MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
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The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.Abstract:
Summary: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data. Availability: The MODELTEST package, including the source code and some documentation is available at http://bioag.byu.edu/zoology/crandall―lab/modeltest.html. Contact: dp47@email.byu.edu.read more
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High-Throughput Genomic Data in Systematics and Phylogenetics
TL;DR: This review presents recent advances in laboratory methods for collection of high-throughput phylogenetic data and challenges and constraints for phylogenetic analysis of these data, and offers recommendations for the most promising protocols and data-analysis workflows currently available.
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Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata)
Laure Guillou,Manon Viprey,Aurélie Chambouvet,Rory M. Welsh,Amy R. Kirkham,Ramon Massana,Dave J. Scanlan,Alexandra Z. Worden +7 more
TL;DR: Given the broad distribution of Syndiniales, this work indicates that parasitism may be a major force in ocean food webs, a force that is neglected in current conceptualizations of the marine carbon cycle.
Journal ArticleDOI
Ancient DNA, pig domestication, and the spread of the Neolithic into Europe
Greger Larson,Umberto Albarella,Keith Dobney,Peter Rowley-Conwy,Joerg Schibler,Anne Tresset,Jean-Denis Vigne,Ceiridwen J. Edwards,Angela Schlumbaum,Alexandru Dinu,Adrian Balacsescu,Gaynor Dolman,Antonio Tagliacozzo,Ninna Manaseryan,Preston T. Miracle,Louise H. Van Wijngaarden-Bakker,Marco Masseti,Daniel G. Bradley,Alan Cooper +18 more
TL;DR: It is demonstrated that domestic pigs of Near Eastern ancestry were definitely introduced into Europe during the Neolithic (potentially along two separate routes), reaching the Paris Basin by at least the early 4th millennium B.C.
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Modeling Compositional Heterogeneity
TL;DR: It is shown using likelihood ratio tests that adequate modeling of compositional heterogeneity can be achieved with few composition parameters, that the data may not need to be modelled with separate composition parameters for each branch in the tree.
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Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification
TL;DR: Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, the analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution.
References
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TL;DR: In this article, a new estimate minimum information theoretical criterion estimate (MAICE) is introduced for the purpose of statistical identification, which is free from the ambiguities inherent in the application of conventional hypothesis testing procedure.
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
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