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).

Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

“…Individuals which did not meet the 0.8 posterior probability threshold for any hybrid class were considered only for the assignment as wild, farmed, or hybrid, and excluded from analyses focusing on specific hybrid classes. Convergence of the MCMC chains in NewHybrids was also confirmed using hybriddetective 49 .…”

“…We used the R 48 package hybriddetective 49 to simulate pure wild, farmed, and hybrid populations to evaluate the power of this panel to identify hybrids and hybrid classes. Using hybriddetective we simulated multigenerational (viz.…”

“…Centering was done following Karlsson et al 33 and has the effect of removing linkage and deviances from Hardy-Weinberg equilibrium that may have been present in a pooled sample of populations. Next, using the centered baselines, individuals in generation t +1 were created by randomly sampling without replacement one allele per locus from each of the parental populations (i.e., wild baseline subsample and farmed baseline subsample) at time t 49 . Three independently simulated datasets were each in turn analyzed three times in parallel using NewHybrids 32 and the R package parallelnewhybrid 50 , with a burn-in of 50,000 followed by 100,000 sweeps.…”

Habitat use and hybridisation between the Rocky Mountain sculpin (Cottussp.) and slimy sculpin (Cottus cognatus)

“…NEWHYBRIDS probabilistically classifies individuals based on their 10 locus genotypes into six genotypic classes: the two parental species, first (F1) and second (F2) generation hybrids and backcrosses to one or other parental species (BC 1 and BC2, respectively) (Anderson & Thompson, ). The NEWHYBRIDS model was built using the genepopedit , paralellnewhybrid , and hybriddetective packages in R software (Stanley, Jeffery, Wringe, Dibacco, & Bradbury, ; Wringe, Stanley, Jeffery, Anderson, & Bradbury, ,b). For our NEWHYBRIDS model, we also used a burn‐in of 50,000 generations and 500,000 MCMC generations to produce assignments of pure RMS, SS and hybrids across five simulated data sets.…”

Editorial 2018

“…New Computer Programs that are expected to become broadly utilized include the program SWINGER (Sandoval‐Castillo et al., ) that determines optimal breeding groups to reduce relatedness and maximize diversity in supportive breeding programmes, the package HYBRIDDETECTIVE (Wringe, Stanley, Jeffery, Anderson, & Bradbury, ) that detects hybridization in nature and a package called TREESPACE (Jombart, Kendall, Almagro‐Garcia, & Colijn, ) that explores multiple phylogenetic estimates to represent the most informative trees. Computer programs continue to be published as “free access” to make them broadly available to the community.…”