Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

(2017) Romain Blanc-Mathieu et al.   PLoS Genetics

Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis

(2017) Toon Janssen et al.   PLoS One

Genetic Drift, Not Life History or RNAi, Determine Long-Term Evolution of Transposable Elements

(2016) Amir Szitenberg et al.   Genome Biology and Evolution

Clustering Genes of Common Evolutionary History

(2016) Kevin Gori et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene conversion and linkage: effects on genome evolution and speciation

(2016) Katharine L. Korunes et al.   MOLECULAR ECOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals

(2016) B. Vernot et al.   SCIENCE

Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution

(2016) Toon Janssen et al.   Scientific Reports

Mitochondrial Haplotype-Based Identification of Ethanol-Preserved Root-Knot Nematodes from Africa

(2015) Chris Pagan et al.   PHYTOPATHOLOGY

Unreduced gametes: meiotic mishap or evolutionary mechanism?

(2015) Annaliese S. Mason et al.   TRENDS IN GENETICS

ReproPhylo: An Environment for Reproducible Phylogenomics

(2015) Amir Szitenberg et al.   PLoS Computational Biology

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

The global spread of crop pests and pathogens

(2014) Daniel P. Bebber et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

The complex hybrid origins of the root knot nematodes revealed through comparative genomics

(2014) David H. Lunt et al.   PeerJ

Hybridization and speciation

(2013) R. Abbott et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Evidence for Widespread GC-biased Gene Conversion in Eukaryotes

(2012) Eugénie Pessia et al.   Genome Biology and Evolution

Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change

(2012) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

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

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

(2009) Benoit Nabholz et al.   BMC EVOLUTIONARY BIOLOGY

Small Subunit rDNA-Based Phylogeny of the Tylenchida Sheds Light on Relationships Among Some High-Impact Plant-Parasitic Nematodes and the Evolution of Plant Feeding

(2009) M. Holterman et al.   PHYTOPATHOLOGY

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Mitotic Recombination: Why? When? How? Where?

(2009) Matthew C. LaFave et al.   PLoS Genetics

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

(2008) David H Lunt   BMC EVOLUTIONARY BIOLOGY

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

Diversity of Meloidogyne arenaria using morphological, cytological and molecular approaches

(2008) Regina Carneiro et al.   NEMATOLOGY

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

(2008) C. H. Opperman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA