Hostname: page-component-78c5997874-t5tsf Total loading time: 0 Render date: 2024-11-13T03:37:41.120Z Has data issue: false hasContentIssue false
  • English
  • Français

Multilevel Lineages and Multidimensional Trees: The Levels of Lineage and Phylogeny Reconstruction

Published online by Cambridge University Press:  01 January 2022

Matthew H. Haber
Get access Rights & Permissions [Opens in a new window]

Abstract

The relation among method, concept, and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: the additional challenges phylogeneticists face when reconstructing phylogeny not at a single level but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory, and concepts may be understood in systematics, which, in turn, provides data for a more general account.

Type
Biology
Information
Philosophy of Science , Volume 79 , Issue 5 , December 2012 , pp. 609 - 623
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

†

I thank Marc Ereshefsky, Joel Velasco, Richard Richards, and Tudor Baetu.

References

Avise, John C., and Robinson, Terence J.. 2008. “Hemiplasy: A New Term in the Lexicon of Phylogenetics.” Systematic Biology 57 (3): 503–7.CrossRefGoogle ScholarPubMed
Avise, John C., and Wollenberg, Kurt. 1997. “Phylogenetics and the Origin of Species.” Proceedings of the National Academy of Sciences 94 (15): 7748–55.CrossRefGoogle ScholarPubMed
Baetu, Tudor. Forthcoming. “Defining Species: A Multi-level Approach.” Acta Biotheoretica.Google Scholar
Bouchard, Frédéric. 2008. “Causal Processes, Fitness, and the Differential Persistence of Lineages.” Philosophy of Science 75 (5): 560–70.CrossRefGoogle Scholar
Bouchard, Frédéric. 2010. “Symbiosis, Lateral Function Transfer and the (Many) Saplings of Life.” Biology and Philosophy 25:623–41.CrossRefGoogle Scholar
Cartwright, Nancy. 1983. How the Laws of Physics Lie. Oxford: Oxford University Press.CrossRefGoogle Scholar
Cech, Thomas R. 1986. “A Model for the RNA-Catalyzed Replication of RNA.” Proceedings of the National Academy of Sciences 83 (12): 4360–63.CrossRefGoogle Scholar
Coyne, Jerry A., and Orr, H. Allen. 2004. Speciation. Sunderland, MA: Sinauer.Google Scholar
Degnan, James H., and Rosenberg, Noah A.. 2006. “Discordance of Species Trees with Their Most Likely Gene Trees.” PLoS Genet 2 (5): e68.CrossRefGoogle ScholarPubMed
Degnan, James H., and Rosenberg, Noah A.. 2009. “Gene Tree Discordance, Phylogenetic Inference and the Multispecies Coalescent.” Trends in Ecology and Evolution 24 (6): 332–40.CrossRefGoogle ScholarPubMed
de Queiroz, Kevin 1998. “The General Lineage Concept of Species, Species Criteria, and the Process of Speciation.” In Endless Forms: Species and Speciation, ed. Howard, Daniel J. and Berlocher, Stewart H., 57–75. Oxford: Oxford University Press.Google Scholar
Doolittle, W. Ford, and Bapteste, Eric. 2007. “Pattern Pluralism and the Tree of Life Hypothesis.” Proceedings of the National Academy of Sciences 104 (7): 2043–49.CrossRefGoogle ScholarPubMed
Doyle, Jeff J. 1992. “Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy.” Systematic Botany 17 (1): 144–63.CrossRefGoogle Scholar
Dupré, John. 1995. The Disorder of Things: Metaphysical Foundations of the Disunity of Science. Cambridge, MA: Harvard University Press.Google Scholar
Dupré, John. 2010. “The Polygenomic Organism.” Sociological Review 58:19–31.CrossRefGoogle Scholar
Dupré, John, and O’Malley, Maureen A.. 2009. “Varieties of Living Things: Life at the Intersection of Lineage and Metabolism.” Philosophy and Theory in Biology 1:1–25.CrossRefGoogle Scholar
Ereshefsky, Marc. 1992. “Eliminative Pluralism.” Philosophy of Science 59 (4): 671–90.CrossRefGoogle Scholar
Ereshefsky, Marc. 2010. “Microbiology and the Species Problem.” Biology and Philosophy 25 (4): 553–68.CrossRefGoogle Scholar
Felsenstein, Joseph. 2004. Inferring Phylogenies. Sunderland, MA: Sinauer.Google Scholar
Galtier, Nicolas, and Daubin, Vincent. 2008. “Dealing with Incongruence in Phylogenomic Analyses.” Philosophical Transactions of the Royal Society B 363 (1512): 4023–29.CrossRefGoogle Scholar
Gánti, Tibor. 2003. The Principles of Life. Trans. Griesemer, James and Szathmáry, Eörs. Oxford: Oxford University Press.CrossRefGoogle Scholar
Ghiselin, Michael T. 1974. “A Radical Solution to the Species Problem.” Systematic Zoology 23 (4): 536–44.CrossRefGoogle Scholar
Giere, Ronald N. 1997. Understanding Scientific Reasoning. 4th ed. Fort Worth, TX: Harcourt Brace.Google Scholar
Godfrey-Smith, Peter. 2009. Darwinian Populations and Natural Selection. Oxford: Oxford University Press.CrossRefGoogle Scholar
Griesemer, James. 2000a. “Development, Culture, and the Units of Inheritance.” Philosophy of Science 67:S348–S368.CrossRefGoogle Scholar
Griesemer, James. 2000b. “The Units of Evolutionary Transition.” Selection 1 (1–3): 67–80.CrossRefGoogle Scholar
Griffiths, Graham C. D. 1974. “On the Foundations of Biological Systematics.” Acta Biotheoretica 23 (3): 85–131.CrossRefGoogle Scholar
Haber, Matthew H. 2013. “Colonies Are Individuals: Revisiting the Superorganism Revival.” In From Groups to Individuals: Perspectives on Biological Associations and Emerging Individuality, ed. Bouchard, Frédéric and Huneman, Philippe. Cambridge, MA: MIT Press, forthcoming.Google Scholar
Hamilton, Andrew, and Haber, Matthew H.. 2006. “Clades Are Reproducers.” Biological Theory 1 (4): 381–91.CrossRefGoogle Scholar
Hamilton, Andrew, Smith, Nathan R., and Haber, Matthew H.. 2009. “Social Insects and the Individuality Thesis: Cohesion and the Colony as a Selectable Individual.” In Organization of Insect Societies, ed. Gadau, Jürgen and Fewell, Jennifer, 572–89. Cambridge, MA: Harvard University Press.Google Scholar
Harrison, Richard G. 1998. “Linking Evolutionary Pattern and Process: The Relevance of Species Concepts for the Study of Speciation.” In Endless Forms: Species and Speciation, ed. Howard, Daniel J. and Berlocher, Stewart H., 19–31. Oxford: Oxford University Press.Google Scholar
Hennig, Willi. 1966. Phylogenetic Systematics. Urbana: University of Illinois Press.Google Scholar
Hudson, Richard R. 1983. “Testing the Constant-Rate Neutral Allele Model with Protein Sequence Data.” Evolution 37 (1): 203–17.CrossRefGoogle ScholarPubMed
Hull, David L. 1976. “Are Species Really Individuals?” Systematic Zoology 25 (2): 174–91.CrossRefGoogle Scholar
Hull, David L.. 1978. “A Matter of Individuality.” Philosophy of Science 45 (3): 335–60.CrossRefGoogle Scholar
Janzen, Daniel H. 1977. “What Are Dandelions and Aphids?” American Naturalist 111 (979): 586–89.CrossRefGoogle Scholar
Kingman, John F. C. 1982. “On the Genealogy of Large Populations.” Journal of Applied Probability 19:27–43.CrossRefGoogle Scholar
Maddison, Wayne P. 1997. “Gene Trees in Species Trees.” Systematic Biology 46 (3): 523–36.CrossRefGoogle Scholar
Martens, Johannes. 2010. “Organisms in Evolution.” History and Philosophy of the Life Sciences 32 (2–3): 373–400.Google Scholar
Maynard-Smith, John, and Szathmáry, Eörs. 1998. The Major Transitions in Evolution. Oxford: Oxford University Press.Google Scholar
Mishler, Brent D. 1999. “Getting Rid of Species.” In Species: New Interdisciplinary Essays, ed. Wilson, Robert A., 141–85. Cambridge, MA: MIT Press.Google Scholar
Okasha, Samir. 2003. “Does the Concept of ‘Clade Selection’ Make Sense?” Philosophy of Science 70 (4): 739–51.CrossRefGoogle Scholar
Okasha, Samir. 2006. Evolution and the Levels of Selection. Oxford: Oxford University Press.CrossRefGoogle Scholar
Okasha, Samir. 2011. “Biological Ontology and Hierarchical Organization: A Defense of Rank Freedom.” In The Major Transitions in Evolution Revisited, ed. Calcott, Brett and Sterelny, Kim, 53–64. Cambridge, MA: MIT Press.CrossRefGoogle Scholar
Pamilo, Pekka, and Nei, Masatoshi. 1988. “Relationships between Gene Trees and Species Trees.” Molecular Biology and Evolution 5 (5): 568–83.Google ScholarPubMed
Potochnik, Angela, and McGill, Brian. 2012. “The Limitations of Hierarchical Organization.” Philosophy of Science 79 (1): 120–40.CrossRefGoogle Scholar
Simpson, George Gaylord. 1961. Principles of Animal Taxonomy. New York: Columbia University Press.CrossRefGoogle Scholar
Sober, Elliott. 1980. “Evolution, Population Thinking, and Essentialism.” Philosophy of Science 47 (3): 350–83.CrossRefGoogle Scholar
Eörs, Szathmáry. 2000. “The Evolution of Replicators.” Philosophical Transactions of the Royal Society of London B 355 (1403): 1669–76.CrossRefGoogle Scholar
Tajima, Fumio. 1983. “Evolutionary Relationship of DNA Sequences in Finite Populations.” Genetics 105 (2): 437–60.CrossRefGoogle ScholarPubMed
Teller, Paul. 2001. “Twilight of the Perfect Model Model.” Erkenntnis 55:393–415.CrossRefGoogle Scholar
Velasco, Joel D. 2008. “Species Concepts Should Not Conflict with Evolutionary History, but Often Do.” Studies in History and Philosophy of Biological and Biomedical Sciences 39 (4): 407–14.CrossRefGoogle ScholarPubMed
Wiley, Edward O. 1978. “The Evolutionary Species Concept Reconsidered.” Systematic Zoology 27 (1): 17–26.CrossRefGoogle Scholar
Wimsatt, William C. 1972. “Complexity and Organization.” In PSA 1972: Proceedings of the 1972 Biennial Meeting of the Philosophy of Science Association, ed. Schaffner, Kenneth F. and Cohen, Robert Sonné, 67–86. East Lansing, MI: Philosophy of Science Association.Google Scholar