论文标题
Sprint:一种快速的新软件工具,用于重建多倍体数据集的进化过去
SPRINT: A fast, new software tool for reconstructing the evolutionary past of polyploid datasets
论文作者
论文摘要
多倍体化是一个重要的进化过程,它会影响从植物到鱼类和真菌的生物。它留下的信号的形式是物种的倍增水平(在单元中发现的完整染色体集的数量),该水平本质上是非真实的。当前可用的工具用于重建多倍体数据集的进化过去通常是从获得感兴趣的数据集获得的多标签树开始,然后以某种方式从该树中得出A(系统发育)网络,以某种方式通过解释过去至少两个作为多倍倍化事件来解释过去的网络。由于获得了这样的树的计算昂贵,因此拥有可用的替代方法,可以将光线放入多倍体数据集的网状进化过去。 Sprint的目的是根据二进制网络重建多倍体数据集的进化过去,该二进制网络实现了数据集的拼写曲线(数据集类群的拼倍水平的向量),并且需要最少的多倍化事件。它通过代表物种X的倍质水平,以从网络的根部到由x标记的网络叶的定向路径的数量。 Sprint分布在GitHub:https://github.com/lmaher1/sprint上。
Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell) which is inherently non-treelike. Currently available tools for reconstructing the evolutionary past of a polyploid dataset generally start with a multi-labelled tree obtained for a dataset of interest and then derive a (phylogenetic) network from that tree in some way that reflects that past by interpreting the networks's vertices of indegree at least two as polyploidization events. Since obtaining such a tree can be computationally expensive it is paramount to have alternative approaches available that allow one to shed light into the reticulate evolutionary past of a polyploid dataset. SPRINT aims to reconstruct the evolutionary past of a polyploid dataset in terms of a binary network which realises the dataset's ploidy profile (vector of ploidy levels of the dataset's taxa) and requires the fewest number of polyploidization events. It does this by representing the ploidy level of a species x in terms of the number of directed paths from the root of the network to the leaf of the network labelled by x. SPRINT is distributed on GitHub: https://github.com/lmaher1/SPRINT.