High Levels Of Homoplasy Research Articles

Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

The Neognathostomata (comprising the orders Clypeasteroida, Oligopygoida, Neolampadoida, and the paraphyletic Cassiduloida) form one of the three major clades of irregular echinoids. Despite the group's apparent success since the Jurassic and impressive peak diversity in the mid-Cretaceous, most included clades are now severely reduced. A phylogeny is essential for reconstructing the taxonomic, environmental and biogeographic patterns of this decline, and understanding the causal processes responsible for them. I examined the distribution of qualitative morphological characters (including those defining genera) for 97 species from 77 non-clypeasteroid genera and the three clypeasteroid suborders. Following preliminary analyses, I reduced the data to 40 characters (having 60 apomorphic states) and 71 representative genera. Goloboff's data decisiveness, the skewness of tree length distributions, and permutation tests all reveal significant phylogenetic structure in the data. Heuristic searches conducted with PAUP found more than 72 500 trees of 217 steps (CI = 0.276), but only the first 30 000 were evaluated. These exhibit considerable instability in the relationships among taxa. Successive approximations weightings did not reduce the numbers of favoured trees. Analyses using only less homoplasious characters failed to improve the resolution. Fisher's stratigraphic debt provides an objective means of selecting a very few of the morphologically most-parsimonious trees. Most nodes are supported by only one to three character changes, and these are generally reversed or paralleled elsewhere. The results suggest some cassiduloid families can not be separated, and support the reassignment of several genera. Despite the high levels of homoplasy, the most-parsimonious trees require fewer changes than had been previously suggested for evolutionary trends in several characters. Whether the rampant homoplasy present in the data reflects incorrect character analysis, limited structural or developmental options, or the effects of parallel selection, its presence raises severe obstacles to phylogenetic analyses.

Cladistic analysis of cassiduloid echinoids: trying to see the phylogeny for the trees

The Neognathostomata (comprising the orders Clypeasteroida, Oligopygoida, Neolampadoida, and the paraphyletic Cassiduloida) form one of the three major clades of irregular echinoids. Despite the group's apparent success since the Jurassic and impressive peak diversity in the mid-Cretaceous, most included clades are now severely reduced. A phylogeny is essential for reconstructing the taxonomic, environmental and biogeographic patterns of this decline, and understanding the causal processes responsible for them. I examined the distribution of qualitative morphological characters (including those defining genera) for 97 species from 77 non-clypeasteroid genera and the three clypeasteroid suborders. Following preliminary analyses, I reduced the data to 40 characters (having 60 apomorphic states) and 71 representative genera. Goloboff's data decisiveness, the skewness of tree length distributions, and permutation tests all reveal significant phylogenetic structure in the data. Heuristic searches conducted with PAUP found more than 72 500 trees of 217 steps (CI = 0.276), but only the first 30,000 were evaluated. These exhibit considerable instability in the relationships among taxa. Successive approximations weightings did not reduce the numbers of favoured trees. Analyses using only less homoplasious characters failed to improve the resolution. Fisher's stratigraphic debt provides an objective means of selecting a very few of the morphologically most-parsimonious trees. Most nodes are supported by only one to three character changes, and these are generally reversed or paralleled elsewhere. The results suggest some cassiduloid families can not be separated, and support the reassignment of several genera. Despite the high levels of homoplasy, the most-parsimonious trees require fewer changes than had been previously suggested for evolutionary trends in several characters. Whether the rampant homoplasy present in the data reflects incorrect character analysis, limited structural or developmental options, or the effects of parallel selection, its presence raises severe obstacles to phylogenetic analyses.

Evolution in the Andean Epiphytic Genus Columnea (Gesneriaceae). I. Morphological Variation

A cladistic analysis was performed on morphological data from seven of the nine species of Columnea section Pentadenia and sixteen of the eighteen species of section Stygnanthe (Gesneriaceae). A nested, global outgroup analysis was performed by including representatives of three other sections of Columnea and two species each of the closely related genera Alloplectus and Drymonia. Twenty characters were scored as binary, and thirteen were scored as multi-state. All characters scored were qualitative. Because of the high levels of homoplasy in the Gesneriaceae, simple characters were not found to be useful and more complex characters comprising several simple characters were necessary to provide resolution. The data were analyzed using Wagner parsimony, resulting in eight most parsimonious trees. In general, the phylogeny was congruent with current classification schemes and phylogenies derived from molecular data and combined molecular and morphological data. However, several phylogenetic relationships that result from the analysis of morphological data are suspect based on other data. The monophyly of Alloplectus is not supported solely with morphological data, although other data support its monophyly. In- ferences regarding the biogeographic history and evolution of Columnea sections Pentadenia and Stygnanthe indicate a southern Andean origin for the genus Columnea with a subsequent migration and radiation northward.

CLADISTIC ANALYSES OF THE COCCINELLIDAE (COLEOPTERA)

Abstract Numerical cladistic method was used for analyzing the phylogeny of ladybirds, based upon adult and larval characters. The analysis of adult characters for 21 tribes, representing all subfamilies proposed by various authors, exhibited 18 equally parsimonious cladograms with high level of homoplasy. Five lineages were roughly revealed in the strict consensus tree: Sticholotidinae, Epilachninae, Coccinellinae (including Singhikalini), Coccidulinae (excluding Noviini) and Scymninae+Chilocorinae. The taxonomic interpretation of the adult analysis was similar to the classification proposed by Chazeauet al. (1990). Comparison of a preliminary analysis based on the larval characters for 14 tribes revealed only one component consistently supported in both analyses (Serangiini+Sukunahikonini). Larval analysis showed that Epi‐lachinae is the most primitive and highly derived group of the Coccinellidae. Larval characters might be more satisfactory in revealing the phylogeny.

Taxonomy, cladistics and biogeography of the Australian genus Putoniessa Kirkaldy (Hemiptera : Cicadelloidea : Cicadellidae)

The morphology of Putoniessa Kirkaldy is reviewed and the genus revised. In total, 28 species are recognised: the type species, P. dignissima Kirkaldy, which is removed from synonymy; one new combination, P. dorsalis (Walker); eight previously described species, P. nigra (Walker), P. minima Evans, P. mackei Evans, P. draba Evans, P. taradalensis Evans, P. sordida Evans, P. nigrella Evans and P. turneri Evans; and 18 new species, P. rieki, P, brisbanensis, P. hickmani, P, neboissi, P. stanthorpensis, P. woodwardi, P. striata, P. evansi, P. variegata, P. tasmaniensis, P. grossi, P. serrata, P. northamensis, P. bifurcata, P. kiataensis, P. watsoni, P. fusca and P. aroka. P. nota Evans is excluded from the genus, and P. maculata Evans is synonymised under P. dorsalis (Walker). P. rivularis (Walker), originally described under Bythoscopus Germar, and P. galliensis Evans are considered as species of uncertain identity. The genus is shown to have a disjunct Bassian distribution with some eastern species extending northwards into the south-east of the Tomesian province. A consensus cladogram for Putoniessa, based on morphological characters, is presented. Large areas of the cladogram remain unresolved because of high levels of homoplasy among the limited number of reliable ingroup characters available. The cladogram does not support a purely vicariant biogeographic hypothesis. Theories that receive qualified support involve an eastern origin for the group followed by either an east-to-west dispersal or a vicariance event affecting a single taxon subsequent to initial speciation. A western origin for the group is strongly refuted.

CYTOLOGICAL STUDIES IN LACCARIA (AGARICALES). II. ASSESSING PHYLOGENETIC RELATIONSHIPS AMONG LACCARIA, HYDNANGIUM, AND OTHER AGARICALES

Laccaria and Hydnangium typically undergo a postmeiotic mitotic nuclear division in basidiospores, basidia, or less commonly, in sterigmata resulting in eight nuclei. Basidiospores formed on tetrasterigmate basidia are binucleate, and those on bisterigmate basidia are tetranucleate in both genera. While Hydnangium and Laccaria likely comprise a monophyletic group-a hypothesis based on a number of shared characters-the presence of multinucleate basidiospores in several putative outgroups precludes using this shared character state as a justification for recognizing these two genera in a separate family, Hydnangiaceae, as had been proposed. Based on a review of the literature, the presence and location of postmeiotic mitotic divisions in basidia and basidiospores of Agaricales do not appear to be appropriate for assessing phylogenetic relationships among genera or families because of a high level of homoplasy.

A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly

The evolutionary relationships of the various orders of placental mammals remain an issue of uncertainty and controversy. Molecular studies of mammalian phylogeny at the DNA level that include more than just a few orders are still relatively meager. Here we report results on mammalian phylogeny deduced from the coding sequence of the single-copy nuclear gene for the interphotoreceptor retinoid binding protein (IRBP). Analysis of 13 species representing eight eutherian orders and one marsupial yielded results that falsify the hypothesis that megachiropteran bats are “flying primates,” only convergently resembling microchiropteran bats. Instead, in agreement with more traditional views, as well as those from other recent molecular studies, the results strongly support a monophyletic Chiroptera (micro- and megabats grouped together). The IRBP results also offer some rare molecular support for the Glires concept, in which rodents and lagomorphs form a superordinal grouping. Also in congruence with other recent molecular evidence, IRBP sequences do not support the view of a superorder Archonta that includes Chiroptera along with Dermoptera (flying lemur), Scandentia (tree shrew), and Primates. IRBP was not however, without its shortcomings as a molecular phylogenetic system: high levels of homoplasy, evident in the marsupial outgroup, did not allow us to properly root the tree, and several of the higher level eutherian clades were only weakly supported (e.g., a Carnivore/Chiroptera clade and an Artiodactyla/Carnivore/Chiroptera clade). We suggest that these shortcomings may be diminished as the phylogenetic density of the data set is increased.

A cladistic analysis of the nomadine bees (Hymenoptera: Apoidea)

Abstract. This study compares the results of Rozen's cladistic analysis of the larvae of fifteen genera of cleptoparasitic bees in the subfamily Nomadinae with an independent data set of adult characters for the same genera. Adult characters exhibited considerably higher levels of homoplasy and poorer resolution of cladistic relationships, with multiple equally parsimonious cladograms. However, comparison of a Nelson consensus tree based on adult characters with the cladogram based on larval characters reveals three components consistently supported in both analyses (the tribes Epeolini and Ammobatini, and Neopasites+Neolarra), one component supported only by adult characters (Isepeolus + Protepeolus), and one terminal component supported only by larval characters (Nomada+ Ammobatini), as well as several more inclusive groupings based on larval characters that are difficult to compare with the adult consensus tree because it shows so much less resolution. When adult and larval characters are combined in a single data matrix, the resulting cladogram closely resembles the cladogram based on larval characters alone, although levels of homoplasy are considerably higher than in the larval analysis.A preliminary analysis of adult characters for thirty‐four genera in the Nomadinae also exhibited high levels of homoplasy and very large numbers of equally parsimonious cladograms. Nevertheless, certain consistent monophyletic groupings, most notably the Epeolini and Ammobatini, were also supported in this analysis. The one currently recognized tribe whose monophyly has received no support from any analysis is the Nomadini.The relevance of these phylogenetic hypotheses to our understanding of host associations and variable features of egg morphology and oviposition behaviour in nomadine bees is briefly discussed.

The amphibian fauna of the East African rainforests, including the description of a new species of toad, genusNectophrynoidesNoble 1926 (Anura Bufonidae)

The East African rainforests are areas of prime biogeographical importance. The significance of the amphibian fauna of the region as a biogeographical indicator group, first recognized by SCHIOTZ (1981) is reiterated. SCHIOTZ' 1981 list of East African rainforest amphibians is corrected and updated. A new species of dwarf toad from the rainforest of the Uzungwe Mountains, Tanzania is described. The new species is tentatively assigned to the genus Nectophrynoides Noble 1926, and comment on the relationships of the new species and of the Nectophrynoides-Didynamipus group is included. It is suggested that many of the African bufonid genera, especially those including dwarf forms, are currently poorly defined; primitive characters, characters involving the loss of structures and characters subject to a high level of homoplasy often being used. Some possible solutions to this problem are given. The need for a better understanding of the biology of rainforest Amphibia, especially the dwarf species, is seen to b...