简约树和解
Unifying Parsimonious Tree Reconciliation
摘要：
进化是一个受各种环境因素影响的过程，例如不同物种，基因和地理特性之间的相互作用。因此，研究多个物种、它们的基因和它们所生活的环境的综合进化历史是很有趣的。一个常见的方法来解决这个问题的研究是描述每一个单独的进化作为一个系统发育树，并构建一个树和解，这是相对于一个给定的事件模型简约。不幸的是，大多数以前的方法都是专为宿主-寄生虫系统，基因树/物种树和解，或植物地理学。因此，需要一种方法，其解决绘制系统发育树并覆盖所有种类的共同进化系统的一般问题，包括例如，捕食者-猎物和共生关系。为了克服这一差距，我们引入了一个广义的cophylogenetic事件模型，考虑局部协同进化事件的组合完备集。我们给出了一个基于动态规划的启发式算法，在O（n^2）的时间内解决最大简约和解问题，对于两个最多有n个叶子的算法。此外，我们提出了一个精确的分支定界算法，它使用的结果从动态规划启发式丢弃部分和解。该方法已实现为Java应用程序，可从http://pacosy.informatik.uni-leipzig.de/coresym免费获得。
英文摘要：
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.
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