Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants
Ultrafast learning of four-node hybridization cycles in phylogenetic networks using algebraic invariants
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DOI：
10.1093/bioadv/vbae014
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发表时间：
2024-02-20
期刊：
影响因子：
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通讯作者：
Solis-Lemus，Claudia
中科院分区：
文献类型：
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作者：
Wu，Zhaoxing;Solis-Lemus，Claudia
生命之树中丰富的基因流挑战了这样一种观念，即进化可以用一个完全分岔的过程来表示，而这个过程不能捕捉重要的生物学现实，如杂交、基因渗入或水平基因转移。基于聚结的网络方法越来越受欢迎，但对于大数据却无法扩展，因为它们需要在网络空间中执行启发式搜索以及可能是np困难的数值优化。本文提出了一种基于代数不变量的系统发育网络重构方法。虽然在系统发育中使用代数不变量有着悠久的传统，但我们的工作是第一个定义一致性因素（输入基因树中四个分类单元分裂的频率）的系统发育不变量，以确定多物种聚结模型下的1级系统发育网络。我们的新型混合检测方法无需优化，因为它只需要对多项式方程进行评估，因此，它绕过了网络空间的遍历，产生的计算速度至少比目前最快的网络方法快10倍。我们用模拟数据和真实数据来说明我们的方法的性能。可用性和实现我们提供了一个公开可用的开源Julia包phylodiamond。可在https://github.com/solislemuslab/PhyloDiamond.jl上获得，在进化社区中具有广泛的适用性。
MotivationThe abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process which cannot capture important biological realities like hybridization, introgression, or horizontal gene transfer. Coalescent-based network methods are increasingly popular, yet not scalable for big data, because they need to perform a heuristic search in the space of networks as well as numerical optimization that can be NP-hard. Here, we introduce a novel method to reconstruct phylogenetic networks based on algebraic invariants. While there is a long tradition of using algebraic invariants in phylogenetics, our work is the first to define phylogenetic invariants on concordance factors (frequencies of four-taxon splits in the input gene trees) to identify level-1 phylogenetic networks under the multispecies coalescent model.ResultsOur novel hybrid detection methodology is optimization-free as it only requires the evaluation of polynomial equations, and as such, it bypasses the traversal of network space, yielding a computational speed at least 10 times faster than the fastest-to-date network methods. We illustrate our method’s performance on simulated and real data from the genusCanis.Availability and implementationWe present an open-source publicly available Julia packagePhyloDiamond.jlavailable at https://github.com/solislemuslab/PhyloDiamond.jl with broad applicability within the evolutionary community.