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A Beta-splitting model for evolutionary trees

机译:进化树的Beta分裂模型

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In this article, we construct a generalization of the Blum–Fran?ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric shares of diversification rates (or diversification ‘potential’) between two sister species in an evolutionarily interpretable manner, as well as the addition of extinction to the model in a natural way. We describe the incremental evolutionary construction of a tree with n leaves by splitting or freezing extant lineages through the generating, organizing and deleting processes. We then give the probability of any (binary rooted) tree under this model with no extinction, at several resolutions: ranked planar trees giving asymmetric roles to the first and second offspring species of a given species and keeping track of the order of the speciation events occurring during the creation of the tree, unranked planar trees, ranked non-planar trees and finally (unranked non-planar) trees. We also describe a continuous-time equivalent of the generating, organizing and deleting processes where tree topology and branch lengths are jointly modelled and provide code in SageMath/Python for these algorithms.
机译:在本文中,我们构建了进化树的Blum–Fran?ois Beta分裂模型的概括,该模型本身是受Aldous的cladogram Beta分裂模型启发的。我们方法的新颖性允许以进化论可解释的方式在两个姊妹物种之间实现不对称的多样化比率(或多样化“潜力”)份额,并以自然方式为模型增加了灭绝能力。我们通过生成,组织和删除过程来分裂或冻结现存谱系,描述了具有n个叶子的树的增量进化构造。然后,我们在几种分辨率下给出了该模型下没有灭绝的任何(二叉根)树的概率:排序的平面树赋予给定物种的第一和第二后代物种不对称的作用,并跟踪物种形成事件的顺序发生在树的创建过程中,未排序的平面树,已排序的非平面树,最后是(未排序的非平面)树。我们还描述了生成,组织和删除过程的连续时间等效过程,在这些过程中,树拓扑和分支长度被联合建模,并在SageMath / Python中为这些算法提供了代码。

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