MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
TLDR
An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.Abstract:
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.read more
Citations
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Journal ArticleDOI
Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop
Khaled M. Hazzouri,Jonathan M. Flowers,Hendrik J. J. Visser,Hussam S. M. Khierallah,Ulises Rosas,Gina M. Pham,Rachel S. Meyer,Rachel S. Meyer,Caryn K. K. Johansen,Zoë Fresquez,Khaled Masmoudi,Nadia Haider,Nabila El Kadri,Youssef Idaghdour,Joel A. Malek,Deborah Thirkhill,Ghulam Sarwar Markhand,Robert Krueger,Abdelouahhab Zaid,Michael D. Purugganan +19 more
TL;DR: A comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars is presented, which documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
Journal ArticleDOI
Comparative genomics shows that viral integrations are abundant and express piRNAs in the arboviral vectors Aedes aegypti and Aedes albopictus
Umberto Palatini,Pascal Miesen,Rebeca Carballar-Lejarazú,Lino Ometto,Ettore Rizzo,Zhijian Tu,Ronald P. van Rij,Mariangela Bonizzoni +7 more
TL;DR: Differences in the number of viral integrations in the genomes of mosquito species from the same geographic area support the conclusion that integrations of viral sequences is not dependent on viral exposure, but that lineage-specific interactions exist, and suggest a role for viral Integrations in antiviral defense in these two mosquito species.
Journal ArticleDOI
Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms
Craig F. Barrett,John V. Freudenstein,Jeff Li,Dustin Mayfield-Jones,Leticia Perez,J. Chris Pires,Cristian Santos +6 more
TL;DR: Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastsome evolution in heterotrophic angiosperms.
Journal ArticleDOI
Genetic characterization of strains named as Xanthomonas axonopodis pv. dieffenbachiae leads to a taxonomic revision of the X. axonopodis species complex
E. C. Constantin,Ilse Cleenwerck,Martine Maes,Steve Baeyen,C. Van Malderghem,P. De Vos,Bart Cottyn +6 more
TL;DR: Each PG was shown to represent a single species, based on average nucleotide identity values, DNA-DNA hybridization data and phenotypic characteristics, and strains named as Xad belong to PG I, PG II and PG III, and not to X. axonopodis.
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Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress
Peng Zhao,Dongdong Wang,Ruoqiu Wang,Nana Kong,Chao Zhang,Chenghui Yang,Wentao Wu,Haoli Ma,Qin Chen +8 more
TL;DR: Analysis of the potato Hsp20 gene family demonstrated that the genes responded to multiple abiotic stresses, such as heat, salt or drought stress, and provided valuable information for clarifying the evolutionary relationship of the StHsp20 family and in aiding functional characterization of StHSP20 genes in further research.
References
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Journal ArticleDOI
MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
Koichiro Tamura,Daniel S. Peterson,Nicholas Peterson,Glen Stecher,Masatoshi Nei,Sudhir Kumar +5 more
TL;DR: The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models, inferring ancestral states and sequences, and estimating evolutionary rates site-by-site.
Journal ArticleDOI
MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Book
The Neutral Theory of Molecular Evolution
TL;DR: The neutral theory as discussed by the authors states that the great majority of evolutionary changes at the molecular level are caused not by Darwinian selection but by random drift of selectively neutral mutants, which has caused controversy ever since.
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