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  • 1.
    Bertrand, Yann
    et al.
    Södertörn University, School of Life Sciences. Muséum National d'Histoire Naturelle, Paris, France / Göteborgs universitet.
    Härlin, Mikael
    Södertörn University, School of Life Sciences.
    Historicism and essentialism in phylogenetic biologyManuscript (preprint) (Other academic)
  • 2.
    Bertrand, Yann
    et al.
    Södertörn University, School of Life Sciences. Muséum National d'Histoire Naturelle, Paris, France / Göteborgs universitet.
    Härlin, Mikael
    Södertörn University, School of Life Sciences.
    Phylogenetic hypotheses, taxonomic sameness and the reference of taxon names2008In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 37, no 3, p. 337-347Article in journal (Refereed)
    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.

  • 3.
    Bertrand, Yann
    et al.
    Södertörn University, School of Life Sciences. Muséum National d'Histoire Naturelle, Paris, France.
    Härlin, Mikael
    Södertörn University, School of Life Sciences.
    Stability and universality in the application of taxon names in phylogenetic nomenclature2006In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 55, no 5, p. 848-858Article in journal (Refereed)
  • 4. Härlin, Carina
    et al.
    Härlin, Mikael
    Södertörn University College, School of Life Sciences.
    Phylogenetic inference using absence/presence coded morphological characters: A phylogenetic hypothesis of Gyrinus (Gyrinidae, Coleoptera)Manuscript (preprint) (Other academic)
  • 5. Härlin, Carina
    et al.
    Härlin, Mikael
    Phylogeny of the eureptantic nemerteans revisited2001In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, 30: 49-58:, Vol. 30, no 1, p. 49-58Article in journal (Refereed)
    Abstract [en]

    In this paper, we revisit the phylogeny of the eureptantic nemerteans. Three species (Kameginemertes parmiornatus, Drepanophoriella histriana, and Polyschista curacaoensis), not present in the original analyses by Härlin & Sundberg (1995), are included, and in the light of the new results we discuss the phylogenetic taxonomy as well as biogeography of the Eureptantia. The biogeography is assessed by dispersal-vicariance analysis (Ronquist 1997), and the new phylogenetic taxonomy is based on developments (Härlin 1998b, 1999b; Härlin & Sundberg 1998) of nomenclatural ideas originally presented by de Queiroz & Gauthier (1990, 1992).

  • 6. Härlin, Carina
    et al.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Towards a historization of aposematism2003In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 17, no 2, p. 197-212Article in journal (Refereed)
    Abstract [en]

    Aposematism is one of the oldest phenomena in evolutionary biology and still a major puzzle to biologists. Despite its evolutionary nature, most attempts to understand aposematism are devoid of phylogenetic components. In addition, most studies that do take phylogeny into account need to bring the analysis even further. We argue that in order to fully understand aposematism we must have a clear picture of the evolutionary history behind present behaviours. In this paper we frame aposematism in a phylogenetic context and argue that most studies still are wanting in terms of demonstrating aposematism. Aposematism is not an end product but rather evolutionary scenarios including character transformations as well as prey-predator interactions. Finally, we suggest that, regardless how we restrict the concept of aposematism, knowing the directions of events facilitate all kinds of comparisons with a promise of uniting functional and evolutionary aspects into a historization of aposematism.

  • 7. Härlin, Mikael
    Biogeographic patterns and the evolution of eureptantic nemerteans1996In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 58, p. 325-342Article in journal (Refereed)
    Abstract [en]

    The origin and evolution of the eureptantic nemerteans is discussed from a biogeographic point of view. It is most likely that East Indian Ocean was part of the ancestral distribution of the Eureptantia. The area cladogram estimated by Brooks parsimony analysis (BPA) is to a high degree congruent with a vicariance explanation of the evolution of the Eureptantia and suggests an ancestral distribution concordant with the Tethys Sea. A general area cladogram based on a combined BPA analysis of eureptantic nemerteans and acanthuroid fishes is reconstructed and suggested as a hypothesis of the relationships between east Indian Ocean, west Indian Ocean, west Pacific Ocean, east Atlantic Ocean, west Atlantic Ocean, and the Mediterranean. This tree is compared with cladograms from the same areas based on other taxa.

  • 8.
    Härlin, Mikael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Classification nomenclature2004In: McGraw-Hill yearbook of science and technology, ISSN 0076-2016, p. 52-54Article in journal (Other academic)
  • 9.
    Härlin, Mikael
    Södertörn University, School of Life Sciences.
    Definitions and phylogenetic nomenclature2005In: Proceedings of the California Academy of Sciences: Volume 56, Supplement I, No. 19, 2005, p. 216-224Conference paper (Refereed)
    Abstract [en]

    Recent developments in biological nomenclature suggest advantages of phylogenetic alternatives to more traditional Linnaean approaches. My aim is to discuss some fundamental aspects underlying biological nomenclature in general and phylogenetic nomenclature in particular. A basic assumption, in both traditional and phylogenetic nomenclature, is that taxon names can and should be defined. From the ontological view of individuality I question this view and argue that taxon names only refer since no defining properties are involved for particular clades. Even if we accept the idea that a taxon is a natural kind with a historical essence, and thus has defining properties, I see problems of definitions from an epistemological and inferential point of view. Our conceptualization of phylogeny is dependent on our hypotheses. Therefore, definitions based on discarded hypotheses are problematic. Instead, each new and accepted hypothesis should form the basis of our conceptualization. Another theme in this paper is what should count as the same taxon under different hypotheses. Can a phylogenetic definition guarantee that a name always refers to the same taxon under different hypotheses? I argue that this is questionable. I conclude by suggesting that we need to rethink the role of definition, sameness, and stability in nomenclature. Rethinking these concepts, I believe, will shed some new light on biological nomenclature. My conclusions strongly favor a phylogenetic approach to nomenclature but also suggest that we, besides some practical problems, still have many interesting theoretical and philosophical aspects to take into account.

  • 10. Härlin, Mikael
    Namn på djur och växter: hur handskas vi med vårt Linneanska arv på 2000-talet2000In: Teknik & vetenskap, ISSN 1402-5701, Vol. 16, no 5, p. 43-43Article in journal (Other (popular science, discussion, etc.))
  • 11.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    On the relationship between content, ancestor, and ancestry in phylogenetic nomenclature2003In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 19, no 2, p. 144-147Article in journal (Refereed)
    Abstract [en]

    In this paper I draw attention to the concepts of content and ancestry in phylogenetic nomenclature. I argue that these concepts are tightly linked and that they cannot be separated as suggested by Bryant and Cantino [Biol. Rev. 77 (2002) 39] in their recent response to a critique of phylogenetic nomenclature. In addition, I argue that the basic assumption in phylogenetic nomenclature that a taxon-name always refers to the same ancestor or ancestry is questionable.

  • 12. Härlin, Mikael
    Phylogenetic approaches to nomenclature: a comparison based on a nemertean case study.1999In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 266, no 1434, p. 2201-2207Article in journal (Refereed)
    Abstract [en]

    Phylogenetic approaches to biological nomenclature are becoming increasingly common. Here I compare the behaviour of two such approaches, the phylogenetic system of definition and the phylogenetic system of reference, when there is a shift in the preference of phylogenetic hypotheses. The comparison is based on a case study from nemertean systematics and is the first to compare two different phylogenetic approaches throughout three stages of change, including two stages of phylogenetic nomenclature. It is concluded that a phylogenetic system of reference in combination with uninomials is superior in conveying phylogenetic information.

  • 13.
    Härlin, Mikael
    Södertörn University College, School of Life Sciences.
    "Tappar vi namnen bort, även kunskap om tingen vi mister"2007In: Tvärsnitt, ISSN 0348-7997, no 2, p. 20-23Article in journal (Other academic)
    Abstract [sv]

    Om relationen mellan biologin idag och Linnés klassificeringssystem

  • 14.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Taxon names as paradigms: the structure of nomenclatural revolutions2003In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 19, no 2, p. 138-143Article in journal (Refereed)
    Abstract [en]

    In the present paper I argue that the two systems of phylogenetic nomenclature hitherto proposed represent, in a generalized sense, two different philosophies for how science develops and progresses. The phylogenetic system of definition. initially proposed by de Queiroz and Gauthier [Syst. Zool. 39 (1990) 307], and later labeled PSD, is typically Popperian in the 'sense that science progresses toward truth by An accumulation of knowledge. Phylogenetic definitions of taxon names are assumed to adapt automatically to each new hypothesis of phylogeny, thereby reflecting better and better hypotheses. The phylogenetic system of reference proposed by Harlin [Zool. Scr. 27 (1998a) 381], on the other hand, is more Kuhnian, because it is built on the idea that successive hypotheses are incommensurable (and thus not cumulative) and that taxon names might be equalled with low-level paradigms.

  • 15. Härlin, Mikael
    Taxonomic names and phylogenetic trees1998In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 27, no 4, p. 381-390Article in journal (Refereed)
    Abstract [en]

    This paper addresses the issue of philosophy of names within the context of biological taxonomy, more specifically how names refer. By contrasting two philosophies of names, one that is based on the idea that names can be defined and one that they cannot be defined, I point out some advantages of the latter within phylogenetic systematics. Due to the changing nature of phylogenetic hypotheses, the former approach tends to rob taxonomy from its unique communicative value since a name that is defined refers to whatever fits the definition. This is particularly troublesome should the hypothesis of phylogenetic relationship change. I argue that, should we decide to accept a new phylogenetic hypothesis, it is also likely that our view of what to name may change. A system where names only refer acknowledge this, and accordingly leaves it open whether to keep a name (and accept the way it refers in the new hypothesis) or discard a name and introduce new names for the parts of the tree that we find scientifically interesting. One of the main differences between a phylogenetic system of definition (PSD) and a phylogenetic system of reference (PSR) is that the former is governed by laws of language while the latter by communicative needs of taxonomists. Thus, a PSR tends to give primacy to phylogenetic trees rather than phylogenetic definitions of names should our views of which phylogenetic hypothesis to accept change.

  • 16. Härlin, Mikael
    The logical priority of the tree over characters and some of its consequences for taxonomy1999In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 68, no 4, p. 497-503Article in journal (Refereed)
    Abstract [en]

    The aim of the present paper is to explore the role of the character in phylogenetic systematics. I argue that too much emphasis is put on particular characters rather than congruence both in the choice of phylogenetic hypotheses and in taxonomic decisions. This means that the logical priority of the tree over the characters is neglected. To a large extent, this is a result of not paying enough attention to the individuality thesis which states that clades are historical individuals and hence contingent in nature.

  • 17. Härlin, Mikael
    Towards a new biological taxonomy – let us give up the Linnean hierachy!2001In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 30, no 4, p. 337-339Article, book review (Other academic)
  • 18. Härlin, Mikael
    Tree-thinking and nemertean systematics, with a systematization of the Eureptantia1998In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 365, no 1-3, p. 33-46Article in journal (Refereed)
    Abstract [en]

    I review how some influential nemertean systematistshave perceived and illustrated phylogenetic trees andargue that the nineteenth century nemerteantaxonomists still influence many contemporarynemertean taxonomists to a high degree. By showing hownineteenth century systematics differs from moremodern views on trees, I hope to convey the advantagesof a cladistic approach to tree-thinking and nemerteansystematics. Furthermore I propose a systematizationof the Eureptantia that illustrates the cladisticapproach to tree-thinking but, more importantly, isalso a better representation of eureptantic phylogenythan previous classifications.

  • 19.
    Härlin, Mikael
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Vetenskapliga namn från ett mångvetenskapligt perspektiv2004In: Teknik & vetenskap, ISSN 1402-5701, Vol. 20, no 1, p. 48-48Article in journal (Other (popular science, discussion, etc.))
  • 20.
    Härlin, Mikael
    et al.
    Södertörn University College, School of Chemistry, Biology, Geography and Environmental Science.
    Thollesson, M
    Fundamentals of phylogenetic (and other) nomenclatures: an exchange of views2005In: Species plantarum 250 years: proceedings of the Species plantarum symposium held in Uppsala August 22-24, 2003 / [ed] Inga Hedberg, Uppsala: Acta Universitatis Upsaliensis , 2005, p. 141-151Conference paper (Other academic)
  • 21. Pleijel, Fredrik
    et al.
    Härlin, Mikael
    Södertörn University, Avdelning Naturvetenskap.
    Phylogenetic nomenclature is compatible with diverse philosophical perspectives2004In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 33, no 6, p. 587-591Article in journal (Refereed)
  • 22. Sundberg, P
    et al.
    Härlin, Mikael
    Cladistic analysis of the eureptantic nemerteans (Nemertea: Hoplonemertea)1995In: Invertebrate taxonomy, ISSN 0818-0164, E-ISSN 1445-4572, Vol. 9, no 6, p. 1211-1229Article in journal (Refereed)
    Abstract [en]

    A phylogeny for the 34 species we consider well enough described in the suborder Eureptantia (phylum Nemertea) is inferred by cladistic analysis based on 38 morphological characters. The phylogenetic reconstruction indicates that many previously recognised genera and families are paraphyletic. These findings are discussed and compared with earlier classifications. We also present an identification key to the species based on the cladistic analysis.

  • 23. Sundberg, Per
    et al.
    Härlin, Mikael
    Taxonomy and philosophy of names1998In: Biology & Philosophy, ISSN 0169-3867, E-ISSN 1572-8404, Vol. 13, no 2, p. 233-244Article in journal (Refereed)
    Abstract [en]

    Although naming biological clades is a major activity in taxonomy, little attention has been paid to what these names actually refer to. In philosophy, definite descriptions have long been considered equivalent to the meaning of names and biological taxonomy is a scientific application of these ideas. One problem with definite descriptions as the meanings of names is that the name will refer to whatever fits the description rather than the intended individual (clade). Recent proposals for explicit phylogenetic definitions of clade names suffer from similar problems and we argue that clade names cannot be defined since they lack intension. Furthermore we stress the importance of "tree-thinking" for phylogenetic reference to work properly.

  • 24. Sundberg, Per
    et al.
    Turbeville, J M
    Härlin, Mikael
    There is no support for Jensen's hypothesis of nemerteans as ancestors to the vertebrates1998In: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 365, no 1-3, p. 47-54Article in journal (Refereed)
    Abstract [en]

    Nemerteans (phylum Nemertea) have been viewed by mostzoologists as descended from, or closely related to,the flatworms. This view is based mainly on theirsupposedly acoelomate body. Their ancestry, however,is a point of controversy and there is evidence for acoelomate, protostomous origin. Notwithstanding thesedifferent views, most zoologists consider nemerteansto be phylogenetically distant from the chordates.Four authors (Hubrecht, Macfarlane, Jensen, Willmer),however, have postulated that nemerteans instead areclosely related to the chordates and that they sharea most recent common ancestor with the vertebrates. We argue that this view is based on a flawed view ofhomology and of seeing evolution as a series ofprogressions, which has no support in modernevolutionary thinking. Since there are nomorphological synapomorphies supporting aChordata-Nemertea clade, these authors instead guesswhat characteristics in extant nemerteans gave rise tocharacters observed in recent chordates. For example,they propose that the nemertean proboscis sheath hasevolved into the notochord. This is mere speculation,lacking testable propositions and is hence void ofinformation, and thus becomes futile in our view. However, the idea of a nemertean-vertebrate sisterrelationship as such is a testable hypotheses, and wetest it by applying the parsimony criterion to a setof morphological characters, and a set of molecular(the 18S rRNA gene) characters. Both tests reject thehypothesis.

1 - 24 of 24
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