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 …

A genomic perspective on hybridization and speciation

BA Payseur, LH Rieseberg - Molecular ecology, 2016 - Wiley Online Library
Hybridization among diverging lineages is common in nature. Genomic data provide a
special opportunity to characterize the history of hybridization and the genetic basis of …

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 …

Hybridization, introgression, and the nature of species boundaries

RG Harrison, EL Larson - Journal of Heredity, 2014 - academic.oup.com
Species can be defined as populations that are diagnosably distinct, reproductively isolated,
cohesive, or exclusive groups of organisms. Boundaries between species in sympatry are …

Adaptive introgression: a plant perspective

A Suarez-Gonzalez, C Lexer… - Biology letters, 2018 - royalsocietypublishing.org
Introgression is emerging as an important source of novel genetic variation, alongside
standing variation and mutation. It is adaptive when such introgressed alleles are …

RAD capture (Rapture): flexible and efficient sequence-based genoty**

OA Ali, SM O'Rourke, SJ Amish, MH Meek, G Luikart… - Genetics, 2016 - academic.oup.com
Massively parallel sequencing has revolutionized many areas of biology, but sequencing
large amounts of DNA in many individuals is cost-prohibitive and unnecessary for many …

Genoty**-by-sequencing in ecological and conservation genomics

SR Narum, CA Buerkle, JW Davey, MR Miller… - Molecular …, 2013 - pmc.ncbi.nlm.nih.gov
The fields of ecological and conservation genetics have developed greatly in recent
decades through the use of molecular markers to investigate organisms in their natural …

High-throughput genomic data in systematics and phylogenetics

EM Lemmon, AR Lemmon - Annual Review of Ecology …, 2013 - annualreviews.org
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by
decreasing the cost and increasing the quantity and rate of data collection by several orders …

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 …