Zenil-Ferguson Rosana, Burleigh J Gordon, Ponciano José Miguel
Department of Biological Science University of Idaho Moscow Idaho 83844 USA.
Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul Minnesota 55108 USA.
Appl Plant Sci. 2018 Apr 11;6(3):e1037. doi: 10.1002/aps3.1037. eCollection 2018 Mar.
Polyploidy has profound evolutionary consequences for land plants. Despite the availability of large phylogenetic and chromosomal data sets, estimating the rates of polyploidy and chromosomal evolution across the tree of life remains a challenging, computationally complex problem. We introduce the R package chromploid, which allows scientists to perform inference of chromosomal evolution rates across large phylogenetic trees.
chromploid is an open-source package in the R environment that calculates the likelihood function of models of chromosome evolution. Models of discrete character evolution can be customized using chromploid. We demonstrate the performance of the BiChroM model, testing for associations between rates of chromosome doubling (as a proxy for polyploidy) and a binary phenotypic character, within chromploid using simulations and empirical data from . In simulations, estimated chromosome-doubling rates were unbiased and the variance decreased with larger trees, but distinguishing small differences in rates of chromosome doubling, even from large data sets, remains challenging. In the data set, a custom model of chromosome number evolution demonstrated higher rates of chromosome doubling in herbaceous species compared to woody.
chromploid enables researchers to perform robust likelihood-based inferences using complex models of chromosome number evolution across large phylogenies.
多倍体对陆生植物具有深远的进化影响。尽管有大量的系统发育和染色体数据集，但估计整个生命之树上多倍体和染色体进化的速率仍然是一个具有挑战性的、计算复杂的问题。我们引入了R包chromploid，它使科学家能够推断大型系统发育树上的染色体进化速率。
chromploid是R环境中的一个开源包，用于计算染色体进化模型的似然函数。可以使用chromploid定制离散性状进化模型。我们展示了BiChroM模型的性能，在chromploid中使用模拟和来自……的实证数据测试染色体加倍速率（作为多倍体的代理）与二元表型性状之间的关联。在模拟中，估计的染色体加倍速率是无偏的，并且方差随着树的增大而减小，但是即使从大数据集中区分染色体加倍速率的微小差异仍然具有挑战性。在……数据集中，一个定制的染色体数目进化模型表明，与木本植物相比，草本物种的染色体加倍速率更高。
chromploid使研究人员能够使用跨越大型系统发育的复杂染色体数目进化模型进行基于似然性的可靠推断。
