Syst. Biol. 50(2) 2001


Abstract.—The importance of fossils to phylogenetic reconstruction is well established. However, analyses of fossil data sets are confounded by problems related to the less complete nature of the specimens. Taxa that are incompletely known are problematic because of the uncertainty of their placement within a tree, leading to a proliferation of most parsimonious solutions and wild card behavior. Problematic taxa are commonly deleted based on a priori criteria of completeness. Paradoxically, a taxon's problematic behavior is tree dependent, and levels of completeness are not directly associated with problematic behavior. Exclusion of taxa based on completeness eliminates real character conflict and, by not allowing incomplete taxa to determine tree topology, the phylogenetic hypothesis is diminished.

The phylogenetic trunk approach is proposed to allow optimization of taxonomic inclusion and tree stability. This method is used in an analysis of the Paleozoic Lepospondyli. A single most parsimonious tree, or trunk, is found after removal of one taxon identified as being problematic. The 38 trees found one additional step from this primary trunk are reduced to two by removal of one additional taxon. These trunks are compared to the trees found by excluding taxa with various degrees of completeness. Effects of incomplete taxa are explored in light of the trunk. Correlated characters associated with limblessness are discussed regarding the assumption of character independence, but inclusion of intermediate taxa is found to be the single best method for breaking down long branches. [Keywords: Paleozoic tetrapods, lepospondyls, missing data, phylogenetic analysis, wild card taxa, aïstopod, nectridean, microsaur, lysorophid, adelospondylid, correlated character]

Cameron and Mardulyn

Abstract. Different views of the pattern of social evolution among the highly eusocial bees have arisen as a result of discordance between past molecular and morphology-based phylogenies. Here we present new data and taxa for four molecular data sets and reassess the morphological characters available to date. We show that there is no significant character incongruence between four molecular data sets (two nuclear and two mitochondrial) but that there is highly significant character incongruence, which leads to topological incongruence, between the molecular and morphological data. We investigate the effects of using different outgroup combinations to root the estimated tree. We also consider various ways in which biases in the sequence data could be misleading, employing several maximum likelihood models, LogDet corrections, and spectral analyses. Ultimately, we concede that there is strong discordance between the molecular and morphological data partitions, and that the conditional combination approach is appropriately applied in this case. We also find for the molecular trees that there are two equally well supported placements of the root, one supported by 16S and 28S sequences, the other supported by cyt b and opsin. The strength of the evidence leads us to accept two equally well supported hypotheses based on analyses of the molecular data sets. These are the most rigorously supported hypotheses of corbiculate bee relationships at this time, and frame our argument that highly eusocial behavior within the corbiculate bees evolved twice independently. [Corbiculate bees; apines; Hymenoptera; insects; molecular phylogeny; combined phylogenetic analysis.]

Danforth and Ji

Abstract.— The bee genus Lasioglossum includes over 1000 species of bees distributed on all continents except Antarctica. Lasioglossum is a major component of the bee fauna in the Holarctic, Ethiopian, and Oriental regions, and is an important group for investigating the evolution of social behavior in bees. Given its cosmopolitan distribution, the historical biogeography of the genus is of considerable interest. We reconstructed phylogenetic relationships among the subgenera and species within Lasioglossum s.s. using DNA sequence data from a slowly evolving nuclear gene, EF-1_. The entire data set includes over 1604 aligned nucleotide sites (including three exons plus two introns) for 89 species (17 outgroups plus 72 ingroups). Parsimony and maximum likelihood analyses provide strong evidence that the primarily Indoaustralian subgenera (Homalictus, Chilalictus, Parasphecodes) form a monophyletic group. Bootstrap support for the Australian clade ranged from 73% to 77% (depending on the method of analysis). Monophyly of the Australian Lasioglossum suggests that a single colonization event (via Southeast Asia and New Guinea) gave rise to a lineage of over 350 native Indoaustralian bees. We discuss the implications of Australian monophyly for resolving the "Australian enigma" -- similarity in social behavior among the Australian halictine bees relative to Holarctic groups. [Key words: biogeography, phylogeny, maximum likelihood, elongation factor-1_, social evolution]

Hibbett and Donoghue

Abstract. Homobasidiomycetes include the majority of wood-decaying fungi. Two basic forms of wood decay are known in homobasidiomycetes: white rot, in which lignin and cellulose are degraded, and brown rot, in which lignin is not appreciably degraded. An apparent correlation has been noted between production of a brown rot, decay of conifer substrates, and possession of a bipolar mating system (which has a single mating type locus, vs. tetrapolar systems, which have two mating type loci). The goals of this study were to infer the historical pattern of transformations in decay mode, mating type, and substrate range characters, and to determine if a causal relationship exists among them. We performed a phylogenetic analysis of 130 species of homobasidiomycetes using nuclear and mitochondrial rDNA sequences, and performed ancestral state reconstructions using parsimony on a range of trees, with various loss:gain cost ratios. We evaluated pairwise character correlations using the concentrated changes test (CCT) of Maddison and the maximum likelihood (ML) method of Pagel. White rot, tetrapolar mating systems, and the ability to decay conifers and hardwoods appear to be plesiomorphic in homobasidiomycetes, whereas brown rot, bipolar mating systems, and exclusive decay of conifers appear to have evolved repeatedly. The only significant correlation among characters was that between brown rot (as the independent character) and exclusive decay of conifer substrates. This correlation was supported by the CCT on a range of plausible trees, although not with every reconstruction of ancestral states, and the ML test. Our findings suggest that the evolution of brown rot has promoted repeated shifts to specialization for conifer substrates. [Ancestral state reconstruction; basidiomycetes; comparative methods; concentrated changes test; Discrete; fungal ecology; Polyporaceae; rDNA; sensitivity analyses; wood decay.]

Smith and Gutberlet

Abstract.— A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is employed to counter the effect of using multiple characters to represent one character. The new method, termed generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and can be applied to both qualitative and quantitative characters. The method was applied to a previously published data set that includes both types of polymorphic multistate characters, and performed well according to congruence with other studies and the g1 and nonparametric bootstrap statistics. The data set was also used to compare GFC to both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, GFC was found to be a better estimator of phylogeny. [Generalized frequency coding; phylogenetic systematics; polymorphic multistate characters; step matrix coding.]


Abstract. The obligate mutualism between pollinating fig wasps in the family Agaonidae (Hymenoptera: Chalcidoidea) and Ficus species (Moraceae) is often regarded as an example of coevolution but little is known about the history of the interaction and understanding the origin of functionally dioecious fig pollination has been especially difficult. The phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus were inferred from mitochondrial cytochrome oxidase gene sequences (mtDNA) and morphology. Separate and combined analyses indicated that the pollinators of functionally dioecious figs are not monophyletic. However, pollinator relationships were generally congruent with host phylogeny and support a revised classification of Ficus. Ancestral changes in pollinator ovipositor length were also correlated with changes in fig breeding system. In particular, the relative elongation of the ovipositor was associated with the repeated loss of functionally dioecious pollination. The concerted evolution of interacting morphologies may bias estimates of phylogeny based on female head characters but homoplasy is not so concerted in other morphological traits. The lesser phylogenetic utility of morphology compared to mtDNA is not due to rampant convergence in morphology but rather to the greater number of potentially informative characters in DNA sequence data and patterns of nucleotide substitution also limit the utility of mtDNA. None the less, inferring the ancestral associations of fig pollinators from the best-supported phylogeny provided strong evidence of host conservatism in this highly specialized mutualism. [coevolution, maximum likelihood, mutualism, parametric bootstrapping, pollination]