Sequence capture versus restriction site associated DNA sequencing for shallow systematics

MG Harvey, BT Smith, TC Glenn, BC Faircloth… - Systematic …, 2016 - academic.oup.com
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two
genomic enrichment strategies for applying next-generation sequencing technologies to …

Deriving genotypes from RAD-seq short-read data using Stacks

NC Rochette, JM Catchen - Nature protocols, 2017 - nature.com
Restriction site-associated DNA sequencing (RAD-seq) allows for the genome-wide
discovery and genotyping of single-nucleotide polymorphisms in hundreds of individuals at …

Genomic approaches to understanding population divergence and speciation in birds

DPL Toews, L Campagna, SA Taylor… - The Auk …, 2016 - academic.oup.com
The widespread application of high-throughput sequencing in studying evolutionary
processes and patterns of diversification has led to many important discoveries. However …

Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation

TJ Devitt, AM Wright… - Proceedings of the …, 2019 - National Acad Sciences
Groundwater-dependent species are among the least-known components of global
biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion …

Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos

C Guo, PF Ma, GQ Yang, XY Ye, Y Guo… - Systematic …, 2021 - academic.oup.com
Rapid evolutionary radiations are among the most challenging phylogenetic problems,
wherein different types of data (eg, morphology and molecular) or genetic markers (eg …

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage

SC Willis, CM Hollenbeck, JB Puritz… - Molecular Ecology …, 2017 - Wiley Online Library
Next‐generation sequencing of reduced‐representation genomic libraries provides a
powerful methodology for genotyping thousands of single‐nucleotide polymorphisms (SNP …

Selecting RAD-Seq data analysis parameters for population genetics: the more the better?

N Díaz-Arce, N Rodríguez-Ezpeleta - Frontiers in genetics, 2019 - frontiersin.org
Restriction site-associated DNA sequencing (RAD-seq) has become a powerful and widely
used tool in molecular ecology studies as it allows to cost-effectively recover thousands of …

Habitat association predicts genetic diversity and population divergence in Amazonian birds

MG Harvey, A Aleixo, CC Ribas… - The American …, 2017 - journals.uchicago.edu
The ecological traits of organisms may predict their genetic diversity and population genetic
structure and mediate the action of evolutionary processes important for speciation and …

Resolving recent plant radiations: power and robustness of genotyping-by-sequencing

M Fernández-Mazuecos, G Mellers… - Systematic …, 2018 - academic.oup.com
Disentangling species boundaries and phylogenetic relationships within recent evolutionary
radiations is a challenge due to the poor morphological differentiation and low genetic …

An empirical pipeline for choosing the optimal clustering threshold in RADseq studies

E McCartney‐Melstad, M Gidiş… - Molecular Ecology …, 2019 - Wiley Online Library
Genomic data are increasingly used for high resolution population genetic studies including
those at the forefront of biological conservation. A key methodological challenge is …