Syst. Biol. 47(2):181-207, 1998

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets

David A. Baum1, Randall L. Small2, and Jonathan F. Wendel2

1 Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, Massachusetts 02138, USA;
Email: dbaum@oeb.harvard.edu

2 Department of Botany, Bessey Hall, Iowa State University, Ames, Iowa, USA

Abstract.---The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction-sites, sequences of the chloroplast rpl16 intron, sequences of the ITS region of nuclear rDNA, and morphology. We sampled at least one accession of all eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were highly concordant. The two chloroplast data sets showed concordance with one another but disagreed with ITS and morphology. This disagreement was found to be significant using a Wilcoxon sign-rank test and an incongruence length difference test. The most likely explanation of the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and, therefore, involved over-water dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution, but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to mammal-pollination in the genus.
[Biogeography, data set conflict, floral evolution, Gondwana, introgression, molecular clock, phylogeny.]


Syst. Biol. 47(2):208-227, 1998

Genetic distances and ordination: the land snail Helix aspersa in North Africa as a test case

Annie Guiller1, Alain Bellido2, and Luc Madec3

1 Laboratoire de Parasitologie Pharmaceutique (CNRS UMR 6553), Facultˇ des Sciences Pharmaceutiques et Biologiques, 35043 Rennes, France;
E-mail: annie.guiller@univ-rennes1.fr

2 Station Biologique de Paimpont (CNRS UMR 6553), 35380 Paimpont, France;
E-mail: alain.bellido@univ-rennes1.fr

3 Laboratoire de Zoologie et d'Ecophysiologie (CNRS UMR 6553, L.A. INRA), Campus de Beaulieu, 35042 Rennes, France;
E-mail: luc.madec@univ-rennes1.fr

Abstract.---We examined the efficiencies of ordination methods in the treatment of gene frequency data at intraspecific level, using metric and nonmetric distance measures (NeiÕs and RogersÕs genetic distances, c2 distance). We assessed initial processes responsible for the geographical distribution of the Mediterranean land snail Helix aspersa. Seventeen enzyme loci from 30 northern African snail populations were considered in the present analysis. Five combinations of distance/multivariate analysis were compared: correspondence analysis (CA), nonmetric multidimensional scaling (NMDS) on NeiÕs, RogersÕs and c2 distances, and principal coordinates analysis on RogersÕs distances. Configuration of the objects resulting from ordination was projected onto three-dimensional graphics with the minimum spanning tree or the relative neighborhood graph surperimposed. Pre- and postordination or clustering distance matrices were compared by means of correlation methods. As expected, all combinations led to a clear west versus east pattern of variation. However, the intraregional relationships and degree of connectivity between pairs of operational taxonomic units were not necessarily constant from one method to another. Ordination methods, when applied with NeiÕs and RogersÕs distances provided the best fit, with original distances (r = 0.98) compared with UPGMA clustering (r » 0.75). The Nei/NMDS combination seems to be a good compromise (distortion index; dt = 10%) between Rogers/NMDS which produces a more confusing pattern of differentiation (dt = 24%) and c2/CA which tends to distort large distances (dt = 31%). NMDS obviously provides a powerful method to summarize relationships between populations, when neither hierarchical structure nor phylogenetic inference are required. These findings led the discussion on the good performance of NMDS, the appropriate distances to be used, and the potential application of this method to other types of allelic data (such as microsatellite loci) or data on nucleotide sequences of genes.
[Allozymes, genetic distances, Helix aspersa, NMDS, ordination.]


Syst. Biol. 47(2):32-42, 1998

Phylogenetic analysis and intraspecific variation: performance of parsimony, likelihood, and distance methods

John J. Wiens1 and Maria R. Servedio2

1 Section of Amphibians and Reptiles, Carnegie Museum of Natural History, Pittsburgh, Pennsylvania 15213-4080, USA;
E-mail: wiensj@clpgh.org

2 Department of Zoology, University of Texas, Austin, Texas 78712-1064, USA;
E-mail: mservedio@mail.utexas.edu

Abstract.---Intraspecific variation is abundant in all types of systematic characters but is rarely addressed in simulation studies of phylogenetic method performance. We compared the accuracy of 15 phylogenetic methods using simulations to: (1) determine the most accurate method(s) for analyzing polymorphic data (under simplified conditions), and (2) test if generalizations about the performance of phylogenetic methods based on previous simulations of fixed (non-polymorphic) characters are robust to a very different evolutionary model that explicitly includes intraspecific variation. Simulated data sets consisted of allele frequencies that evolved by genetic drift. The phylogenetic methods included eight parsimony coding methods, continuous maximum likelihood, and three distance methods (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (NeiÕs and the modified Cavalli-Sforza and Edwards chord distance). Two sets of simulations were performed. The first examined the effects of different branch lengths, sample sizes (individuals sampled per species), numbers of characters, and numbers of alleles per locus in the eight-taxon case. The second examined more extensively the effects of branch length in the four-taxon, two-allele case. Overall, the most accurate methods were likelihood, the additive distance methods (neighbor joining and Fitch-Margoliash), and the frequency parsimony method. Despite the use of a very different evolutionary model in the present paper, many of the results are similar to those from simulations of fixed characters. Similarities include the presence of the ŅFelsenstein ZoneÓ where methods often fail, which suggests that long-branch attraction may occur among closely related species through genetic drift. Differences between the results of fixed and polymorphic data simulations include the following: (1) UPGMA is as accurate or more accurate than nonfrequency parsimony methods across nearly all combinations of branch lengths, (2) likelihood and the additive distance methods are not positively misled under any combination of branch lengths tested (even when the assumptions of the methods are violated and few characters are sampled). We found that sample size is an important determinant of accuracy and affects the relative success of methods (i.e., distance and likelihood methods outperform parsimony at small sample sizes). Attempts to generalize about the behavior of phylogenetic methods should consider the extreme examples offered by fixed-mutation models of DNA sequence data and genetic-drift models of allele frequencies.
[Accuracy; distance methods; maximum likelihood; parsimony; polymorphism; simulations.]


Syst. Biol. 47(2):254-263, 1998

Landmark based thin-plate spline relative warp analysis of gastropod shells

J. R. Stone1

Department of Zoology, University of Toronto, Toronto, Ontario, Canada M5S 3G5

Abstract.---In the analysis of organismal form, landmark-based geometrical morphometrics now are preferred to traditional morphometrics by many systematists. However, certain forms have eluded geometrical morphometric analysis because landmarks on them are difficult to define; this situation is a problem of logistics rather than an inadequacy of the landmark-based approach. In this article, a landmark-based geometrical morphometric analysis is performed on one such form (the gastropod shell), and the results obtained are compared to those obtained using more traditional methods of morphometric analysis.
[Gastropods; geometric morphometrics; landmarks; principal components; thin-plate spline.]

1 Present address: Department of Ecology and Evolution, State University of New York, Stony Brook, New York 11794-5425, USA;
Email: stone@life.bio.sunysb.edu


Syst. Biol. 47(2):264-281, 1998

The relative success of methods for measuring and describing the shape of complex objects

Tracy McLellan1 and John A. Endler2

1 Department of Zoology and Genetics, Iowa State University, Ames, Iowa 50011, USA;
E-mail: gnaylor@iastate.edu

2 Department of Biology, University of Michigan, Ann Arbor, Michigan, USA

Abstract.---We examined and compared several morphometric methods for describing complex shapes. We chose the leaves of maples (Acer) and other tree species because they can all be visually discriminated from each other solely by leaf shape. We digitized the leaf outlines with a video camera and then examined the outlines with several morphometric methods to determine the extent to which margin details could be quantified and compared. Elliptic Fourier analysis provides complete and accurate descriptions of complex outlines and can be used to reconstruct images accurately. We compared several metrics that summarize overall shape complexity. A new measure of margin roughness is useful for quantifying and comparing margin detail independently of overall shape. Fractal dimension is highly correlated with the ratio of perimeter to area (dissection index) and reveals little additional information about shape. In combination, the summaries of shape complexity provide good discrimination of groups. We used canonical discriminant analysis to compare methods for outlines to traditional morphometric analysis of measurements taken between landmark points. Groups were discriminated from each other more clearly with outline methods than with landmark-based analyses.
[Morphometrics, leaf shape, Fourier analysis, margin roughness, fractal dimension, landmark analysis, Acer, Quercus, Liquidambar.]


Syst. Biol. 47(2):282-310, 1998

Data decisiveness, data quality, and incongrunce in phylogenetic analysis: and example from the monocotyledons using mitochondrial atpA sequences

Jerrold I. Davis1, Mark P. Simmons1, Dennis W. Stevenson2, and Jonathan F. Wendel3

1 L. H. Bailey Hortorium, Cornell University, Ithaca, New York 14853, USA

2 New York Botanical Garden, Bronx, New York 10458, USA

3 Department of Botany, Iowa State University, Ames, Iowa 50011, USA

Abstract.---We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the mitochondrion-encoded gene atpA, the latter of which encodes the *-subunit of mitochondrial ATP synthase. The plant mitochondrial genome has been little-used in plant systematics, in part because nucleotide sequence evolution in enzyme-encoding genes of this genome evolve relatively slowly. The three data sets were examined in separate and combined analyses, with a focus on patterns of congruence, homoplasy, and data decisiveness. Data decisiveness (described by P. Goloboff) is a measure of robustness of support for most-parsimonious trees by a data set in terms of the degree to which those trees are shorter than the average length of all possible trees. Because indecisive data sets require relatively fewer additional steps than decisive ones to be optimized on nonparsimonious trees, they will have a lesser tendency to be incongruent with other data sets. One consequence of this relationship between decisiveness and character incongruence is that if incongruence is used as a criterion of noncombinability, decisive data sets, which provide robust support for relationships, are more likely to be assessed as noncombinable with other data sets than are indecisive data sets, which provide weak support for relationships. For the sampling of taxa in this study, the atpA data set has about half as many cladistically informative nucleotides as the rbcL data set per site examined, and is less homoplastic and more decisive. The rbcL data set, which is the least decisive of the three, exhibits the lowest levels of character incongruence. Whatever the molecular evolutionary cause of this phenomenon, it seems likely that the poorer performance of rbcL than atpA, in terms of data decisiveness, is due to both its higher overall level of homoplasy and the fact that it is performing especially poorly at nonsynonymous sites.
[atpA; character incongruence; cladistics; data decisiveness; monocotyledons; plant mitochondrial DNA; rbcL; restriction sites.]


Syst. Biol. 47(2):311-335, 1998

Phylogeny of frogs of the Physalaemus pustulosus species group with an examination of data incongruence

David C. Cannatella1,2, David M. Hillis1, Paul T. Chippindale1,3, Lee Weight4, A. Stanley Rand4,5, and Michael J. Ryan1,4

1 Department of Zoology, University of Texas, Austin, Texas 78712-1064, USA;
E-mail: (D.M.H.) hillis@bull.zo.utexas.edu, (M.J.R.) mryan@mail.utexas.edu

2 Texas Memorial Museum, University of Texas, Austin, Texas 78705, USA;
E-mail: catfish@mail.utexas.edu

Abstract.---Characters derived from advertisement calls, morphology, allozymes, and the sequences of the small subunit of the mitochondrial ribosomal gene (12S) and the COI mitochondrial gene were used to estimate the phylogeny of frogs of the Physalaemus pustulosus group (Leptodactylidae). The combinability of these data partitions was assessed in several ways: measures of phylogenetic signal, character support for trees, congruence of tree topologies, compatibility of data partitions with suboptimal trees, and homogeneity of data partitions. Combined parsimony analysis of all data equally weighted yielded the same tree as the 12S partition analyzed under parsimony and maximum likelihood. The COI, allozyme, and morphology partitions were generally congruent and compatible with the tree derived from combined data. The call data were significantly different from all other partitions, whether considered in terms of tree topology alone, partition homogeneity, or compatibility of data with trees derived from other partitions. The lack of effect of the call data on the topology of the combined tree is probably due to the small number of call characters. The general incongruence of the call data with other data partitions is consistent with the idea that the advertisement calls of this group of frogs are under strong sexual selection.
[Advertisement calls; behavior; combined-data analysis; data partitions; frogs; Leptodactylidae;Physalaemus; sensory exploitation hypothesis.]

3 Present Address: Department of Biology, University of Texas, Arlington, Texas 76019, USA;
E-mail: paulc@albert.uta.edu

4 Smithsonian Tropical Research Institute, Unit 0948, APO AA 34002;
Present address (L.W.): Field Museum of Natural History, Roosevelt Road at Lake Shore Dr., Chicago, Illinois 60605;
E-mail: weigt@fmppr.fmnh.org

5 E-mail: rand@gamboa.si.edu