Estimating dispersal using close kin dyads: The kindisperse R package
Estimating dispersal using close kin dyads: The kindisperse R package
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DOI：
10.1111/1755-0998.13520
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发表时间：
2021-10-10
影响因子：
7.7
通讯作者：
Schmidt, Thomas L.
中科院分区：
文献类型：
--
作者：
Jasper, Moshe E.;Hoffmann, Ary A.;Schmidt, Thomas L.
调查动物种群的扩散可能很困难，特别是对于那些难以直接观察的类群，例如那些小的或稀有的类群。一个有前途的解决方案可能来自新的方法，使用全基因组序列数据来检测近亲二联体，并估计这些二联体的分布的扩散参数。迄今为止，这些方法仅适用于蚊子种群。然而，他们应该有广泛的适用性，一系列的类群，虽然还没有评估其性能在不同的传播条件和研究设计。在这里，我们开发了一个R包和闪亮的应用程序kindispose，它可以用来从近亲的空间分布中估计分散参数。kindisperate可以处理研究设计，针对不同的生命阶段，并允许一系列的分散内核形状和生物体的生活史;我们提供了一个脊椎动物（Antechinus）和无脊椎动物（伊蚊）的实施例。我们使用kindispose模拟运行的两个公布的近亲方法的性能进行比较，表明一种方法产生无偏估计，而另一种产生向下偏估计。我们还使用kindispose模拟研究设计如何影响分散估计，我们提供的样本网站的大小和形状以及准确估计所需的近亲数量的指导方针。kindisperse很容易适用于从入侵害虫到受威胁物种的各种研究环境，其中非侵入性DNA采样可用于检测近亲。
Investigating dispersal in animal populations can be difficult, particularly for taxa that are hard to directly observe such as those that are small or rare. A promising solution may come from new approaches that use genome-wide sequence data to detect close kin dyads and estimate dispersal parameters from the distribution of these dyads. These methods have so far only been applied to mosquito populations. However, they should have broad applicability to a range of taxa, although no assessment has yet been made on their performance under different dispersal conditions and study designs. Here we develop an R package and shiny app, kindisperse, that can be used to estimate dispersal parameters from the spatial distribution of close kin. kindisperse can handle study designs that target different life stages and allows for a range of dispersal kernel shapes and organismal life histories; we provide implementation examples for a vertebrate (Antechinus) and an invertebrate (Aedes). We use simulations run in kindisperse to compare the performance of two published close kin methodologies, showing that one method produces unbiased estimates whereas the other produces downward-biased estimates. We also use kindisperse simulations to investigate how study design affects dispersal estimates, and we provide guidelines for the size and shape of sample sites as well as the number of close kin needed for accurate estimates. kindisperse is easily adaptable for application to a variety of research contexts ranging from invasive pests to threatened species where noninvasive DNA sampling can be used to detect close kin.