Abstract.---As an initial step toward developing a model system to study requirements for and consequences of transitions to mutualism, the phylogeny of a group of closely related lichenized and nonlichenized basidiomycetes (Omphalina) was reconstructed. The phylogenetic analyses are based on four data sets representing different regions of the nuclear ribosomal repeat unit (ITS1, 5.8S, ITS2, and 25S) obtained from 30 species of Omphalina and related genera. The resulting phylogenetic trees from each of these four data sets, when analyzed separately, were not identical. Testing for the combinability of these four data sets suggested that they could not be combined in their entirety. The removal of ambiguous alignments and saturated sites was sufficient, after reapplying the combinability test on the pruned data sets, to explain the topological discrepancies. In this process, the first of two complementary tests developed by Rodrigo et al. (1993, N.Z. J. Bot. 31:257--268) to assess whether two data sets are the result of the same phylogenetic history was found to be biased, rejecting the combinability of two data sets even when they are samples of the same phylogenetic history. Combining the four pruned data sets yielded phylogenies that suggest the five lichen-forming species of Omphalina form a monophyletic group. The sister group to this symbiotic clade consists mostly of dark brown Omphalina species intermixed with species from the genera Arrhenia and Phaeothellus. The genera Omphalina and Gerronema are shown to be polyphyletic. The lichen-forming species O. ericetorum and the nonmutualistic species O. velutipes, O. epichysium, and O. sphagnicola are the best candidates for experimental work designed to gain a better understanding of mechanisms involved in symbiotic interactions and the role symbiosis has played in the evolution of fungi.
[Basidiomycetes; data set combinability; data set homogeneity; fungi; lichen symbiosis; model system; molecular phylogenies; mutualism; nuclear ribosomal RNA; Omphalina; phylogenetic signal.]
1 Present address: Department of Botany, Field Museum of Natural History, Roosevelt Road at Lake Shore Drive, Chicago, Illinois 60605, USA. E-mail: lutzoni@fmppr.fmnh.org.

Abstract.---Two parsimony analyses based on morphological data of the subtribe Blennospermatinae (Asteraceae, Senecioneae) were performed to generate a hypothesis for the phylogenetic relationships within the subtribe, which comprises four genera and 27 species of both radiate and disciform genera distributed around the Pacific Rim. Heterogeneity of the group is concomitant with coding problems such as absence of organs leading to inapplicable states, also termed missing entries. Morphological data were therefore coded by two differing methods: (1) using the separate state "absent" or (2) using the state "inapplicable." Substantial support for Blennospermatinae monophyly was obtained. A well-supported sister-group relationship, based on floral characters, was established between the two genera Blennosperma and Ischnea. Their ancestor evolved a specialized type of tubeless ray florets and male disc florets. These two genera are confined to the New World and to New Guinea, respectively. Their sister taxon is the monotypic North American genus Crocidium, and its status as a separate genus was supported. Abrotanella is a genus of 19 species confined to alpine habitats in the Southern Hemisphere. Monophyly and the isolated position of Abrotanella was strengthened. One clade of the genus has evolved functionally male central florets with a progressing trend toward cypsela reduction. Different floral colors have evolved in Abrotanella, and the deep yellow color found in the other genera is lost. Among the flowering plants confined to New Zealand, there is a remarkably high ratio of white-flowered species. Results of this study indicate that the white-flowered capitulum is a derived character within Abrotanella originating in New Zealand. A purple-flowered capitulum, also restricted to Abrotanella, is a repeatedly evolved apomorphic character found in species confined to southern South America and the sub-Antarctic Campbell and Auckland islands.
[Abrotanella; Asteraceae; Blennosperma; Blennospermatinae; cladistic analysis; Crocidium; floral evolution; flower color; Ischnea; male floret; New Zealand; phylogenetic reconstruction; Senecioneae.]

Abstract.---Mice of the Peromyscus aztecus species group occur at mid to high elevations in several mountain ranges in the highlands of Middle America (Mexico and Central America), a region of high endemicity. We examined the biogeography of this group by conducting phylogenetic analyses of 668 bp of the mitochondrial cytochrome b (cyt b) gene. Phylogenetic analyses under both parsimony and likelihood frameworks produced the same topologies, but estimates of nodal support were artificially high in weighted parsimony analyses. This difference is attributed to the inability of parsimony to optimize branch lengths when evaluating topologies. These data indicate that the P. aztecus-like populations from south and east of the Isthmus of Tehuantepec currently assigned to P. a. oaxacensis represent a distinct species, with genetic distances as high as 0.091. In addition, P. hylocetes is strongly divergent from Mexican populations of P. aztecus (genetic distances of 0.044--0.069), supporting the recognition of this taxon as a distinct species. The history of divergence in this group can be explained by a series of apparently early to middle Pleistocene vicariance events associated with glacial cycles. The Sierra Madre Occidental and Cordillera Transvolcanica each appear to be faunistically isolated, the Isthmus of Tehuantepec appears to have been a strong Pleistocene barrier, and the Sierra Madre Oriental has affinities with the Sierra Madre del Sur and the highlands of central Oaxaca.
[Cytochrome b; highlands; maximum likelihood; Middle America; parsimony; Peromyscus; phylogeography; vicariance.]

Abstract.---We critically reviewed the homologies of the jaw muscles in tetraodontiform fishes (Triacanthoidea, Balistoidea, Tetraodontoidea), as first described in Winterbottom's phylogenetic monograph (1974, Smithson. Contrib. Zool. 155:1--201), as a case study in structural duplication. Within this order of teleost fishes, the two main adductor mandibulae muscles, A1 and A2, are duplicated one or more times in some subclades. The number of descendant A1 and A2 muscles ranges from as few as the original two muscles in triplespines to as many as eight muscles in some filefishes. As first pointed out by Winterbottom, the homologies of some muscles are unclear, particularly in comparisons between the superfamilies Balistoidea (boxfishes, triggerfishes, filefishes) and Tetraodontoidea (pursefishes, molas, puffers, porcupinefishes). We reassessed the homologies (orthologs and paralogs) of these A1 and A2 muscles based on their origins, insertions, and relative masses in representative taxa and their congruence with a phylogeny for these taxa. New names that reflect the homologies of these muscles are presented. Ten muscle duplications by subdivision and three phylogenetic losses of muscles have occurred in this system. No relationship was found between the number of separate muscles and the relative masses of the A1 or A2 muscles, suggesting that muscle duplication events essentially repackage existing muscle tissue. However, both A1 and A2 muscle masses are correlated with each other and with the feeding ecology of these fishes. Durophagous taxa have relatively larger A1 and A2 muscles, whereas planktivores and benthic grazers have relatively smaller A2 muscles.
[Homology; morphological duplications; muscle evolution; orthology; paralogy; Tetraodontiformes.]

Abstract.---The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.
[Congruence; incongruence tests; maximum likelihood; phylogenetic accuracy; six-parameter parsimony; successive weighting; transversion parsimony; weighted parsimony.]

Abstract.---Although morphological data have historically favored a basal position for the Indian gharial (Gavialis gangeticus) within Crocodylia and a Mesozoic divergence between Gavialis and all other crocodylians, several recent molecular data sets have argued for a sister-group relationship between Gavialis and the Indonesian false gharial (Tomistoma schlegelii) and a divergence between them no earlier than the Late Tertiary. Fossils were added to a matrix of 164 discrete morphological characters and subjected to parsimony analysis. When morphology was analyzed alone, Gavialis was the sister taxon of all other extant crocodylians whether or not fossil ingroup taxa were included, and a sister-group relationship between Gavialis and Tomistoma was significantly less parsimonious. In combination with published sequence and restriction site fragment data, Gavialis was the sister taxon of all other living crocodylians, but the position of Tomistoma depended on the inclusion of fossil ingroup taxa; with or without fossils, preferred morphological and molecular topologies were not significantly different. Fossils closer to Gavialis than to Tomistoma can be recognized in the Late Cretaceous, and fossil relatives of Tomistoma are known from the basal Eocene, strongly indicating a divergence long before the Late Tertiary. Comparison of minimum divergence time from the fossil record with different measures of molecular distance indicates evolutionary rate heterogeneity within Crocodylia. Fossils strongly contradict a post-Oligocene divergence between Gavialis and any other living crocodylian, but the phylogenetic placement of Gavialis is best viewed as unresolved.
[Combined data sets; Crocodylia; fossils; molecular clock; parsimony analysis; stratigraphy.]

Abstract.---Exploration of the relationship between gene trees and their containing species trees leads to consideration of how to reconstruct species trees from gene trees and of the concept of phylogeny as a cloud of gene histories. When gene copies are sampled from various species, the gene tree relating these copies might disagree with the species phylogeny. This discord can arise from horizontal transfer (including hybridization), lineage sorting, and gene duplication and extinction. Lineage sorting could also be called deep coalescence, the failure of ancestral copies to coalesce (looking backwards in time) into a common ancestral copy until deeper than previous speciation events. These events depend on various factors; for instance, deep coalescence is more likely if the branches of the species tree are short (in generations) and wide (in population size). A similar dependence on process is found in historical biogeography and host--parasite relationships. Each of the processes of discord could yield a different parsimony criterion for reconstructing the species tree from a set of gene trees: with horizontal transfer, choose the species tree that minimizes the number of transfer events; with deep coalescence, choose the tree minimizing the number of extra gene lineages that had to coexist along species lineages; with gene duplication, choose the tree minimizing duplication and;shor extinction events. Maximum likelihood methods for reconstructing the species tree are also possible because coalescence theory provides the probability that a particular gene tree would occur given a species tree (with branch lengths and widths specified). In considering these issues, one is provoked to reconsider precisely what is phylogeny. Perhaps it is misleading to view some gene trees as agreeing and other gene trees as disagreeing with the species tree; rather, all of the gene trees are part of the species tree, which can be visualized like a fuzzy statistical distribution, a cloud of gene histories. Alternatively, phylogeny might be (and has been) viewed not as a history of what happened, genetically, but as a history of what could have happened, i.e., a history of changes in the probabilities of interbreeding.
[Biogeography; coalescence; coevolution; evolution; gene duplication; gene genealogy; gene trees; horizontal transfer; hybridization; lineage sorting; parsimony; phylogeny; species concepts; species trees; tree reconciliation.]

Abstract.---The construction and interpretation of gene trees is fundamental in molecular systematics. If the gene is defined in a historical (coalescent) sense, there can be multiple gene trees within the single contiguous set of nucleotides, and attempts to construct a single tree for such a sequence must deal with homoplasy created by conflict among divergent histories. On a larger scale, incongruence is expected among gene tree topologies at different loci of individuals within sexually reproducing species, and it has been suggested that this discordance can be used to delimit species. A practical concern for such topological methods is that polymorphisms may be maintained through numerous cladogenic events; this polymorphism problem is less of a concern for nontopological approaches to species delimitation using molecular data. Although a central theoretical concern in molecular systematics is discordance between a given gene tree and the true "species tree," the primary empirical problem faced in reconstructing taxic phylogeny is incongruence among the trees inferred from different sequences. Linkage relationships limit character independence and thus have important implications for handling multiple data sets in phylogenetic analysis, particularly at the species level, where incongruence among different historically associated loci is expected. Gene trees can also be reconstructed for loci that influence phenotypic characters, but there is at best a tenuous relationship between phenotypic homoplasy and homoplasy in such gene trees. Nevertheless, expression patterns and orthology relationships of genes involved in the expression of phenotypes can in theory provide criteria for homology assessment of morphological characters.
[Gene trees; homoplasy; linkage; morphology; orthology; phylogeny; species delimitation.]