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2025
Population genetics of Macrognathus siamensis (Synbranchiformes: Mastacembelidae): Implications for non-migratory fishery resources in the Mekong River basin
Fisheries Research
2025
COI barcoding can distinguish bisexual and parthenogenetic populations of Haemaphysalis longicornis in Japan: Revisiting methods with SNP analysis as another possible method
International Journal for Parasitology: Parasites and Wildlife
2025
Hawaiian black coral (Antipatharia) complete mitochondrial genomes have limited phylogenetic signal for taxonomic resolution of species
PeerJ
2025
Global stock structure of the Silky shark (Carcharhinus falciformis, Carcharhinidae) assessed with high-throughput DNA sequencing
PeerJ
2025
A genomic approach to Porites (Anthozoa: Scleractinia) megadiversity from the Indo-Pacific
Molecular Phylogenetics and Evolution
2025
Gut Microbial Diversity and Genome‐Wide Variation of the Cape Sea Urchin (Parechinus angulosus) Across a Thermal Gradient
Austral Ecology
2025
Population genetics and the importance of migration in the facultative migratory fish, Labeo chrysophekadion, in the Lower Mekong Basin
Conservation Genetics
2025
Molecular phylogeny of the operculated land snail family Pupinidae (Caenogastropoda, Cyclophoroidea) in mainland Southeast Asia
Zoologica Scripta
2025
Climate-driven range expansion via long-distance larval dispersal
Marine Ecology Progress Series
2025
Optimizing ddRAD sequencing for population genomic studies with ddgRADer
Molecular Ecology Resources
2025
Sustainable Warm-Climate Forage Legumes: Versatile Products and Services
Grasses
2025
Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa
Molecular Ecology Resources
2024
Genetic structuring and species boundaries in the Atlantic stony coral Favia (Scleractinia, Faviidae)
Zoologica Scripta
2024
The estimation of additive genetic variance of body size in a wild passerine is sensitive to the method used to estimate relatedness among the individuals
Ecology and Evolution
2024
The complete mitochondrial genome of a species of Cirrhipathes de Blainville, 1830 from Kauaʻi, Hawaiʻi (Hexacorallia: Antipatharia)
Mitochondrial DNA Part B
2024
Cryptic diversity and phylogeographic patterns of Mediodactylus species in the Eastern Mediterranean region
Molecular Phylogenetics and Evolution
2023
Genomic evidence indicates small island-resident populations and sex-biased behaviors of Hawaiian reef Manta Rays
BMC Ecology and Evolution
2023
The complete mitochondrial genome of the Reef Manta Ray, Mobula alfredi, from Hawaii
Mitochondrial DNA Part B
2023
Urbanization drives adaptive evolution in a Neotropical bird
Current Zoology
2023
A critically endangered estuarine limpet’s only two populations are genomically and morphologically distinct
Aquatic Conservation: Marine and Freshwater Ecosystems
2023
Methods in Molecular Biology
2023
Geographic destiny trumps taxonomy in the Roundtail Chub, Gila robusta species complex (Teleostei, Leuciscidae)
Scientific Reports
2023
A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture
Frontiers in Marine Science
2022
Phylogenomics of Palythoa (Hexacorallia: Zoantharia): probing species boundaries in a globally distributed genus
Coral Reefs
2022
The complete mitochondrial genome of Dendrophyllia minuscula (Cnidaria: Scleractinia) from the NEOM region of the Northern Red Sea
Mitochondrial DNA Part B
2022
Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo′orea and their symbionts (Symbiodiniaceae)
Molecular Ecology
2022
The RadOrgMiner pipeline: Automated genotyping of organellar loci from RADseq data
Methods in Ecology and Evolution
2022
A phylogenomic examination of Palmyra Atoll’s corallimorpharian invader
Coral Reefs
2022
Distinct lineages and population genomic structure of the coral Pachyseris speciosa in the small equatorial reef system of Singapore
Coral Reefs
2022
Next-Generation Plant Breeding Approaches for Stress Resilience in Cereal Crops
2022
Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing
Scientific Reports
2022
Methods in Molecular Biology
2022
Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review
Life
2022
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia
Frontiers in Genetics
2022
The New Green Challenge in Urban Planning: The Right Genetics in the Right Place
Horticulturae
2022
Drainage rearrangements and in situ diversification of an endemic freshwater fish genus from north‐eastern Brazilian rivers
Freshwater Biology
2022
Range expansion and first observation of Tridacna noae (Cardiidae: Tridacninae) in American Sāmoa
Ecology and Evolution
2022
A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (Salvelinus alpinus)
Evolutionary Applications
2022
Application of phylogenomic tools to unravel anthozoan evolution
Coral Reefs
2022
High-throughput single nucleotide polymorphism genotyping reveals population structure and genetic diversity of tall fescue (
Crop & Pasture Science
2022
Taming DNA clustering in massive datasets with SLYMFAST
ACM SIGAPP Applied Computing Review
2021
Development of genetic tools for the redbait species Pyura herdmani and P. stolonifera, important bioengineers along African coastlines
African Journal of Marine Science
2021
Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing
BMC Genomics
2021
Neither historical climate nor contemporary range fully explain the extant patterns of molecular diversity in marine species
Journal of Biogeography
2021
Comparison of sequence-capture and ddRAD approaches in resolving species and populations in hexacorallian anthozoans
Molecular Phylogenetics and Evolution
2021
Identify and characterize the SNP markers for traceability of scallop spiny lobster Panulirus homarus (Decapoda, Palinuridae) in Vietnam
IOP Conference Series: Earth and Environmental Science
2021
Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly dispersive mud crab Scylla olivacea (Herbst, 1796) in the Sulu Sea
Ecology and Evolution
2021
Genomic divergence and differential gene expression between crustacean ecotypes across a marine thermal gradient
Marine Genomics
2021
Distinct interspecific and intraspecific vulnerability of coastal species to global change
Global Change Biology
2021
ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)
BMC Genomics
2021
Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data
Molecular Ecology Resources
2021
Applying genomic data to seagrass conservation
Biodiversity and Conservation
2021
Phylogenomics of Porites from the Arabian Peninsula
Molecular Phylogenetics and Evolution
2021
Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?
Molecular Genetics and Genomics
2021
Genetic and phenotypic variation exhibit both predictable and stochastic patterns across an intertidal fish metapopulation
Molecular Ecology
2021
Evolutionary genomics of endangered Hawaiian tree snails (Achatinellidae: Achatinellinae) for conservation of adaptive capacity
PeerJ
2021
Genetic diversity across the mitochondrial genome of eastern oysters (Crassostrea virginica) in the northern Gulf of Mexico
PeerJ
2021
Genetic effects of long-term captive breeding on the endangered pygmy hog
PeerJ
2021
Global connections with some genomic differentiation occur between Indo‐Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish
Journal of Biogeography
2021
Genetic variation and differentiation of Quercus variabilis populations at phosphate and non-phosphate rock sites in southwestern China
Plant Systematics and Evolution
2021
High‐throughput NGS‐based genotyping and phenotyping: Role in genomics‐assisted breeding for soybean improvement
Legume Science
2021
Customize and get the most out of your reduced‐representation sequencing experiment with the new simulation software RADinitio
Molecular Ecology Resources
2021
Proceedings of the 36th Annual ACM Symposium on Applied Computing
2020
Estimating and accounting for genotyping errors in RAD‐seq experiments
Molecular Ecology Resources
2020
Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides
PLOS ONE
2020
Multiple and Extra-Pair Mating in a Pair-Living Hermaphrodite, the Intertidal LimpetSiphonaria gigas
Integrative Organismal Biology
2020
The First Genetic Map for a Psoraleoid Legume (Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes
Plants
2020
Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing
Ecology and Evolution
2020
Unraveling the systematics and evolution of the ‘Geophagus’ brasiliensis (Cichliformes: Cichlidae) species complex
Molecular Phylogenetics and Evolution
2020
Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic
PeerJ
2020
Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs
BMC Genomics
2020
Unexpectedly high genetic diversity in a rare and endangered seabird in the Hawaiian Archipelago
PeerJ
2020
Attack of the PCR clones: Rates of clonality have little effect on RAD‐seq genotype calls
Molecular Ecology Resources
2020
Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies
Frontiers in Genetics
2020
Population genetics of two chromatic morphs of the Chagas disease vector Rhodnius pallescens Barber, 1932 in Panamá
Infection, Genetics and Evolution
2020
Supporting Fisheries Management With Genomic Tools: A Case Study of Kingklip (Genypterus capensis) Off Southern Africa
Frontiers in Marine Science
2020
Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis
PLOS ONE
2020
New genomic resources for three exploited Mediterranean fishes
Genomics
2020
Host-symbiont coevolution, cryptic structure, and bleaching susceptibility, in a coral species complex (Scleractinia; Poritidae)
Scientific Reports
2020
Genomics versus mtDNA for resolving stock structure in the silky shark (Carcharhinus falciformis)
PeerJ
2020
Towards a rigorous species delimitation framework for scleractinian corals based on RAD sequencing: the case study of Leptastrea from the Indo-Pacific
Coral Reefs
2020
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species
BMC Evolutionary Biology
2020
Anthropogenic pressures negatively impact genomic diversity of the vulnerable seagrass Zostera capensis
Journal of Environmental Management
2020
Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish
Journal of Evolutionary Biology
2019
3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae)
Molecular Phylogenetics and Evolution
2019
Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora
BMC Evolutionary Biology
2019
Host hybridization as a potential mechanism of lateral symbiont transfer in deep‐sea vesicomyid clams
Molecular Ecology
2019
Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)
PeerJ
2019
Population genomics of the peripheral freshwater fish Polynemus melanochir (Perciformes, Polynemidae) in a changing Mekong Delta
Conservation Genetics
2019
Historical demography of the Caribbean spiny lobster Panulirus argus (Latreille, 1804) (Decapoda: Achelata: Palinuridae) in the Florida Keys, USA inferred using single nucleotide polymorphisms (SNPs)
Journal of Crustacean Biology
2019
Plant Biotechnology: Progress in Genomic Era
2019
Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics
Molecular Ecology
2019
Genome-wide SNP analyses reveal population structure of Portunus pelagicus along Vietnam coastline
PLOS ONE
2019
RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
BMC Evolutionary Biology
2019
RADseq as a valuable tool for plants with large genomes—A case study in cycads
Molecular Ecology Resources
2019
Diversity of zoantharian species and their symbionts from the Macaronesian and Cape Verde ecoregions demonstrates their widespread distribution in the Atlantic Ocean
Coral Reefs
2019
Shared genomic outliers across two divergent population clusters of a highly threatened seagrass
PeerJ
2019
Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden
Agronomy
2019
Tools for Chrysanthemum genetic research and breeding: Is genotyping-by-sequencing (GBS) the best approach?
Horticulture, Environment, and Biotechnology
2019
The Development of Plant Conservation in Botanic Gardens and the Current and Future Role of Conservation Genetics for Enhancing Those Conservation Efforts
Molecular Frontiers Journal
2019
Innovations in Sustainable Agriculture
2019
The complete mitochondrial genome of the Band-rumped Storm Petrel (Oceanodroma castro)
Mitochondrial DNA Part B
2018
These aren’t the loci you’e looking for: Principles of effective SNP filtering for molecular ecologists
Molecular Ecology
2018
Divergence times in demosponges (Porifera): first insights from new mitogenomes and the inclusion of fossils in a birth-death clock model
BMC Evolutionary Biology
2018
Using ezRAD to reconstruct the complete mitochondrial genome of Porites fontanesii (Cnidaria: Scleractinia)
Mitochondrial DNA Part B
2018
Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current
Ecology and Evolution
2018
Practical considerations for plant phylogenomics
Applications in Plant Sciences
2018
Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci
PeerJ
2018
Applications of genotyping by sequencing in aquaculture breeding and genetics
Reviews in Aquaculture
2018
Geopolitical species revisited: genomic and morphological data indicate that the roundtail chubGila robustaspecies complex (Teleostei, Cyprinidae) is a single species
PeerJ
2018
Would an RRS by any other name sound as RAD?
Methods in Ecology and Evolution
2018
Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations
Aquatic Living Resources
2018
A comparison of mitochondrial genomes from five species in three genera suggests polyphyly in the subfamily Achatinellinae (Gastropoda: Pulmonata: Stylommatophora: Achatinellidae)
Mitochondrial DNA Part B
2018
Host‐targeted RAD‐Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast
Molecular Ecology
2018
Complex signatures of genomic variation of two non-model marine species in a homogeneous environment
BMC Genomics
2018
Population connectivity of the plating coral Agaricia lamarcki from southwest Puerto Rico
Coral Reefs
2018
Corallite skeletal morphological variation in Hawaiian Porites lobata
Coral Reefs
2018
Genome-wide divergence patterns support fine-scaled genetic structuring associated with migration tendency in brown trout
Canadian Journal of Fisheries and Aquatic Sciences
2017
Genotyping‐by‐sequencing approaches to characterize crop genomes: choosing the right tool for the right application
Plant Biotechnology Journal
2017
Deriving genotypes from RAD-seq short-read data using Stacks
Nature Protocols
2017
Bioinformatics in Aquaculture
2017
Genomic variation across cervid species in respect to the estimation of red deer diversity
Acta Veterinaria
2017
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador
PLOS Neglected Tropical Diseases
2017
Deep reefs are not universal refuges: Reseeding potential varies among coral species
Science Advances
2017
Resequencing Helminth Genomes for Population and Genetic Studies
Trends in Parasitology
2017
Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral,Acropora palmata
PeerJ
2017
Methods in Molecular Biology
2017
Phylogenomics
2017
Species boundaries in the absence of morphological, ecological or geographical differentiation in the Red Sea octocoral genus Ovabunda (Alcyonacea: Xeniidae)
Molecular Phylogenetics and Evolution
2017
Salvia Biotechnology
2017
quaddRAD: a new high‐multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage
Molecular Ecology
2017
Optimized double-digest genotyping by sequencing (ddGBS) method with high-density SNP markers and high genotyping accuracy for chickens
PLOS ONE
2017
SNPs markers for the heavily overfished tambaqui Colossoma macropomum, a Neotropical fish, using next-generation sequencing-based de novo genotyping
Conservation Genetics Resources
2017
Application of PE‐RADSeq to the study of genomic diversity and divergence of two Brazilian marmoset species (Callithrix jacchusandC. penicillata)
American Journal of Primatology
2017
Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa
Molecular Phylogenetics and Evolution
2017
Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Molecular Plant
2017
A genomic glance through the fog of plasticity and diversification in Pocillopora
Scientific Reports
2017
Integrative taxonomy of the ornamental ‘peppermint’ shrimp public market and population genetics ofLysmata boggessi, the most heavily traded species worldwide
PeerJ
2017
Invertebrate population genetics across Earth's largest habitat: The deep‐sea floor
Molecular Ecology
2016
Harnessing the power of RADseq for ecological and evolutionary genomics
Nature Reviews Genetics
2016
Next-generation biology: Sequencing and data analysis approaches for non-model organisms
Marine Genomics
2016
A field ornithologist's guide to genomics: Practical considerations for ecology and conservation
The Auk
2016
simMSG: an experimental design tool for high‐throughput genotyping of hybrids
Molecular Ecology Resources
2016
Seaweed Phylogeography
2016
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
Electronic Journal of Biotechnology
2016
De novo SNP markers development for the Neotropical gilded catfish Brachyplatystoma rousseauxii using next-generation sequencing-based genotyping
Conservation Genetics Resources
2016
Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis
G3 Genes|Genomes|Genetics
2016
A decade of seascape genetics: contributions to basic and applied marine connectivity
Marine Ecology Progress Series
2016
The complete mitochondrial genome ofAchatinella sowerbyana(Gastropoda: Pulmonata: Stylommatophora: Achatinellidae)
Mitochondrial DNA Part B
2016
Design of efficient simplified genomic DNA and bisulfite sequencing in large plant populations
Quantitative Biology
2016
The complete mitochondrial genome of the lobe coral Porites lobata (Anthozoa: Scleractinia) sequenced using ezRAD
Mitochondrial DNA Part B
2016
Box JellyfishAlatina alataHas a Circumtropical Distribution
The Biological Bulletin
2016
Applying SNP-Derived Molecular Coancestry Estimates to Captive Breeding Programs
Journal of Heredity
2016
A highly robust and optimized sequence-based approach for genetic polymorphism discovery and genotyping in large plant populations
Theoretical and Applied Genetics
2016
Fishing for divergence in a sea of connectivity: The utility of ddRADseq genotyping in a marine invertebrate, the black-lip pearl oyster Pinctada margaritifera
Marine Genomics
2016
Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species
Molecular Phylogenetics and Evolution
2016
Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants
Plant Methods
2016
The complete mitochondrial genome ofAchatinella mustelina(Gastropoda: Pulmonata: Stylommatophora)
Mitochondrial DNA Part B
2016
Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding
Frontiers in Genetics
2016
Plant responses to global change: next generation biogeography
Physical Geography
2015
Cryptic species obscure introduction pathway of the blue Caribbean sponge (Haliclona(Soestella)caerulea), (order: Haplosclerida) to Palmyra Atoll, Central Pacific
PeerJ
2015
The aggregate site frequency spectrum for comparative population genomic inference
Molecular Ecology
2015
Genomic signatures of geographic isolation and natural selection in coral reef fishes
Molecular Ecology
2015
SNP discovery in nonmodel organisms: strand bias and base‐substitution errors reduce conversion rates
Molecular Ecology Resources
2015
Could polyp pulsation be the key to species boundaries in the genus Ovabunda (Octocorallia: Alcyonacea: Xeniidae)?
Hydrobiologia
2015
Low-cost ddRAD method of SNP discovery and genotyping applied to the periwinkleLittorina saxatilis
Journal of Molluscan Studies
2015
Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular‐based research in ecology and evolution
Ecology and Evolution
2015
Marker-Assisted Plant Breeding: Principles and Practices
2014
Demystifying the RAD fad
Molecular Ecology
2014
Recent novel approaches for population genomics data analysis
Molecular Ecology
2014
Can novel genetic analyses help to identify low‐dispersal marine invasive species?
Ecology and Evolution
2014
Genotyping-By-Sequencing for Plant Genetic Diversity Analysis: A Lab Guide for SNP Genotyping
Diversity
2014
Detection and Removal of PCR Duplicates in Population Genomic ddRAD Studies by Addition of a Degenerate Base Region (DBR) in Sequencing Adapters
The Biological Bulletin
2014
Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges
The Biological Bulletin
2014
Trade‐offs and utility of alternative RADseq methods: Reply to Puritz et al.
Molecular Ecology
2014
SimRAD: an R package for simulation‐based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches
Molecular Ecology Resources
2014
dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms
PeerJ
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