First Insights into Population Structure and Genetic Diversity Versus Host Specificity in Trypanorhynch Tapeworms Using Multiplexed Shotgun Genotyping

A synergistic, global approach to revising the trypanorhynch tapeworm family Rhinoptericolidae (Trypanobatoida)

(2022) Kaylee S. Herzog et al.   PeerJ

High levels of inbreeding with spatial and host‐associated structure in lice of an endangered freshwater seal

(2022) Stephany Virrueta Herrera et al.   MOLECULAR ECOLOGY

Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

(2021) José Cerca et al.   Methods in Ecology and Evolution

Evolutionary transitions in broad tapeworms (Cestoda: Diphyllobothriidea) revealed by mitogenome and nuclear ribosomal operon phylogenetics

(2021) Natalia Fraija-Fernández et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Improved Environmental DNA Reference Library Detects Overlooked Marine Fishes in New Jersey, United States

(2020) Mark Y. Stoeckle et al.   Frontiers in Marine Science

Minor allele frequency thresholds strongly affect population structure inference with genomic datasets

(2019) Ethan Linck et al.   Molecular Ecology Resources

New insights into the identities of the elasmobranch fauna of Sri Lanka

(2019) DANIEL FERNANDO et al.   ZOOTAXA

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Five new species of the tapeworm genus Anthocephalum (Rhinebothriidea: Anthocephaliidae) parasitizing a single species of Indo-Pacific stingray, and a revised diagnosis of the genus

(2018) Kaylee S. Herzog et al.   JOURNAL OF PARASITOLOGY

Migratory connectivity and philopatry of cownose rays Rhinoptera bonasus along the Atlantic coast, USA

(2018) MB Ogburn et al.   MARINE ECOLOGY PROGRESS SERIES

Migratory connectivity and philopatry of cownose rays Rhinoptera bonasus along the Atlantic coast, USA

(2018) MB Ogburn et al.   MARINE ECOLOGY PROGRESS SERIES

The role of parasite dispersal in shaping a host-parasite system at multiple evolutionary scales

(2018) Andrew D. Sweet et al.   MOLECULAR ECOLOGY

Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice

(2018) Jana Martinů et al.   Ecology and Evolution

Summer and fall movement of cownose ray, Rhinoptera bonasus, along the east coast of United States observed with pop-up satellite tags

(2017) Kristen L. Omori et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Role of parasite transmission in promoting inbreeding: I. Infection intensities drive individual parasite selfing rates

(2017) Jillian T. Detwiler et al.   MOLECULAR ECOLOGY

Role of parasite transmission in promoting inbreeding: II. Pedigree reconstruction reveals sib-transmission and consequent kin-mating

(2017) Jillian T. Detwiler et al.   MOLECULAR ECOLOGY

Structure_threader : An improved method for automation and parallelization of programs structure , fastStructure and MavericK on multicore CPU systems

(2017) Francisco Pina-Martins et al.   Molecular Ecology Resources

Genetic variability of Taenia solium cysticerci recovered from experimentally infected pigs and from naturally infected pigs using microsatellite markers

(2017) Mónica J. Pajuelo et al.   PLoS Neglected Tropical Diseases

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Paralogues of nuclear ribosomal genes conceal phylogenetic signals within the invasive Asian fish tapeworm lineage: evidence from next generation sequencing data

(2016) Jan Brabec et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Genetic polymorphism and population structure of Echinococcus ortleppi

(2016) F. ADDY et al.   PARASITOLOGY

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

Prochristianella mattisi sp. n. (Trypanorhyncha: Eutetrarhynchidae) from the wedgenose skate, Dipturus whitleyi (Rajiformes: Rajidae), from Tasmania (Australia)

(2014) Bjoern C. Schaeffner et al.   FOLIA PARASITOLOGICA

A Digest of Elasmobranch Tapeworms

(2014) Janine N. Caira et al.   JOURNAL OF PARASITOLOGY

The trypanorhynch cestode fauna of Borneo

(2014) BJOERN C. SCHAEFFNER et al.   ZOOTAXA

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

A DNA Sequence–Based Approach To the Identification of Shark and Ray Species and Its Implications for Global Elasmobranch Diversity and Parasitology

(2012) G. J. P. Naylor et al.   BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Estimates of Genetic Differentiation Measured by FST Do Not Necessarily Require Large Sample Sizes When Using Many SNP Markers

(2012) Eva-Maria Willing et al.   PLoS One

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Habitat-specific feeding by cownose rays (Rhinoptera bonasus) of the northern Gulf of Mexico

(2011) Matthew Joseph Ajemian et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Population genetic structure and phylogeography of Mesokalliapseudes macsweenyi (Crustacea: Tanaidacea) in the northwestern Atlantic and Gulf of Mexico

(2011) David T. Drumm et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

(2011) A. Branca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

Discriminant analysis of principal components: a new method for the analysis of genetically structured populations

(2010) Thibaut Jombart et al.   BMC GENETICS

ZUSAMMENSETZUNG VON POPULATIONEN UND KORRELATIONSERSCHEINUNGEN VOM STANDPUNKT DER VERERBUNGSLEHRE AUS BETRACHTET

(2010) STEN WAHLUND   HEREDITAS

Panbiogeographical analysis of the shark genus Rhizoprionodon (Chondrichthyes, Carcharhiniformes, Carcharhinidae)

(2010) V. Gallo et al.   JOURNAL OF FISH BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evolution of the trypanorhynch tapeworms: Parasite phylogeny supports independent lineages of sharks and rays

(2009) Peter D. Olson et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Interplay of host specificity and biogeography in the population structure of a cosmopolitan endoparasite: microsatellite study ofLigula intestinalis(Cestoda)

(2009) J. ŠTEFKA et al.   MOLECULAR ECOLOGY

Geographic pattern of genetic variation in the fox tapeworm Echinococcus multilocularis

(2009) Minoru Nakao et al.   PARASITOLOGY INTERNATIONAL

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Phylogenies without roots? A plea for the use of vouchers in molecular phylogenetic studies

(2008) F. Pleijel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION