Data from: Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots

Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while simultaneously allowing for evolutionary transitions between character states. We used BiChroM to test whether polyploidy is more frequent in woody or herbaceous plants, based on tree with 4,711 eudicot species. Although polyploidy occurs in woody species, rates of chromosome doubling were over six times higher in herbaceous species. Rates of single chromosome increases or decreases were also far higher in herbaceous than woody species. Simulation experiments indicate that BiChroM performs well with little to no bias and relatively little variance at a wide range of tree depths when trees have at least 500 taxa. Thus, BiChroM provides a first step towards a rigorous statistical framework for assessing the traits that facilitate polyploidy.

尽管已有诸多研究探讨了不同植物性状与多倍体（polyploidy）的关联频率，但目前鲜有可用的统计工具用于识别潜在促进多倍体形成的影响因素。本研究提出了一种全新的概率模型BiChroM，旨在将系统发育（phylogeny）框架下的多倍体与染色体变异频率，与二元表型性状建立关联。BiChroM提供了一套稳健的统计框架，可用于检验系统发育过程中与表型性状相关的多倍体发生速率差异，同时允许性状状态间发生演化转变。我们基于包含4711个真双子叶植物（eudicot）物种的系统发育树，使用BiChroM检验多倍体在木本植物还是草本植物中更为普遍。尽管木本植物中亦存在多倍体现象，但草本植物的染色体加倍速率是木本植物的六倍以上；同时，草本植物的单染色体增减速率也远高于木本植物。模拟实验结果表明，当系统发育树包含至少500个分类单元时，BiChroM在广泛的树深范围内均可表现优异，几乎无偏倚且方差相对较低。综上，BiChroM为构建用于评估促进多倍体形成的相关性状的严谨统计框架迈出了关键的第一步。