Journal ArticleDOI
A comparison of nrDNA ITS and ETS loci for phylogenetic inference in the Umbelliferae: an example from tribe Tordylieae.
Maria D. Logacheva,C.M. Valiejo-Roman,Galina V. Degtjareva,Jenny M. Stratton,Stephen R. Downie,Tagir H. Samigullin,Michael G. Pimenov +6 more
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TLDR
This work investigates the utility of nuclear ribosomal DNA external transcribed spacer (ETS) sequences for phylogenetic inference in Umbelliferae tribe Tordylieae, and reports that the ETS region evolves at a slightly faster rate and has a higher percentage of parsimony informative characters than that of ITS and all chloroplast DNA loci examined to date.About:
This article is published in Molecular Phylogenetics and Evolution.The article was published on 2010-10-01. It has received 54 citations till now. The article focuses on the topics: Phylogenetics & Molecular phylogenetics.read more
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Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus
Mariangela Arca,Damien Daniel Hinsinger,Corinne Cruaud,Annie Tillier,Jean Bousquet,Nathalie Frascaria-Lacoste,Nathalie Frascaria-Lacoste,Nathalie Frascaria-Lacoste +7 more
TL;DR: The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus was investigated and it is suggested that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome.
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Species discrimination in Sisyrinchium (Iridaceae): assessment of DNA barcodes in a taxonomically challenging genus.
TL;DR: The study illustrates the difficulties for DNA barcoding to identify species in evolutionary complex lineages by testing the DNA barcode paradigm among the genera of the tribe Sisyrinchieae (Iridoideae), with the best taxonomic resolution obtained with Bayesian inference.
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Adaptation and convergent evolution within the Jamesonia-Eriosorus complex in high-elevation biodiverse Andean hotspots.
TL;DR: Testing for phylogenetic and morphological evidence of adaptive radiation and convergent evolution to novel habitats (exposed, high-altitude páramo habitats) in the Andean fern genera Jamesonia and Eriosorus finds rates of speciation are significantly higher among páramso than non-párama lineages supporting the hypothesis of adaptation and divergence in the unique Párami biodiversity hotspot.
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New Insights into the Phylogeny of Angelica and its Allies (Apiaceae) with Emphasis on East Asian Species, Inferred from nrDNA, cpDNA, and Morphological Evidence
TL;DR: Preliminary phylogenetic analyses of nrDNA ITS and ETS sequences, cpDNA sequences, and morphological data, supplemented by observations of fruit anatomy and micromorphology, provide new insights into the phylogeny and classification of the Angelica group.
References
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Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/ nt
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MrBayes 3: Bayesian phylogenetic inference under mixed models
TL;DR: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models to analyze heterogeneous data sets and explore a wide variety of structured models mixing partition-unique and shared parameters.
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MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.