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- Insect Systematics (9)
- Sequence Alignment and Phylogenetics (7)
- Ephemeroptera (2)
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- Bayesian; maximum likelihood; maximum parsimony; multiple sequence alignment; neighbor joining; phylogenetics; simulation; tree reconstruction (1)
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- Clustal; DNA sequence alignment; Evolutionary distance; Gap character coding; Homology; Indel; Parsimony; Simulation; Tree reconstruction (1)
- ClustalW; direct optimization; multiple sequence alignment; parsimony; phylogenetics; POY; sensitivity analysis; simulation; tree reconstruction (1)
- Ephemeroptera; MayXies; Molecular phylogeny; Evolution of Xight; Origin of wings; Pterygota; Mandibular tusks; Sensitivity analysis; Direct optimization (1)
- Ephemeroptera; Mayflies; Molecular phylogeny; Pannota; Ephemerellidae (1)
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- [Bayesian; maximum likelihood; maximum parsimony; multiple sequence alignment; neighbor joining; phylogenetics; simulation; tree reconstruction (1)
Articles 1 - 14 of 14
Full-Text Articles in Biotechnology
Polyphyly Of The Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial Dna Sequences, T. Heath Ogden
Polyphyly Of The Pikeminnows (Teleostei: Cyprinidae) Inferred Using Mitochondrial Dna Sequences, T. Heath Ogden
T. Heath Ogden
The phylogenetic relationships of the Colorado pikeminnow Ptychocheilus lucius, northern pikeminnow P. oregonensis, Sacramento pikeminnow P. grandis, Umpqua pikeminnow P. umpquae, and hardhead Mylopharodon conocephalus were examined by using molecular data to investigate monophyly of the genus Ptychocheilus. Phylogenies generated using DNA sequence data from the cytochrome b and 16S ribosomal DNA genes of the mitochondrial genome reveal that Ptychocheilus is a polyphyletic genus and suggest that the taxonomy of the group is in need of further revision. These data yield insights into the evolution of the pikeminnows and help place the significant evolutionary events in context with the geological …
The Evolution Of Flight In Insects: Insights From Mayflies And Dna, T. Heath Ogden
The Evolution Of Flight In Insects: Insights From Mayflies And Dna, T. Heath Ogden
T. Heath Ogden
No abstract provided.
Towards A New Paradigm In Mayfly Phylogeny (Ephemeroptera): Combined Analysis Of Morphological And Molecular Data, T. Heath Ogden
Towards A New Paradigm In Mayfly Phylogeny (Ephemeroptera): Combined Analysis Of Morphological And Molecular Data, T. Heath Ogden
T. Heath Ogden
This study represents the first formal morphological and combined (morphological and molecular) phylogenetic analyses of the order Ephemeroptera. Taxonomic sampling comprised 112 species in 107 genera, including 42 recognized families (all major lineages of Ephemeroptera). Morphological data consisted of 101 morphological characters. Molecular data were acquired from DNA sequences of the 12S, 16S, 18S, 28S and H3 genes. The Asian genus Siphluriscus (Siphluriscidae) was supported as sister to all other mayflies. The lineages Carapacea, Furcatergalia, Fossoriae, Pannota, Caenoidea and Ephemerelloidea were supported as monophyletic, as were many of the families. However, some recognized families (for example, Ameletopsidae and Coloburiscidae) and …
Combined Morphological And Molecular Phylogeny Of Ephemerellidae (Ephemeroptera), T. Heath Ogden
Combined Morphological And Molecular Phylogeny Of Ephemerellidae (Ephemeroptera), T. Heath Ogden
T. Heath Ogden
This study represents the first combined molecular and morphological analysis for the mayfly family Ephemerellidae (Ephemeroptera), with a focus on the relationships of genera and species groups of the subfamily Ephemerellinae. The phylogeny was constructed based on DNA sequence data from 3 nuclear (18S rDNA, 28S rDNA, histone H3) and 2 mitochondrial (12S rDNA, 16S rDNA) genes, and 23 morphological characters. Taxon sampling for Ephemerellidae included exemplars from all 25 extant genus groups and additional representatives from those genera with the highest diversity. Ephemerellidae appears to consist of three major clades. Ephemerella, the largest genus of Ephemerellidae, and Serratella were …
Pisciforma, Setisura, And Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based On 18s Rdna Sequences: A Reply To Sun Et Al. (2006), T. Heath Ogden
Pisciforma, Setisura, And Furcatergalia (Order: Ephemeroptera) Are Not Monophyletic Based On 18s Rdna Sequences: A Reply To Sun Et Al. (2006), T. Heath Ogden
T. Heath Ogden
No abstract provided.
Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden
Molecules, Morphology And Fossils: A Comprehensive Approach To Odonate Phylogeny And The Evolution Of The Odonate Wing, T. Heath Ogden
T. Heath Ogden
We undertook a comprehensive morphological and molecular phylogenetic analysis of dragonfly phylogeny, examining both extant and fossil lineages in simultaneous analyses. The legitimacy of higher-level family groups and the phylogenetic relationship between families were tested. Thirteen families were supported as monophyletic (Aeshnidae, Calopterygidae, Chlorocyphidae, Euphaeidae, Gomphidae, Isostictidae, Lestidae, Libellulidae, Petaluridae, Platystictidae, Polythoridae, Pseudostigmatidae and Synthemistidae) and eight as non-monophyletic (Amphipterygidae, Coenagrionidae, Corduliidae, Megapodagrionidae, Protoneuridae and Synlestidae), although Perilestidae and Platycnemididae were recovered as monophyletic under Bayesian analyses. Nine families were represented by one species, thus monophyly was not tested (Epiophlebiidae, Austropetaliidae, Chlorogomphidae, Cordulegastridae, Macromiidae, Chorismagrionidae, Diphlebiidae, Lestoideidae and Pseudolestidae). Epiprocta …
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 …
Taxonomy And Biology Of A New Oecophoridae (Lepidoptera) From Central Chile, T. Heath Ogden
Taxonomy And Biology Of A New Oecophoridae (Lepidoptera) From Central Chile, T. Heath Ogden
T. Heath Ogden
The adult, larva, and pupa of Afdera jimenae Ogden & Parra sp. nov. are described and illustrated. Larvae live in leaf litter throughout all instars and are generalists feeding upon the fallen leaves of a number of different plant species of sclerophyllous forests. Comments on morphological details and bionomics of this species are given. This is the second species of Afdera know for Chile.