quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage

Incipient speciation driven by hypertrophied lips in Midas cichlid fishes?

(2017) Gonzalo Machado-Schiaffino et al.   MOLECULAR ECOLOGY

The Role of microRNAs in the Repeated Parallel Diversification of Lineages of Midas Cichlid Fish from Nicaragua

(2016) Paolo Franchini et al.   Genome Biology and Evolution

RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

(2016) Sandra L. Hoffberg et al.   Molecular Ecology Resources

Making sense of genomic islands of differentiation in light of speciation

(2016) Jochen B. W. Wolf et al.   NATURE REVIEWS GENETICS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Genetic linkage of distinct adaptive traits in sympatrically speciating crater lake cichlid fish

(2016) Carmelo Fruciano et al.   Nature Communications

Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related speciesArchocentrus centrarchus

(2016) Carmelo Fruciano et al.   Ecology and Evolution

Multispecies Outcomes of Sympatric Speciation after Admixture with the Source Population in Two Radiations of Nicaraguan Crater Lake Cichlids

(2016) Andreas F. Kautt et al.   PLoS Genetics

Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters

(2016) Hannah Schweyen et al.   BIOLOGICAL BULLETIN

Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing

(2015) Adam D. Leaché et al.   Genome Biology and Evolution

Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

(2015) Pablo Saenz-Agudelo et al.   MOLECULAR ECOLOGY

Speciation genomics and a role for the Z chromosome in the early stages of divergence between Mexican ducks and mallards

(2015) Philip Lavretsky 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

Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy

(2015) M. M. Y. Tin et al.   Molecular Ecology Resources

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

(2014) Deren A. R. Eaton   BIOINFORMATICS

Sampling strategies for frequency spectrum-based population genomic inference

(2014) John D Robinson et al.   BMC EVOLUTIONARY BIOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping

(2014) Frederico Henning et al.   MOLECULAR ECOLOGY

Genomics and the origin of species

(2014) Ole Seehausen et al.   NATURE REVIEWS GENETICS

Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes

(2014) Kathryn R. Elmer et al.   Nature Communications

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations

(2014) Jeffrey L. Feder et al.   Frontiers in Genetics

Ecological and evolutionary implications of genomic structural variations

(2014) Frédéric J. J. Chain et al.   Frontiers in Genetics

Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes

(2013) Paolo Franchini et al.   MOLECULAR ECOLOGY

The evolutionary history ofXiphophorusfish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing

(2013) Julia C. Jones et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

ezRAD: a simplified method for genomic genotyping in non-model organisms

(2013) Robert J. Toonen et al.   PeerJ

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

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

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

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

Phylogeography, colonization and population history of the Midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes

(2010) Marta Barluenga et al.   BMC EVOLUTIONARY BIOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Local variation and parallel evolution: morphological and genetic diversity across a species complex of neotropical crater lake cichlid fishes

(2010) K. R. Elmer et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

COLOR ASSORTATIVE MATING CONTRIBUTES TO SYMPATRIC DIVERGENCE OF NEOTROPICAL CICHLID FISH

(2009) Kathryn R. Elmer et al.   EVOLUTION

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One