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Darwin and Phylogenetics: Past and Present

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Abstract

Phylogenetics is the science of tree reconstruction. The evolution and transformations of phylogenetics is analyzed from the unique illustration included in Darwin’s On the Origin of Species. From the nineteenth century up to the present the various treatments of the concept of pattern and process applied to relationships and evolutionary modes are discussed. Emphasis is put on the Hennigian phylogenetics and successive cladistic and probability approaches. The fate of the concept of homology is explored from Darwin’s time up to contemporaneous molecular methods.

T he mental features discoursed of as the analytical, are, in themselves, but little susceptible of analysis. We appreciate them only in their effects

(Edgar A. Poe, Murders in the Rue Morgue).

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Notes

  1. 1.

    Group of organisms classified at any level of classification (example: Homo, taxon on the rank of genus).

  2. 2.

    On this theme, cf. among others, Hall (1994), Sanderson and Hufford (1996).

  3. 3.

    The form’s permanence even if it declines as variations of the archetype.

  4. 4.

    Differentiation of a mother species into daughter species (=speciation).

  5. 5.

    Organisms without a nucleus, with a cell membrane made of certain lipids, generally living in harsh environments.

  6. 6.

    Organisms whose cells have a nucleus.

  7. 7.

    Horizontal gene transfer: a case where genes are transferred from one species to another and not from one generation to another within a same species (for example, bacteria recuperate DNA from their hosts, DNA exchanges between different bacteria).

  8. 8.

    Mobile, multi-celled organisms with collagen; synonym for Animalia, animals.

  9. 9.

    In French, cf. Dupuis (1986) and Tassy (1983).

  10. 10.

    For a brief history of structural cladistics, cf. Tassy (2005).

  11. 11.

    Bayesian probabilities: probability statistics named in reference to English mathematician Thomas Bayes (1702–1761). In phylogenetics, probability methods for building kinship trees.

  12. 12.

    Evolutionary step: unit of evolution linked to the transformation from one character state to another.

  13. 13.

    Two types of mutations affecting genes (transition: substitution of a purine base for another and of a pyrimidine base for another, and transversion: substitution of a purine base for a pyrimidine base).

  14. 14.

    Cf. the discussion, among others, in Tassy (1991: 248–250).

  15. 15.

    Branch: in the phylogenetic tree, a segment connecting to nodes (internal branch) or a node and a terminal taxon (external branch).

  16. 16.

    Nucleotide substitution: in a gene, replacement of a nucleotide by another (e.g. adenine by guanine, two purine bases).

  17. 17.

    This is what Deleporte (2004) and Lecointre (2004) argue.

  18. 18.

    Two groups of organisms (clades) descended from one exclusive ancestral species.

  19. 19.

    Unsaturated gene: a gene for which there are not multiple nucleotide substitutions at a given site.

  20. 20.

    Gingerich and Russell (1981), Gingerich et al. (2001), Thewissen et al. (2001).

  21. 21.

    Regular rhythm of nucleotide substitution.

  22. 22.

    Cf. discussion and references in Burbrink and Pyron (2008).

  23. 23.

    Total evidence, supermatrix: the sum total of data (characters) that is accessible and analysed simultaneously during a phylogenetic analysis.

  24. 24.

    Tree of synthesis built from the combination of several trees that does not necessarily have the same taxa.

  25. 25.

    Baum and Ragan (1992), Cotton and Wilkinson (2007), Steel and Rodrigo (2008).

  26. 26.

    Group of metazoans with debated affinities, including one single marine species, Trichoplax adhaerens, an organism in the form of a pancake measuring 0.5 mm in diameter, with an extremely simple organisational plan.

  27. 27.

    Out-group: group of organisms not belonging to a phylogenetically analysed group, chosen to orient the transformation of characters from the primitive to the derived. Example: in order to study Primates phylogeny, any other group(s) of Mammalia can be used as extra-groups.

  28. 28.

    Group of animals comprising hydra, sea anemones, corals, and jellyfish.

  29. 29.

    Animals with bilateral symmetry.

  30. 30.

    Hypothesised derived traits at the node: resemblances assumed to be due to common ancestry.

  31. 31.

    Retention index: measure of characters’ degree of homology (which takes into account the number of observed transformations on the tree in relation to the minimum and maximum number of possible transformations).

  32. 32.

    Group comprising true animals, characterised by the presence of true embryonic layers.

  33. 33.

    Posterior probabilities: in Bayesian probabilities applied to phylogenetics, calculation of the degree of solidity of the tree’s different nodes.

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Authors and Affiliations

  1. CR2P CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum national d’Histoire naturelle, CP 38, 57 Cuvier, 75230, Paris Cedex 05, France

    Pascal Tassy

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  1. Génétique Animale et Biologie Intégrative, INRA, UMR 1313, Jouy-en-Josas, France

    Thomas Heams

  2. Institut d’Histoire et de Philosophie des Sciences et des Techniques, CNRS/Université Paris I Sorbonne/ENS, Paris, France

    Philippe Huneman

  3. Museum National d'Histoire Naturelle (MNHN), Paris, France

    Guillaume Lecointre

  4. Éditions Matériologiques, Paris, France

    Marc Silberstein

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Tassy, P. (2015). Darwin and Phylogenetics: Past and Present. In: Heams, T., Huneman, P., Lecointre, G., Silberstein, M. (eds) Handbook of Evolutionary Thinking in the Sciences. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9014-7_18

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