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hybriddetective: A workflow and package to facilitate the detection of hybridization using genomic data in r
Authors:Brendan F. Wringe  Ryan R. E. Stanley  Nicholas W. Jeffery  Eric C. Anderson  Ian R. Bradbury
Affiliation:1. Salmonids Section, Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, NL, Canada;2. Coastal Ecosystem Sciences Division, Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, NS, Canada;3. Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
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 ).
Keywords:assignment tests  hybrid  introgression  population genetics  population structure  simulation
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