Syst. Biol. 47(3):351-366, 1998

Reassessment of homology of morphological characters in tetractinellid sponges based on molecular data

Catherine Chombard1, 2, Nicole Boury-Esnault3, and Simon Tillier1, 2, 4

1 Service de Systematique Moleculaire, CNRS GDR 1005, 43 rue Cuvier, Museum National d'Histoire Naturelle, 75005 Paris, France

2 Laboratoire de Biologie des Invertebres Marins et Malacologie, URA CNRS 699 55 rue Buffon, Museum National d'Histoire Naturelle, 75005 Paris, France

3 Centre d'Oceanologie de Marseille, Station Marine d'Endoume, UMR CNRS 6540 rue de la Batterie des Lions, 13007 Marseille, France

4 Email: tillier@mnhn.fr

Abstract.---In sponges, as in other taxa with simple organization, the evaluation and use of morphological characters is difficult. Phylogenetic analysis of the first 850 nucleotides from the 5’ end of the 28S rRNA gene is used here to assess the homology of spicules used in the classification of the subclass Tetractinellida. A single well supported MP tree was obtained. The monophyly of the 9 Tetractinellida species studied confirms the tetraxon megasclere as a morphological synapomorphy for the Tetractinellida. Two species are reallocated, Penares helleri as a Geodiidae, now thought to have lost sterraster microscleres, and Stryphnus mucronatus to the Streptosclerophorida. SEM micrographs of Stryphnus microscleres show that the morphology of the sanidasters is compatible with the hypothesis that they are homologous with streptoscleres and confirm this reallocation. Two other synapomorphies are confirmed within the tetractinellid clade, the simultaneous presence of tetraxon megasclere and aster-type microsclere (Astrophorida) and the loss of the streptosclere and persistence of the euaster s.s. microscleres (Euastrophorida) evidenced by the reallocation of Stryphnus mucronatus. The streptosclere microscleres cannot be evaluated in terms of homology because Streptosclerophorida may be paraphyletic (although these nodes are not supported by reliable bootstrap proportions) contrary to the currently accepted classification.
[Astrophorida, Demospongiae, homology, molecular systematics, phylogeny, ribosomal DNA, skeleton, spicule, Tetractinellida.]


Syst. Biol. 47(3):367-396, 1998

Data sets, partitions, and characters: philosophies and procedures for analyzing multiple data sets

J. William O. Ballard1, 2, Margaret K. Thayer1, Alfred F. Newton, Jr.1, and Elizabeth R. Grismer3, 4

1 Department of Zoology, Field Museum, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA

2 Department of Zoology, Field Museum, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA;
E-mail: ballard@fmnh.org

3 Biochemistry Laboratory, Field Museum, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA

4 Stratagene Cloning Systems, Protein Dept., 11011 N. Torrey Pines, La Jolla, California 92037, USA

Abstract.---We compared four approaches for analyzing three data sets derived from staphylinoid beetles, a superfamily whose known species diversity is roughly comparable to that of vertebrates. One data set is derived from adult morphology and the two molecular data sets are from 12S ribosomal RNA and cytochrome b mitochondrial DNA. We found that taxonomic congruence following conditional data combination, herein called compatible evidence (CE), resolved more nodes compatible with an initial conservative hypothesis than did total evidence (TE), conditional data combination (CDC), or taxonomic congruence (TC). CE sets a base of nodes obtained by CDC analysis and then investigates what further agreement may arise in a universe where these nodes are accepted as given. We suggest that CE75-75 may be appropriate for future studies that aim to both generate a well-corroborated tree and investigate conflicts between data sets, partitions, and characters. CE75-75 is a 75% bootstrap consensus CDC tree followed by combinable-component consensus of a 75% bootstrap consensus of each homogeneous set of partitions having hierarchical structure.
[Beetles; Compatible Evidence; Conditional Data Combination; Staphylinidae; Taxonomic Congruence; Total Evidence.]


Syst. Biol. 47(3):397-413, 1998

The accuracy of methods for coding and sampling higher-level taxa for phylogenetic analysis: a simulation study

John J. Wiens

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

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 (Nei’s 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 “Felsenstein Zone” 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(3):414-426, 1998

Generalizing phylogenetic parsimony from the tree to the forest

Allan W. Dickerman

NCGR, 1800-A Old Pecos Trail, Santa Fe, New Mexico 87505, USA;
Email: awd@ncgr.org

Abstract.---Phylogenetic analysis is usually limited to considering descent relationships structured as a tree. Descent patterns with structures other than a tree characterize evolutionary systems when entities can inherit genetic material from more than one source, i.e. hybrid ancestry. Descent patterns in a phylogenetic system with a single hybrid event can be described as the sum of two gene trees, each describing the history of part of the genetic material comprising the system. Systems with more than one hybrid event will require a larger set of trees. This set of gene trees is called a phylogenetic forest. A potentially reticulate data structure, the hypertree, can represent a forest-structured phylogenetic hypothesis and simplify the calculation of parsimony costs. A workable parsimony criterion for hypertrees is the simultaneous minimization of mutation costs and the complexity of the forest. A method is presented to perform data-directed permutations on hypertrees in a heuristic search for parsimonious solutions. For any given data set, parsimonious hypertrees will range from zero hybrid events and a certain amount of homoplasy to multiple hybrid events with no homoplasy. Choosing from among this set of parsimonious hypertrees is a conceptually difficult problem that will depend on how likely hybrid events are in the particular system. This multitree approach is a simple generalization of cladistic parsimony to reticulate systems of common ancestry.
[Algorithm; forest; gene trees; hybridization; hypertree; parsimony; phylogeny; reticulation.]


Syst. Biol. 47(3):427-444, 1998

Testing phylogenetic methods with tree congruence: phylogenetic analysis of polymorphic morphological characters in phrynosomatid lizards

John Wiens

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

Abstract.---Congruence between trees from separately analyzed data sets is a powerful approach for assessing the performance of phylogenetic methods but has been applied primarily to the analysis of molecular data. In this study, different methods for treating polymorphic characters were compared using morphological data from phrynosomatid lizards. Clades were identified that are both traditionally recognized and supported by recent molecular analyses, and species were sampled from these clades to make three RknownS phylogenies of eight species each. The ability of different methods to estimate these "known" phylogenies with a finite sample of characters was tested. The phylogenetic methods included eight parsimony methods for coding polymorphism, three distance approaches (UPGMA, neighbor joining, and Fitch-Margoliash) applied to two genetic distance measures (Nei's and the modified Cavalli-Sforza and Edwards chord distance), and continuous maximum likelihood. The effects of excluding polymorphic characters and character weighting (a priori and successive) were also tested. Among the different parsimony approaches, the fixed-only method (excluding all polymorphic characters) performed relatively poorly, whereas the frequency method (including all polymorphic characters) performed relatively well. However, frequency-based distance methods consistently outperformed parsimony, especially with a small sample size (n= 1 individual per species). These results agree closely with those from recent simulation studies of polymorphic data and argue against the common practices of excluding polymorphic morphological characters, ignoring the frequencies of traits within species, and the exclusive use of parsimony to analyze morphological data.
[Accuracy; congruence; distance; likelihood; morphology; parsimony; polymorphic characters.]


Syst. Biol. 47(3):445-456, 1998

Weighted ancestral area analysis and a solution of the redundant distribution problem

Bernhard Hausdorf

Zoologisches Institut und Zoologisches Museum der Universitat Hamburg, Martin-Luther-King-Platz 3, D-20146 Hamburg, Germany;
E-mail: hausdorf@zoologie.uni-hamburg.de

Abstract.---A new cladistic method for the estimation of ancestral areas is based on reversible parsimony in combination with a weighting scheme that weights steps in positionally plesiomorphic branches higher than steps in positionally apomorphic branches. By applying this method to cladograms of human mitochondrial DNA, the method is superior to previously proposed algorithms. The method is also an appropriate tool for the solution of the redundant distribution problem in area cladograms. Under the assumption of allopatric speciation, redundant distributions, i.e., sympatry of sister groups, show that dispersal has occurred. Thus, the ancestral area of at least one sister group was smaller than the combined distribution of its descendants. With the weighted ancestral area analysis, the ancestral areas can be confined and at least some dispersal events can be distinguished from possible vicariance events. As applied to a cladogram of the Polypteridae, weighted ancestral area analysis is superior to Brooks parsimony analysis (assumption 0) and component analysis under assumptions 1 and 2 (Nelson and Platnick, 1981, Systematics and biogeography: Cladistics and vicariance. Columbia Univ. Press, New York.) in resolving redundancies. The results of the weighted ancestral area analysis may differ from the results of dispersal-vicariance analysis, because the rules of dispersal-vicariance analysis indirectly favour the questionable assumption that the ancestral species occupied only one unit area.
[Ancestral area; biogeography; dispersal; human mtDNA; Polypteridae; redundant distribution; sympatry.]


Syst. Biol. 47(3):457-474, 1998

The phylogenetic position of the dusky rat-kangaroo and the evolution of bipedal hopping in kangaroos (Macropodidae: Diprotodontia)

Angela Burk1, Michael Westerman2, and Mark Springer1

1 Department of Biology, University of California, Riverside, California 92521, USA;
E-mail: angburk@citrus.ucr.edu

2 Department of Genetics and Human Variation, La Trobe University, Melbourne, Victoria 3083, Australia

Abstract.---Kangaroos and their relatives (family Macropodidae) are divided into the subfamilies Macropodinae (kangaroos, wallabies, pademelons) and Potoroinae (rat-kangaroos, potoroos, bettongs). The musky rat-kangaroo, Hypsiprymnodon moschatus, is traditionally allied with other potoroines based primarily on osteological characters and aspects of the female reproductive system. Unlike other macropodids, however, which are capable of bipedal hopping, Hypsiprymnodon is a quadrupedal bounder and lacks several derived features of the pes and tarsus that are presumably adaptations for bipedal hopping. Other derived features, such as a complex stomach, loss of P2 with the eruption of P3, and reduction of litter size to one, are also lacking in Hypsiprymnodon but occur in all other macropodids. Thus, available evidence suggests that Hypsiprymnodon either is part of a monophyletic Potoroinae or is a sister taxon to other living macropodids. To test these hypotheses, we sequenced 1,170 base pairs of the mitochondrial genome for 16 macropodids. Maximum parsimony, minimum evolution, maximum likelihood, and quartet puzzling all support the hypothesis that macropodines and potoroines are united to the exclusion of Hypsiprymnodon. This hypothesis implies that characters such as bipedal hopping evolved only once in macropodid evolution. Aside from Hypsiprymnodon, the remaining macropodids separate into the traditional Macropodinae and Potoroinae. Macropodines further separate into two clades: one containing the New Guinean forest wallabies Dorcopsis and Dorcopsulus, and one consisting of the genera Macropus, Setonix, Thylogale, Onychogalea, Wallabia, Dendrolagus, Peradorcas, and Lagorchestes. Among potoroines, there is moderate support for the association of Bettongia and Aepyprymnus to the exclusion of Potorous. Divergence times were estimated using 12S ribosomal RNA transversions. At the base of the macropodid radiation, Hypsiprymnodon diverged from other macropodids approximately 45 million years ago. This estimate is comparable to divergence estimates among families of Australasian possums based on single-copy DNA hybridization and 12S rRNA transversions. Macropodines and potoroines, in turn, diverged approximately 30 million years ago. Among macropodines Dorcopsis and Dorcopsulus separated from other taxa approximately 10 million years ago.
[kangaroo, ribosomal RNA, bipedal hopping, Hypsiprymnodon]


Syst. Biol. 47(3):475-494, 1998

Incongruence between morphological and mitochondrial-DNA characters suggests hybrid origins of parthenogenic weevil lineages (Genus Aramigus)

Benjamin Normark1 and Analia A. Lanteri2

1 Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;
E-mail: bnormark@oeb.harvard.edu

2 Departamento Cientifico de Entomologia, Museo de La Plata, Paseo del Bosque, 1900 La Plata, Argentina;
E-mail: lanteri@isis.unlp.edu.ar

Abstract.---We present an expanded matrix of morphological characters for the genus Aramigus (Coleoptera: Curculionidae), which includes numerous polyploid parthenogenetic lineages, and compare and combine it with a published matrix of mitochondrial DNA (mtDNA) characters. The matrix of morphological characters provides little resolution of the A. tessellatus and A. uruguayensis species complexes, but does resolve previously unresolved relationships among other morphologically defined species (A. globoculus + A. intermedius and A. curtulus + A. planioculus). The morphological and mtDNA characters are significantly incongruent (0.435 ≤ IM ≤ 0.463; IMF = 0.0735), according to the test of Farris et al. (p = .010) and Templeton’s test (p <0.005), which we interpret as likely to be due to hybrid origins of polyploid parthenogenetic lineages. For the few sexual lineages included in both matrices, morphology and mtDNA provide congruent estimates of phylogeny. In spite of recent injunctions not to combine data sets that are incongruent due to differing histories, we perform combined analyses and use the results to select one of the most parsimonious mtDNA trees as the best estimate of maternal-lineage genealogy. We use this topology to reconstruct the evolution of parthenogenesis under the assumption that transitions from sexuality to parthenogenesis are irreversible. Where cytogenetically justified, as in weevils, the irreversibility assumption is useful for producing conservative estimates of the age of parthenogenetic lineages in spite of potential sampling bias against sexuals.
[Ancient asexuals; Entiminae; hybridization; incongruence; Naupactini; parthenogenesis; reticulation; root weevils.]