Finding the genomic basis of local adaptation: pitfalls, practical solutions, and future directions

S Hoban, JL Kelley, KE Lotterhos… - The American …, 2016 - journals.uchicago.edu
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of
evolutionary biology. The recent development of cost-effective methods for obtaining high …

Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation

SP Flanagan, BR Forester, EK Latch… - Evolutionary …, 2018 - Wiley Online Library
Identifying and monitoring locally adaptive genetic variation can have direct utility for
conserving species at risk, especially when management may include actions such as …

Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics

NC Rochette, AG Rivera‐Colón… - Molecular ecology, 2019 - Wiley Online Library
For half a century population genetics studies have put type II restriction endonucleases to
work. Now, coupled with massively‐parallel, short‐read sequencing, the family of RAD …

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 …

These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists

SJ O'Leary, JB Puritz, SC Willis, CM Hollenbeck… - 2018 - Wiley Online Library
Sequencing reduced‐representation libraries of restriction site‐associated DNA (RAD seq)
to identify single nucleotide polymorphisms (SNP s) is quickly becoming a standard …

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

ABA Shafer, CR Peart, S Tusso… - Methods in Ecology …, 2017 - Wiley Online Library
Restriction site‐associated DNA sequencing (RAD‐seq) provides high‐resolution
population genomic data at low cost, and has become an important component in ecological …

A decade of seascape genetics: contributions to basic and applied marine connectivity

KA Selkoe, CCD Aloia, ED Crandall, M Iacchei… - Marine Ecology …, 2016 - int-res.com
Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that
draws on ecology, oceanography and geography to address challenges in basic …

Applications of genotyping by sequencing in aquaculture breeding and genetics

D Robledo, C Palaiokostas, L Bargelloni… - Reviews in …, 2018 - Wiley Online Library
Selective breeding is increasingly recognized as a key component of sustainable production
of aquaculture species. The uptake of genomic technology in aquaculture breeding has …

Demystifying the RAD fad

JB Puritz, MV Matz, RJ Toonen, JN Weber, DI Bolnick… - 2014 - Wiley Online Library
We are writing in response to the population and phylogenomics meeting review by
Andrews & Luikart () entitled 'Recent novel approaches for population genomics data …

Signatures of selection underpinning rapid coral adaptation to the world's warmest reefs

EG Smith, KM Hazzouri, JY Choi, P Delaney… - Science …, 2022 - science.org
Coral populations in the world's warmest reefs, the Persian/Arabian Gulf (PAG), represent an
ideal model system to understand the evolutionary response of coral populations to past and …