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 …

Genomic selection in aquaculture: application, limitations and opportunities with special reference to marine shrimp and pearl oysters

KR Zenger, MS Khatkar, DB Jones… - Frontiers in …, 2019 - frontiersin.org
Within aquaculture industries, selection based on genomic information (genomic selection)
has the profound potential to change genetic improvement programs and production …

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

ZN Kamvar, JC Brooks, NJ Grünwald - Frontiers in genetics, 2015 - frontiersin.org
To gain a detailed understanding of how plant microbes evolve and adapt to hosts,
pesticides, and other factors, knowledge of the population dynamics and evolutionary history …

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 …

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 …

How to identify sex chromosomes and their turnover

DH Palmer, TF Rogers, R Dean, AE Wright - Molecular ecology, 2019 - Wiley Online Library
Although sex is a fundamental component of eukaryotic reproduction, the genetic systems
that control sex determination are highly variable. In many organisms the presence of sex …

Practical considerations for plant phylogenomics

MR McKain, MG Johnson… - Applications in plant …, 2018 - Wiley Online Library
The past decade has seen a major breakthrough in our ability to easily and inexpensively
sequence genome‐scale data from diverse lineages. The development of high‐throughput …

Conservation genomics of natural and managed populations: building a conceptual and practical framework

LM Benestan, AL Ferchaud, PA Hohenlohe, BA Garner… - 2016 - Wiley Online Library
The boom of massive parallel sequencing (MPS) technology and its applications in
conservation of natural and managed populations brings new opportunities and challenges …