The Experts below are selected from a list of 27 Experts worldwide ranked by ideXlab platform
Johannes Bergsten - One of the best experts on this subject based on the ideXlab platform.
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a review of long branch attraction
Cladistics, 2005Co-Authors: Johannes BergstenAbstract:The history of long-branch attraction, and in particular methods suggested to detect and avoid the artifact to date, is reviewed. Methods suggested to avoid LBA-artifacts include excluding long-branch taxa, excluding faster evolving third codon positions, using inference methods less sensitive to LBA such as likelihood, the Aguinaldo et al. approach, sampling more taxa to break up long branches and sampling more characters especially of another kind, and the pros and cons of these are discussed. Methods suggested to detect LBA are numerous and include methodological disconcordance, RASA, Separate Partition analyses, parametric simulation, random outgroup sequences, long-branch extraction, split decomposition and spectral analysis. Less than 10 years ago it was doubted if LBA occurred in real datasets. Today, examples are numerous in the literature and it is argued that the development of methods to deal with the problem is warranted. A 16 kbp dataset of placental mammals and a morphological and molecular combined dataset of gall wasps are used to illustrate the particularly common problem of LBA of problematic ingroup taxa to outgroups. The preferred methods of Separate Partition analysis, methodological disconcordance, and long branch extraction are used to demonstrate detection methods. It is argued that since outgroup taxa almost always represent long branches and are as such a hazard towards misplacing long branched ingroup taxa, phylogenetic analyses should always be run with and without the outgroups included. This will detect whether only the outgroup roots the ingroup or if it simultaneously alters the ingroup topology, in which case previous studies have shown that the latter is most often the worse. Apart from that LBA to outgroups is the major and most common problem; scanning the literature also detected the ill advised comfort of high support values from thousands of characters, but very few taxa, in the age of genomics. Taxon sampling is crucial for an accurate phylogenetic estimate and trust cannot be put on whole mitochondrial or chloroplast genome studies with only a few taxa, despite their high support values. The placental mammal example demonstrates that parsimony analysis will be prone to LBA by the attraction of the tenrec to the distant marsupial outgroups. In addition, the murid rodents, creating the classic ‘‘the guinea-pig is not a rodent’’ hypothesis in 1996, are also shown to be attracted to the outgroup by nuclear genes, although including the morphological evidence for rodents and Glires overcomes the artifact. The gall wasp example illustrates that Bayesian analyses with a Partition-specific GTR + G + I model give a conflicting resolution of clades, with a posterior probability of 1.0 when comparing ingroup alone versus outgroup rooted topologies, and this is due to long-branch attraction to the outgroup. � The Willi Hennig Society 2005.
Jonathan Tennyson - One of the best experts on this subject based on the ideXlab platform.
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temperature dependent Partition functions and equilibrium constant for hcn and hnc
Journal of Chemical Physics, 2002Co-Authors: R J Barber, G J Harris, Jonathan TennysonAbstract:Ab initio vibration-rotation energy levels are summed to estimate a Partition function for the total HCN system. By assigning individual levels to HCN and HNC, Separate Partition functions are obtained for the isomers. These are used to give a temperature dependent equilibrium constant which suggests that at temperatures typical of cool carbon stars, about 20% of the HCN system is actually HNC. Errors in the Partition functions and equilibrium constant are estimated.
R J Barber - One of the best experts on this subject based on the ideXlab platform.
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temperature dependent Partition functions and equilibrium constant for hcn and hnc
Journal of Chemical Physics, 2002Co-Authors: R J Barber, G J Harris, Jonathan TennysonAbstract:Ab initio vibration-rotation energy levels are summed to estimate a Partition function for the total HCN system. By assigning individual levels to HCN and HNC, Separate Partition functions are obtained for the isomers. These are used to give a temperature dependent equilibrium constant which suggests that at temperatures typical of cool carbon stars, about 20% of the HCN system is actually HNC. Errors in the Partition functions and equilibrium constant are estimated.
Michael F. Whiting - One of the best experts on this subject based on the ideXlab platform.
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phylogenetic approaches for the analysis of mitochondrial genome sequence data in the hymenoptera a lineage with both rapidly and slowly evolving mitochondrial genomes
Molecular Phylogenetics and Evolution, 2009Co-Authors: Mark Dowto, Stephe L Camero, Andrew D Austi, Michael F. WhitingAbstract:We entirely sequenced two new hymenopteran mitochondrial genomes (Cephus cinctus and Orussus occidentalis), and a substantial portion of another three hymenopterans (Schlettererius cinctipes, Venturia canescens, and Enicospilus). We analyze them together with nine others reported in the literature. We establish that the rate of genetic divergence is two to three times higher among some Hymenoptera when compared with others, making this a group with both long and short phylogenetic branches. We then assessed the ability of a range of phylogenetic approaches to recover seven uncontroversial relationships, when lineages show markedly different rates of molecular evolution. This range encompassed maximum parsimony and Bayesian analysis of (i) amino acid data, (ii) nucleotide data, and (iii) nucleotide data excluding third codon positions. UnPartitioned analyses were compared with Partitioned analyses, with the data Partitioned by codon position (ribosomal genes were placed in a Separate Partition). These analyses indicated that Partitioned, Bayesian analysis of nucleotide data, excluding 3rd codon positions, recovered more of the uncontroversial relationships than any other approach. These results suggest that the analysis of complete mitochondrial genome sequences holds promise for the resolution of hymenopteran superfamily relationships.
G J Harris - One of the best experts on this subject based on the ideXlab platform.
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temperature dependent Partition functions and equilibrium constant for hcn and hnc
Journal of Chemical Physics, 2002Co-Authors: R J Barber, G J Harris, Jonathan TennysonAbstract:Ab initio vibration-rotation energy levels are summed to estimate a Partition function for the total HCN system. By assigning individual levels to HCN and HNC, Separate Partition functions are obtained for the isomers. These are used to give a temperature dependent equilibrium constant which suggests that at temperatures typical of cool carbon stars, about 20% of the HCN system is actually HNC. Errors in the Partition functions and equilibrium constant are estimated.
