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Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden
Does Direct Optimization Produce More Accurate Alignments And Topologies? Poy Vs. Clustalw+Paup*, T. Heath Ogden
T. Heath Ogden
Direct optimization frameworks for simultaneously estimating alignments and phylogenies have recently been developed. One such method, implemented in the program POY, is becoming more common for analyses of variable length sequences (e.g., analyses using ribosomal genes) and for combined evidence analyses (morphology + multiple genes). Simulation of sequences containing insertion and deletion events was performed in order to directly compare a widely used method of multiple sequence alignment (ClustalW) and subsequent parsimony analysis in PAUP* with direct optimization via POY. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (clocklike, non-clocklike, and ultrametric). Alignment accuracy …
How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
T. Heath Ogden
Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps …
Multiple Sequence Alignment Accuracy And Phylogenetic Inference, T. Heath Ogden, Michael S. Rosenberg
Multiple Sequence Alignment Accuracy And Phylogenetic Inference, T. Heath Ogden, Michael S. Rosenberg
T. Heath Ogden
Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our …
Multiple Sequence Alignment Accuracy And Phylogenetic Inference, T. Heath Ogden
Multiple Sequence Alignment Accuracy And Phylogenetic Inference, T. Heath Ogden
T. Heath Ogden
Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our …
Poor Taxon Sampling, Poor Character Sampling, And Non-Repeatable Analyses Of A Contrived Dataset Do Not Provide A More Credible Estimate Of Insect Phylogeny: A Reply To Kjer., T. Heath Ogden
T. Heath Ogden
The wealth of data available for phylogenetic analysis of the insect orders, from both morphological and molecular sources, is steadily increasing. However, controversy exists among the methodologies one can use to reconstruct ordinal relationships. Recently, Kjer (2004) presented an analysis of insect ordinal relationships based exclusively on a single source of information: 18S rDNA sequence data. Kjer claims that his analysis resulted in a more ‘‘credible’’ phylogeny for the insect orders and strongly criticized our previous phylogenetic results. However, Kjer only used a subset of the data that are currently available for insect ordinal phylogeny, misrepresented our analyses, and omitted …
Phylogeny Of Ephemeroptera (Mayflies) Based On Molecular Evidence, T. Heath Ogden
Phylogeny Of Ephemeroptera (Mayflies) Based On Molecular Evidence, T. Heath Ogden
T. Heath Ogden
This study represents the Wrst molecular phylogeny for the Order Ephemeroptera. The analyses included 31 of the 37 families, representing »24% of the genera. Fifteen families were supported as being monophyletic, Wve families were supported as nonmonophyletic, and 11 families were only represented by one species, and monophyly was not testable. The suborders Furcatergalia and Carapacea were supported as monophyletic while Setisura and Pisciforma were not supported as monophyletic. The superfamilies Ephemerelloidea and Caenoidea were supported as monophyletic while Baetoidea, Siphlonuroidea, Ephemeroidea, and Heptagenioidea were not. Baetidae was recovered as sister to the remaining clades. The mayXy gill to wing …
The Problem With The Paleoptera Problem: Sense And Sensitivity, T. Heath Ogden
The Problem With The Paleoptera Problem: Sense And Sensitivity, T. Heath Ogden
T. Heath Ogden
While the monophyly of winged insects (Pterygota) is well supported, phylogenetic relationships among the most basal extant pterygote lineages are problematic. Ephemeroptera (mayflies) and Odonata (dragonflies) represent the two most basal extant lineages of winged insects, and determining their relationship with regard to Neoptera (remaining winged insects) is a critical step toward understanding insect diversification. A recent molecular analysis concluded that Paleoptera (Odonata +Ephemeroptera) is monophyletic. However, we demonstrate that this result is supported only under a narrow range of alignment parameters. We have further tested the monophyly of Paleoptera using additional sequence data from 18SrDNA, 28S rDNA, and Histone …