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 …

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 …

From next-generation resequencing reads to a high-quality variant data set

SP Pfeifer - Heredity, 2017‏ - nature.com
Sequencing has revolutionized biology by permitting the analysis of genomic variation at an
unprecedented resolution. High-throughput sequencing is fast and inexpensive, making it …

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 …

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 …

[HTML][HTML] A phylogenomic supertree of birds

RT Kimball, CH Oliveros, N Wang, ND White, FK Barker… - Diversity, 2019‏ - mdpi.com
It has long been appreciated that analyses of genomic data (eg, whole genome sequencing
or sequence capture) have the potential to reveal the tree of life, but it remains challenging …

RAD cap: sequence capture of dual‐digest RAD seq libraries with identifiable duplicates and reduced missing data

SL Hoffberg, TJ Kieran, JM Catchen… - Molecular ecology …, 2016‏ - Wiley Online Library
Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to
thousands of individuals at minimal cost per sample. Current methods, such as restriction …

Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism in ants

DB Booher, JC Gibson, C Liu, JT Longino… - PLoS …, 2021‏ - journals.plos.org
Evolutionary innovations underlie the rise of diversity and complexity—the 2 long-term
trends in the history of life. How does natural selection redesign multiple interacting parts to …

On the causes, consequences, and avoidance of PCR duplicates: towards a theory of library complexity

NC Rochette, AG Rivera‐Colón, J Walsh… - Molecular Ecology …, 2023‏ - Wiley Online Library
Library preparation protocols for most sequencing technologies involve PCR amplification of
the template DNA, which open the possibility that a given template DNA molecule is …

Museums are biobanks: unlocking the genetic potential of the three billion specimens in the world's biological collections

DK Yeates, A Zwick, AS Mikheyev - Current opinion in insect science, 2016‏ - Elsevier
Highlights•Museum and herbarium collections store near inexhaustible genetic
resources.•We overview next-generation sequencing tools for the analysis of museum and …