Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection

(2021) Giobbe Forni et al.   Ecology and Evolution

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The tuatara genome reveals ancient features of amniote evolution

(2020) Neil J. Gemmell et al.   NATURE

Genomic Features of Parthenogenetic Animals

(2020) Kamil S Jaron et al.   JOURNAL OF HEREDITY

CAFE 5 models variation in evolutionary rates among gene families

(2020) Fábio K Mendes et al.   BIOINFORMATICS

Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution

(2019) Changcheng Wu et al.   Genes

Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea)

(2019) Andrea Luchetti et al.   Zoological Letters

A new calmanostracan crustacean species from the Cretaceous Yixian Formation and a simple approach for differentiating fossil tadpole shrimps and their relatives

(2019) Philipp Wagner et al.   Zoological Letters

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOSCIENCE

Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

(2018) Martin Schwentner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

(2018) Castrense Savojardo et al.   Molecular Ecology Resources

A New Standard for Crustacean Genomes: The Highly Contiguous, Annotated Genome Assembly of the Clam Shrimp Eulimnadia texana Reveals HOX Gene Order and Identifies the Sex Chromosome

(2017) James G Baldwin-Brown et al.   Genome Biology and Evolution

ABySS 2.0: resource-efficient assembly of large genomes using a Bloom filter

(2017) Shaun D. Jackman et al.   GENOME RESEARCH

Contrasting Rates of Molecular Evolution and Patterns of Selection among Gymnosperms and Flowering Plants

(2017) Amanda R. De La Torre et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the CollembolanOrchesella cincta

(2016) Anna Faddeeva-Vakhrusheva et al.   Genome Biology and Evolution

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

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

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

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

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Dating the origin of the major lineages of Branchiopoda

(2016) Xiao-Yan Sun et al.   Palaeoworld

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

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

No Accumulation of Transposable Elements in Asexual Arthropods

(2015) Jens Bast et al.   MOLECULAR BIOLOGY AND EVOLUTION

The oldest notostracan (Upper Devonian Strud locality, Belgium)

(2015) Linda Lagebro et al.   PALAEONTOLOGY

Fast Dating Using Least-Squares Criteria and Algorithms

(2015) Thu-Hien To et al.   SYSTEMATIC BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Evolutionary dynamics of R2 retroelement and insertion inheritance in the genome of bisexual and parthenogeneticBacillus rossiuspopulations (Insecta Phasmida)

(2014) L. Bonandin et al.   INSECT MOLECULAR BIOLOGY

Identification, expression, and molecular evolution of microRNAs in the “living fossil”Triops cancriformis(tadpole shrimp)

(2014) Kahori T. Ikeda et al.   RNA

Why coelacanths are not ‘living fossils’

(2013) Didier Casane et al.   BIOESSAYS

Improving Genome-Wide Scans of Positive Selection by Using Protein Isoforms of Similar Length

(2013) José Luis Villanueva-Cañas et al.   Genome Biology and Evolution

Onychocaudata (Branchiopoda: Diplostraca), a new high-level taxon in branchiopod systematics

(2013) Jørgen Olesen et al.   JOURNAL OF CRUSTACEAN BIOLOGY

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

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

Molecular phylogeny of the Notostraca

(2013) Michael Korn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’

(2013) Thomas C. Mathers et al.   PeerJ

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

(2012) Limin Fu et al.   BIOINFORMATICS

Transposon proliferation in an asexual parasitoid

(2012) KEN KRAAIJEVELD et al.   MOLECULAR ECOLOGY

Toward a Global Phylogeny of the “Living Fossil" Crustacean Order of the Notostraca

(2012) Bram Vanschoenwinkel et al.   PLoS One

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

(2010) Sarah Schaack et al.   GENOME BIOLOGY

Correlates of substitution rate variation in mammalian protein-coding sequences

(2009) John J Welch et al.   BMC EVOLUTIONARY BIOLOGY

Molecular taxonomy and phylogeny of ItalianLepidurustaxa (Branchiopoda: Notostraca)

(2009) B. Mantovani et al.   ITALIAN JOURNAL OF ZOOLOGY

Genetic variability and reproductive modalities in European populations ofTriops cancriformis(Crustacea, Branchiopoda, Notostraca)

(2009) A. Velonà et al.   ITALIAN JOURNAL OF ZOOLOGY

Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes

(2008) ELIE S. DOLGIN et al.   Genetics Research

Mitochondrial and nuclear DNA variability in the living fossil Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda, Notostraca)

(2008) B Mantovani et al.   HEREDITY

The Association Between Breeding System and Transposable Element Dynamics in Daphnia Pulex

(2008) Pegah Valizadeh et al.   JOURNAL OF MOLECULAR EVOLUTION

The genome of the model beetle and pest Tribolium castaneum

(2008) Stephen Richards et al.   NATURE

Rapid molecular evolution in a living fossil

(2008) Jennifer M. Hay et al.   TRENDS IN GENETICS

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics