swinger: a user‐friendly computer program to establish captive breeding groups that minimize relatedness without pedigree information

Abstract

Captive breeding programmes are often a necessity for the continued persistence of a population or species. They typically have the goal of maintaining genetic diversity and minimizing inbreeding. However, most captive breeding programmes have been based on the assumption that the founding breeders are unrelated and outbred, even though in situ anthropogenic impacts often mean these founders may have high relatedness and substantial inbreeding. In addition, polygamous group-breeding species in captivity often have uncertain pedigrees, making it difficult to select the group composition for subsequent breeding. Molecular-based estimates of relatedness and inbreeding may instead be used to select breeding groups (≥two individuals) that minimize relatedness and filter out inbred individuals. swinger constructs breeding groups based on molecular estimates of relatedness and inbreeding. The number of possible combinations of breeding groups quickly becomes intractable by hand. swinger was designed to overcome this major issue in ex situ conservation biology. The user can specify parameters within swinger to reach breeding solutions that suit the mating system of the target species and available resources. We provide evidence of the efficiency of the software with an empirical example and using simulations. The only data required are a typical molecular marker data set, such as a microsatellite or SNP data set, from which estimates of inbreeding and pairwise relatedness may be obtained. Such molecular data sets are becoming easier to gather from non-model organisms with next-generation sequencing technology. swinger is an open-source software with a user-friendly interface and is available at http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ and https://github.com/Yuma248/Swinger.

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

“…The mean IR was estimated as −0.61 with a range of −0.43 to 0.23 (Table ). Following the parameter selection methodology of Sandoval‐Castillo et al () we obtained one list of 12 females and 13 males with an average PR of −0.075 and a mean IR of −0.45.…”

“…Our assurance colony management strategy depends on minimizing the average PR across the group and IR of individuals included in the group. Therefore, we ran SWINGER (Sandoval‐Castillo et al, ), utilizing the IR table incorporating sex information of the individuals and the PR table. The threshold values for maximum IR and maximum PR were both set to average values of the data.…”

Assessing the benefits and risks of translocations in depauperate species: A theoretical framework with an empirical validation

“…Wild‐to‐wild releases also generally show greater rates of success (Christie, Marine, French, & Blouin, ; Snyder et al, ). If there is sufficient time before demographic collapse (Woodruff, ), improvements in the wild‐to‐wild release could include genetic assessment of wild individuals (or populations) prior to translocation to identify the optimal strategy for selection of founder individuals (Miller et al, 2017; Sandoval‐Castillo et al, ). If the source population is not robust enough to support wild‐to‐wild translocation, captive breeding may be required.…”

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.…”