A hybrid micro-macroevolutionary approach to gene tree reconstruction

Dannie Durand, Bjarni V. Halldórsson, Benjamin Vernot*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

203 Citations (Scopus)


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 phytogeny 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 phytogeny reconstruction stands in contrast to most formulations of phytogeny 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 phytogeny 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.

Original languageEnglish
Pages (from-to)320-335
Number of pages16
JournalJournal of Computational Biology
Issue number2
Publication statusPublished - Mar 2006

Other keywords

  • Duplication/loss Parsimony
  • Gene duplication
  • Gene family
  • Phylogeny
  • Reconciliation


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