Social insect colony size is correlated with rates of molecular evolution

Overlooked roles of DNA damage and maternal age in generating human germline mutations

(2019) Ziyue Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RERconverge: an R package for associating evolutionary rates with convergent traits

(2019) Amanda Kowalczyk et al.   BIOINFORMATICS

Rate variation in the evolution of non-coding DNA associated with social evolution in bees

(2019) Benjamin E. R. Rubin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

A review of the Pseudomyrmex ferrugineus and Pseudomyrmex goeldii species groups: acacia-ants and relatives (Hymenoptera: Formicidae)

(2017) PHILIP S. WARD   ZOOTAXA

The Nuclear and Mitochondrial Genomes of the Facultatively Eusocial Orchid Bee Euglossa dilemma

(2017) Philipp Brand et al.   G3-Genes Genomes Genetics

Subterranean mammals show convergent regression in ocular genes and enhancers, along with adaptation to tunneling

(2017) Raghavendran Partha et al.   eLife

Darwinism for the Genomic Age: Connecting Mutation to Diversification

(2017) Xia Hua et al.   Frontiers in Genetics

Defensive traits exhibit an evolutionary trade-off and drive diversification in ants

(2016) Benjamin D. Blanchard et al.   EVOLUTION

The Genome and Methylome of a Subsocial Small Carpenter Bee,Ceratina calcarata

(2016) Sandra M. Rehan et al.   Genome Biology and Evolution

Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals

(2016) Maria Chikina et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Comparative genomics reveals convergent rates of evolution in ant–plant mutualisms

(2016) Benjamin E. R. Rubin et al.   Nature Communications

Reciprocal genomic evolution in the ant–fungus agricultural symbiosis

(2016) Sanne Nygaard et al.   Nature Communications

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A generation-time effect on the rate of molecular evolution in bacteria

(2015) Cory Weller et al.   EVOLUTION

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Macroevolutionary assembly of ant/plant symbioses:Pseudomyrmexants and their ant-housing plants in the Neotropics

(2015) Guillaume Chomicki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic signatures of evolutionary transitions from solitary to group living

(2015) K. M. Kapheim et al.   SCIENCE

The genomes of two key bumblebee species with primitive eusocial organization

(2015) Ben M Sadd et al.   GENOME BIOLOGY

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

(2014) Matthew W. Pennell et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Finding the missing honey bee genes: lessons learned from a genome upgrade

(2014) Christine G Elsik et al.   BMC GENOMICS

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Colony size explains the lifespan differences between queens and workers in eusocial Hymenoptera

(2013) Boris H. Kramer et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Parasitic plants have increased rates of molecular evolution across all three genomes

(2013) Lindell Bromham et al.   BMC EVOLUTIONARY BIOLOGY

TESTING THE MUSEUM VERSUS CRADLE TROPICAL BIOLOGICAL DIVERSITY HYPOTHESIS: PHYLOGENY, DIVERSIFICATION, AND ANCESTRAL BIOGEOGRAPHIC RANGE EVOLUTION OF THE ANTS

(2013) Corrie S. Moreau et al.   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

Population size and the rate of evolution

(2013) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Rate of de novo mutations and the importance of father’s age to disease risk

(2012) Augustine Kong et al.   NATURE

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

Phylogeny, diversification patterns and historical biogeography of euglossine orchid bees (Hymenoptera: Apidae)

(2010) SANTIAGO R. RAMÍREZ et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Cancer and neurologic degeneration in xeroderma pigmentosum: long term follow-up characterises the role of DNA repair

(2010) P. T. Bradford et al.   JOURNAL OF MEDICAL GENETICS

A Generation Time Effect on the Rate of Molecular Evolution in Invertebrates

(2010) Jessica A. Thomas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Watching the clock: Studying variation in rates of molecular evolution between species

(2010) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Why do species vary in their rate of molecular evolution?

(2009) L. Bromham   Biology Letters

Fast Statistical Alignment

(2009) Robert K. Bradley et al.   PLoS Computational Biology

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE