Algebraic Invariants for Inferring 4-leaf Semi-directed Phylogenetic networks
Algebraic Invariants for Inferring 4-leaf Semi-directed Phylogenetic networks
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DOI：
10.1101/2023.09.11.557152
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发表时间：
2023-09
期刊：
影响因子：
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通讯作者：
Samuel Martin;Vincent Moulton;R. Leggett
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文献类型：
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作者：
Samuel Martin;Vincent Moulton;R. Leggett
系统基因组学的核心目标是从生物序列数据中确定一组物种的进化史。系统发生网络能够描述比系统发生树更复杂的进化现象，但更难以准确重建。最近，人们对开发推断半定向系统发育网络的方法越来越感兴趣。由于计算这样的网络可能是计算密集型的，构建这样的网络的一种方法是将较小的网络拼在一起。因此，必须有可靠的方法来推断少量分类群的半定向系统发育网络。本文通过分析叶片模式概率的分布，研究了一种从4叶半定向系统发育网络的核苷酸序列数据进行系统发育网络推断的代数方法。在模拟数据中，我们发现当序列长度接近10Mbp时，我们可以正确识别高精度的半定向网络，并且我们能够使用我们的方法识别树状进化并确定底层树。我们还将我们的方法应用于剑尾鱼已发表的转录组数据，将其性能与推断半有向网络的伪似然方法进行比较。
A core goal of phylogenomics is to determine the evolutionary history of a set of species from biological sequence data. Phylogenetic networks are able to describe more complex evolutionary phenomena than phylogenetic trees but are more difficult to accurately reconstruct. Recently, there has been growing interest in developing methods to infer semi-directed phylogenetic networks. As computing such networks can be computationally intensive, one approach to building such networks is to puzzle together smaller networks. Thus, it is essential to have robust methods for inferring semi-directed phylogenetic networks on small numbers of taxa. In this paper, we investigate an algebraic method for performing phylogenetic network inference from nucleotide sequence data on 4-leaved semi-directed phylogenetic networks by analysing the distribution of leaf-pattern probabilities. On simulated data, we found that we can correctly identify with high accuracy semi-directed networks as sequences approach 10Mbp in length, and that we are able to use our approach to identify tree-like evolution and determine the underlying tree. We also applied our approach to published transcriptome data from swordtail fish to compare its performance with a pseudolikelihood method for inferring semi-directed networks.