Sandoval-Castillo Jonathan, Attard Catherine R M, Marri Shashikanth, Brauer Chris J, Möller Luciana M, Beheregaray Luciano B
Molecular Ecology Lab, School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
Cetacean Ecology, Behaviour and Evolution Lab, School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia.
Mol Ecol Resour. 2017 Mar;17(2):278-287. doi: 10.1111/1755-0998.12609. Epub 2016 Nov 14.
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.
圈养繁殖计划通常是一个种群或物种持续生存的必要手段。它们的目标通常是维持遗传多样性并尽量减少近亲繁殖。然而，大多数圈养繁殖计划都是基于这样的假设，即初始繁殖者之间没有亲缘关系且为远交个体，尽管在原地的人为影响往往意味着这些初始繁殖者可能具有高度的亲缘关系和大量的近亲繁殖。此外，圈养中的多配偶群体繁殖物种的谱系往往不确定，这使得难以选择后续繁殖的群体组成。基于分子的亲缘关系和近亲繁殖估计可用于选择亲缘关系最小化且排除近亲个体的繁殖群体（≥两个个体）。swinger基于亲缘关系和近亲繁殖的分子估计构建繁殖群体。手动计算繁殖群体的可能组合数量很快就会变得难以处理。swinger旨在克服迁地保护生物学中的这一主要问题。用户可以在swinger中指定参数，以获得适合目标物种交配系统和可用资源的繁殖解决方案。我们通过一个实证例子和模拟提供了该软件效率的证据。所需的唯一数据是一个典型的分子标记数据集，例如微卫星或SNP数据集，从中可以获得近亲繁殖和成对亲缘关系的估计值。随着下一代测序技术的发展，从非模式生物中收集此类分子数据集变得越来越容易。swinger是一款具有用户友好界面的开源软件，可在http://www.molecularecology.flinders.edu.au/molecular-ecology-lab/software/swinger/swinger/ 和https://github.com/Yuma248/Swinger获取。
