Abstract.---An effective method yielding taxon-specific markers from
the genome of a single individual would be valuable for many types of
scientific investigations, including systematic, forensic, conservation, and
evolutionary studies. We explored the use of cosmid libraries, with insert
sizes averaging 35 kb, to streamline the process of locating sequences of DNA
that can serve as taxonomic markers from the specific to the ordinal levels.
By screening approximately 2.6% of the leaf-nosed bat (Macrotus waterhousii)
genome, we identified several potential DNA fragments that appear to be
synapomorphic for a variety of taxonomic levels. A more thorough analysis of
the markers documented that 17 Macrotus-specific clones represent three
distinct DNA generic markers, whereas 30 microchiropteran clones represent
multiple copies of a single family of repetitive DNA. The Microchiroptera
taxon markers hybridize with representatives of most of the Microchiroptera
families; however, no hybridization was detected for members of the
superfamily Rhinolophoidea. These results demonstrate that cosmid libraries
can be a valuable source for isolating taxon-specific markers from mammals
even when the insert size is as large as 35 kb.
3 Present address: Department of Zoology, Life Sciences West, Oklahoma State University, Stillwater, Oklahoma 74078, USA; E-mail: firstname.lastname@example.org (M.J.H.), email@example.com (R.V.D.B.).
Abstract.---NEXUS is a file format designed to contain systematic data for use by computer programs. The goals of the format are to allow future expansion, to include diverse kinds of information, to be independent of particular computer operating systems, and to be easily processed by a program. To this end, the format is modular, with a file consisting of separate blocks, each containing one particular kind of information, and consisting of standardized commands. Public blocks (those containing information utilized by several programs) house information about taxa, morphological and molecular characters, distances, genetic codes, assumptions, sets, trees, etc.; private blocks contain information of relevance to single programs. A detailed description of commands in public blocks is given. Guidelines are provided for reading and writing NEXUS files and for extending the format.
Abstract.---Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canid fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canid species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canid endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canid clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.
Abstract.---Relationships among representatives of the five major Hawaiian Drosophila species groups were examined using data from eight different gene regions. A simultaneous analysis of these data resulted in a single most-parsimonious tree that (1) places the adiastola picture-winged subgroup as sister taxon to the other picture-winged subgroups, (2) unites the modified-tarsus species group with flies from the Antopocerus species group, and (3) places the white-tip scutellum species group as the most basal taxon. Because of the different gene sources used in this study, numerous process partitions can be erected within this data set. We examined the incongruence among these various partitions and the ramifications of these data for the taxonomic consensus, prior agreement, and simultaneous analysis approaches to phylogenetic reconstruction. Separate analyses and taxonomic consensus appear to be inadequate methods for dealing with the partitions in this study. Although detection of incongruence is possible and helps elucidate particular areas of disagreement among data sets, separation of partitions on the basis of incongruence is problematic for many reasons. First, analyzing all genes separately and then either presenting them all as possible hypotheses or taking their consensus provides virtually no information concerning the relationships among these flies. Second, despite some evidence of incongruence, there are no clear delineations among the various gene partitions that separate only heterogeneous data. Third, to the extent that problematic genes can be identified, these genes have nearly the same information content, within a combined analysis framework, as the remaining nonproblematic genes. Our data suggest that significant incongruence among data partitions may be isolated to specific relationships and the "false" signal creating this incongruence is most likely to be overcome by a simultaneous analysis. We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree.
Abstract.---Portions of the large ribosomal subunit RNA gene (28S rDNA) encompassing the D1 and the D7 region were obtained from 16 dipteran species and families to reconstruct early phylogenetic events in the order Diptera. For outgroup comparison, the corresponding sequences were used from representative taxa of the Siphonaptera, Mecoptera, and Lepidoptera. A subset of 488 unambiguously alignable sites was analyzed with respect to important sequence evolution parameters. We found (1) sequence variability is significantly higher in double-stranded sites than in single-stranded sites, (2) transitions are close to saturation in most pairwise sequence comparisons, (3) significant substitution rate heterogeneity exists across sites, and (4) significant substitution rate heterogeneity exists among lineages. Tree reconstruction was carried out with the neighbor joining, maximum parsimony, and maximum likelihood methods. Four major subgroups are consistently and robustly supported: the Brachycera, the Culicomorpha, the Tipulomorpha sensu stricto, and the hitherto controversial Bibionomorpha sensu lato, which includes the families Sciaridae, Mycetophilidae, Cecidomyiidae, Bibionidae, Scatopsidae, and Anisopodidae. The phylogenetic relationships within or among these subclades and the positions of the families Psychodidae and Trichoceridae were not robustly resolved. These results support the view that the mouthparts of extant dipteran larvae evolved from a derived ground state characterized by subdivided and obliquely moving mandibles. Furthermore, sequence divergence and the paleontological record consistently indicate that a period of rapid cladogenesis gave rise to the major dipteran subgroups.
Abstract.---The empirical performance of the ontogenetic criterion for determining character polarities was tested based on three published and one new data set originating from a study of larval Sepsidae (Diptera). The ontogenetic criterion polarizes about as many characters as does outgroup comparison. However, for the four data sets conflicting polarities were inferred for 4--45% of all characters for which both polarization methods were applicable. Four different versions of the ontogenetic criterion were identified from the literature and were empirically tested. The version used by de Queiroz (1985, Syst. Zool. 34:280--299) and Wheeler (1990, Cladistics 6:225--268) fared best, as determined by low levels of homoplasy and a small number of inferred equally parsimonious tree roots. For three of four empirical data sets, hypothetical ancestors based on outgroup comparison and the ontogenetic criterion resulted in identical tree roots. Hypothetical ancestors based on outgroup comparison implied less homoplasy than did those based on the ontogenetic criterion, so the ougroup method appears to be superior for character polarization. To test whether polarity decisions from both polarization methods should be combined into one hypothetical ancestor, two different "composite" ancestors were reconstructed. One comprised only the plesiomorphic states of the characters for which both criteria predicted the same polarity ( consensus ). It inferred multiple parsimonious roots without distinctly lowering the level of homoplasy. The second ancestor comprised the plesiomorphic states as predicted by one or both methods ( composite ). It tended to infer single roots, even for data sets for which very different rooting positions were identified by the two polarization criteria, thereby obscuring conflict between the two methods. High levels of homoplasy in hypothetical ancestors based on the ontogenetic criterion are not due to the inclusion of presence;shabsence characters in the data set, for which the application of the ontogenetic criterion would require hypotheses of homology for "absent" character states across ontogenetic stages of different species. Instead, the ratio of terminal deletions to terminal additions is a better predictor for the success of the ontogenetic criterion for any particular data set.
Abstract.---A phylogenetic analysis of the genus Gonioctena (Coleoptera, Chrysomelidae) based on allozyme data (17 loci) and mitochondrial DNA sequence data (three gene fragments, 1,391 sites) was performed to study the evolutionary history of host-plant shifts among these leaf beetles. This chrysomelid genus is characteristically associated with a high number of different plant families. The diverse molecular data gathered in this study are to a large extent congruent, and the analyses provide a well-supported phylogenetic hypothesis to address questions about the evolution of host-plant shifts in the genus Gonioctena. The most-parsimonious reconstruction of the ancestral host-plant associations, based on the estimated phylogeny, suggests that the Fabaceae was the ancestral host-plant family of the genus. Although most of the host-plant shifts (between different host species) in Gonioctena have occurred within the same plant family or within the same plant genus, at least eight shifts have occurred between hosts belonging to distantly related and chemically dissimilar plant families. In these cases, host shifts may have been simply directed toward plant species available in the environment. Yet, given that two Gonioctena lineages have independently colonized the same three new plant families, including four of the same new genera, some constraints are likely to have limited the different possibilities of interfamilial host-plant shifts.