Conti Angela, Casagrande Pierantoni Debora, Robert Vincent, Cardinali Gianluigi, Corte Laura
Department of Pharmaceutical Sciences, University of Perugia, 06121 Perugia, Italy.
Westerdjik Institute for Biodiversity, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
Microorganisms. 2021 Jan 28;9(2):273. doi: 10.3390/microorganisms9020273.
Homoplasy is a sort of noise in phylogenetic reconstructions, due to the accumulation of backmutations, convergent evolution and horizontal gene transfer (HGT), which is considered the major trigger of homoplasy in microorganism for its massive presence. It is also known that homoplasy increases with the complexity of the tree with both real and simulated data. In this paper, we analyzed the variation of homoplasy with the two widely used taxonomic markers and in four taxonomic models characterized by differences in the intra-specific distances. An algorithm (HomoDist) was developed to analyze the homoplasy index (HI) variation upon addition of a single element (strain or species) in increasing distance from a starting element. This algorithm allows to follow changes of the consistency index (CI), complementary to the HI, with the increase of the number of taxa and with the increase of the distance among elements. Results show that homoplasy increases-as expected-with the number of taxa, but also as a function of the overall distance among species, often with an almost linear relationship between distance and HI. No HI change was observed in trees with few taxa spanning through short distances, indicating that this noise is not prohibitive in this context, although the analysis of the ratio between HI and distance can be recommended as a criterion for tree acceptance. The absence of large changes of the HI within the species, and its increase when new species are added by HomoDist, suggest that homoplasy variation can be used as an auxiliary test in distance-based species delimitation with any type of marker.
同塑性是系统发育重建中的一种噪声，这是由于回复突变、趋同进化和水平基因转移（HGT）的积累造成的，由于HGT在微生物中大量存在，它被认为是微生物中同塑性的主要触发因素。同样已知的是，无论是真实数据还是模拟数据，同塑性都随着树的复杂性增加而增加。在本文中，我们分析了同塑性在两个广泛使用的分类标记以及四种以内种间距离差异为特征的分类模型中的变化。我们开发了一种算法（HomoDist）来分析在从起始元素开始以递增距离添加单个元素（菌株或物种）时同塑性指数（HI）的变化。该算法允许跟踪与HI互补的一致性指数（CI）随着分类单元数量的增加以及元素之间距离的增加而发生的变化。结果表明，同塑性正如预期的那样随着分类单元数量的增加而增加，但也作为物种间总体距离的函数而增加，距离与HI之间通常存在近似线性关系。在分类单元少且跨度短的树中未观察到HI变化，这表明在这种情况下这种噪声并不碍事，尽管可以推荐分析HI与距离之间的比率作为树接受度的一个标准。在物种内HI没有大的变化，并且当通过HomoDist添加新物种时HI增加，这表明同塑性变化可以用作基于距离的物种界定中使用任何类型标记的辅助测试。
