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 …

A practical guide to environmental association analysis in landscape genomics

C Rellstab, F Gugerli, AJ Eckert, AM Hancock… - Molecular …, 2015 - Wiley Online Library
Landscape genomics is an emerging research field that aims to identify the environmental
factors that shape adaptive genetic variation and the gene variants that drive local …

DnaSP 6: DNA sequence polymorphism analysis of large data sets

J Rozas, A Ferrer-Mata… - Molecular biology …, 2017 - academic.oup.com
We present version 6 of the DNA Sequence Polymorphism (DnaSP) software, a new version
of the popular tool for performing exhaustive population genetic analyses on multiple …

Breaking RAD: An evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation

DB Lowry, S Hoban, JL Kelley, KE Lotterhos, LK Reed… - 2017 - Wiley Online Library
Understanding how and why populations evolve is of fundamental importance to molecular
ecology. Restriction site‐associated DNA sequencing (RAD seq), a popular reduced …

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 …

Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies

AD Leaché, BL Banbury, J Felsenstein… - Systematic …, 2015 - academic.oup.com
Single nucleotide polymorphisms (SNPs) are useful markers for phylogenetic studies owing
in part to their ubiquity throughout the genome and ease of collection. Restriction site …

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 genoty** 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 …

Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genoty**‐by‐sequencing data from natural populations

GJ McKinney, RK Waples, LW Seeb… - Molecular Ecology …, 2017 - Wiley Online Library
Whole‐genome duplications have occurred in the recent ancestors of many plants, fish, and
amphibians, resulting in a pervasiveness of paralogous loci and the potential for both …