hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r

Brendan F. Wringe; Ryan R.E. Stanley; Nicholas W. Jeffery; Eric C. Anderson; Ian R. Bradbury

doi:10.1111/1755-0998.12704

hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r

Brendan F. Wringe, Ryan R.E. Stanley, Nicholas W. Jeffery, Eric C. Anderson, Ian R. Bradbury

Research output: Contribution to journal › Article › peer-review

52 Citations (Scopus)

Abstract

The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the magnitude of, and timescale over which, hybridization has been or is occurring. Here, we present an r package and associated workflow developed for the detection, with estimates of efficiency and accuracy, of multigenerational hybrid individuals using genetic or genomic data in conjunction with the program newhybrids. This package includes functions for the identification and testing of diagnostic panels of markers, the simulation of multigenerational hybrids, and the quantification and visualization of the efficiency and accuracy with which hybrids can be detected. Overall, this package delivers a streamlined hybrid analysis platform, providing improvements in speed, ease of use and repeatability over current ad hoc approaches. The latest version of the package and associated documentation are available on GitHub (https://github.com/bwringe/hybriddetective).

Original language	English
Pages (from-to)	e275-e284
Journal	Molecular Ecology Resources
Volume	17
Issue number	6
DOIs	https://doi.org/10.1111/1755-0998.12704
Publication status	Published - Nov 2017
Externally published	Yes

Bibliographical note

Funding Information:
The authors wish to thank Marion Sinclair-Waters, Justine Létourneau and Anne-Laure Ferchaud for their help bug-checking the code. We also thank Thierry Gosselin for encouraging us to publish this package. The manuscript was greatly improved by comments from Sarah Lehnert and three anonymous reviewers. This work was supported by a Natural Sciences and Engineering Research Council Strategic Project Grant, a Natural Sciences and Engineering Research Discovery Grant, and Canadian Healthy Oceans Network, and Fisheries and Oceans Canada funding

Funding Information:
Natural Sciences and Engineering Research Council Strategic Project Grant; Natural Sciences and Engineering Research Discovery Grant; Canadian Healthy Oceans Network; Fisheries and Oceans Canada

Publisher Copyright:
© 2017 John Wiley & Sons Ltd

ASJC Scopus Subject Areas

Biotechnology
Ecology, Evolution, Behavior and Systematics
Genetics

PubMed: MeSH publication types

Journal Article

Access to Document

10.1111/1755-0998.12704

Cite this

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title = "hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r",

abstract = "The ability to detect and characterize hybridization in nature has long been of interest to many fields of biology and often has direct implications for wildlife management and conservation. The capacity to identify the presence of hybridization, and quantify the numbers of individuals belonging to different hybrid classes, permits inference on the magnitude of, and timescale over which, hybridization has been or is occurring. Here, we present an r package and associated workflow developed for the detection, with estimates of efficiency and accuracy, of multigenerational hybrid individuals using genetic or genomic data in conjunction with the program newhybrids. This package includes functions for the identification and testing of diagnostic panels of markers, the simulation of multigenerational hybrids, and the quantification and visualization of the efficiency and accuracy with which hybrids can be detected. Overall, this package delivers a streamlined hybrid analysis platform, providing improvements in speed, ease of use and repeatability over current ad hoc approaches. The latest version of the package and associated documentation are available on GitHub (https://github.com/bwringe/hybriddetective).",

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hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r

Abstract

Bibliographical note

ASJC Scopus Subject Areas

PubMed: MeSH publication types

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