Homoplasy as an Auxiliary Criterion for Species Delimitation.
Homoplasy as an Auxiliary Criterion for Species Delimitation.
复制标题
同质性作为物种界定的辅助标准。
DOI：
10.3390/microorganisms9020273
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发表时间：
2021-01-28
期刊：
影响因子：
4.5
通讯作者：
Corte L
中科院分区：
文献类型：
--
作者：
Conti A;Casagrande Pierantoni D;Robert V;Cardinali G;Corte L
同源性是微生物系统发育重建中的一种噪声，是由于回复突变、趋同进化和水平基因转移（HGT）的积累而引起的，而水平基因转移是微生物系统同源性的主要触发因素。还已知的是，对于真实的和模拟的数据，同构性随着树的复杂性而增加。本文分析了ITS和LSU两个常用的分类学标记在四个以种内距离差异为特征的分类模型中的同源性变化。开发了一种算法（HomoDist），用于分析在距离起始元素增加的情况下添加单个元素（菌株或物种）后的同质性指数（HI）变化。该算法允许遵循一致性指数（CI）的变化，与HI互补，随着分类群数量的增加和元素之间距离的增加。结果表明，同质性增加，正如预期的那样，随着类群的数量，但也作为一个功能的物种之间的整体距离，往往与距离和HI之间几乎呈线性关系。没有HI的变化，在树木中观察到几个类群跨越短距离，表明这种噪音是不禁止在这种情况下，虽然HI和距离之间的比率的分析可以建议作为一个标准，树接受。物种内的HI的大的变化的情况下，它的增加时，新的物种被添加到HomoDist，表明同源性变化可以被用作一个辅助测试，在基于距离的物种界定与任何类型的标记。
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 ITS and LSU 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.
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影响因子：
6.5
作者：
Brandley, Matthew C.;Warren, Dan L.;McGuire, Jimmy A.
通讯作者：
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影响因子：
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作者：
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DOI：
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发表时间：
2009-05-01
影响因子：
2.8
作者：
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通讯作者：
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影响因子：
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作者：
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