Literature DB >> 28382730

Responsible RAD: Striving for best practices in population genomic studies of adaptation.

David B Lowry1,2, Sean Hoban3,4, Joanna L Kelley5, Katie E Lotterhos6, Laura K Reed7, Michael F Antolin8, Andrew Storfer5.   

Abstract

Two recent articles were written in response to our paper "Breaking RAD: An evaluation of the utility of restriction site associated DNA sequencing scans of adaptation." While we agree with some of the comments made by the authors of these two response papers, we still believe caution should be employed in RADseq studies that aim to detect loci that contribute to adaptation. In this rebuttal, we evaluate the key points made in these papers, attempt to identify a middle ground and make suggestions for responsibly conducting future studies to understand the genomewide mechanisms of adaptation.
© 2017 John Wiley & Sons Ltd.

Entities:  

Keywords:  genome scan; genome-environment association; genotyping by sequencing; local adaptation; outlier analysis

Mesh:

Year:  2017        PMID: 28382730     DOI: 10.1111/1755-0998.12677

Source DB:  PubMed          Journal:  Mol Ecol Resour        ISSN: 1755-098X            Impact factor:   7.090


  16 in total

1.  Decimation by sea star wasting disease and rapid genetic change in a keystone species, Pisaster ochraceus.

Authors:  Lauren M Schiebelhut; Jonathan B Puritz; Michael N Dawson
Journal:  Proc Natl Acad Sci U S A       Date:  2018-06-18       Impact factor: 11.205

2.  Genome-wide scan reveals signatures of selection related to pollution adaptation in non-model estuarine Atlantic killifish (Fundulus heteroclitus).

Authors:  J S Osterberg; K M Cammen; T F Schultz; B W Clark; R T Di Giulio
Journal:  Aquat Toxicol       Date:  2018-04-25       Impact factor: 4.964

Review 3.  Navigating the Interface Between Landscape Genetics and Landscape Genomics.

Authors:  Andrew Storfer; Austin Patton; Alexandra K Fraik
Journal:  Front Genet       Date:  2018-03-13       Impact factor: 4.599

4.  Strong Selection Against Early Generation Hybrids in Joshua Tree Hybrid Zone Not Explained by Pollinators Alone.

Authors:  Anne M Royer; Jackson Waite-Himmelwright; Christopher Irwin Smith
Journal:  Front Plant Sci       Date:  2020-05-26       Impact factor: 5.753

5.  Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra.

Authors:  Odile Rogier; Aurélien Chateigner; Souhila Amanzougarene; Marie-Claude Lesage-Descauses; Sandrine Balzergue; Véronique Brunaud; José Caius; Ludivine Soubigou-Taconnat; Véronique Jorge; Vincent Segura
Journal:  BMC Genomics       Date:  2018-12-12       Impact factor: 3.969

Review 6.  Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation.

Authors:  Sarah P Flanagan; Brenna R Forester; Emily K Latch; Sally N Aitken; Sean Hoban
Journal:  Evol Appl       Date:  2017-12-02       Impact factor: 5.183

7.  The genetic legacy of 50 years of desert bighorn sheep translocations.

Authors:  Joshua P Jahner; Marjorie D Matocq; Jason L Malaney; Mike Cox; Peregrine Wolff; Mitchell A Gritts; Thomas L Parchman
Journal:  Evol Appl       Date:  2018-10-16       Impact factor: 5.183

Review 8.  Conservation insights from wild bee genetic studies: Geographic differences, susceptibility to inbreeding, and signs of local adaptation.

Authors:  Evan P Kelemen; Sandra M Rehan
Journal:  Evol Appl       Date:  2021-03-25       Impact factor: 5.183

9.  Migration-Selection Balance Drives Genetic Differentiation in Genes Associated with High-Altitude Function in the Speckled Teal (Anas flavirostris) in the Andes.

Authors:  Allie M Graham; Philip Lavretsky; Violeta Muñoz-Fuentes; Andy J Green; Robert E Wilson; Kevin G McCracken
Journal:  Genome Biol Evol       Date:  2018-01-01       Impact factor: 3.416

10.  Whole-genome amplification in double-digest RADseq results in adequate libraries but fewer sequenced loci.

Authors:  Bruno A S de Medeiros; Brian D Farrell
Journal:  PeerJ       Date:  2018-07-17       Impact factor: 2.984

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