Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

Comparative phylogeography of black mangroves (Avicennia germinans ) and red mangroves (Rhizophora mangle ) in Florida: Testing the maritime discontinuity in coastal plants

(2016) Richard G. J. Hodel et al.   AMERICAN JOURNAL OF BOTANY

Identifying patterns of dispersal, connectivity and selection in the sea scallop,Placopecten magellanicus,using RADseq-derived SNPs

(2016) Mallory Van Wyngaarden et al.   Evolutionary Applications

Contrasting genetic effects of red mangrove (Rhizophora mangle L.) range expansion along West and East Florida

(2016) John Paul Kennedy et al.   JOURNAL OF BIOGEOGRAPHY

New view of population genetics of zooplankton: RAD-seq analysis reveals population structure of the North Atlantic planktonic copepod Centropages typicus

(2016) L. Blanco-Bercial et al.   MOLECULAR ECOLOGY

Genomic signatures of rapid adaptive evolution in the bluespotted cornetfish, a Mediterranean Lessepsian invader

(2016) Giacomo Bernardi et al.   MOLECULAR ECOLOGY

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp,Carassius carassius,L.

(2016) Daniel L. Jeffries et al.   MOLECULAR ECOLOGY

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

(2016) Naiara Rodríguez-Ezpeleta et al.   Molecular Ecology Resources

Harnessing the power of RADseq for ecological and evolutionary genomics

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

Relationships of morphological groups in the northern flicker superspecies complex (Colaptes auratus & C. chrysoides)

(2016) Joseph D. Manthey et al.   SYSTEMATICS AND BIODIVERSITY

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

A New Resource for the Development of SSR Markers: Millions of Loci from a Thousand Plant Transcriptomes

(2016) Richard G. J. Hodel et al.   Applications in Plant Sciences

The Report of My Death was an Exaggeration: A Review for Researchers Using Microsatellites in the 21st Century

(2016) Richard G. J. Hodel et al.   Applications in Plant Sciences

Transatlantic secondary contact in Atlantic Salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction-site associated DNA sequencing for the resolution of complex spatial structure

(2015) Ian R. Bradbury et al.   MOLECULAR ECOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

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

Population Structure and Phylogeography in Nassau Grouper (Epinephelus striatus), a Mass-Aggregating Marine Fish

(2014) Alexis M. Jackson et al.   PLoS One

Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

(2014) Rezwana Reaz et al.   PLoS One

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Population genomic analyses from low-coverage RAD-Seq data: a case study on the non-model cucurbit bottle gourd

(2013) Pei Xu et al.   PLANT JOURNAL

An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping

(2013) Humira Sonah et al.   PLoS One

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The effect of RAD allele dropout on the estimation of genetic variation within and between populations

(2012) Mathieu Gautier et al.   MOLECULAR ECOLOGY

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

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

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Rise of the machines - recommendations for ecologists when using next generation sequencing for microsatellite development

(2011) MICHAEL G. GARDNER et al.   Molecular Ecology Resources

Current trends in microsatellite genotyping

(2011) E. GUICHOUX et al.   Molecular Ecology Resources

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Microsatellite markers: an overview of the recent progress in plants

(2010) Rajwant K. Kalia et al.   EUPHYTICA

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

(2010) A. M. Smith et al.   NUCLEIC ACIDS RESEARCH

Comparative Performance of Single Nucleotide Polymorphism and Microsatellite Markers for Population Genetic Analysis

(2009) Brad S. Coates et al.   JOURNAL OF HEREDITY

Comparison of information content for microsatellites and SNPs in poultry and cattle

(2008) G. C. B. Schopen et al.   ANIMAL GENETICS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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