Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals

Mammalian transposable elements and their impacts on genome evolution

(2018) Roy N. Platt et al.   CHROMOSOME RESEARCH

Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling

(2018) Alexander T Xue et al.   Genome Biology and Evolution

Assessing the Impacts of Positive Selection on Coalescent-Based Species Tree Estimation and Species Delimitation

(2018) Richard H Adams et al.   SYSTEMATIC BIOLOGY

Dynamics of genome size evolution in birds and mammals

(2017) Aurélie Kapusta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis

(2017) Robert P. Ruggiero et al.   Frontiers in Genetics

The Deep Origin and Recent Loss of Venom Toxin Genes in Rattlesnakes

(2016) Noah L. Dowell et al.   CURRENT BIOLOGY

Effects of Linked Selective Sweeps on Demographic Inference and Model Selection

(2016) D. R. Schrider et al.   GENETICS

Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution

(2016) Richard H. Adams et al.   GENOME

The devil is in the details: the effect of population structure on demographic inference

(2016) P Orozco-terWengel   HEREDITY

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes

(2016) Emeric Figuet et al.   MOLECULAR BIOLOGY AND EVOLUTION

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-whiteFicedulaflycatchers

(2016) Krystyna Nadachowska-Brzyska et al.   MOLECULAR ECOLOGY

Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach

(2016) Simon Boitard et al.   PLoS Genetics

Transposons, Genome Size, and Evolutionary Insights in Animals

(2015) Adriana Canapa et al.   CYTOGENETIC AND GENOME RESEARCH

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Body sizes and diversification rates of lizards, snakes, amphisbaenians and the tuatara

(2015) Anat Feldman et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

On the importance of being structured: instantaneous coalescence rates and human evolution—lessons for ancestral population size inference?

(2015) O Mazet et al.   HEREDITY

GenBank

(2015) Karen Clark 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

Demographic inference using genetic data from a single individual: Separating population size variation from population structure

(2015) Olivier Mazet et al.   THEORETICAL POPULATION BIOLOGY

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps

(2015) Arthur Georges et al.   GigaScience

Population Genomics of Transposable Elements inDrosophila

(2014) Maite G. Barrón et al.   Annual Review of Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes

(2014) Alexander Suh et al.   Genome Biology and Evolution

Endogenous hepadnaviruses, bornaviruses and circoviruses in snakes

(2014) C. Gilbert et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

(2014) R. E. Green et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes

(2013) R Pyron et al.   BMC EVOLUTIONARY BIOLOGY

An Age-of-Allele Test of Neutrality for Transposable Element Insertions

(2013) J. P. Blumenstiel et al.   GENETICS

Lizards and LINEs: Selection and Demography Affect the Fate of L1 Retrotransposons in the Genome of the Green Anole (Anolis carolinensis)

(2013) Marc Tollis et al.   Genome Biology and Evolution

Widespread horizontal transfer of retrotransposons

(2013) A. M. Walsh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

(2013) T. A. Castoe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alu elements in primates are preferentially lost from areas of high GC content

(2013) Elizabeth HB Hellen et al.   PeerJ

Active Transposition in Genomes

(2012) Cheng Ran Lisa Huang et al.   Annual Review of Genetics

Accumulation and Rapid Decay of Non-LTR Retrotransposons in the Genome of the Three-Spine Stickleback

(2012) Eryn Blass et al.   Genome Biology and Evolution

Reconstructing the Evolutionary History of Transposable Elements

(2012) Arnaud Le Rouzic et al.   Genome Biology and Evolution

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Co-evolution between transposable elements and their hosts: a major factor in genome size evolution?

(2011) J. Arvid Ågren et al.   CHROMOSOME RESEARCH

Discovery of Highly Divergent Repeat Landscapes in Snake Genomes Using High-Throughput Sequencing

(2011) Todd A. Castoe et al.   Genome Biology and Evolution

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

The genome of the green anole lizard and a comparative analysis with birds and mammals

(2011) Jessica Alföldi et al.   NATURE

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Unique structural characteristics and evolution of a cluster of venom phospholipase A2 isozyme genes of Protobothrops flavoviridis snake

(2010) Naoki Ikeda et al.   GENE

Population Genomics of Transposable Elements in Drosophila melanogaster

(2010) D. A. Petrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

A role for host–parasite interactions in the horizontal transfer of transposons across phyla

(2010) Clément Gilbert et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Independent and parallel lateral transfer of DNA transposons in tetrapod genomes

(2009) Peter Novick et al.   GENE

Statistical inferences in phylogeography

(2009) RASMUS NIELSEN et al.   MOLECULAR ECOLOGY

Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence

(2009) TODD A. CASTOE et al.   Molecular Ecology Resources

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

NCBI BLAST: a better web interface

(2008) M. Johnson et al.   NUCLEIC ACIDS RESEARCH