Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution.
Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution.
复制标题
DOI：
10.1186/gb-2007-8-7-r141
复制
发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
Hahn, Matthew W.
中科院分区：
文献类型：
--
作者：
Hahn, Matthew W.
比较基因组学研究揭示了整个基因通过复制和假基因的频繁获得和丢失。推断基因得失的数量和时间的一种常用方法是使每个基因家族的基因树与所考虑的分类群的物种树相一致。最近使用这种方法的研究发现，脊椎动物基因组中存在大量的古代复制和最近的丢失。我证明，当推断的基因树不正确时，树协调方法是有偏见的。这种偏向将重复放置在树根上，并将损失放置在树的顶端。我证明了当在多个哺乳动物和果蝇基因组上进行树协调时，这种偏见是存在的，并且基因树上较低的引导截止值会导致更极端的偏见。我还建议了一种处理调和偏差的方法，尽管这种方法只修正了物种树某些分支上的基因增益数量。根据所给出的结果，很可能大多数树协调分析都显示出偏差，除非所使用的基因树特别好地分辨和得到很好的支持。这些结果对之前的结论提出了质疑，即脊椎动物基因组历史的特点是许多古代复制和许多最近的基因丢失。
Comparative genomic studies are revealing frequent gains and losses of whole genes via duplication and pseudogenization. One commonly used method for inferring the number and timing of gene gains and losses reconciles the gene tree for each gene family with the species tree of the taxa considered. Recent studies using this approach have found a large number of ancient duplications and recent losses among vertebrate genomes. I show that tree reconciliation methods are biased when the inferred gene tree is not correct. This bias places duplicates towards the root of the tree and losses towards the tips of the tree. I demonstrate that this bias is present when tree reconciliation is conducted on both multiple mammal and Drosophila genomes, and that lower bootstrap cut-off values on gene trees lead to more extreme bias. I also suggest a method for dealing with reconciliation bias, although this method only corrects for the number of gene gains on some branches of the species tree. Based on the results presented, it is likely that most tree reconciliation analyses show biases, unless the gene trees used are exceptionally well-resolved and well-supported. These results cast doubt upon previous conclusions that vertebrate genome history has been marked by many ancient duplications and many recent gene losses.
登录
查看更多内容
影响因子：
3.7
作者：
Demuth JP;De Bie T;Stajich JE;Cristianini N;Hahn MW
通讯作者：
Hahn MW
影响因子：
3.4
作者：
Stefanović S;Rice DW;Palmer JD
通讯作者：
Palmer JD
影响因子：
4.5
作者：
Pollard DA;Iyer VN;Moses AM;Eisen MB
通讯作者：
Eisen MB
影响因子：
10.7
作者：
SAITOU, N;NEI, M
通讯作者：
NEI, M
影响因子：
7
作者：
Hahn, MW;De Bie, T;Cristianini, N
通讯作者：
Cristianini, N