Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree:: application to trichomonad parasites
Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree:: application to trichomonad parasites
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DOI：
10.1099/00207713-51-3-731
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发表时间：
2001-05-01
影响因子：
2.8
通讯作者：
Flegr, J
中科院分区：
文献类型：
--
作者：
Hampl, V;Pavlícek, A;Flegr, J
本文介绍了Win95/98/NT环境下的FreeTree程序，该程序可根据RAPD、RFLP和等位酶数据计算距离矩阵和构建系统树或表型树。与其他类似软件相比，程序FreeTree（可在http://www.natur.cuni.cz/similar上获得，以flegr/programs/freetree或http：//ijs.sgmjournals.org/content/vol51/issue3/）也可以通过自举、折刀或操作分类单元折刀分析来评估树拓扑的鲁棒性。此外，该程序还可以用于分析在几个独立的实验中获得的数据进行不相同的类群子集。通过对10种42株毛滴虫的RAPD分析，验证了该程序的功能。在FreeTree构建的系统发育树上，胎猪三毛滴虫14株分支的自举值较高，末端分支较短，表明该菌可能是较新的克隆辐射。阴道毛滴虫20- 24的自举值相对较低，末端分支较长，菌株分支表明该物种的更古老的辐射和在该人类病原体中可能存在遗传重组（有性生殖）。低的Bootstrap值和整个毛滴虫科树的星形拓扑结构证实了RAPD方法不适用于原生动物在高等类群水平上的系统发育分析，重复Bootstrap分析应是任何RAPD研究的必要部分。它可以评估所获得的树的可靠性，并根据所分析的分类群的RAPD数据中的系统发育信号的数量来调整收集的数据量（随机引物的数量）。FreeTree程序使这种分析成为可能。
The Win95/98/NT program FreeTree for computation of distance matrices and construction of phylogenetic or phenetic trees on the basis of random amplified polymorphic DNA (RAPD), RFLP and allozyme data is presented. In contrast to other similar software, the program FreeTree (available at http://www.natur.cuni.cz/similar to flegr/programs/freetree or http://ijs.sgmjournals.org/content/vol51/issue3/) can also assess the robustness of the tree topology by bootstrap, jackknife or operational taxonomic unit-jackknife analysis. Moreover, the program can be also used for the analysis of data obtained in several independent experiments performed with non-identical subsets of taxa. The function of the program was demonstrated by an analysis of RAPD data from 42 strains of 10 species of trichomonads. On the phylogenetic tree constructed using FreeTree, the high bootstrap values and short terminal branches for the Tritrichomonas foetus/suis 14-strain branch suggested relatively recent and probably clonal radiation of this species, At the same time, the relatively lower bootstrap values and long terminal branches for the Trichomonas vaginalis 20-strain branch suggested more ancient radiation of this species and the possible existence of genetic recombination (sexual reproduction) in this human pathogen. The low bootstrap values and the star-like topology of the whole Trichomonadidae tree confirm that the RAPD method is not suitable for phylogenetic analysis of protozoa at the level of higher taxa, It is proposed that the repeated bootstrap analysis should be an obligatory part of any RAPD study. It makes it possible to assess the reliability of the tree obtained and to adjust the amount of collected data (the number of random primers) to the amount of phylogenetic signals in the RAPD data of the taxon analysed. The FreeTree program makes such analysis possible.