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Character Optimization (character + optimization)
Selected AbstractsA Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character OptimizationCLADISTICS, Issue 2 2000Gonzalo Giribet Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropod groups. Sequences of 139 taxa (23 outgroup and 116 ingroup taxa) representing all extant arthropod "classes" except Remipedia and Cephalocarida are analyzed using direct character optimization exploring six parameter sets. Parameter choice appears to be crucial to phylogenetic inference. The high level of sequence heterogeneity in the 18S rRNA gene (sequence length from 1350 to 2700 bp) makes placement of certain taxa with "unusual" sequences difficult and underscores the necessity of combining ribosomal gene data with other sources of information. Monophyly of Pycnogonida, Chelicerata, Chilopoda, Chilognatha, Malacostraca, Branchiopoda (excluding Daphnia), and Ectognatha are among the higher groups that are supported in most of the analyses. The positions of the Pauropoda, Symphyla, Protura, Collembola, Diplura, Onychophora, Tardigrada, and Daphnia are unstable throughout the parameter space examined. [source] Phylogeny of the Cocculinoidea (Mollusca, Gastropoda)INVERTEBRATE BIOLOGY, Issue 2 2003Ellen E. Strong Abstract. The superfamily Cocculinoidea is a group of marine, deep-water, limpet-like gastropods. Recent speculation surrounding their affinities has concentrated on their placement within the Gastropoda. However, phylogenetic relationships within the Cocculinoidea, especially the monophyly of families and genera within the group, remain poorly understood. Phylogenetic analysis of 31 morphological characters for 15 cocculinoidean taxa and 2 outgroups resulted in a single most parsimonious tree, length=70, CI=0.62, and RI=0.71. Monophyly of the Cocculinoidea, Cocculinidae, and the genera Cocculina and Coccopigya was supported; Paracocculina and Coccocrater were found to be paraphyletic. Character optimization demonstrates that many characters often cited as diagnostic of various taxa, are often homoplastic and/or synapomorphies at different hierarchical levels. [source] Parallel evolution of larval morphology and habitat in the snail-killing fly genus TetanoceraJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2006E. G. CHAPMAN Abstract In this study, we sequenced one nuclear and three mitochondrial DNA loci to construct a robust estimate of phylogeny for all available species of Tetanocera. Character optimizations suggested that aquatic habitat was the ancestral condition for Tetanocera larvae, and that there were at least three parallel transitions to terrestrial habitat, with one reversal. Maximum likelihood analyses of character state transformations showed significant correlations between habitat transitions and changes in four larval morphological characteristics (cuticular pigmentation and three characters associated with the posterior spiracular disc). We provide evidence that phylogenetic niche conservatism has been responsible for the maintenance of aquatic-associated larval morphological character states, and that concerted convergence and/or gene linkage was responsible for parallel morphological changes that were derived in conjunction with habitat transitions. These habitat,morphology associations were consistent with the action of natural selection in facilitating the morphological changes that occurred during parallel aquatic to terrestrial habitat transitions in Tetanocera. [source] Phylogenetically structured variance in felid bite force: the role of phylogeny in the evolution of biting performanceJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 3 2010M. SAKAMOTO Abstract A key question in evolution is the degree to which morphofunctional complexes are constrained by phylogeny. We investigated the role of phylogeny in the evolution of biting performance, quantified as bite forces, using phylogenetic eigenvector regression. Results indicate that there are strong phylogenetic signals in both absolute and size-adjusted bite forces, although it is weaker in the latter. This indicates that elimination of size influences reduces the level of phylogenetic inertia and that the majority of the phylogenetic constraint is a result of size. Tracing the evolution of bite force through phylogeny by character optimization also supports this notion, in that relative bite force is randomly distributed across phylogeny whereas absolute bite force diverges according to clade. The nonphylogenetically structured variance in bite force could not be sufficiently explained by species-unique morphology or by ecology. This study demonstrates the difficulties in identifying causes of nonphylogenetically structured variance in morphofunctional character complexes. [source] A Review of Arthropod Phylogeny: New Data Based on Ribosomal DNA Sequences and Direct Character OptimizationCLADISTICS, Issue 2 2000Gonzalo Giribet Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropod groups. Sequences of 139 taxa (23 outgroup and 116 ingroup taxa) representing all extant arthropod "classes" except Remipedia and Cephalocarida are analyzed using direct character optimization exploring six parameter sets. Parameter choice appears to be crucial to phylogenetic inference. The high level of sequence heterogeneity in the 18S rRNA gene (sequence length from 1350 to 2700 bp) makes placement of certain taxa with "unusual" sequences difficult and underscores the necessity of combining ribosomal gene data with other sources of information. Monophyly of Pycnogonida, Chelicerata, Chilopoda, Chilognatha, Malacostraca, Branchiopoda (excluding Daphnia), and Ectognatha are among the higher groups that are supported in most of the analyses. The positions of the Pauropoda, Symphyla, Protura, Collembola, Diplura, Onychophora, Tardigrada, and Daphnia are unstable throughout the parameter space examined. [source] Unstable taxa in cladistic analysis: identification and the assessment of relevant charactersCLADISTICS, Issue 5 2009Diego Pol A common problem in phylogenetic analysis is the presence of unstable taxa that are depicted in multiple positions in optimal topologies. These uncertainties are reflected in strict consensus trees with polytomies that hamper the interpretation of the phylogenetic results. We propose a protocol for detecting unstable branches (either terminal taxa or clades) and identifying particular characters related to their instability in cladistic analysis. This procedure is based on an iterative evaluation of the agreement of triplets among the optimal topologies (i.e. most-parsimonious trees, MPTs) and examination of character optimizations on these trees. Different types of characters underlying the unstable behaviour of taxa are detected: those with conflicting scorings that support alternative positions of problematic taxa and those with missing data in the unstable taxa that could reduce their instability if they are scored. The entire process is automated through a TNT script that provides a list of characters related to the instability of each unstable taxon. The outcome of this procedure can be used as a guide for further research efforts focused on the revision or addition of (morphological or molecular) phylogenetic data for elucidating the affinities of unstable taxa. ,© The Willi Hennig Society 2009. [source] | ||||||||||