Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish

MitoFinder: Efficient automated large‐scale extraction of mitogenomic data in target enrichment phylogenomics

(2020) Rémi Allio et al.   Molecular Ecology Resources

SuperCRUNCH: A bioinformatics toolkit for creating and manipulating supermatrices and other large phylogenetic datasets

(2020) Daniel M. Portik et al.   Methods in Ecology and Evolution

Temperature transcends partner specificity in the symbiosis establishment of a cnidarian

(2020) Marcela Herrera et al.   ISME Journal

Natural strain variation reveals diverse biofilm regulation in squid-colonizing Vibrio fischeri

(2019) Ella R. Rotman et al.   JOURNAL OF BACTERIOLOGY

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment

(2019) Lydia J Baker et al.   eLife

Shedding Light on Specificity: Population Genomic Structure of a Symbiosis Between a Coral Reef Fish and Luminous Bacterium

(2019) Alison L. Gould et al.   Frontiers in Microbiology

Ongoing Transposon-Mediated Genome Reduction in the Luminous Bacterial Symbionts of Deep-Sea Ceratioid Anglerfishes

(2018) Tory A. Hendry et al.   mBio

The complete mitochondrial genome of the five-lined cardinalfish Cheilodipterus quinquelineatus (Apogonidae)

(2018) Ambrocio Melvin Matias et al.   Mitochondrial DNA Part B-Resources

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

(2017) Marc Troussellier et al.   Frontiers in Microbiology

A genomic comparison of 13 symbiotic Vibrio fischeri isolates from the perspective of their host source and colonization behavior

(2016) Clotilde Bongrand et al.   ISME Journal

Life history of the symbiotically luminous cardinalfishSiphamia tubifer(Perciformes: Apogonidae)

(2016) A. L. Gould et al.   JOURNAL OF FISH BIOLOGY

Repeated and Widespread Evolution of Bioluminescence in Marine Fishes

(2016) Matthew P. Davis et al.   PLoS One

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

(2015) Sarah M. Hykin et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Genomic signatures of obligate host dependence in the luminous bacterial symbiont of a vertebrate

(2013) Tory A. Hendry et al.   ENVIRONMENTAL MICROBIOLOGY

Features governing symbiont persistence in the squid-vibrio association

(2013) Eric J. Koch et al.   MOLECULAR ECOLOGY

Marine bacteria exhibit a bipolar distribution

(2013) W. J. Sul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiosis catalyses niche expansion and diversification

(2013) J. B. Joy   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Gimme shelter: how Vibrio fischeri successfully navigates an animal’s multiple environments

(2013) Allison N. Norsworthy et al.   Frontiers in Microbiology

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Symbiosis initiation in the bacterially luminous sea urchin cardinalfishSiphamia versicolor

(2012) P. V. Dunlap et al.   JOURNAL OF FISH BIOLOGY

Global biogeography of SAR11 marine bacteria

(2012) Mark V Brown et al.   Molecular Systems Biology

Bio-ORACLE: a global environmental dataset for marine species distribution modelling

(2011) Lennert Tyberghein et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY

Genome Sequence of Photobacterium mandapamensis Strain svers.1.1, the Bioluminescent Symbiont of the Cardinal Fish Siphamia versicolor

(2011) H. Urbanczyk et al.   JOURNAL OF BACTERIOLOGY

Functional morphology of the luminescence system of Siphamia versicolor (Perciformes: Apogonidae), a bacterially luminous coral reef fish

(2011) Paul V. Dunlap et al.   JOURNAL OF MORPHOLOGY

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

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

Phylogeographical Patterns among Mediterranean Sepiolid Squids and TheirVibrioSymbionts: Environment Drives Specificity among Sympatric Species

(2010) D. J. Zamborsky et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

(2009) Christine E. Thacker et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Population Structure of Vibrio fischeri within the Light Organs of Euprymna scolopes Squid from Two Oahu (Hawaii) Populations

(2008) M. S. Wollenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY