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 …

Phylogenomics and the flowering plant tree of life

C Guo, Y Luo, LM Gao, TS Yi, HT Li… - Journal of Integrative …, 2023 - Wiley Online Library
The advances accelerated by next‐generation sequencing and long‐read sequencing
technologies continue to provide an impetus for plant phylogenetic study. In the past …

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 …

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 genoty** populations of model and non‐model organisms. Generating a …

Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies

L Gorgannezhad, M Umer, MN Islam, NT Nguyen… - Lab on a Chip, 2018 - pubs.rsc.org
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in
almost all body fluids, including blood, and is involved in various physiological and …

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 …

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

TC Glenn, RA Nilsen, TJ Kieran, JG Sanders… - PeerJ, 2019 - peerj.com
Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors
include:(1) start-up (ie, purchasing initial reagents and equipment);(2) buyin (ie, getting the …

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 …

Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies

J Sunde, Y Yıldırım, P Tibblin, A Forsman - Frontiers in genetics, 2020 - frontiersin.org
Population genetic studies reveal biodiversity patterns and inform about drivers of
evolutionary differentiation and adaptation, including gene flow, drift and selection. This can …

Sequence capture of ultraconserved elements from bird museum specimens

JE McCormack, WLE Tsai… - Molecular ecology …, 2016 - Wiley Online Library
New DNA sequencing technologies are allowing researchers to explore the genomes of the
millions of natural history specimens collected prior to the molecular era. Yet, we know little …