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 …

Lost in parameter space: a road map for stacks

JR Paris, JR Stevens… - Methods in Ecology and …, 2017 - Wiley Online Library
Restriction site‐Associated DNA sequencing (RAD‐seq) has become a widely adopted
method for genotyping populations of model and non‐model organisms. Generating a …

RADseq approaches and applications for forest tree genetics

TL Parchman, JP Jahner, KA Uckele… - Tree Genetics & …, 2018 - Springer
As tree species vary extensively in genome size, complexity, and resource development,
reduced representation methods have been increasingly employed for the generation of …

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

RGJ Hodel, S Chen, AC Payton, SF McDaniel… - Scientific Reports, 2017 - nature.com
The widespread adoption of RAD-Seq data in phylogeography means genealogical
relationships previously evaluated using relatively few genetic markers can now be …

Population genomics: advancing understanding of nature

G Luikart, M Kardos, BK Hand, OP Rajora… - Population genomics …, 2019 - Springer
Population genomics is advancing our understanding of evolution, ecology, conservation,
agriculture, forestry, and human health by allowing new and long-standing questions to be …

Estimating effective population size using RADseq: Effects of SNP selection and sample size

F Marandel, G Charrier, JB Lamy… - Ecology and …, 2020 - Wiley Online Library
Effective population size (Ne) is a key parameter of population genetics. However, Ne
remains challenging to estimate for natural populations as several factors are likely to bias …

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

M Van Wyngaarden, PVR Snelgrove… - Evolutionary …, 2017 - Wiley Online Library
Understanding patterns of dispersal and connectivity among marine populations can directly
inform fisheries conservation and management. Advances in high‐throughput sequencing …

RADSex: A computational workflow to study sex determination using restriction site‐associated DNA sequencing data

R Feron, Q Pan, M Wen, B Imarazene… - Molecular Ecology …, 2021 - Wiley Online Library
The study of sex determination and sex chromosome organization in nonmodel species has
long been technically challenging, but new sequencing methodologies now enable precise …

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 …

Population genomics applied to fishery management and conservation

L Benestan - Population genomics: Marine organisms, 2020 - Springer
In times of overfishing and climate change, marine resources are extremely vulnerable, and
the vast majority of the world's fish stocks have already collapsed. In this fragile context, the …