Venom Gene Sequence Diversity and Expression Jointly Shape Diet Adaptation in Pitvipers

The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype

(2021) Mark J. Margres et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics

(2021) Pedro G Nachtigall et al.   BRIEFINGS IN BIOINFORMATICS

Phylogenetically diverse diets favor more complex venoms in North American pitvipers

(2021) Matthew L. Holding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements

(2021) Solomon T. C. Chak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Venom systems as models for studying the origin and regulation of evolutionary novelties

(2020) Giulia Zancolli et al.   MOLECULAR BIOLOGY AND EVOLUTION

The origin and diversification of a novel protein family in venomous snakes

(2020) Matt W. Giorgianni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates

(2020) Agneesh Barua et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetics is the New Genetics (for Most of Biodiversity)

(2020) Stacey D. Smith et al.   TRENDS IN ECOLOGY & EVOLUTION

The molecular basis of venom resistance in a rattlesnake‐squirrel predator‐prey system

(2020) H. Lisle Gibbs et al.   MOLECULAR ECOLOGY

A broad mutational target explains a fast rate of phenotypic evolution

(2020) Fabrice Besnard et al.   eLife

Structurally Robust and Functionally Highly Versatile—C-Type Lectin (-Related) Proteins in Snake Venoms

(2019) Johannes Eble   Toxins

When one phenotype is not enough: divergent evolutionary trajectories govern venom variation in a widespread rattlesnake species

(2019) Giulia Zancolli et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bayesian detection of convergent rate changes of conserved noncoding elements on phylogenetic trees

(2019) Zhirui Hu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes

(2019) Drew R. Schield et al.   GENOME RESEARCH

Many options, few solutions: over 60 million years snakes converged on a few optimal venom formulations

(2019) Agneesh Barua et al.   MOLECULAR BIOLOGY AND EVOLUTION

Convergent regulatory evolution and loss of flight in paleognathous birds

(2019) Timothy B. Sackton et al.   SCIENCE

Intraspecific sequence and gene expression variation contribute little to venom diversity in sidewinder rattlesnakes ( Crotalus cerastes )

(2019) Rhett M. Rautsaw et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals

(2019) Nicholas R. Casewell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel phylogenetic methods are needed for understanding gene function in the era of mega-scale genome sequencing

(2019) László G Nagy et al.   NUCLEIC ACIDS RESEARCH

Coevolution of Snake Venom Toxic Activities and Diet: Evidence that Ecological Generalism Favours Toxicological Diversity

(2019) Emma-Louise Davies et al.   Toxins

A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin

(2018) A Carl Whittington et al.   MOLECULAR BIOLOGY AND EVOLUTION

Replicability and Prediction: Lessons and Challenges from GWAS

(2018) Urko M. Marigorta et al.   TRENDS IN GENETICS

Phenotypic Variation in Mojave Rattlesnake (Crotalus scutulatus) Venom Is Driven by Four Toxin Families

(2018) Jason Strickland et al.   Toxins

Evaluating the Performance of De Novo Assembly Methods for Venom-Gland Transcriptomics

(2018) Matthew Holding et al.   Toxins

phylopath: Easy phylogenetic path analysis in R

(2018) Wouter van der Bijl   PeerJ

Venom gland size and venom complexity - essential trophic adaptations of venomous predators: a case study using spiders

(2018) Stano Pekár et al.   MOLECULAR ECOLOGY

Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake (Crotalus cerastes) lineages reveal little differential expression despite individual variation

(2018) Erich P. Hofmann et al.   Scientific Reports

Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom

(2017) Mark J. Margres et al.   GENETICS

Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus

(2017) Qing Li et al.   Genome Biology and Evolution

Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry

(2017) Steven D. Aird et al.   Genome Biology and Evolution

Quantity, Not Quality: Rapid Adaptation in a Polygenic Trait Proceeded Exclusively through Expression Differentiation

(2017) Mark J Margres et al.   MOLECULAR BIOLOGY AND EVOLUTION

Selection To Increase Expression, Not Sequence Diversity, Precedes Gene Family Origin and Expansion in Rattlesnake Venom

(2017) Mark J. Margres et al.   GENETICS

Dietary breadth is positively correlated with venom complexity in cone snails

(2016) Mark A. Phuong et al.   BMC GENOMICS

Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders

(2016) Robert A. Haney et al.   Genome Biology and Evolution

Venom Resistance as a Model for Understanding the Molecular Basis of Complex Coevolutionary Adaptations

(2016) Matthew L. Holding et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Ecological venomics: How genomics, transcriptomics and proteomics can shed new light on the ecology and evolution of venom

(2016) Kartik Sunagar et al.   Journal of Proteomics

Coevolution of venom function and venom resistance in a rattlesnake predator and its squirrel prey

(2016) Matthew L. Holding et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Snake venoms are integrated systems, but abundant venom proteins evolve more rapidly

(2015) Steven D. Aird et al.   BMC GENOMICS

Commentary: When does understanding phenotypic evolution require identification of the underlying genes?

(2015) Mark D. Rausher et al.   EVOLUTION

Expression Differentiation Is Constrained to Low-Expression Proteins over Ecological Timescales

(2015) M. J. Margres et al.   GENETICS

The transcriptomic and proteomic basis for the evolution of a novel venom phenotype within the Timber Rattlesnake (Crotalus horridus)

(2015) Darin R. Rokyta et al.   TOXICON

Post-transcriptional Mechanisms Contribute Little to Phenotypic Variation in Snake Venoms

(2015) Darin R. Rokyta et al.   G3-Genes Genomes Genetics

The Rise and Fall of an Evolutionary Innovation: Contrasting Strategies of Venom Evolution in Ancient and Young Animals

(2015) Kartik Sunagar et al.   PLoS Genetics

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods

(2014) Dan Chang et al.   BMC EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms

(2014) N. R. Casewell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

Spider genomes provide insight into composition and evolution of venom and silk

(2014) Kristian W. Sanggaard et al.   Nature Communications

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

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

(2012) Limin Fu et al.   BIOINFORMATICS

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

(2012) Darin R Rokyta et al.   BMC GENOMICS

DISENTANGLING EVOLUTIONARY CAUSE-EFFECT RELATIONSHIPS WITH PHYLOGENETIC CONFIRMATORY PATH ANALYSIS

(2012) Achaz von Hardenberg et al.   EVOLUTION

Venom evolution through gene duplications

(2012) Emily S.W. Wong et al.   GENE

Novel venom peptides from the cone snail Conus pulicarius discovered through next-generation sequencing of its venom duct transcriptome

(2012) Arturo O. Lluisma et al.   Marine Genomics

Extensive and Continuous Duplication Facilitates Rapid Evolution and Diversification of Gene Families

(2012) Dan Chang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Gene duplication as a mechanism of genomic adaptation to a changing environment

(2012) F. A. Kondrashov   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

C-type lectin-like proteins from snake venoms

(2012) Franziska T. Arlinghaus et al.   TOXICON

The long road of research on snake venom serine proteinases

(2012) Solange M.T. Serrano   TOXICON

Phospholipases A2: Unveiling the secrets of a functionally versatile group of snake venom toxins

(2012) José María Gutiérrez et al.   TOXICON

Complex cocktails: the evolutionary novelty of venoms

(2012) Nicholas R. Casewell et al.   TRENDS IN ECOLOGY & EVOLUTION

Dynamic evolution of venom proteins in squamate reptiles

(2012) Nicholas R. Casewell et al.   Nature Communications

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

Host characteristics and environmental factors differentially drive the burden and pathogenicity of an ectoparasite: a multilevel causal analysis

(2011) Maxime Cardon et al.   JOURNAL OF ANIMAL ECOLOGY

Deconstructing a Complex Molecular Phenotype: Population-Level Variation in Individual Venom Proteins in Eastern Massasauga Rattlesnakes (Sistrurus c. catenatus)

(2011) H. Lisle Gibbs et al.   JOURNAL OF MOLECULAR EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

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

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

Picante: R tools for integrating phylogenies and ecology

(2010) S. W. Kembel et al.   BIOINFORMATICS

The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms

(2009) Bryan G. Fry et al.   Annual Review of Genomics and Human Genetics

Coevolution of diet and prey-specific venom activity supports the role of selection in snake venom evolution

(2009) A. Barlow et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Phospholipase A2 Homologues of Snake Venoms: Biological Activities and Their Possible Adaptive Roles

(2009) Bruno Lomonte et al.   PROTEIN AND PEPTIDE LETTERS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?

(2008) David L. Stern et al.   EVOLUTION

Rapid Evolution by Positive Selection and Gene Gain and Loss: PLA2 Venom Genes in Closely Related Sistrurus Rattlesnakes with Divergent Diets

(2008) H. Lisle Gibbs et al.   JOURNAL OF MOLECULAR EVOLUTION

Variation and evolution of toxin gene expression patterns of six closely related venomous marine snails

(2008) T. F. DUDA JR et al.   MOLECULAR ECOLOGY

Evolution of ecological specialization and venom of a predatory marine gastropod

(2008) E. A. REMIGIO et al.   MOLECULAR ECOLOGY