J. Mol. Evol. 22:160--174) and assumes that the nucleotide sites are evolving independently of each other. The methods examined are maximum likelihood, maximum parsimony, and neighbor joining with uncorrected, Jukes--Cantor-corrected, and Kimura-corrected distances. All methods, including maximum likelihood, are inconsistent for certain model trees. Maximum likelihood only shows a Felsenstein zone if sequence sites are not evolving independently. The location of the border of the Felsenstein zone indicates that maximum likelihood is very robust against violation of the independence assumption. The other tree reconstruction methods are more sensitive to violation of this assumption. Moreover, the addition of dependence to a model of sequence evolution does not change the boundary of the Felsenstein zone very much if tree reconstruction methods that are already inconsistent for certain model trees are applied.
[Maximum likelihood; neighbor joining; maximum parsimony; correlated sites; inconsistency; power of phylogenetic inferences; Felsenstein zone.]