Genetic drift and mutational hazard in the evolution of salamander genomic gigantism

Early genome size increase in urodeles

(2016) Michel Laurin et al.   COMPTES RENDUS PALEVOL

Low Levels of LTR Retrotransposon Deletion by Ectopic Recombination in the Gigantic Genomes of Salamanders

(2015) Matthew Blake Frahry et al.   JOURNAL OF MOLECULAR EVOLUTION

Babelomics 5.0: functional interpretation for new generations of genomic data

(2015) Roberto Alonso et al.   NUCLEIC ACIDS RESEARCH

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

(2015) Tyler A. Elliott et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

(2015) Melissa C. Keinath et al.   Scientific Reports

Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds

(2014) Toni I. Gossmann et al.   Genome Biology and Evolution

Hellbender Genome Sequences Shed Light on Genomic Expansion at the Base of Crown Salamanders

(2014) C. Sun et al.   Genome Biology and Evolution

Acquisition of Germ Plasm Accelerates Vertebrate Evolution

(2014) T. Evans et al.   SCIENCE

Why Do More Divergent Sequences Produce Smaller Nonsynonymous/Synonymous Rate Ratios in Pairwise Sequence Comparisons?

(2013) M. dos Reis et al.   GENETICS

Inference of Functional Divergence Among Proteins When the Evolutionary Process is Non-stationary

(2013) Rachael A. Bay et al.   JOURNAL OF MOLECULAR EVOLUTION

Meiotic Recombination Strongly Influences GC-Content Evolution in Short Regions in the Mouse Genome

(2013) Yves Clément et al.   MOLECULAR BIOLOGY AND EVOLUTION

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

(2012) Zhang Zhang et al.   BMC BIOINFORMATICS

The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

(2012) Iker Irisarri et al.   BMC GENOMICS

LOW METABOLIC RATES IN SALAMANDERS ARE CORRELATED WITH WEAK SELECTIVE CONSTRAINTS ON MITOCHONDRIAL GENES

(2012) Rebecca A. Chong et al.   EVOLUTION

Slow DNA Loss in the Gigantic Genomes of Salamanders

(2012) Cheng Sun et al.   Genome Biology and Evolution

Fast Molecular Evolution Associated with High Active Metabolic Rates in Poison Frogs

(2012) Juan C. Santos   MOLECULAR BIOLOGY AND EVOLUTION

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

(2012) Robi Tacutu et al.   NUCLEIC ACIDS RESEARCH

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

(2011) Michael Lynch et al.   Annual Review of Genomics and Human Genetics

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

(2011) Cheng Sun et al.   Genome Biology and Evolution

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

(2011) R. Alexander Pyron et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The genome as a life-history character: why rate of molecular evolution varies between mammal species

(2011) L. Bromham   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reduced Selective Constraint in Endosymbionts: Elevation in Radical Amino Acid Replacements Occurs Genome-Wide

(2011) Jennifer J. Wernegreen   PLoS One

Paleogenomic data suggest mammal-like genome size in the ancestral amniote and derived large genome size in amphibians

(2010) C. L. ORGAN et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The Positive Correlation between dN/dS and dS in Mammals Is Due to Runs of Adjacent Substitutions

(2010) Nina Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

A multilocus timescale for the origin of extant amphibians

(2010) Diego San Mauro   MOLECULAR PHYLOGENETICS AND EVOLUTION

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

A time-invariant principle of genome evolution

(2010) S. De et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Did Genetic Drift Drive Increases in Genome Complexity?

(2010) Kenneth D. Whitney et al.   PLoS Genetics

Reduced Effectiveness of Selection Caused by a Lack of Recombination

(2009) Andrea J. Betancourt et al.   CURRENT BIOLOGY

Protein Rates of Evolution Are Predicted by Double-Strand Break Events, Independent of Crossing-over Rates

(2009) Claudia C. Weber et al.   Genome Biology and Evolution

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

(2009) Jochen B. W. Wolf et al.   Genome Biology and Evolution

The consequences of genetic drift for bacterial genome complexity

(2009) C.-H. Kuo et al.   GENOME RESEARCH

Correlation Between Ka/Ks and Ks is Related to Substitution Model and Evolutionary Lineage

(2009) Jun Li et al.   JOURNAL OF MOLECULAR EVOLUTION

No effect of recombination on the efficacy of natural selection in primates

(2008) K. Bullaughey et al.   GENOME RESEARCH

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS