PACo: a novel procrustes application to cophylogenetic analysis.
PACo: a novel procrustes application to cophylogenetic analysis.
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DOI：
10.1371/journal.pone.0061048
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Blasco-Costa I
中科院分区：
文献类型：
--
作者：
Balbuena JA;Míguez-Lozano R;Blasco-Costa I
我们提出了一种新的统计工具来测试系统发育树之间的一致性，或相关类群的系统发育距离矩阵之间的一致性。与以前的测试不同，PACo评估了一种遗传学对另一种遗传学的依赖性。这使得它特别适合于测试经典的共同进化模型，该模型假设寄生虫在其宿主体内或宿主身上度过部分生命，跟踪其宿主的生殖过程。新方法不需要完全解决的寄生虫，并允许多个主机-寄生虫协会。PACo产生了一个Procrustes叠加图，使图形评估的寄生虫的寄生虫发生到主机的寄生虫发生和拟合优度的统计，其显着性是建立随机化的主机-寄生虫的关联数据。每个单独的主机-寄生虫关联的全球拟合的贡献是通过折刀估计各自的平方残差和置信区间相关联的每个主机-寄生虫链接。我们进行了不同的模拟，以评估性能的PACo的第一类和第二类错误相对于两个类似的出版测试。在大多数情况下，PACo的表现至少与其他测试一样好，并显示出更高的总体统计功效。此外，折刀估计平方残差使更详细的验证有关的性质，个别的链接比ParaFitLink 1测试的程序ParaFit。为了证明它如何在真实的生物学情况下使用，我们使用公共领域统计软件R编写的脚本将PACo应用于两项已发表的研究。
We present Procrustean Approach to Cophylogeny (PACo), a novel statistical tool to test for congruence between phylogenetic trees, or between phylogenetic distance matrices of associated taxa. Unlike previous tests, PACo evaluates the dependence of one phylogeny upon the other. This makes it especially appropriate to test the classical coevolutionary model that assumes that parasites that spend part of their life in or on their hosts track the phylogeny of their hosts. The new method does not require fully resolved phylogenies and allows for multiple host-parasite associations. PACo produces a Procrustes superimposition plot enabling a graphical assessment of the fit of the parasite phylogeny onto the host phylogeny and a goodness-of-fit statistic, whose significance is established by randomization of the host-parasite association data. The contribution of each individual host-parasite association to the global fit is measured by means of jackknife estimation of their respective squared residuals and confidence intervals associated to each host-parasite link. We carried out different simulations to evaluate the performance of PACo in terms of Type I and Type II errors with respect to two similar published tests. In most instances, PACo performed at least as well as the other tests and showed higher overall statistical power. In addition, the jackknife estimation of squared residuals enabled more elaborate validations about the nature of individual links than the ParaFitLink1 test of the program ParaFit. In order to demonstrate how it can be used in real biological situations, we applied PACo to two published studies using a script written in the public-domain statistical software R.
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影响因子：
64.8
作者：
Buckling, A;Rainey, PB
通讯作者：
Rainey, PB
影响因子：
4
作者：
BARKER, SC;CRIBB, TH;ADLARD, RD
通讯作者：
ADLARD, RD
影响因子：
6.5
作者：
de Vienne, Damien M.;Aguileta, Gabriela;Ollier, Sebastien
通讯作者：
Ollier, Sebastien
影响因子：
5.8
作者：
de Vienne, Damien M.;Giraud, Tatiana;Martin, Olivier C.
通讯作者：
Martin, Olivier C.
DOI：
10.1073/pnas.2533751100
发表时间：
2003-12-23
影响因子：
11.1
作者：
Clayton, DH;Bush, SE;Johnson, KP
通讯作者：
Johnson, KP