Hostname: page-component-78c5997874-8bhkd Total loading time: 0 Render date: 2024-11-13T03:53:58.584Z Has data issue: false hasContentIssue false
  • English
  • Français

The Future of Systematics: Tree Thinking without the Tree

Published online by Cambridge University Press:  01 January 2022

Joel D. Velasco
Get access Rights & Permissions [Opens in a new window]

Abstract

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”

Type
Biology
Information
Philosophy of Science , Volume 79 , Issue 5 , December 2012 , pp. 624 - 636
Copyright
Copyright © The Philosophy of Science Association

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

Footnotes

†

Thanks to audiences at the 2010 PSA meeting, the 2011 ISHPSSB meeting, Caltech, Ohio State, Gustavus Adolphus, and Texas Tech who heard parts of versions of this article and to Matt Barker, Kenny Easwaran, Luke Glynn, Matt Haber, Matt Slater, and Elliott Sober who also provided comments on this article.

References

Andreasen, Robin O. 2004. “The Cladistic Race Concept: A Defense.” Biology and Philosophy 19:425–42.CrossRefGoogle Scholar
Archibald, John M. 2009. “The Puzzle of Plastid Evolution.” Current Biology 19 (2): R81–R88. http://dx.doi.org/10.1016/j.cub.2008.11.067.CrossRefGoogle ScholarPubMed
Avise, John C. 2000. Phylogeography: The History and Formation of Species. Cambridge, MA: Harvard University Press.CrossRefGoogle Scholar
Baum, David A., and Smith, Stacy D.. 2012. Tree Thinking: An Introduction to Phylogenetic Biology. Greenwood Village, CO: Roberts.Google Scholar
Brown, Duncan, and Sjölander, Kimmen. 2006. “Functional Classification Using Phylogenomic Inference.” PLoS 2 (6): e77.Google ScholarPubMed
Cartwright, Nancy. 1989. Nature's Capacities and Their Measurement. Oxford: Oxford University Press.Google Scholar
Darwin, Charles. 1859. The Origin of Species. London: Murray.Google Scholar
Doolittle, W. Ford. 1999. “Phylogenetic Classification and the Universal Tree.” Science 284 (5423): 2124–28.CrossRefGoogle ScholarPubMed
Franklin-Hall, Laura R. 2010. “Trashing Life's Tree.” Biology and Philosophy 25 (4): 689–709.CrossRefGoogle Scholar
Frigg, Roman, and Hartmann, Stephan. 2012. “Models in Science.” In Stanford Encyclopedia of Philosophy, ed. Zalta, Edward N.. Stanford, CA: Stanford University. http://plato.stanford.edu/archives/spr2012/entries/models-science/.Google Scholar
Kitcher, Philip. 2001. Science, Truth, and Democracy. Oxford: Oxford University Press.CrossRefGoogle Scholar
Mallet, James. 2005. “Hybridization as an Invasion of the Genome.” Trends in Ecology and Evolution 20:229–37.CrossRefGoogle ScholarPubMed
McMullin, Ernan. 1985. “Galilean Idealization.” Studies in History and Philosophy of Science 16:247–73.CrossRefGoogle Scholar
O’Hara, Robert. 1988. “Homage to Clio; or, Toward an Historical Philosophy for Evolutionary Biology.” Systematic Zoology 37 (2): 142–55.Google Scholar
O’Hara, Robert. 1997. “Population Thinking and Tree Thinking in Systematics.” Zoologica Scripta 26 (4): 326–29.Google Scholar
O’Malley, Maureen A. 2010. “The First Eukaryote Cell: An Unfinished History of Contestation.” Studies in History and Philosophy of Biological and Biomedical Sciences 41 (3): 212–24.CrossRefGoogle ScholarPubMed
O’Malley, Maureen A., and Boucher, Yan. 2005. “Paradigm Change in Evolutionary Microbiology.” Studies in History and Philosophy of Biological and Biomedical Sciences 36:183–208.CrossRefGoogle ScholarPubMed
O’Malley, Maureen A., Martin, William, and Dupré, John. 2010. “The Tree of Life: Introduction to an Evolutionary Debate.” Biology and Philosophy 25:441–53.CrossRefGoogle Scholar
Sapp, Jan. 2009. The New Foundations of Evolution: On the Tree of Life. Oxford: Oxford University Press.Google Scholar
Soares, Pedro, Ermini, Luca, Thomson, Noel, Mormina, Maru, Rito, Teresa, Rohl, Arne, Salas, Antonio, Oppenheimer, Stephen, Macaulay, Vincent, and Richards, Martin B.. 2009. “Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock.” American Journal of Human Genetics 84:740–59.CrossRefGoogle ScholarPubMed
Sober, Elliott. 2008. Evidence and Evolution. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Templeton, Alan R. 1998. “Human Races: A Genetic and Evolutionary Perspective.” American Anthropologist 100 (3): 632–50.CrossRefGoogle Scholar
Toulmin, Stephen. 1953. The Philosophy of Science: An Introduction. London: Hutchinson's University Library.Google Scholar
Velasco, Joel D. 2010. “Species, Genes, and the Tree of Life.” British Journal for the Philosophy of Science 61:599–619.CrossRefGoogle Scholar
Velasco, Joel D.. 2013. “The Tree of Life.” In The Cambridge Encyclopedia of Darwin and Evolutionary Thought, ed. Ruse, Michael. Cambridge: Cambridge University Press, forthcoming.Google Scholar
Velasco, Joel D., and Sober, Elliott. 2010. “Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection.” Biology and Philosophy 25:675–87.CrossRefGoogle Scholar
Weisberg, Michael. 2007. “Three Kinds of Idealization.” Journal of Philosophy 104 (12): 639–59.CrossRefGoogle Scholar