Abstract
A phylogeny that allows for lateral gene transfer (LGT) can be thought of as a strictly branching tree (all of whose branches are vertical) to which lateral branches have been added. Given that the goal of phylogenetics is to depict evolutionary history, we should look for the best supported phylogenetic network and not restrict ourselves to considering trees. However, the obvious extensions of popular tree-based methods such as maximum parsimony and maximum likelihood face a serious problem—if we judge networks by fit to data alone, networks that have lateral branches will always fit the data at least as well as any network that restricts itself to vertical branches. This is analogous to the well-studied problem of overfitting data in the curve-fitting problem. Analogous problems often have analogous solutions and we propose to treat network inference as a case of model selection and use the Akaike Information Criterion (AIC). Strictly tree-like networks are more parsimonious than those that postulate lateral as well as vertical branches. This leads to the conclusion that we should not always infer LGT events whenever it would improve our fit-to-data, but should do so only when the improved fit is larger than the penalty for adding extra lateral branches.
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Notes
It may not be possible to recover the true network. The data might be structured so that a false lateral branch will reduce the parsimony score more than one or more of the real lateral branches. In this case, no matter what the threshold, parsimony cannot recover the true network.
To derive the AIC, a few background assumptions are needed. For example, there are certain regularity conditions that have to hold for the likelihood function to be asymptotically normal and there has to be enough data to ensure that the likelihood function will approximate its asymptotic properties. See Forster and Sober (1994) and Burnham and Anderson (2002) for more details.
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Acknowledgments
We thank David Baum, Rob Beiko, Matt Haber, Ehud Lamm, Bret Larget, Luay Nakhleh, Mike Steel, and an anonymous referee for helpful discussion. This paper was first presented at the workshop, Perspectives on the Tree of Life, sponsored by the Leverhulme Trust and held in Halifax, Nova Scotia, July, 2009.
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Velasco, J.D., Sober, E. Testing for treeness: lateral gene transfer, phylogenetic inference, and model selection. Biol Philos 25, 675–687 (2010). https://doi.org/10.1007/s10539-010-9222-6
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DOI: https://doi.org/10.1007/s10539-010-9222-6