Syst. Biol. 52(6) 2003

Hugot et al.
Abstract.—Previous studies have demonstrated that the agent of Pneumocystis pneumonia (PcP), Pneumocystis carinii, corresponds to a complex of eukaryotic organisms and suggested that cophylogeny could explain the distribution of the hosts and parasites. In the present work, the hypothesis of cophylogeny between the primates-derived Pneumocystis and their hosts is tested. Specific strains isolated from 20 primate species, including humans are used to produce a phylogeny of the parasites. Aligned sequences corresponding to DNA sequences of 3 genes (DHPS, mtSSU-rRNA, and mtLSU-rRNA) are separately analysed and then combined in a single data set. The resulting parasite phylogeny is compared with different controversial phylogenies for the hosts. This comparison demonstrates that, depending upon which topology is accepted for the hosts, at least 61 % and perhaps 77 % of the homologous nodes of the respective cladograms of the hosts and parasites may be interpreted as resulting from codivergence events. This and the high specificity of these parasites, suggests that cophylogeny may be considered the dominant pattern of evolution for Pneumocystis organisms. This represents a new example of parallel evolution between primates and their specific parasites. As the phylogeny of the Pneumocystis followed very closely the differentiation of their hosts at the specific level, the study of the parasites could provide valuable information on the phylogeny of their hosts. This is used to discuss controversial hypotheses of the phylogeny of the Platyrrhini by comparison with the phylogeny of their specific Pneumocystis. If these organisms were closely associated as lung parasites with primates through the ages, the hypothesis of the Pneumocystis spp. being new pathogenic agents can be refuted. They rather are opportunistic "symbionts," able to express a pathogenic power whenever the immunological defences of their hosts decline. This study also provides evidences for the hypothesis that the different Pneumocystis species are genetically independent organisms, and helps to clarify their taxonomic status.

Wiegmann et al.
Abstract.—The insect order Diptera, true flies, contains one of the four largest Mesozoic-aged insect radiations within its suborder Brachycera. Estimates of phylogenetic relationships and divergence dates among the major brachyceran lineages have been problematic or vague due to a lack of consistent evidence and to the rarity of well-preserved fossils. Here we combine new evidence from nucleotide sequence data, morphological re-interpretations, and fossils to improve estimates of brachyceran evolutionary relationships and ages. The 28S ribosomal gene was sequenced for a broad diversity of taxa and combined with recently published morphological scorings for parsimony-based phylogenetic analysis. The phylogenetic topology inferred from the combined 28S rDNA and morphology dataset supports brachyceran monophyly, the monophyly of the four major brachyceran infraorders and suggests relationships largely consistent with previous classifications. Weak support is found for a basal brachyceran clade comprising the infraorders Stratiomyomorpha (soldier flies and relatives), Xylophagomorpha (xylophagid flies) and Tabanomorpha (horse flies, snipe flies, and relatives). This topology, and similar alternative arrangements, were used to obtain Bayesian estimates of divergence times, both with and without the assumption of a constant evolutionary rate. The estimated times were found to be relatively robust to the choice of prior distributions. Divergence times based on the 28S rDNA and several fossil constraints indicate that the Brachycera originated in the late Triassic or earliest Mesozoic and that all major lower brachyceran fly lineages had near contemporaneous origins in the mid-Jurassic prior to the origin of flowering plants (Angiosperms). This study provides increased resolution of brachyceran phylogeny and our revised estimates of fly ages should improve the temporal context of evolutionary inferences and genomic comparisons between fly model organisms.

Jennings et al.
Abstract.—We conducted a phylogenetic study of pygopodid lizards, a group of 38 species endemic to Australia and New Guinea, with two major goals: to reconstruct a taxonomically-complete and robustly-supported phylogeny for the group; then use this information to gain insights into the tempo, mode, and timing of the pygopodid radiation. Phylogenetic analyses of mtDNA, nDNA, and previously published morphological data (Kluge, 1976) using parsimony, maximum likelihood, and Bayesian methods on the independent and combined three data sets yielded trees with similar and largely stable ingroup topologies. However, relationships among the six most inclusive and unambiguously supported clades (Aprasia, Delma, Lialis, Ophidiocephalus, Pletholax, and Pygopus) varied depending on data set analyzed. We used parametric bootstrapping to help us understand which of the three-branch schemes linking these six taxa was most plausible given our data. We conclude based on our results that the arrangement ((((Delma, Lialis), Pygopus), Pletholax), (Aprasia, Ophidiocephalus)) represents the best present hypothesis of intergeneric relationships. A second major problem to arise in our study concerned the inability of our two outgroup taxa (Diplodactylus) to root trees properly, as three different rooting locations were suggested depending upon analysis. This long-branch attraction problem was so severe that the outgroup branch also interfered with estimation of ingroup relationships. We therefore used the molecular clock method to root the pygopodid tree. Results of two independent molecular clock analyses (mtDNA and nDNA) converged upon the same root location (branch leading to Delma). We are confident that we have found the correct root because the possibility of our clock estimates agreeing by chance alone is remote given that there are 65 possible root locations (branches) on the pygopodid tree (∼ 1 in 5000 odds). Our analysis also indicated that Delma fraseri is not monophyletic, a result supported by a parametric bootstrapping test. We elevated the Western Australian race, Delma f. petersoni, to species status (i.e., Delma petersoni) because hybridization and incomplete lineage sorting could be ruled out as potential causes of this paraphyletic gene tree, and because D. grayii is broadly sympatric with its sister species D. fraseri. Climate changes over the past 23 million years, which transformed Australia from a wet-green continent to one that is largely dry and brown, have been suspected as playing a major role in the diversification of Australia's temperate biotas. Our phylogenetic-based analyses of pygopodid speciation and biogeography revealed four important findings consistent with this climate-change diversification model: (1) our fossil-calibrated phylogeny shows that although some extant pygopodid lineages predate the onset of aridification, 28 of 33 pygopodid species included in our study seem to have originated in the last 23 my; (2) relative cladogenesis tests suggest that several major clades underwent higher than expected rates of speciation; (3) our findings support earlier studies showing that speciation of mesic-adapted biotas in the southeastern and southwestern corners of Australia largely occurred within each of these regions between 12-23 mya, as opposed to repeated dispersal between them; and (4) we have identified for the first time the existence of several pairs of sympatric sister species of lizards living in arid and semi-arid ecosystems. We also found that these sympatric sister species seem to be younger than allopatric or parapatric sister-species pairs, which is not consistent with previous beliefs.

Aris-Brosou
Abstract.—Several tests of molecular phylogenies were proposed over the last decades, but most of them lead to strikingly different p-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To support this, two new tests are described. Both consider the composite null hypothesis that all the topologies are equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis at the least favorable distribution (frequentist significance test, or FST), or to the maximum likelihood topology (frequentist hypothesis test, or FHT). In both cases, the reduced null hypothesis is tested against each topology included in the analysis. The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a non-parametric bootstrap adjusting p-values for multiple comparisons. The new tests are applied to the reanalysis of two chloroplastic genes, psaA and psbB, and are compared with previously described tests. As expected, the FST and the FHT behave approximately like the Shimodaira-Hasegawa test and the bootstrap, respectively. While the tests are found to give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex models, incorporating heterogeneity among codon positions, resolve some conflicts. To further investigate the influence of the null hypothesis, a power study was conducted. Simulations showed that FST and the Shimodaira-Hasegawa test are least powerful, while FHT was most powerful across the parameter space. Although the size of all the tests is affected by misspecification, the two new tests appear more robust against misspecification of the model of evolution, and consistently support the hypothesis that the Gnetales are nested within the Gymnosperms.

Evans et al.
Abstract.—The interface of the Asian and Australian faunal zones is defined by a network of deep ocean trenches that separate intervening islands of the Philippines and Wallacea (Sulawesi, the Lesser Sundas, and the Moluccas). Studies of this region by Wallace marked the genesis of the field of biogeography, yet few workers have used molecular methods to investigate the biogeography of taxa whose distribution spans this interface. Some taxa, such as the fanged frogs of the ranid genus Limnonectes, have distributions on either side of Wallace's and Huxley's zoogeographical lines, offering an opportunity to ask how frequently these purported barriers were crossed and by what paths. To examine diversification of Limnonectes in Southeast Asia, the Philippines, and Wallacea, we estimated a phylogeny from mitochondrial DNA sequences obtained from a robust geographic sample. Our analyses suggest that these frogs dispersed from Borneo to the Philippines at least twice, from Borneo to Sulawesi once or twice, from Sulawesi to the Philippines once, and from the Philippines to Sulawesi once. Dispersal to the Moluccas occurred from Sulawesi and to the Lesser Sundas from Java/Bali. Species distributions are generally concordant with Pleistocene aggregate island complexes of the Philippines and with areas of endemism on Sulawesi. We conclude that that the recognition of zoogeographic lines, though insightful, may oversimplify the biogeography of widespread taxa in this region.

Nepokroeff et al.
Abstract.—Systematic and biogeographical relationships within the Hawaiian clade of the pantropical understory shrub genus Psychotria (Rubiaceae) were investigated using phylogenetic analysis of 18S-26S rDNA internal (ITS) and external (ETS) transcribed spacers. Phylogenetic analyses strongly suggest that the Hawaiian Psychotria are monophyletic and the result of a single introduction to the Hawaiian Islands. The results of phylogenetic analyses of ITS and ETS partitions alone give slightly different topologies among basal lineages of the Hawaiian clade; however, such differences are not well supported. Relationships in the section Straussia clade in particular are not well resolved due to few nucleotide changes on internal branches, suggesting extremely rapid radiation in the lineage. Parsimony and likelihood-based reconstructions of ancestral geographical distributions using the topologies inferred from both parsimony and likelihood analysis of combined data, and using different combinations of models and branch lengths gave highly congruent results. However, for one internal node, (corresponding to the majority of the "greenwelliae" clade) parsimony reconstructions were unable to distinguish between three possible island states, whereas likelihood reconstructions resulted in clear ordering of possible states, with the island of O'ahu slightly more probable than other islands under all but one model and branch length combination considered (the JC-like model with branch lengths inferred under parsimony, under which conditions Maui Nui is more probable). A pattern of colonization from oldest to youngest islands was inferred from the phylogeny, using maximum parsimony and maximum likelihood. Additionally, a much higher incidence of within-island versus inter-island speciation was inferred.

Bininda-Emonds
Abstract.—MRP supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such "unsupported clades" may also occur using other supertree methods; however, their incidence is largely unknown. In this study, I investigate the frequency of unsupported clades in both simulated and empirical MRP supertrees. I also propose a new index, QS, to quantify the qualitative support for a supertree and its clades among the set of source trees. Results show that unsupported clades are very rare in MRP supertrees, occurring most often when there are few source trees that all possess the same set of taxa. However, even here, the frequency of unsupported clades was < 0.2%. Unsupported clades were absent from both the Carnivora and Lagomorpha supertrees, reflecting the use of large numbers of source trees for both. The proposed QS indices correlate broadly with another measure of quantitative clade support (bootstrap frequencies, as derived from resampling of the MRP matrix), but appear to be more sensitive. More importantly, they sample at the level of the source trees and thus, unlike the bootstrap, are suitable for summarizing the support of MRP supertree clades.