COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE - ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE
COULD A CLADOGRAM THIS SHORT HAVE ARISEN BY CHANCE ALONE - ON PERMUTATION TESTS FOR CLADISTIC STRUCTURE
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DOI：
10.1111/j.1096-0031.1991.tb00020.x
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发表时间：
1991-03-01
期刊：
影响因子：
3.6
通讯作者：
CRANSTON, PS
中科院分区：
文献类型：
--
作者：
FAITH, DP;CRANSTON, PS
评估分支分析的绝对标准是有用的，不仅因为分支算法强加了结构，而且因为分支结果的应用需要对分支图的证实程度进行一些评估。这里提出了一种基于树长的定量评估方法。最简约树的长度反映了观察到的特征共变的程度，使得单个树拓扑可以解释类群之间共享的特征状态。这种“分支共变”可以通过将观察到的数据集的最简约树的长度与具有随机特征共变的数据集的长度进行比较来量化。随机数据集被定义为其中保持原始字符数及其字符状态的数据集，但对于每个字符，状态被随机重新分配给分类单元。分支排列尾部概率 (PTP) 定义为对发现树比原始树短或短的时间比例的估计。如果 PTP 小于规定值（例如 0.05），则存在显着的分支共变。在基于分子和形态学数据集的案例研究中，PTP的应用表明：1在哺乳动物目四种不同分子数据集的比较中，α血红蛋白的序列数据集不具有显着的分支共变，而α晶状体蛋白的序列数据集具有高度显着性。然而，当每个数据集减少到 11 个常见分类群以便标准化比较时，发现分支共变水平降低，而 α 晶状体蛋白数据没有明显的优势。这 11 个分类群的形态学数据具有高度显着的 PTP，生成的树与具有边际或显着 PTP 值的三个分子集的树大致一致。合并所有数据集，排除结构不良的 α 血红蛋白数据，产生具有显着 PTP 的数据集，并提供对这 11 个哺乳动物目之间的系统发育关系的估计。2在对四个分类群的乳清蛋白和溶菌酶 DNA 序列数据的分析中，嘌呤-嘧啶编码产生具有显着分支共变的数据集，而其他编码产生具有显着分支共变的数据集。 失败。密码子位置 3 的数据单独显示出最强的分支协变。3基于蓼类群中类黄酮的数据集最初产生显着的 PTP；然而，删除相同评分的类群不会留下显着的分支共变。 4对于四种凤头蝾螈种群基因组类型的线粒体DNA数据，所有基因组类型集以及其中一个物种内的五种线粒体DNA基因组类型之间都存在显着的分支共变。然而，假设物种单系的条件 PTP 测试表明，这些数据的毛皮物种之间不存在显着的分支共变。 5 在对一组淡水昆虫进行测试的应用中，作为生物监测的初步，代表幼虫、蛹和成虫阶段的分类数据的各个子集具有不显着的 PTP，而完整的数据集显示出显着的分支结构。
Absolute criteria for evaluating cladistic analyses are useful, not only because cladistic algorithms impose structure, but also because applications of cladistic results demand some assessment of the degree of corroboration of the cladogram. Here, a means of quantitative evaluation is presented based on tree length. The length of the most‐parsimonious tree reflects the degree to which the observed characters co‐vary such that a single tree topology can explain shared character states among the taxa. This “cladistic covariation” can be quantified by comparing the length of the most parsimonious tree for the observed data set to that found for data sets with random covariation of characters. A random data set is defined as one in which the original number of characters and their character states are maintained, but for each character, the states are randomly reassigned to the taxa. The cladistic permutation tail probability, PTP, is defined as the estimate of the proportion of times that a tree can be found as short or shorter than the original tree. Significant cladistic covariation exists if the PTP is less than a prescribed value, for example, 0.05. In case studies based on molecular and morphological data sets, application of the PTP shows that:1In the comparison of four different molecular data sets for orders of mammals, the sequence data set for alpha hemoglobin does not have significant cladistic covariation, while that for alpha crystallin is highly significant. However, when each data set was reduced to the 11 common taxa in order to standardize comparison, reduced levels of cladistic covariation, with no clear superiority of the alpha crystallin data, were found. Morphological data for these 11 taxa had a highly significant PTP, producing a tree roughly congruent with those for the three molecular sets with marginal or significant PTP values. Merging of all data sets, with the exclusion of the poorly structured alpha hemoglobin data, produced a data set with a significant PTP, and provides an estimate of the phylogenetic relationships among these 11 orders of mammals.2In an analysis of lactalbumin and lysozyme DNA sequence data for four taxa, purine‐pyrimidine coding yields a data set with significant cladistic covariation, while other codings fail. The data for codon position 3 taken alone exhibit the strongest cladistic covariation.3A data set based on flavonoids in taxa ofPolygonuminitially yields a significant PTP; however, deletion of identically scored taxa leaves no significant cladistic covariation.4For mitochondrial DNA data on population genome types for four species of the crested newt, there is significant cladistic covariation for the set of all genome types, and among the five mtDNA genome types within one of the species. However, a conditional PTP test that assumes species monophyly shows that no significant cladistic covariation exists among the fur species for these data.5In an application of the test to a group of freshwater insects, as preliminary to biological monitoring, individual subsets of the taxonomic data representing larval, pupal, and adult stages had non‐significant PTPs, while the complete data set showed significant cladistic structure.