Gaps: an elusive source of phylogenetic information.
Gaps: an elusive source of phylogenetic information.
复制标题
差距：系统发育信息的难以捉摸的来源。
作者：
K. Saurabh;B. Holland;G. Gibb;D. Penny
在本文中，我们使用一个示例滨鸟数据集来探索关于对齐和遗传估计之间相互作用的三个相关问题：
1)gap-rich比对是否可以用于合理准确和无偏的系统发育推断？2)gap中包含了多少系统发育信息
与单独的核苷酸相比，这些特征如何？3)插入/缺失过程的模型是否有利，如果有利，在什么水平的系统发育分化？我们报告说，有相当多的信息创建的插入/缺失（插入/缺失）的过程中，是潜在的系统发育推断。理想情况下，我们应该能够独立地获得相同的树从核苷酸字符和间隙字符，但是，仍然有相当大的变化，在不同的程序产生的比对，我们预测，更好的和更容易处理的计算模型的indel过程之前，间隙中的信息可以充分利用系统发育推断。
In this paper, we use an example shorebird data set to explore three related questions regarding the interplay between alignment and phylogeny estimation:
1) can gap-rich alignments be used for reasonably accurate and unbiased phylogenetic inference? 2) How much phylogenetic information is contained in gap
characters as compared with the nucleotides alone? 3) Are models of the insertion/deletion process advantageous and if so at what level of phylogenetic divergence? We report that there is considerable information created by the indel (insertion/deletion) process that is potentially available for phylogenetic inference. Ideally, we should be able to independently obtain the same tree from both nucleotide characters and from gap characters; however, there is still considerable variability in the alignments produced by different programs.We predict that better and more computationally tractable models of the indel process will be required before the information in gaps can be fully exploited for phylogenetic inference.