Cophylogeny reconstruction via an approximate Bayesian computation.
Cophylogeny reconstruction via an approximate Bayesian computation.
复制标题
通过近似贝叶斯计算进行的cophyly重建。
DOI：
10.1093/sysbio/syu129
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发表时间：
2015-05
影响因子：
6.5
通讯作者：
Sagot MF
中科院分区：
文献类型：
--
作者：
Baudet C;Donati B;Sinaimeri B;Crescenzi P;Gautier C;Matias C;Sagot MF
尽管关于研究寄主-寄生虫关联的共生重建的文献越来越多，但了解这类系统的共同进化史仍然是一个远未解决的问题。大多数宿主-寄生虫调节算法使用基于事件的模型，其中事件通常包括协同指定、复制、丢失和宿主切换(子集)。所有已知的节俭的基于事件的方法然后将成本分配给每种类型的事件，以便找到最小成本的重建。这种做法的主要问题是，事件的费用严重影响了所取得的和解结果。一些早期的方法试图通过寻找Pareto解集来避免这个问题，因此通过在一些最小化约束下考虑事件成本。为了解决这个问题，我们开发了一种称为Coala的算法，用于基于近似贝叶斯计算方法估计事件的频率。这种方法的好处有两个方面：(1)它提供了对用于对账的费用集合的更大信心，(2)在数据集由具有大量分类群的树组成的情况下，它允许估计事件的频率。我们在模拟数据集和生物数据集上对我们的方法进行了评估。我们表明，在这两种情况下，对于同一对寄主和寄生树，不同的事件频率集导致同样可能的解决方案。此外，这些解决方案通常在推断事件的数量方面存在很大差异。在试图对这种和解进行任何进一步的生物学解释之前，考虑到这一点似乎至关重要。更广泛地说，我们还表明，根据输入宿主和寄生树的不同，这组频率可能会有很大的不同。因此，不分青红皂白地应用标准成本向量可能不是一个好策略。
Despite an increasingly vast literature on cophylogenetic reconstructions for studying host–parasite associations, understanding the common evolutionary history of such systems remains a problem that is far from being solved. Most algorithms for host–parasite reconciliation use an event-based model, where the events include in general (a subset of) cospeciation, duplication, loss, and host switch. All known parsimonious event-based methods then assign a cost to each type of event in order to find a reconstruction of minimum cost. The main problem with this approach is that the cost of the events strongly influences the reconciliation obtained. Some earlier approaches attempt to avoid this problem by finding a Pareto set of solutions and hence by considering event costs under some minimization constraints. To deal with this problem, we developed an algorithm, called Coala, for estimating the frequency of the events based on an approximate Bayesian computation approach. The benefits of this method are 2-fold: (i) it provides more confidence in the set of costs to be used in a reconciliation, and (ii) it allows estimation of the frequency of the events in cases where the data set consists of trees with a large number of taxa. We evaluate our method on simulated and on biological data sets. We show that in both cases, for the same pair of host and parasite trees, different sets of frequencies for the events lead to equally probable solutions. Moreover, often these solutions differ greatly in terms of the number of inferred events. It appears crucial to take this into account before attempting any further biological interpretation of such reconciliations. More generally, we also show that the set of frequencies can vary widely depending on the input host and parasite trees. Indiscriminately applying a standard vector of costs may thus not be a good strategy.
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影响因子：
1.9
作者：
Baroni, M;Grünewald, S;Semple, C
通讯作者：
Semple, C
影响因子：
4.1
作者：
Guigo, R;Muchnik, I;Smith, TF
通讯作者：
Smith, TF
影响因子：
2
作者：
DAY, WHE
通讯作者：
DAY, WHE
DOI：
10.1186/1748-7188-5-16
发表时间：
2010-02-03
期刊：
Algorithms for molecular biology : AMB
影响因子：
--
作者：
Conow C;Fielder D;Ovadia Y;Libeskind-Hadas R
通讯作者：
Libeskind-Hadas R
DOI：
10.1109/tcbb.2009.32
发表时间：
2009-07-01
影响因子：
4.5
作者：
Bryant, David;Steel, Mike
通讯作者：
Steel, Mike