Mind the gap! The mitochondrial control region and its power as a phylogenetic marker in echinoids

DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

(2017) Xuhua Xia   JOURNAL OF HEREDITY

Phylogeny and taxonomy of the genus Ilyodon Eigenmann, 1907 (Teleostei: Goodeidae), based on mitochondrial and nuclear DNA sequences

(2017) Rosa Gabriela Beltrán-López et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Deep Phylogeographic Breaks in Magpie Pica pica Across the Holarctic: Concordance with Bioacoustics and Phenotypes

(2017) Alexey P. Kryukov et al.   ZOOLOGICAL SCIENCE

Cryptic speciation in pan-tropical sea urchins: a case study of an edge-of-range population of Tripneustes from the Kermadec Islands

(2017) Omri Bronstein et al.   Scientific Reports

Analyses of Mitogenome Sequences Revealed that Asian Citrus Psyllids (Diaphorina citri) from California Were Related to Those from Florida

(2017) Fengnian Wu et al.   Scientific Reports

Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship

(2016) Z.H. Huang et al.   GENETICS AND MOLECULAR RESEARCH

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web

(2016) Oscar Robinson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Do genes lie? Mitochondrial capture masks the Red Sea collector urchin’s true identity (Echinodermata: Echinoidea: Tripneustes )

(2016) Omri Bronstein et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Characterization of the complete mitochondrial genome of Bombyx huttoni (Lepidoptera: Bombycidae)

(2015) Xiao-Yi Peng et al.   Mitochondrial DNA Part A

AliView: a fast and lightweight alignment viewer and editor for large datasets

(2014) Anders Larsson   BIOINFORMATICS

Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes

(2014) Han Gan et al.   BMC EVOLUTIONARY BIOLOGY

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria

(2014) Robert Ekblom et al.   BMC GENOMICS

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq

(2014) Jonathan L. King et al.   Forensic Science International-Genetics

Development and assessment of an optimized next-generation DNA sequencing approach for the mtgenome using the Illumina MiSeq

(2014) Jennifer A. McElhoe et al.   Forensic Science International-Genetics

Natural Selection on Coding and Noncoding DNA Sequences Is Associated with Virulence Genes in a Plant Pathogenic Fungus

(2014) Gabriel E. Rech et al.   Genome Biology and Evolution

Phylogenomics of strongylocentrotid sea urchins

(2013) Kord M Kober et al.   BMC EVOLUTIONARY BIOLOGY

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

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

The Taxonomy and Phylogeny of Echinometra (Camarodonta: Echinometridae) from the Red Sea and Western Indian Ocean

(2013) Omri Bronstein et al.   PLoS One

Twin mitochondrial sequence analysis

(2013) Yosr Bouhlal et al.   Molecular Genetics & Genomic Medicine

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Contrasting Evolutionary Dynamics and Information Content of the Avian Mitochondrial Control Region and ND2 Gene

(2012) F. Keith Barker et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Comparison of complete mitochondrial DNA control regions among five Asian freshwater turtle species and their phylogenetic relationships

(2011) Y. Jiang et al.   GENETICS AND MOLECULAR RESEARCH

The phylogeny and classification of post-Palaeozoic echinoids

(2011) Andreas Kroh et al.   JOURNAL OF SYSTEMATIC PALAEONTOLOGY

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees

(2011) Marina Marcet-Houben et al.   NUCLEIC ACIDS RESEARCH

raxmlGUI: a graphical front-end for RAxML

(2011) Daniele Silvestro et al.   ORGANISMS DIVERSITY & EVOLUTION

Next generation sequencing has lower sequence coverage and poorer SNP-detection capability in the regulatory regions

(2011) Weixin Wang et al.   Scientific Reports

Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata

(2010) T. B. HOAREAU et al.   Molecular Ecology Resources

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae

(2009) Luis Cadahía et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Investigation of Heteroplasmy in the Human Mitochondrial DNA Control Region: A Synthesis of Observations from More Than 5000 Global Population Samples

(2009) Jodi A. Irwin et al.   JOURNAL OF MOLECULAR EVOLUTION

DNA barcoding discriminates echinoderm species

(2009) ROBERT D. WARD et al.   Molecular Ecology Resources

Complex population structure in African village dogs and its implications for inferring dog domestication history

(2009) A. R. Boyko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bird Mitochondrial Gene Order: Insight from 3 Warbler Mitochondrial Genomes

(2008) Tiratha Raj Singh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Variable Selective Pressures at a Large Secondary Structure of the Human Mitochondrial DNA Control Region

(2008) F. Pereira et al.   MOLECULAR BIOLOGY AND EVOLUTION