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Relationships between nomenclature, phylogenetics and systematics
Södertörn University, School of Life Sciences. Göteborgs universitet.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Systematists have become increasingly aware of the limits imposed by the current system of nomenclature for accurately representing evolutionary relationships and managing efficiently names associated with clades. In reaction, a new system of nomenclature, the PhyloCode is being developed that fully recognizes the historical nature of taxonomy and the importance of the cladistics revolution. As a consequence, questions emerge about the new historical entities of systematics, questions that can be apprehended through the lens of epistemology, philosophy of language and metaphysics. What is the ontological nature of entities that lack any other essential features besides spatiotemporal properties? How to depart from the fixed realm of immutable and transcendental essence into a worldview wherein all biological entities are characterized by their temporality and materiality? What are the consequences of nomenclatural decisions on other sectors of biology? With the ever growing sequencing capacity and tree reconstructing abilities, our conceptualization of phylogenetic relationships is changing at an unprecedented pace. Then it begs the question, what prevents communication break down when the references of clades’ names are changing almost on a daily basis. These are some of the fundamental issues I am tackling in the present work. Addressing the ontological issue, I argue that species and clades are best perceived as mereological sums of individuals, which means that each biological individual is the unique individual composed of all its less inclusive individuals and nothing more. I propose to separate the meanings of “clade” and “monophyletic group”. I suggest to use “monophyletic” for an epithet referring to a defining property of a set (a natural kind) and “clade” for a noun which corresponds to a historical entity (an individual) resulting from evolutionary process. I present the idea that a phyloname is not attached to a single clade but to a natural kind containing as members the clades that would be selected in counterfactual phylogenies. The defining properties of this natural kind are provided by the phylogenetic definition. Finally I stress that taxonomists are also driven by the will to narrate the same sort of history, when they adjust the reference of names in light of new phylogenetic data, which leads me to submit that taxa can also be perceived as narratives.

Place, publisher, year, edition, pages
Göteborg: Göteborgs universitet, 2008. , 44 p.
Keyword [en]
PhyloCode, philosophy, systematics, individuality, natural kind, possible worlds, causal theory of reference
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:sh:diva-31241ISBN: 978-91-628-7544-2OAI: oai:DiVA.org:sh-31241DiVA: diva2:1050529
Public defence
2008-09-26, Föreläsningssalen, Department of Zoology, Medicinaregatan 18, Göteborg, 10:00 (English)
Opponent
Supervisors
Available from: 2016-11-29 Created: 2016-11-29 Last updated: 2016-11-29Bibliographically approved
List of papers
1. Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks
Open this publication in new window or tab >>Taxonomic surrogacy in biodiversity assessments, and the meaning of Linnaean ranks
2006 (English)In: Systematics and Biodiversity, ISSN 1477-2000, E-ISSN 1478-0933, Vol. 4, no 2, 149-159 p.Article in journal (Refereed) Published
Abstract [en]

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non-nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy tacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad-scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family-level classifications of polychaetes. We use families as a surrogate for species, and present Shannon-Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.

National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-14295 (URN)10.1017/S1477200005001908 (DOI)000238588700004 ()2-s2.0-33744806071 (ScopusID)
Available from: 2011-12-20 Created: 2011-12-20 Last updated: 2016-11-29Bibliographically approved
2. Stability and universality in the application of taxon names in phylogenetic nomenclature
Open this publication in new window or tab >>Stability and universality in the application of taxon names in phylogenetic nomenclature
2006 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 5, 848-858 p.Article in journal (Refereed) Published
National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6070 (URN)10.1080/10635150600960061 (DOI)000246721800012 ()2-s2.0-39049175702 (ScopusID)
Available from: 2011-02-08 Created: 2011-02-07 Last updated: 2016-11-29Bibliographically approved
3. Species individuality and integration
Open this publication in new window or tab >>Species individuality and integration
(English)Manuscript (preprint) (Other academic)
National Category
Biological Sciences
Identifiers
urn:nbn:se:sh:diva-31240 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2016-11-29 Created: 2016-11-29 Last updated: 2016-11-29Bibliographically approved
4. Contrasting the general with the particular in phylogenetics - a proposal to keep the meanings of mono/paraphyletic and clade/grade separated
Open this publication in new window or tab >>Contrasting the general with the particular in phylogenetics - a proposal to keep the meanings of mono/paraphyletic and clade/grade separated
2008 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 57, no 3, 705-708 p.Article in journal (Refereed) Published
Abstract [en]

Clade and monophyletic group on one hand and grade and paraphyletic group on the other hand are commonly used as pairs of interchangeable terms. I question this apparent synonymy and propose that "monophyly" and "paraphyly" should refer to a property of a set, whereas "clade" and "grade" should apply to individuals resulting from evolutionary process.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:sh:diva-14140 (URN)000258974600003 ()2-s2.0-52249108872 (ScopusID)
Available from: 2011-12-18 Created: 2011-12-16 Last updated: 2016-11-29Bibliographically approved
5. Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names
Open this publication in new window or tab >>Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names
2008 (English)In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 3, 337-347 p.Article in journal (Refereed) Published
Abstract [en]

When scientists use a taxon name like Mammalia, it is important that they talk about the same thing. But, what does it mean to be the same thing in different phylogenetic hypotheses? And, how is taxonomic reference maintained across hypotheses? Here, we discuss the differences between real and hypothetical clades, and how such a distinction relates to the sameness problem. Since hypotheses influence how we perceive things and pursue science, we find it important to have a functioning nomenclatural system for clades as perceived in phylogenetic hypotheses. As a solution to the sameness problem for such clades, we argue that a taxon name does not primarily refer to a single clade that somehow mirror the reality of branches in the tree of life. Instead we suggest that a taxon name refers to a set, or natural kind, of counterfactual and reconstructed clades.

National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6100 (URN)10.1111/j.1463-6409.2007.00323.x (DOI)000254954700008 ()2-s2.0-42149140801 (ScopusID)
Available from: 2011-02-08 Created: 2011-02-08 Last updated: 2016-11-29Bibliographically approved
6. Historicism and essentialism in phylogenetic biology
Open this publication in new window or tab >>Historicism and essentialism in phylogenetic biology
(English)Manuscript (preprint) (Other academic)
National Category
Natural Sciences
Identifiers
urn:nbn:se:sh:diva-6137 (URN)
Note

Som manuskript i avhandling. As manuscript in dissertation.

Available from: 2011-02-10 Created: 2011-02-10 Last updated: 2016-11-29Bibliographically approved

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