Responsible RAD: Striving for best practices in population genomic studies of adaptation.
David B. Lowry,Sean Hoban,Sean Hoban,Joanna L. Kelley,Katie E. Lotterhos,Laura K. Reed,Michael F. Antolin,Andrew Storfer +7 more
TLDR
This rebuttal attempts to identify a middle ground and make suggestions for responsibly conducting future studies to understand the genomewide mechanisms of adaptation in RADseq studies that aim to detect loci that contribute to adaptation.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.read more
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Annual Review of Ecology, Evolution and Systematics
TL;DR: Twenty-four articles by biologists, ecologists, and other scientists represent a year's progress in the field of paleobiogeography, genetics and geographic structure, and time as an ecological resource are addressed.
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Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics
TL;DR: This paper describes the first software natively capable of using paired‐end sequencing to derive short contigs from de novo RAD data, and shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired‐ end de noVO data sets.
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Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations
TL;DR: No single WGR approach fulfils all requirements of conservation genetics, and each method has its own limitations and sources of potential bias; proposed ways to minimize such biases are discussed.
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Stacks 2: Analytical Methods for Paired-end Sequencing Improve RADseq-based Population Genomics
TL;DR: This paper describes the first software capable of using paired-end sequencing to derive short contigs from de novo RAD data natively, and shows that the latest version of Stacks is highly accurate and outperforms other software in assembling and genotyping paired- end de noVO datasets.
Journal ArticleDOI
Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation.
TL;DR: An adaptive management framework is offered to help conservation biologists and managers decide when genomics is likely to be effective in detecting local adaptation, and how to plan assessment and monitoring of adaptive variation to address conservation objectives.
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The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones,Manfred Grabherr,Manfred Grabherr,Yingguang Frank Chan,Pamela Russell,Evan Mauceli,Evan Mauceli,Jeremy Johnson,Ross Swofford,Mono Pirun,Mono Pirun,Michael C. Zody,Simon D. M. White,Ewan Birney,Stephen M. J. Searle,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Richard M. Myers,Craig Miller,Craig Miller,Brian R. Summers,Anne K. Knecht,Shannon D. Brady,Haili Zhang,Alex A. Pollen,Timothy R. Howes,Chris T. Amemiya,Eric S. Lander,Federica Di Palma,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,David M. Kingsley,David M. Kingsley +33 more
TL;DR: A high-quality reference genome assembly for threespine stickleback fish is developed and it is indicated that reuse of globally shared standing genetic variation has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation.
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Widespread Parallel Evolution in Sticklebacks by Repeated Fixation of Ectodysplasin Alleles
Pamela F. Colosimo,Kim E. Hosemann,Sarita Balabhadra,Guadalupe Villarreal,Mark Dickson,Jane Grimwood,Jeremy Schmutz,Richard M. Myers,Dolph Schluter,David M. Kingsley +9 more
TL;DR: The authors used positional cloning methods to identify the major chromosome locus controlling armor plate patterning in wild threespine sticklebacks and found that members of this clade of low-plated alleles are present at low frequencies in marine fish, which suggests that standing genetic variation can provide a molecular basis for rapid, parallel evolution of dramatic phenotypic change in nature.
The genomic basis of adaptive evolution in threespine sticklebacks
Felicity C. Jones,Manfred Grabherr,Yingguang Frank Chan,Pamela Russell,Evan Mauceli,Jeremy A. Johnson,Ross Swofford,Mono Pirun,Michael C. Zody,Simon D. M. White,Ewan Birney,Stephen M. J. Searle,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Richard M. Myers,Craig Miller,Brian R. Summers,Anne K. Knecht,Shannon D. Brady,Haili Zhang,Alex A. Pollen,Timothy R. Howes,Chris T. Amemiya,Jen Baldwin,Toby Bloom,David B. Jaffe,Robert Nicol,Jane E. Wilkinson,Eric S. Lander,Federica Di Palma,Kerstin Lindblad-Toh,David M. Kingsley +32 more
Journal ArticleDOI
Genetic Consequences of Range Expansions
TL;DR: Interestingly, most of these patterns had been previously attributed to distinct selective processes, showing that taking into account the dynamic nature of a species range can lead to a paradigm shift in the authors' perception of evolutionary processes.
Journal ArticleDOI
Ecological genomics of local adaptation
TL;DR: Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation.