Functional colour genes and signals of selection in colour‐polymorphic salamanders

Linking a mutation to survival in wild mice

(2019) Rowan D. H. Barrett et al.   SCIENCE

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

(2019) Pedro Andrade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The conspicuous postmetamorphic coloration of fire salamanders, but not their toxicity, is affected by larval background albedo

(2019) Eugenia Sanchez et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

More yellow more toxic? Sex rather than alkaloid content is correlated with yellow coloration in the fire salamander

(2019) K. Preißler et al.   JOURNAL OF ZOOLOGY

The population genetics of crypsis in vertebrates: recent insights from mice, hares, and lizards

(2019) Rebecca B. Harris et al.   HEREDITY

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

A salamander’s toxic arsenal: review of skin poison diversity and function in true salamanders, genus Salamandra

(2018) Tim Lüddecke et al.   NATURWISSENSCHAFTEN

Conspicuousness, color resemblance, and toxicity in geographically diverging mimicry: The pan-Amazonian frogAllobates femoralis

(2017) Adolfo Amézquita et al.   EVOLUTION

Parallel habitat acclimatization is realized by the expression of different genes in two closely related salamander species (genus Salamandra)

(2017) D J Goedbloed et al.   HEREDITY

Revealing the Biochemical and Genetic Basis of Color Variation in a Polymorphic Lizard

(2017) Claire A. McLean et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring the shallow phylogeny of true salamanders ( Salamandra ) by multiple phylogenomic approaches

(2017) Ariel Rodríguez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Deriving genotypes from RAD-seq short-read data using Stacks

(2017) Nicolas C Rochette et al.   Nature Protocols

Loci associated with skin pigmentation identified in African populations

(2017) Nicholas G. Crawford et al.   SCIENCE

Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Ambystoma mexicanum

(2017) M. Ryan Woodcock et al.   Scientific Reports

Identification of genomic variants putatively targeted by selection during dog domestication

(2016) Alex Cagan et al.   BMC EVOLUTIONARY BIOLOGY

Salamandra

(2016) Wouter Beukema et al.   CURRENT BIOLOGY

Colour polymorphism in Salamandra salamandra (Amphibia: Urodela), revealed by a lack of genetic and environmental differentiation between distinct phenotypes

(2016) Wouter Beukema et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Exon capture optimization in amphibians with large genomes

(2016) Evan McCartney-Melstad et al.   Molecular Ecology Resources

Developmental mechanisms of stripe patterns in rodents

(2016) Ricardo Mallarino et al.   NATURE

Database Resources of the National Center for Biotechnology Information

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Sympatric ecological divergence associated with a color polymorphism

(2015) Henrik Kusche et al.   BMC BIOLOGY

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Double-digest RAD sequencing using Ion Proton semiconductor platform (ddRADseq-ion) with nonmodel organisms

(2015) Hans Recknagel et al.   Molecular Ecology Resources

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

(2015) Aaron K. Wong et al.   NUCLEIC ACIDS RESEARCH

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

The Genome 10K Project: A Way Forward

(2015) Klaus-Peter Koepfli et al.   Annual Review of Animal Biosciences

Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing

(2015) Melissa C. Keinath et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Assortative Mating in a Polymorphic Salamander

(2014) Megan A. Acord et al.   COPEIA

Questioning the use of an amphibian colour morph as an indicator of climate change

(2014) Jean-David Moore et al.   GLOBAL CHANGE BIOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Nuclear and mitochondrial multilocus phylogeny and survey of alkaloid content in true salamanders of the genus Salamandra (Salamandridae)

(2014) Miguel Vences et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Leucophores are similar to xanthophores in their specification and differentiation processes in medaka

(2014) T. Kimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

(2014) J. W. Poelstra et al.   SCIENCE

Natural Selection Reduced Diversity on Human Y Chromosomes

(2014) Melissa A. Wilson Sayres et al.   PLoS Genetics

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

(2013) Erik Axelsson et al.   NATURE

oca2regulation of chromatophore differentiation and number is cell type specific in zebrafish

(2013) Alisha J. Beirl et al.   Pigment Cell & Melanoma Research

Coordinated Regulation of Chromatophore Differentiation and Melanogenesis during the Ontogeny of Skin Pigmentation of Solea senegalensis (Kaup, 1858)

(2013) Maria J. Darias et al.   PLoS One

Adaptive colouration in amphibians

(2013) Andreas Rudh et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

pavo: an R package for the analysis, visualization and organization of spectral data

(2013) Rafael Maia et al.   Methods in Ecology and Evolution

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

transparent, a gene affecting stripe formation in Zebrafish, encodes the mitochondrial protein Mpv17 that is required for iridophore survival

(2013) J. Krauss et al.   Biology Open

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

Poison Frog Colors Are Honest Signals of Toxicity, Particularly for Bird Predators

(2011) Martine E. Maan et al.   AMERICAN NATURALIST

Epidermal Keratinocytes from Light vs. Dark Skin Exhibit Differential Degradation of Melanosomes

(2011) Jody P. Ebanks et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Diversity of human hair pigmentation as studied by chemical analysis of eumelanin and pheomelanin

(2011) S. Ito et al.   JOURNAL OF THE EUROPEAN ACADEMY OF DERMATOLOGY AND VENEREOLOGY

Linking the evolution and form of warning coloration in nature

(2011) M. Stevens et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Increasing melanism along a latitudinal gradient in a widespread amphibian: local adaptation, ontogenic or environmental plasticity?

(2010) Jussi S Alho et al.   BMC EVOLUTIONARY BIOLOGY

Vertebrate pigmentation: from underlying genes to adaptive function

(2010) Joanna K. Hubbard et al.   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Camouflage, communication and thermoregulation: lessons from colour changing organisms

(2008) D. Stuart-Fox et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Not just black and white: Pigment pattern development and evolution in vertebrates

(2008) Margaret G. Mills et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY