On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations.
On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations.
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DOI：
10.1186/1471-2148-10-343
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发表时间：
2010-11-09
影响因子：
3.4
通讯作者：
Spencer M
中科院分区：
文献类型：
--
作者：
Sangaralingam A;Susko E;Bryant D;Spencer M
基于基因含量的系统发育重建方法常常将所有寄生和内共生真细菌（简称寄生虫）归为一类。许多其他证据表明这个寄生虫类群是一种假象。这种假象可能是构建直系同源数据库所使用方法（由于某些未知的偏差）的结果，也可能是用于估计系统发育的方法的结果，或者两者皆是。
我们通过分析三个不同的直系同源数据库（COG、TRIBES和OFAM）来检验寄生虫类群是直系同源鉴定假象这一观点，这些数据库是使用不同方法构建的，因此不太可能有相同的偏差。在每种情况下，我们使用改进版的条件对数行列式距离方法来估计系统发育。如果寄生虫类群在来自所有三个数据库的树中都出现，那么它不太可能是直系同源鉴定假象。
寄生虫中一部分基因家族加速丢失（一种异速进化形式）可能导致从基因含量数据估计系统发育的困难。我们通过应用两种不同的混合模型（系统发育的和非系统发育的）与条件对数行列式相结合，来检验异速进化是估计出假象寄生虫类群的根本原因这一观点。在这些模型中，基因家族分为两类，其中一类在寄生虫中加速丢失。通过条件对数行列式分别从每一类估计距离。如果异速进化是估计寄生虫类群的根本原因，这应该会减少树估计方法将寄生虫归为一类的趋势。
寄生虫类群出现在从所有三个数据库估计出的条件对数行列式树中。这使得它不太可能是数据库构建的假象。非系统发育混合模型给出的树中没有寄生虫类群。然而，系统发育混合模型仍然得出一个有寄生虫类群的树。因此，异速进化是否是估计寄生虫类群的根本原因并不完全清楚。模拟研究表明，系统发育混合模型方法可能不成功，因为它所使用的基因家族增减模型不能充分描述真实数据。
从基因含量数据估计寄生和内共生真细菌可靠系统发育树最成功的方法仍然是诸如SHOT距离方法之类的特定方法。然而，我们在此开发的改进的条件对数行列式方法可能对非寄生虫有用，可在http://www.liv.ac.uk/~cgrbios/cond_logdet.html获取。
Phylogenetic reconstruction methods based on gene content often place all the parasitic and endosymbiotic eubacteria (parasites for short) together in a clan. Many other lines of evidence point to this parasites clan being an artefact. This artefact could be a consequence of the methods used to construct ortholog databases (due to some unknown bias), the methods used to estimate the phylogeny, or both. We test the idea that the parasites clan is an ortholog identification artefact by analyzing three different ortholog databases (COG, TRIBES, and OFAM), which were constructed using different methods, and are thus unlikely to share the same biases. In each case, we estimate a phylogeny using an improved version of the conditioned logdet distance method. If the parasites clan appears in trees from all three databases, it is unlikely to be an ortholog identification artefact. Accelerated loss of a subset of gene families in parasites (a form of heterotachy) may contribute to the difficulty of estimating a phylogeny from gene content data. We test the idea that heterotachy is the underlying reason for the estimation of an artefactual parasites clan by applying two different mixture models (phylogenetic and non-phylogenetic), in combination with conditioned logdet. In these models, there are two categories of gene families, one of which has accelerated loss in parasites. Distances are estimated separately from each category by conditioned logdet. This should reduce the tendency for tree estimation methods to group the parasites together, if heterotachy is the underlying reason for estimation of the parasites clan. The parasites clan appears in conditioned logdet trees estimated from all three databases. This makes it less likely to be an artefact of database construction. The non-phylogenetic mixture model gives trees without a parasites clan. However, the phylogenetic mixture model still results in a tree with a parasites clan. Thus, it is not entirely clear whether heterotachy is the underlying reason for the estimation of a parasites clan. Simulation studies suggest that the phylogenetic mixture model approach may be unsuccessful because the model of gene family gain and loss it uses does not adequately describe the real data. The most successful methods for estimating a reliable phylogenetic tree for parasitic and endosymbiotic eubacteria from gene content data are still ad-hoc approaches such as the SHOT distance method. however, the improved conditioned logdet method we developed here may be useful for non-parasites and can be accessed at http://www.liv.ac.uk/~cgrbios/cond_logdet.html
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DOI：
10.1073/pnas.0400975101
发表时间：
2004-06-29
影响因子：
11.1
作者：
Boussau, B;Karlberg, EO;Andersson, SGE
通讯作者：
Andersson, SGE
树突镜：大型系统发育树的互动观众。
影响因子：
3
作者：
Huson, Daniel H.;Richter, Daniel C.;Rausch, Christian;Dezulian, Tobias;Franz, Markus;Rupp, Regula
通讯作者：
Rupp, Regula
影响因子：
5.8
作者：
Iwasaki, Wataru;Takagi, Toshihisa
通讯作者：
Takagi, Toshihisa
影响因子：
4.1
作者：
Bailey, CD;Fain, MG;Houde, P
通讯作者：
Houde, P
影响因子：
10.7
作者：
Gascuel, O
通讯作者：
Gascuel, O