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Standard Parsimony (standard + parsimony)
Selected AbstractsMolecular phylogenetics of tribe Synandreae, a North American lineage of lamioid mints (Lamiaceae)CLADISTICS, Issue 3 2008Anne-Cathrine Scheen The five mint genera Brazoria, Macbridea, Physostegia, Synandra and Warnockia (Lamioideae: Lamiaceae) are all North American endemics. Together with the monotypic European genus Melittis and the Asian genus Chelonopsis, these taxa have been classified as subtribe Melittidinae. Previous morphological studies have failed to uncover synapomorphic characters for this group. We sequenced the plastid trnL-trnF region and trnS-trnG spacer and the nuclear ribosomal 5S non-transcribed spacer (5S-NTS) to assess phylogenetic relationships within Melittidinae. Standard parsimony and direct optimization (POY) analyses show Melittis, the type genus of the subtribe, as sister to Stachys. Thus, the monophyly of subtribe Melittidinae is not supported either by molecular or morphological data. However, the North American endemics form a monophyletic group that can be recognized as the recircumscribed tribe Synandreae. The molecular relationships among these genera are corroborated by both morphological and cytological data. The expected close relationship between the south-central endemics Warnockia and Brazoria and their sister relationship to the widespread genus Physostegia is confirmed. Nevertheless, most of the North American endemics are restricted to the south-east of the continent. Dispersal westwards and northwards is correlated with an increase in chromosome numbers. No specific Eurasian origin (i.e., transatlantic or transpacific) can be determined, but Synandreae are clearly distinct from the large Stachys clade, and therefore represent a separate migration into North America. © The Willi Hennig Society 2007. [source] Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeographyJOURNAL OF BIOGEOGRAPHY, Issue 5 2005Lyn G. Cook Abstract Aim, Phylogenies are increasingly being used to attempt to answer biogeographical questions. However, a reliance on tree topology alone has emerged without consideration of earth processes or the biology of the organisms in question. Most ancestral-state optimization methods have inherent problems, including failure to take account of asymmetry, such as unequal probabilities of losses and gains, and the lack of use of independent cost estimates. Here we discuss what we perceive as shortcomings in most current tree-based biogeography interpretation methods and show that consideration of processes and their likelihoods can turn the conventional biogeographical interpretation on its head. Location, Southern hemisphere focus but applicable world-wide. Methods, The logic of existing methods is reviewed with respect to their adequacy in modelling processes such as geographical mode of speciation and likelihood of dispersal, including directional bias. Published reconstructions of dispersal of three plant taxa between Australia and New Zealand were re-analysed using standard parsimony and maximum likelihood (ML) methods with rate matrices to model expected asymmetry of dispersal. Results, Few studies to date incorporate asymmetric dispersal rate matrices or question the simplistic assumption of equal costs. Even when they do, cost matrices typically are not derived independently of tree topology. Asymmetrical dispersal between Australia and New Zealand could be reconstructed using parsimony but not with ML. Main conclusions, The inadequacy of current models has important consequences for our interpretation of southern hemisphere biogeography, particularly in relation to dispersal. For example, if repeated directional dispersals and colonization in the direction of prevailing winds have occurred, with intervening periods of speciation, then there is no need to infer dispersals against those winds. Failure to take account of directionality and other biases in reconstruction methods has implications beyond the simple misinterpretation of the biogeography of a taxonomic group, such as calibration of molecular clocks, the dating of vicariance events, and the prioritization of areas for conservation. [source] PHYLOGENY OF PHAGOTROPHIC EUGLENIDS (EUGLENOZOA): A MOLECULAR APPROACH BASED ON CULTURE MATERIAL AND ENVIRONMENTAL SAMPLES,JOURNAL OF PHYCOLOGY, Issue 4 2003Ingo Busse Molecular studies based on small subunit (SSU) rDNA sequences addressing euglenid phylogeny hitherto suffered from the lack of available data about phagotrophic species. To extend the taxon sampling, SSU rRNA genes from species of seven genera of phagotrophic euglenids were investigated. Sequence analyses revealed an increasing genetic diversity among euglenid SSU rDNA sequences compared with other well-known eukaryotic groups, reflecting an equally broad diversity of morphological characters among euglenid phagotrophs. Phylogenetic inference using standard parsimony and likelihood approaches as well as Bayesian inference and spectral analyses revealed no clear support for euglenid monophyly. Among phagotrophs, monophyly of Petalomonas cantuscygni and Notosolenus ostium, both comprising simple ingestion apparatuses, is strongly supported. A moderately supported clade comprises phototrophic euglenids and primary osmotrophic euglenids together with phagotrophs, exhibiting a primarily flexible pellicle composed of numerous helically arranged strips and a complex ingestion apparatus with two supporting rods and four curved vanes. Comparison of molecular and morphological data is used to demonstrate the difficulties to formulate a hypothesis about how the ingestion apparatus evolved in this group. [source] Cladogenesis and reticulation in the Hawaiian endemic mints (Lamiaceae)CLADISTICS, Issue 6 2003Charlotte Lindqvist The Hawaiian endemic mints, which comprise 58 species of dry-fruited Haplostachys and fleshy-fruited Phyllostegia and Stenogyne, represent a major island radiation that likely originated from polyploid hybrid ancestors in the temperate North American Stachys lineage. In contrast with considerable morphological and ecological diversity among taxa, sequence variation in the nrDNA 5S non-transcribed spacer was found to be remarkably low, which when analyzed using standard parsimony resulted in a lack of phylogenetic resolution among accessions of insect-pollinated Phyllostegia and bird-pollinated Stenogyne. However, many within-individual nucleotide polymorphisms were observed, and under the assumption that they could contain phylogenetic information, these ambiguities were recoded as new character states. Substantially more phylogenetic structure was obtained with these data, including the resolution of most Stenogyne species into a monophyletic group with an apparent recent origin on O'ahu (3.0 My) or the Maui Nui island complex (2.2 My). Subsequent diversification appears to have involved multiple inter-island dispersal events. Intergeneric placements for a few morphotypes, seemingly misplaced within either Phyllostegia or Stenogyne, may indicate reticulation as one polymorphism-generating force. For a finer scale exploration of hybridization, preliminary AFLP fragment data were examined among putative hybrids of Stenogyne microphylla and S. rugosa from Mauna Kea, Hawai'i, that had been identified based on morphology. Cladistic analysis (corroborated by multivariate correspondence analysis) showed the morphologically intermediate individuals to group in a strongly supported monophyletic clade with S. microphylla. Therefore, reticulation could be both historic and active in Stenogyne, and perhaps a force of general importance in the evolution of the Hawaiian mints. The relatively greater extent of lineage-sorted polymorphisms in Stenogyne may indicate selective differentiation from other fleshy-fruited taxa, perhaps through the agency of highly specialized bird pollinators that restricted gene flow with other Hawaiian mint morphotypes. [source] | ||||||||||