David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Ezio Di Nucci
Jack Alan Reynolds
Learn more about PhilPapers
Biology and Philosophy 25 (4):675-687 (2010)
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.
|Keywords||Philosophy Evolutionary Biology Philosophy of Biology|
|Categories||categorize this paper)|
Setup an account with your affiliations in order to access resources via your University's proxy server
Configure custom proxy (use this if your affiliation does not provide a proxy)
|Through your library|
References found in this work BETA
Elliott Sober (2008). Evidence and Evolution: The Logic Behind the Science. Cambridge University Press.
Malcolm Forster & Elliott Sober (1994). How to Tell When Simpler, More Unified, or Less Ad Hoc Theories Will Provide More Accurate Predictions. British Journal for the Philosophy of Science 45 (1):1-35.
Citations of this work BETA
Joel D. Velasco (2012). The Future of Systematics: Tree Thinking Without the Tree. Philosophy of Science 79 (5):624-636.
Similar books and articles
Jacqueline Lück, Hermann B. Lück & Mohammed Bakkali (1990). A Comprehensive Model for Acrotonic, Mesotonic and Basitonic Branchings in Plants. Acta Biotheoretica 38 (3-4):257-288.
Frédéric Bouchard (2010). Symbiosis, Lateral Function Transfer and the (Many) Saplings of Life. Biology and Philosophy 24 (4):623-641.
Gregory J. Morgan (2010). Evaluating Maclaurin and Sterelny's Conception of Biodiversity in Cases of Frequent, Promiscuous Lateral Gene Transfer. Biology and Philosophy 25 (4):603-621.
Jeffrey G. Lawrence & Adam C. Retchless (2010). The Myth of Bacterial Species and Speciation. Biology and Philosophy 25 (4):569-588.
Elliott Sober (2002). Instrumentalism, Parsimony, and the Akaike Framework. Proceedings of the Philosophy of Science Association 2002 (3):S112-S123.
Eric Bapteste & Richard M. Burian (2010). On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation. Biology and Philosophy 25 (4):711-736.
Maureen A. O’Malley (2010). Ernst Mayr, the Tree of Life, and Philosophy of Biology. Biology and Philosophy 25 (4):529-552.
W. Ford Doolittle (2010). The Attempt on the Life of the Tree of Life: Science, Philosophy and Politics. Biology and Philosophy 25 (4):455-473.
Joel D. Velasco (2013). Phylogeny as Population History. Philosophy and Theory in Biology 5 (20130604).
Robert G. Beiko (2010). Gene Sharing and Genome Evolution: Networks in Trees and Trees in Networks. Biology and Philosophy 25 (4):659-673.
Added to index2010-05-12
Total downloads52 ( #79,500 of 1,793,261 )
Recent downloads (6 months)14 ( #54,553 of 1,793,261 )
How can I increase my downloads?