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 genotyping of single-nucleotide polymorphisms in hundreds of individuals at …

Significance and limitations of the use of next-generation sequencing technologies for detecting mutational signatures

A Abbasi, LB Alexandrov - DNA repair, 2021 - Elsevier
Next generation sequencing technologies (NGS) have been critical in characterizing the
genomic landscape and untangling the genetic heterogeneity of human cancer. Since its …

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

NJ Bayona-Vásquez, TC Glenn, TJ Kieran, TW Pierson… - PeerJ, 2019 - peerj.com
Molecular ecologists frequently use genome reduction strategies that rely upon restriction
enzyme digestion of genomic DNA to sample consistent portions of the genome from many …

A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture

L Casas, F Saborido-Rey - Frontiers in Marine Science, 2023 - frontiersin.org
Stock assessments serve to monitor the condition of fish stocks and exploit them sustainably
but require accurate data such as growth and mortality rates as input parameters. Most …

Strong and lasting impacts of past global warming on baleen whales and their prey

AA Cabrera, E Schall, M Bérubé… - Global change …, 2022 - Wiley Online Library
Global warming is affecting the population dynamics and trophic interactions across a wide
range of ecosystems and habitats. Translating these real‐time effects into their long‐term …

Rapid and parallel adaptive evolution of the visual system of Neotropical Midas cichlid fishes

J Torres-Dowdall, MER Pierotti, A Härer… - Molecular biology …, 2017 - academic.oup.com
Midas cichlid fish are a Central American species flock containing 13 described species that
has been dated to only a few thousand years old, a historical timescale infrequently …

Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data

AG Rivera‐Colón, NC Rochette… - Molecular ecology …, 2021 - Wiley Online Library
Restriction‐site associated DNA sequencing (RADseq) has become a powerful and
versatile tool in modern population genomics, enabling large‐scale evolutionary and …

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

SA Kitchen, G Von Kuster, KLV Kuntz, HG Reich… - Scientific reports, 2020 - nature.com
Standardized identification of genotypes is necessary in animals that reproduce asexually
and form large clonal populations such as coral. We developed a high-resolution …

Tool for genomic selection and breeding to evolutionary adaptation: Development of a 100K single nucleotide polymorphism array for the honey bee

JC Jones, ZG Du, R Bernstein, M Meyer… - Ecology and …, 2020 - Wiley Online Library
High‐throughput high‐density genotyping arrays continue to be a fast, accurate, and cost‐
effective method for genotyping thousands of polymorphisms in high numbers of individuals …

Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete

S Bamberger, J Xu, B Hausdorf - Systematic Biology, 2022 - academic.oup.com
Delimiting species in radiations is notoriously difficult because of the small differences
between the incipient species, the star-like tree with short branches between species …