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A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates

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Molecular genetic approaches to the study of primate behavior, social organization, and reproduction
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A New Method for Genome-wide Marker Development and Genotyping Holds Great Promise for Molecular Primatology
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The Promise and Practicality of Population Genomics Research with Endangered Species
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Letter to the Editor
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The use of museum specimens with high-throughput DNA sequencers
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Applications of next-generation sequencing to phylogeography and phylogenetics
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Primate molecular phylogenetics in a genomic era
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inferredcites →https://doi.org/10.1016/j.ympev.2014.07.016openalex-snapshot
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Trans-Pacific RAD-Seq population genomics confirms introgressive hybridization in Eastern Pacific Pocillopora corals
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The misbegotten: long lineages, long branches and the interrelationships of Aotus, Callicebus and the saki–uacaris*
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Applications of next generation sequencing in molecular ecology of non-model organisms
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Target-enrichment strategies for next-generation sequencing
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ModelFinder: fast model selection for accurate phylogenetic estimates
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inferredcites →https://doi.org/10.1038/s41598-018-20427-9openalex-snapshot
Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces
inferredcites →https://doi.org/10.1073/pnas.0810346106openalex-snapshot
Successive radiations, not stasis, in the South American primate fauna
inferredcites →https://doi.org/10.1073/pnas.1006538107openalex-snapshot
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inferredcites →https://doi.org/10.1080/10635150290069913openalex-snapshot
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inferredcites →https://doi.org/10.1080/10635150500354928openalex-snapshot
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inferredcites →https://doi.org/10.1080/10635150500481390openalex-snapshot
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inferredcites →https://doi.org/10.1080/10635150802044011openalex-snapshot
Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)
inferredcites →https://doi.org/10.1086/688018openalex-snapshot
Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions
inferredcites →https://doi.org/10.1093/bfgp/elq031openalex-snapshot
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A survey of tools for variant analysis of next-generation genome sequencing data
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/bioinformatics/btu530openalex-snapshot
Quartet Inference from SNP Data Under the Coalescent Model
inferredcites →https://doi.org/10.1093/bioinformatics/btu719openalex-snapshot
deML: robust demultiplexing of Illumina sequences using a likelihood-based approach
inferredcites →https://doi.org/10.1093/bioinformatics/btz966openalex-snapshot
ipyrad: Interactive assembly and analysis of RADseq datasets
inferredcites →https://doi.org/10.1093/gbe/evv026openalex-snapshot
Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
inferredcites →https://doi.org/10.1093/molbev/msu300openalex-snapshot
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
inferredcites →https://doi.org/10.1093/molbev/msu325openalex-snapshot
Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”
inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot
MUSCLE: multiple sequence alignment with high accuracy and high throughput
inferredcites →https://doi.org/10.1093/nar/gkv1157openalex-snapshot
Ensembl 2016
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a026201openalex-snapshot
Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference
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A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony.
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Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
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Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants
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Potential for female kin associations in wild western gorillas despite female dispersal
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Identification of SNP markers for inferring phylogeny in temperate bamboos ( P oaceae: B ambusoideae) using RAD sequencing
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Sim RAD : an R package for simulation‐based prediction of the number of loci expected in RAD seq and similar genotyping by sequencing approaches
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Assessing the utility of whole genome amplified DNA for next‐generation molecular ecology
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Explosive Pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys
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On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 SNPs
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04650.xopenalex-snapshot
Genome-enabled development of DNA markers for ecology, evolution and conservation
inferredcites →https://doi.org/10.1111/j.1365-294x.2010.04888.xopenalex-snapshot
Genomic-scale capture and sequencing of endogenous DNA from feces
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Genome‐wide patterns of divergence and gene flow across a butterfly radiation
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05749.xopenalex-snapshot
Molecular evolutionary and population genomic analysis of the nine‐spined stickleback using a modified restriction‐site‐associated DNA tag approach
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IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
inferredcites →https://doi.org/10.1111/j.1755-0998.2010.02967.xopenalex-snapshot
Next‐generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout
inferredcites →https://doi.org/10.1111/jbi.12945openalex-snapshot
Capuchin monkey biogeography: understandingSapajusPleistocene range expansion and the current sympatry betweenCebusandSapajus
inferredcites →https://doi.org/10.1111/mec.12023openalex-snapshot
Genome‐wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the L ake V ictoria cichlid adaptive radiation
inferredcites →https://doi.org/10.1111/mec.12083openalex-snapshot
Population genomic signatures of divergent adaptation, gene flow and hybrid speciation in the rapid radiation of L ake V ictoria cichlid fishes
inferredcites →https://doi.org/10.1111/mec.12084openalex-snapshot
Special features of RAD Sequencing data: implications for genotyping
inferredcites →https://doi.org/10.1111/mec.12228openalex-snapshot
Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics
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Sturgeon conservation genomics: SNP discovery and validation using RAD sequencing
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Genotyping‐by‐sequencing in ecological and conservation genomics
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Stacks: an analysis tool set for population genomics
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Recent novel approaches for population genomics data analysis
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Field Methods for Capture and Measurement of Three Monkey Species in Costa Rica
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inferredcites →https://doi.org/10.1186/1471-2164-15-275openalex-snapshot
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inferredcites →https://doi.org/10.1186/s12915-015-0119-3openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pgen.1000862openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pgen.1001333openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0018561openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0037135openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0049521openalex-snapshot
Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix
inferredcites →https://doi.org/10.1371/journal.pone.0071148openalex-snapshot
Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest
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inferredcites →https://doi.org/10.1371/journal.pone.0093975openalex-snapshot
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inferredcites →https://doi.org/10.1371/journal.pone.0102272openalex-snapshot
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inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1525/auk.2010.127.1.4openalex-snapshot
Prospects for the Use of Next-Generation Sequencing Methods in Ornithology
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High-Density Detection of Restriction-Site-Associated DNA Markers for Rapid Mapping of Mutated Loci in Neurospora
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inferredcites →https://doi.org/10.3732/ajb.1500519openalex-snapshot
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VSEARCH: a versatile open source tool for metagenomics

What points at this work

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

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Mitochondrial genes as strong molecular markers for species identification
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Allopatric instead of parapatric divergence in an ectomycorrhizal fungus (Laccaria trichodermophora) in tropical sky-islands
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Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism
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Signatures of adaptive evolution in platyrrhine primate genomes
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Achieving high-quality ddRAD-like reference catalogs for non-model species: the power of overlapping paired-end reads
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Whole genomes of the amazonian Cacajao reveal complex connectivity and fast differentiation driven by high environmental dynamism
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Hepatitis C outreach project and cross-sectional epidemiology in high-risk populations in Trondheim, Norway
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Stock structure and effective population size of the commercially exploited gummy shark Mustelus antarcticus
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Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation
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Genetic and behavioral correlates of pair living in coppery titi monkeys (Plecturocebus cupreus)
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