scholarly journals CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

2013 ◽  
Vol 30 (6) ◽  
pp. 1270-1280 ◽  
Author(s):  
Manuel Gil ◽  
Marcelo Serrano Zanetti ◽  
Stefan Zoller ◽  
Maria Anisimova
Keyword(s):  
Maximum Likelihood ◽  
Codon Substitution ◽  
Substitution Models ◽  
Phylogeny Estimation ◽  
Maximum Likelihood Phylogeny

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

2020 ◽  
Vol 190 (2) ◽  
pp. 709-736
Author(s):  
Jae-Cheon Sohn ◽  
Shigeki Kobayashi ◽  
Yutaka Yoshiyasu
Keyword(s):  
Maximum Likelihood ◽  
East Asia ◽  
Host Plants ◽  
Morphological Characters ◽  
Species Group ◽  
Geological History ◽  
Dna Barcodes ◽  
History Of ◽  
Species Groups ◽  
Maximum Likelihood Phylogeny

Abstract A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

scholarly journals Bayesian Comparisons of Codon Substitution Models

Genetics ◽  
2008 ◽  
Vol 180 (3) ◽  
pp. 1579-1591 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Nicolas Lartillot ◽  
Hervé Philippe
Keyword(s):  
Codon Substitution ◽  
Substitution Models

Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates

2005 ◽  
Vol 12 (9) ◽  
pp. 1166-1182 ◽  
Author(s):  
Ole F. Christensen ◽  
Asger Hobolth ◽  
Jens L. Jensen
Keyword(s):  
Codon Substitution ◽  
Pseudo Likelihood ◽  
Likelihood Analysis ◽  
Substitution Models

Codon substitution models based on residue similarity and their applications

Gene ◽  
2012 ◽  
Vol 509 (1) ◽  
pp. 136-141 ◽  
Author(s):  
Xinsheng Liu ◽  
Hui Liu ◽  
Wanlin Guo ◽  
Keming Yu
Keyword(s):  
Codon Substitution ◽  
Substitution Models
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