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Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

https://doi.org/10.1101/205799

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ece3.4147openalex-snapshot

Double‐digest RAD seq loci using standard Illumina indexes improve deep and shallow phylogenetic resolution of Lophodermium, a widespread fungal endophyte of pine needles

inferredcites →https://doi.org/10.1002/ece3.512openalex-snapshot

Is RAD ‐seq suitable for phylogenetic inference? An in silico assessment and optimization

inferredcites →https://doi.org/10.1007/978-3-319-31350-4_3openalex-snapshot

Targeted DNA Region Re-sequencing

inferredcites →https://doi.org/10.1016/j.ympev.2013.06.011openalex-snapshot

Molecular phylogenetics of the mud and musk turtle family Kinosternidae

inferredcites →https://doi.org/10.1016/j.ympev.2017.11.008openalex-snapshot

Resolving taxonomic turbulence and uncovering cryptic diversity in the musk turtles (Sternotherus) using robust demographic modeling

inferredcites →https://doi.org/10.1016/s0076-6879(05)95013-1openalex-snapshot

Isolating Microsatellite DNA Loci

inferredcites →https://doi.org/10.1038/hdy.2014.105openalex-snapshot

Use of RAD sequencing for delimiting species

inferredcites →https://doi.org/10.1038/nmeth.2023openalex-snapshot

2b-RAD: a simple and flexible method for genome-wide genotyping

inferredcites →https://doi.org/10.1038/nrg.2015.28openalex-snapshot

Harnessing the power of RADseq for ecological and evolutionary genomics

inferredcites →https://doi.org/10.1038/nrg3012openalex-snapshot

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

inferredcites →https://doi.org/10.1089/cmb.2009.0179openalex-snapshot

How Many Bootstrap Replicates Are Necessary?

inferredcites →https://doi.org/10.1093/bioinformatics/btu121openalex-snapshot

PyRAD: assembly of de novo RADseq loci for phylogenetic analyses

inferredcites →https://doi.org/10.1093/jhered/esi017openalex-snapshot

On the Estimation of Genome-wide Heterozygosity Using Molecular Markers

inferredcites →https://doi.org/10.1093/jhered/esv030openalex-snapshot

Population Genetic Structure of the Bonnethead Shark,Sphyrna tiburo, from the Western North Atlantic Ocean Based on mtDNA Sequences

inferredcites →https://doi.org/10.1093/jmedent/47.2.152openalex-snapshot

Population Genetics ofAmblyomma americanum(Acari: Ixodidae) Collected From Arkansas

inferredcites →https://doi.org/10.1093/molbev/msv347openalex-snapshot

Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes)

inferredcites →https://doi.org/10.1093/sysbio/syv058openalex-snapshot

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

inferredcites →https://doi.org/10.1093/sysbio/syw036openalex-snapshot

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics

inferredcites →https://doi.org/10.1101/049114openalex-snapshot

Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

inferredcites →https://doi.org/10.1101/gr.5681207openalex-snapshot

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

inferredcites →https://doi.org/10.1111/1755-0998.12404openalex-snapshot

Impacts of degraded DNA on restriction enzyme associated DNA sequencing ( RADS eq)

inferredcites →https://doi.org/10.1111/1755-0998.12566openalex-snapshot

RAD cap: sequence capture of dual‐digest RAD seq libraries with identifiable duplicates and reduced missing data

inferredcites →https://doi.org/10.1111/1755-0998.12574openalex-snapshot

Capturing Darwin's dream

inferredcites →https://doi.org/10.1111/2041-210x.12700openalex-snapshot

Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference

inferredcites →https://doi.org/10.1111/j.1365-294x.2005.02757.xopenalex-snapshot

Gene lineages and eastern North American palaeodrainage basins: phylogeography and speciation in salamanders of the Eurycea bislineata species complex

inferredcites →https://doi.org/10.1111/j.1365-294x.2006.02933.xopenalex-snapshot

Global phylogeography of the scalloped hammerhead shark ( Sphyrna lewini )

inferredcites →https://doi.org/10.1111/j.1471-8286.2005.01155.xopenalex-snapshot

genalex 6: genetic analysis in Excel. Population genetic software for teaching and research

inferredcites →https://doi.org/10.1111/mec.12354openalex-snapshot

Stacks: an analysis tool set for population genomics

inferredcites →https://doi.org/10.1111/mec.12964openalex-snapshot

Trade‐offs and utility of alternative RADseq methods: Reply to Puritz et al .

inferredcites →https://doi.org/10.1111/mec.13441openalex-snapshot

Selection and sex‐biased dispersal in a coastal shark: the influence of philopatry on adaptive variation

inferredcites →https://doi.org/10.1371/journal.pone.0003376openalex-snapshot

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

inferredcites →https://doi.org/10.1371/journal.pone.0016607openalex-snapshot

Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

inferredcites →https://doi.org/10.1371/journal.pone.0019379openalex-snapshot

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

inferredcites →https://doi.org/10.1371/journal.pone.0042543openalex-snapshot

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

inferredcites →https://doi.org/10.1371/journal.pone.0120520openalex-snapshot

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

inferredcites →https://doi.org/10.1534/g3.111.000240openalex-snapshot

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

inferredcites →https://doi.org/10.1534/g3.118.200101openalex-snapshot

A High-Quality Reference Genome for the Invasive Mosquitofish Gambusia affinis Using a Chicago Library

inferredcites →https://doi.org/10.3835/plantgenome2012.05.0005openalex-snapshot

Genotyping‐by‐Sequencing for Plant Breeding and Genetics

inferredcites →https://doi.org/10.7717/peerj.203openalex-snapshot

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/aps3.1038openalex-snapshot

Practical considerations for plant phylogenomics

inferred← citeshttps://doi.org/10.1016/j.ympev.2018.12.032openalex-snapshot

Phylogenomics of the adaptive radiation of Triturus newts supports gradual ecological niche expansion towards an incrementally aquatic lifestyle

inferred← citeshttps://doi.org/10.1016/j.ympev.2019.04.019openalex-snapshot

3RAD-based systematics of the transitional Nearctic-Neotropical lubber grasshopper genus Taeniopoda (Orthoptera: Romaleidae)

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Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions

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Species limits and diversification of the Dendropsophus rubicundulus subgroup (Anura, Hylidae) in Neotropical savannas

inferred← citeshttps://doi.org/10.1093/cz/zoad048openalex-snapshot

Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation

inferred← citeshttps://doi.org/10.1101/049114openalex-snapshot

Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

inferred← citeshttps://doi.org/10.1111/evo.14377openalex-snapshot

Displaced clines in an avian hybrid zone (Thamnophilidae:Rhegmatorhina) within an Amazonian interfluve*

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Formation of a recent hybrid zone offers insight into the geographic puzzle and maintenance of species boundaries in musk turtles

inferred← citeshttps://doi.org/10.1111/mec.15112openalex-snapshot

Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle

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Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome‐wide SNP data from seven native species

inferred← citeshttps://doi.org/10.1111/mec.15588openalex-snapshot

Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq

inferred← citeshttps://doi.org/10.1111/syen.12373openalex-snapshot

Genetic structure, species limits and evolution of the parasitoid wasp genus Stenocorse (Braconidae: Doryctinae) based on nuclear 3RAD and mitochondrial data

inferred← citeshttps://doi.org/10.1371/journal.pone.0231367openalex-snapshot

Phylogenetic diversity of 200+ isolates of the ectomycorrhizal fungus Cenococcum geophilum associated with Populus trichocarpa soils in the Pacific Northwest, USA and comparison to globally distributed representatives

inferred← citeshttps://doi.org/10.22541/au.166079895.54947645/v1openalex-snapshot

Migratory beekeeping facilitates genetic admixture in populations of the honeybee parasite Varroa destructor

inferred← citeshttps://doi.org/10.22541/au.166079895.54947645/v2openalex-snapshot

Migratory beekeeping facilitates genetic admixture in populations of the honeybee parasite Varroa destructor

inferred← citeshttps://doi.org/10.3389/fgene.2019.00719openalex-snapshot

Extensive Cryptic Diversity Within the Physalaemus cuvieri–Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic Markers

inferred← citeshttps://doi.org/10.70675/508f00cdze410z49cdzbb52z1d5a7113b3caopenalex-snapshot

The ongoing speciation ina neotropical ant species complex

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Mitogenomes reveal the timing and distribution of divergence events among trans-Beringian birds

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