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 …
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 …
method for genotyping populations of model and non‐model organisms. Generating a …
RADseq approaches and applications for forest tree genetics
As tree species vary extensively in genome size, complexity, and resource development,
reduced representation methods have been increasingly employed for the generation of …
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 …
The widespread adoption of RAD-Seq data in phylogeography means genealogical
relationships previously evaluated using relatively few genetic markers can now be …
relationships previously evaluated using relatively few genetic markers can now be …
Population genomics: advancing understanding of nature
Population genomics is advancing our understanding of evolution, ecology, conservation,
agriculture, forestry, and human health by allowing new and long-standing questions to be …
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 …
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 …
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
The study of sex determination and sex chromosome organization in nonmodel species has
long been technically challenging, but new sequencing methodologies now enable precise …
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 …
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 …
the vast majority of the world's fish stocks have already collapsed. In this fragile context, the …