Harnessing the power of RADseq for ecological and evolutionary genomics

KR Andrews, JM Good, MR Miller, G Luikart… - Nature Reviews …, 2016 - nature.com
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq)
are enabling the low-cost discovery and genoty** of thousands of genetic markers for any …

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 …

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 genoty** 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 …

RAD genoty** reveals fine‐scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the a Merican Lobster (H …

L Benestan, T Gosselin, C Perrier… - Molecular …, 2015 - Wiley Online Library
Deciphering genetic structure and inferring connectivity in marine species have been
challenging due to weak genetic differentiation and limited resolution offered by traditional …

Sequence capture versus restriction site associated DNA sequencing for shallow systematics

MG Harvey, BT Smith, TC Glenn, BC Faircloth… - Systematic …, 2016 - academic.oup.com
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two
genomic enrichment strategies for applying next-generation sequencing technologies to …

Species delimitation in endangered groundwater salamanders: Implications for aquifer management and biodiversity conservation

TJ Devitt, AM Wright… - Proceedings of the …, 2019 - National Acad Sciences
Groundwater-dependent species are among the least-known components of global
biodiversity, as well as some of the most vulnerable because of rapid groundwater depletion …

Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos

C Guo, PF Ma, GQ Yang, XY Ye, Y Guo… - Systematic …, 2021 - academic.oup.com
Rapid evolutionary radiations are among the most challenging phylogenetic problems,
wherein different types of data (eg, morphology and molecular) or genetic markers (eg …

Speciation Hypotheses from Phylogeographic Delimitation Yield an Integrative Taxonomy for Seal Salamanders (Desmognathus monticola)

RA Pyron, KA O'Connell, SC Duncan… - Systematic …, 2023 - academic.oup.com
Significant advances have been made in species delimitation and numerous methods can
test precisely defined models of speciation, though the synthesis of phylogeography and …

Shared and nonshared genomic divergence in parallel ecotypes of Littorina saxatilis at a local scale

M Ravinet, A Westram, K Johannesson… - Molecular …, 2016 - Wiley Online Library
Parallel speciation occurs when selection drives repeated, independent adaptive
divergence that reduces gene flow between ecotypes. Classical examples show parallel …