Abstract
Gene family evolution is determined by microevolutionary processes (e.g., point mutations) and macroevolutionary processes (e.g., gene duplication and loss), yet macroevolutionary considerations are rarely incorporated into gene phylogeny reconstruction methods. We present a dynamic program to find the most parsimonious gene family tree with respect to a macroevolutionary optimization criterion, the weighted sum of the number of gene duplications and losses. The existence of a polynomial delay algorithm for duplication/loss phylogeny reconstruction stands in contrast to most formulations of phylogeny reconstruction, which are NP-complete. We next extend this result to obtain a two-phase method for gene tree reconstruction that takes both micro- and macroevolution into account. In the first phase, a gene tree is constructed from sequence data, using any of the previously known algorithms for gene phylogeny construction. In the second phase, the tree is refined by rearranging regions of the tree that do not have strong support in the sequence data to minimize the duplication/lost cost. Components of the tree with strong support are left intact. This hybrid approach incorporates both micro- and macroevolutionary considerations, yet its computational requirements are modest in practice because the two-phase approach constrains the search space. Our hybrid algorithm can also be used to resolve nonbinary nodes in a multifurcating gene tree. We have implemented these algorithms in a software tool, NOTUNG 2.0, that can be used as a unified framework for gene tree reconstruction or as an exploratory analysis tool that can be applied post hoc to any rooted tree with bootstrap values. The NOTUNG 2.0 graphical user interface can be used to visualize alternate duplication/loss histories, root trees according to duplication and loss parsimony, manipulate and annotate gene trees, and estimate gene duplication times. It also offers a command line option that enables high-throughput analysis of a large number of trees.
Highlights
The evolutionary history of a gene family is determined by a combination of microevolutionary events and macroevolutionary events
Gene tree reconstruction should be based on a model that incorporates both micro- and macroevolutionary events (Goodman et al, 1979), yet few phylogeny reconstruction tools based on such a unified model are available
Given a species tree and the number of gene family members found in each species as input, our algorithm will construct a tree with the fewest duplications and losses required to explain the data
Summary
The evolutionary history of a gene family is determined by a combination of microevolutionary events (sequence evolution) and macroevolutionary events. In contrast to most phylogeny reconstruction problems, which are NP-complete (Chor and Tuller, 2005; Day et al, 1986; Day, 1987), our results show that macroevolutionary parsimony can be solved in polynomial time per output tree Using this result, we develop a two-phase approach to gene tree reconstruction that incorporates sequence evolution, gene duplication and gene loss in the evaluation of alternate phylogenies. By reserving consideration of macroevolutionary events until phase two and focusing only on those areas where the sequence data cannot resolve the topology, this hybrid approach reduces the search space, leading to a method that incorporates both types of events, yet has modest computational requirements This hybrid approach can be used to resolve non-binary nodes in a multifurcating tree.
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