Next-generation data filtering in the genomics era

W Hemstrom, JA Grummer, G Luikart… - Nature Reviews …, 2024 - nature.com
Genomic data are ubiquitous across disciplines, from agriculture to biodiversity, ecology,
evolution and human health. However, these datasets often contain noise or errors and are …

Big data in conservation genomics: Boosting skills, hedging bets, and staying current in the field

RM Schweizer, N Saarman, KM Ramstad… - Journal of …, 2021 - academic.oup.com
A current challenge in the fields of evolutionary, ecological, and conservation genomics is
balancing production of large-scale datasets with additional training often required to handle …

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 …

A GT‐seq panel for walleye (Sander vitreus) provides important insights for efficient development and implementation of amplicon panels in non‐model organisms

ML Bootsma, KM Gruenthal… - Molecular Ecology …, 2020 - Wiley Online Library
Targeted amplicon sequencing methods, such as genotyping‐in‐thousands by sequencing
(GT‐seq), facilitate rapid, accurate, and cost‐effective analysis of hundreds of genetic loci in …

Estimating and accounting for genotyping errors in RAD‐seq experiments

L Bresadola, V Link, CA Buerkle… - Molecular Ecology …, 2020 - Wiley Online Library
In non‐model organisms, evolutionary questions are frequently addressed using reduced
representation sequencing techniques due to their low cost, ease of use, and because they …

Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq …

JT Chang, CT Chao, K Nakamura, HL Liu… - Frontiers in Plant …, 2022 - frontiersin.org
The divergence process of incipient species is fascinating but elusive by incomplete lineage
sorting or gene flow. Species delimitation is also challenging among those morphologically …

Effective double‐digest RAD sequencing and genotyping despite large genome size

R Gargiulo, T Kull, MF Fay - Molecular Ecology Resources, 2021 - Wiley Online Library
Obtaining informative data is the ambition of any genomic project, but in nonmodel species
with very large genomes, pursuing such a goal requires surmounting a series of analytical …

Palau's warmest reefs harbor thermally tolerant corals that thrive across different habitats

HE Rivera, AL Cohen, JR Thompson, IB Baums… - Communications …, 2022 - nature.com
Ocean warming is killing corals, but heat-tolerant populations exist; if protected, they could
replenish affected reefs naturally or through restoration. Palau's Rock Islands experience …

Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection

AT Sendell-Price, KC Ruegg, SM Clegg - Heredity, 2020 - nature.com
Abstract Theory predicts that when populations are established by few individuals, random
founder effects can facilitate rapid phenotypic divergence even in the absence of selective …

A reference‐free approach to analyse RADseq data using standard next generation sequencing toolkits

R Heller, C Nursyifa, G Garcia‐Erill… - Molecular Ecology …, 2021 - Wiley Online Library
Genotyping‐by‐sequencing methods such as RADseq are popular for generating genomic
and population‐scale data sets from a diverse range of organisms. These often lack a …