David Bourget (Western Ontario)
David Chalmers (ANU, NYU)
Rafael De Clercq
Jack Alan Reynolds
Learn more about PhilPapers
Philosophy and Theory in Biology 5 (20130604) (2013)
The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species
|Keywords||No keywords specified (fix it)|
|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
No references found.
Citations of this work BETA
Joel D. Velasco (2013). Philosophy and Phylogenetics. Philosophy Compass 8 (10):990-998.
Similar books and articles
Olivier Rieppel (2010). The Series, the Network, and the Tree: Changing Metaphors of Order in Nature. Biology and Philosophy 25 (4):475-496.
Bengt Autzen (2011). Constraining Prior Probabilities of Phylogenetic Trees. Biology and Philosophy 26 (4):567-581.
Joel D. Velasco (2008). Species Concepts Should Not Conflict with Evolutionary History, but Often Do. Studies in History and Philosophy of Science Part C 39 (4):407-414.
Davide Pisani, Michael J. Benton & Mark Wilkinson (2007). Congruence of Morphological and Molecular Phylogenies. Acta Biotheoretica 55 (3):269-281.
Joel D. Velasco (2009). When Monophyly is Not Enough: Exclusivity as the Key to Defining a Phylogenetic Species Concept. Biology and Philosophy 24 (4):473-486.
Frederic Tremblay (2013). Nicolai Hartmann and the Metaphysical Foundation of Phylogenetic Systematics. Biological Theory 7 (1):56-68.
Joel D. Velasco & Elliott Sober (2010). Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. Biology and Philosophy 25 (4):675-687.
Wybo Houkes (2012). Tales of Tools and Trees: Phylogenetic Analysis and Explanation in Evolutionary Archaeology. In Henk W. de Regt (ed.), Epsa Philosophy of Science: Amsterdam 2009. Springer. 89--100.
Matthew H. Haber (2012). Multilevel Lineages and Multidimensional Trees: The Levels of Lineage and Phylogeny Reconstruction. Philosophy of Science 79 (5):609-623.
Joel D. Velasco (2008). The Prior Probabilities of Phylogenetic Trees. Biology and Philosophy 23 (4):455-473.
Christopher D. Horvath (1997). Discussion: Phylogenetic Species Concept: Pluralism, Monism, and History. [REVIEW] Biology and Philosophy 12 (2):225-232.
Richard Richards (2003). Character Individuation in Phylogenetic Inference. Philosophy of Science 70 (2):264-279.
Jeffrey Schwartz (2009). Reflections on Systematics and Phylogenetic Reconstruction. Acta Biotheoretica 57 (1-2):295-305.
Carl Chung (2003). On the Origin of the Typological/Population Distinction in Ernst Mayr's Changing Views of Species, 1942-1959. Studies in History and Philosophy of Science Part C 34 (2):277-296.
Anya Plutynski (2004). Seeing the Forst for the Trees. [REVIEW] Biology and Philosophy 19 (2):299-303.
Added to index2011-10-19
Total downloads23 ( #83,968 of 1,413,339 )
Recent downloads (6 months)1 ( #154,160 of 1,413,339 )
How can I increase my downloads?