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), FacultŽ 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 CavalliSforza 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 ÒFelsenstein 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
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