General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability.
General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability.
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DOI：
10.1186/1471-2148-8-86
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发表时间：
2008-03-18
影响因子：
3.4
通讯作者：
Grimm GW
中科院分区：
文献类型：
--
作者：
Göker M;Grimm GW
植物系统发育研究中最常用的分子标记是核核糖体内转录间隔区（ITS）。这些多拷贝区域的个体内变异是植物中非常常见的现象，其原因在文献中存在争议。在这些条件下进行系统发育重建本质上是困难的。我们的方法是将这个问题视为一般生物学问题的一个特例，即如何从宿主（此处由植物个体代表）的特征（此处由克隆序列代表）推断宿主的特征。介绍了六个通用变换函数，涵盖关联字符到离散和连续主字符的变换，以及关联距离到主距离的变换。建立了一个纯粹的基于距离的框架，其中这些变换函数应用于从被子植物宏碁属、水青冈属和榉树属收集的 ITS 序列。这些公式也适用于从蔷薇属获得的三个不同基因座的等位基因数据。这些功能通过（1）独立于系统发育的树状测量来验证； (2)与独立宿主性状的相关性； (3) 使用分割图进行可视化并与测试生物体的已发表数据进行比较。结果与这三种测量方法和检查的数据集以及理论预测和文献中的先前结果非常吻合。使用六个变换公式中的四个可以获得高质量的距离矩阵。我们证明其中之一代表了索伦森系数的推广，该系数在生态学中广泛应用。由于它们的通用性，变换函数可以应用于可以用宿主和同事来解释的广泛的生物学问题。关于克隆序列，这些公式很有可能准确反映被子植物属内的进化关系，并鉴定杂交种和祖先类群。这些结果证实了早期的结果，表明树状度量是生物距离函数比较研究中的一个有价值的工具。
Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here). Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology. Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.
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影响因子：
3.3
作者：
Comes, HP;Abbott, RJ
通讯作者：
Abbott, RJ
影响因子：
1.9
作者：
Denk, T;Grimm, G;Hemleben, V
通讯作者：
Hemleben, V
影响因子：
10.7
作者：
Bryant, D;Moulton, V
通讯作者：
Moulton, V
DOI：
10.1101/sqb.1974.038.01.054
发表时间：
1973-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
BROWN, DD;SUGIMOTO, K
通讯作者：
SUGIMOTO, K
DOI：
10.2307/2992205
发表时间：
1990-03-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
BROOKS, DR
通讯作者：
BROOKS, DR