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W3087554614 abstract "No one is more desirous of the improvement of science than myself; but reform implies something more than change; and it is precisely because I do not consider that the proposed changes are for the better, that I enter my protest against them. On a superficial view of the case, it may certainly appear, that to change a less appropriate scientific name for one that is more so, is a change for the better: but what is the result? If, to take the most favorable view of the case, the scientific world should agree to adopt an “improved” nomenclature, yet, even then, all our standard works on natural history would become, in great measure, a dead letter; every museum in the world would require to be relabelled; and the disentanglement of synonyms (already a sufficiently laborious though necessary duty) would become almost hopeless. But if, as would almost certainly be the case, these “improved nomenclatures” should be only partially adopted, the disentanglement of synonyms would then become quite hopeless, and the curse of Babel would be entailed on the scientific world. (H. E. Strickland, 1837) At last, the long-awaited PhyloCode has been published in a permanent and immutable form. Rather than haunting the ether as an unsubstantiated, protean sketch, now it exists as a physical entity which we may examine and lay to rest, or as the case may be, commit to the flames. Stemming from proposals offered in the 1990s, the current version of this prolonged undertaking presents rules for coining new names (or coopting existing names) for taxa, focusing––at least initially––on names for inclusive clades corresponding to taxa above the family rank. As discussed below, the PhyloCode’s rules now ultimately depend upon nomenclatural types governed by the existing Zoological, Botanical and other Codes, (“the Codes”: International Code of Zoological Nomenclature (4th ed.), 1999; International Code of Nomenclature for Algae, Fungi and Plants, 2017; International Code of Virus Classification and Nomenclature, 2018; International Code of Nomenclature of Prokaryotes, 2019), yet the PhyloCode remains premised upon the hypocritical postulate that the traditional Codes are metaphysically incorrect. The publication of the PhyloCode provides occasion to review purportedly objectionable issues with traditional biological nomenclature, and to address the historical and philosophical underpinnings of efforts to replace or supplement it with a rankless system of names for clades. Why reinvent biological nomenclature? The kernel of dissatisfaction that led to the Phylocode was essentialism, purportedly embedded in traditional biological classification and the rank-based Codes of biological nomenclature. It sprouted some 35 years ago, among a group of metaphysically inclined systematists at UC Berkeley and the California Academy of Sciences. Ghiselin (1984), Rowe (1987) and de Queiroz (1988) suggested an alternative, ostensibly nonessentialist nomenclatural proposal, which was developed explicitly by de Queiroz and Gauthier (1990), and, following a 1998 meeting at Harvard, was proposed formally as an alternative “code” of biological nomenclature in 2000 (the first and subsequent drafts of the PhyloCode, all apparently authored by Cantino and de Queiroz, may be found at http://phylonames.org/documents). Advocacy for (de Queiroz, 1992, 1994, 1995, 1997, 1998, 1999, 2000; de Queiroz and Gauthier, 1992, 1994; Bryant, 1994, 1996; Sundberg and Pleijel, 1994; Lee, 1996a,b, 1998; Cantino et al., 1997; Cantino, 1998, 2000, 2004; Bryant and Cantino, 2002; Pleijel and Harlin, 2004; Laurin et al., 2005, 2006) and criticism of the nascent PhyloCode (Schander and Thollesson, 1995; Lidén and Oxelman, 1996; Lidén et al., 1997; Nixon and Carpenter, 2000; Forey, 2002; Carpenter, 2003; Keller et al., 2003; Kojima, 2003; Nixon et al., 2003; Schuh, 2003; Pickett, 2005a, b; Sereno, 2005; Rieppel, 2006; Benton, 2007) was most intense in the decade between 1996 and 2006. As the published PhyloCode’s citations indicate, interest in the topic had dwindled by 2014 (Fig. 1). But now, seven years later, here is Phylocode 6.0, heralded with the same sophomoric triumphalism we saw back in the day: “This is truly the most significant contribution to the scientific naming system since Linnaeus.” (Nico Cellinese, quoted in van Hoose, 2020). One reason for the prolonged delay in publication of the PhyloCode may have been to synchronize with the publication of Phylonyms (de Queiroz et al., 2020), a compendium of some 300 phylogenetically defined names for higher taxa (mainly plants and vertebrates; just two insect clades were included). Not coincidentally, the “start date” of the PhyloCode (30 April 2020) coincides with the publication date of Phylonyms – simultaneously discounting the efforts of anyone who has attempted to publish a phylogenetically defined name before that date, and cementing nomenclatural immortality for the modern Prometheus (Nixon and Carpenter, 2000) and his collaborators, at least until the PhyloCode meets the fate of predecessor schemes (e.g. Michener, 1964; Hull, 1966; Hennig, 1969; Griffiths, 1974). Note that although the Codes are all freely available online, as is the newly published PhyloCode (www.phylonames.org/code/), this is a commercial endeavour: if you want to read Phylonyms, that will set you back US$234. You can see the chapter titles, which correspond to the clade names, in CRC’s advertisement online. For those who need a refresher in what the PhyloCode was intended to accomplish (and for those too young to remember), I offer some background on the challenges of classification, and explore arguments, most recently expressed by Cantino and de Queiroz (2020), rationalizing the need to replace (or, in later versions, augment) the Linnean system of classification embodied in the Codes. Quotations from the newly published PhyloCode are italicized in the text below. A false premise to dispense with at the start is the notion that revising the Linnean System is an idea original to Kevin de Queiroz, Jacques Gauthier and Philip Cantino: “We just kind of stumbled on this idea. We were trying to decide where to place certain names on a phylogenetic tree. In the process of talking about it, we realized that there could be a different way of defining names – by describing evolutionary relationships. Since definitions are the foundations of any naming system, this opened up a possibility for a new system: the PhyloCode.” (de Queiroz, quoted in van Hoose, 2020). A long-recognized feature of the traditional Linnean taxonomic hierarchy, considered a practical disadvantage by some, is that its categories (kingdom, phylum, class, order etc.) embody a hierarchical structure of nonoverlapping ranks. Thus, as our hypotheses of groups nested within groups become more detailed, the Linnean system presents the Procrustean impediment of intercalating ever more categories between the most and least inclusive levels of the hierarchy. The problem is two-pronged: the structure of large clades demands too many successive categories to fit comfortably into the Linnean hierarchy, and this is compounded by the notion that sister taxa must bear comparable category names, even if they contain only a single terminal (Farris, 1976; Colless, 1977; Nelson, 1978). For example, Archaeopteryx lithographica, as the monotypic sister taxon to all other birds (suppose there are 20 000 recognized extant and fossil species), must bear at an absolute minimum 15 additional supergeneric group names, and could bear as many as 20 000 group names, if the cladogram for the rest of the birds were fully pectinate (or even 40 000, if we recognized both the stem and crown clade definitions advocated in the PhyloCode). The modern improvements of science, and the vast additions of new species, have multiplied the number of divisions in the system to an extent greatly beyond the five originally employed by the Swedish naturalist. In many cases, they exceed twenty in number. In order to give to each of these groups an appropriate title, naturalists have denominated them as divisions, classes, orders, tribes, legions, families, sections, subdivisions, &c. We have already stated the want of co-ordination between these groups, and are therefore disposed to prefer distinct appellations for each, expressive, if practicable, of their essential character, rather than to designate them by terms, which, while they occur frequently, have never the same equivalent expression. (Fleming, 1822, p. 158) Somewhat more recently, Griffiths (1974, 1976) echoed Fleming’s recommendation to eliminate Linnean categories. He proposed many of the ideas for an alternative classification system suggested later by de Queiroz and Gauthier (1990, 1992, 1994) and, like them, couched his argument in terms of a rejection of Aristotelian logical division and essentialism. (The similarity between Griffiths’ system and the PhyloCode is striking, but, conveniently outside the sliding window of historical memory of those who covet credit for predecessors’ ideas; Fig. 1). Comparison of Fleming’s and Griffiths’ comments suggests complete agreement on the practical solution to this problem: disposing of fixed categorical ranks across taxa. That Aristotelians and anti-Aristotelians can make the same argument against Linnean categories suggests that the problem of multiplicity of group names in the Linnean hierarchy is not dependent upon essentialism or the nature of group definition, but rather addresses the epistemological problem of managing a large hierarchical database. There are just too many ranks to name. The practical solution adopted by users of both the Linnean system of classification embodied in the Codes and the PhyloCode is the same: don’t name them all. De Queiroz and Gauthier (1994) claimed that under their proposed system, group names could be subordinated under other group names that formerly represented groups of equivalent rank (cf. their Box 5, in which Chamaeleonidae is a subclade of Agamidae). As expressed in the PhyloCode, …clear communication and efficient storage and retrieval of biological information require names that explicitly and unambiguously refer to clades that do not change over time. The current rank-based codes fail to provide such names for clades. (p. vii). Cantino and de Queiroz apparently object to the fact that people have sometimes applied the same family-group (superfamilial, familial, subfamilial or tribal) name to different clades, or different names to the same clade, which they claim promotes “instability” (My Bruchidae is your Bruchinae – chaos!). Although it impacts a relatively limited number of names (family-group names in Zoology, plus ordinal-group names in Botany), this was one of the major points of contention in the debates of 20 years ago: the “advantage” of such a system (a debatable increase in nomenclatorial stability––see Nixon and Carpenter, 2000) comes at the price of abandonment of the hierarchical meaning of the names themselves. Under the PhyloCode, there is no longer any mnemonic clue in a name to indicate whether group x is a part of group y, group y is a part of group x, the two are sister groups, or exist in some other relationship. For example, which of these clade names do you think is more inclusive: Archosauria, Archosauriformes or Archosauromorpha? Are these taxa nested within one another? Who knows? The meaning of phylogenetic names comes from their placement at nodes on a cladogram, or from enumeration in complex Boolean lists (cf. appendix in Cantino et al., 1997). Perhaps the expression of concern over the loss of the hierarchical implications of group names is trivial, given the complexity of modern phylogenetic hypotheses. But then, as Colless (1977) argued in his discussion of Cracraft’s (1974) “phyletic sequencing,” “(i)t is not at all clear to me why a nested list of names… should be preferred over the more succinct and synoptic cladogram itself.” Names, after all, are only labels for concepts we want to talk about. A perhaps more significant challenge to stability is the changing content of taxonomic circumscriptions resulting from increased knowledge of patterns of relationship. Since the Hennigian revolution in the 1970s, traditional nomenclature has been steadily modified under the existing Codes to apply names to clades, recognized on the basis of synapomorphies. Farris (1980) showed that cladistic classifications maximize information content. There is nothing incompatible between the Codes and cladistic classification (Nixon et al, 2003; Schuh, 2003). The circumscription of taxa is, wisely, not regulated by the Codes, and stability of nomenclature is generally achieved by consensus among systematists. However, in a period of scientific history when new methods and data sources have led to substantial changes in our understanding of relationships in many taxa, it should be no surprise that there has been some “instability” in the groups that we wish to name. The claim that fixing names to particular hypotheses of branching promotes stability assumes that those patterns are permanent and will not change in the future. Systematists generally presume that there is only one irregularly bifurcating pattern of phylogenetic relationships that reflects evolutionary history, but the further presumption that we can state accurately and unequivocally what that pattern is, and that our understanding of it will not change in the future, is, shall we say, naive: all scientific knowledge must at least be open to “change over time.” The only advantage the PhyloCode holds over traditional nomenclature in this regard is that it starts in 2020 with a clean slate, informed by the efforts of systematists to improve existing nomenclature over more than two centuries. If we believe that classification should reflect the nonoverlapping, nested pattern of taxa discovered by empirical grouping of synapomorphies1 (and regardless of our views on the monophyletic origins of taxa that this pattern implies), then branching diagrams summarizing character distributions should suffice as a framework upon which names (conveying mnemonic hierarchical information or not) can be affixed to as many or as few clades as we see fit. Such a change does not require retooling traditional nomenclatorial practice, except to relax the impractical idea of exhaustive parallel categorical ranking. This has been done implicitly since the beginning of modern systematics: the logical divisions yielding Linnaeus’ (1758) classification of orders imply superordinal groups which are not named; the inclusion of more than two species per Linnean genus likewise implies additional, unresolved and unnamed infrageneric levels. H. E. Strickland (1844), the author of the first Rules of Zoological Nomenclature, explicitly called for inclusion of unnamed categories. In modern practice, authors who have named groups that are not of general interest have been criticized, and their names have simply been ignored (e.g. Boudreaux’s (1979) exhaustive insect group names). Explicitly rankless classification thus would do little to improve the practicality of the traditional system, and adopting it would disrupt everything that has come before (Lidén and Oxelman, 1996). If the point of nomenclature is to make our taxonomic groups easy to talk about, it is hard to imagine how discarding or arbitrarily redefining the common reference system used in all our museums and libraries will facilitate this task. Valuable and important as phylogenetic speculations are, as guides to, and suggestions of, investigation, they are pure hypotheses incapable of any objective test; and there is no little danger of introducing confusion into science by mixing up such hypotheses with Taxonomy, which should be a precise and logical arrangement of verifiable facts. (T.H. Huxley, 1874) (R)eference to a particular ancestor is the essential component of a phylogenetic definition of a taxon name. (H.N. Bryant, 1994 (italics added)) In order to understand the perceived need for a philosophically superior alternative to the traditional nomenclatural Codes, some historical background is valuable. One could adopt the view that systematists need not be particularly concerned with logical definitions of taxa, but should instead provide them with names and diagnostic characters to create a handy reference system for communicating with each other and for telling one organism from another. Following Popper (1962), de Queiroz (1994) referred to such an outlook as methodological nominalism, and claimed this to be his own position. Popper (1965, p. 279) summarized: “…(O)utside mathematics and logic problems of definability are mostly gratuitous. We need many undefined terms whose meaning is only precariously fixed by usage -- by the manner in which they are used in the context of theories, and by the procedures and practices of the laboratory. Thus, the meaning of these concepts will be changeable. But this is so with all concepts, including defined ones, since a definition can only reduce the meaning of the defined term to that of undefined terms.” Such a circumspect view obviates the need for semantic dispute about the meanings of words, because they are employed as heuristic tools only. If we can agree on a stable, albeit completely arbitrary connection between a name and a referent taxonomic group, ontological impedimenta regarding the group’s definition2 can be simply shucked off and discarded. Such pragmatism seems to have been the motivation of the early framers of the Zoological Code, who held that, “the permanency of names and convenience of practical application (are) the two chief requisites of any code of rules for scientific nomenclature…” (Verrill, 1869). For generations, however, systematists have felt that classifications should reflect something more than a practical list. Darwin’s (1859) “hidden bond” springs to mind, but the quest for a “natural system,” or, Systema Naturae, of classification reflecting the empirical pattern of groups within groups observed in nature is well over two centuries old (Linnaeus, 1758). Traditionally, attempts at natural classifications have been rooted empirically in characters (the evidence upon which our understanding of taxa and the relationships among them is based), and since Hennig (1966), taxa have been diagnosed on the basis of synapomorphies. Phylogenetic nomenclature also rests on the conviction that classification should reflect something more than arbitrary convenience. But rather than basing classifications on patterns implied by characters, its advocates make the evolutionary process the central tenet, or axiom, of systematics: “Taxa are monophyletic if and only if they share a common ancestor, irrespective of evidence or belief” (Ghiselin, 1984); “Here the definitions of taxon names are ontological statements in that they refer to monophyletic entities (clades) which are presumed to exist under the central tenet of common descent independent of our ability to recognize them” (de Queiroz and Gauthier, 1990). In the PhyloCode, the wording is less bombastic, but the metaphysical premise is the same: clades are products of evolution that have an objective existence regardless of whether they are named (p. x). Evolution, ancestors and cladograms are theories, based on interpretations of character data from systematic research. Reifying historical processes and entities while at the same time trivializing or discounting entirely the evidence that empirically supports those theories (cf. footnote 1) puts the cart before the horse (Brady, 1985). Ghiselin (1966, 1984), asserted the following semantic distinctions: 1, a definition states the attributes necessary and sufficient for a name to apply; 2, taxa are individuals (spatiotemporally restricted wholes, as opposed to classes which are universal and eternal); 3, individuals do not possess defining properties; and therefore 4, taxa can only be defined ostensively (given proper names associated with a particular referent thing). According to this viewpoint, taxa may be diagnosed but cannot be defined by the presence or absence of any attributes. De Queiroz and Gauthier (1992, pp. 461–462) concurred: “Definitions are statements specifying the meanings of taxon names (words); they are stated in terms of ancestry. Diagnoses are statements specifying how to determine whether a given species or organism is a representative of the taxon (clade) to which a particular name refers; they are most commonly stated in terms of characters.” With these semantic pronouncements, de Queiroz and Gauthier dismissed character-based classification as metaphysically incorrect and obsolete: “Definitions of taxon names based on organismal traits are fundamentally non-evolutionary. Such definitions were in use long before the widespread acceptance of an evolutionary world view, and furthermore, they make no reference to common descent or any other evolutionary phenomenon” (de Queiroz and Gauthier, 1992). Despite professing nominalism (de Queiroz, 1994)––a perspective under which the nature and basis of group definitions should not matter––the authors evidently consider traditional taxonomy’s reliance on characters to be a dire philosophical error, and aim to correct it by exchanging their own metaphysical credo (common ancestry) for the empirical differentiae they find objectionable as the basis for defining taxon names. Systematists and historians have called out such “origin essentialism” (Brower, 2000; 2019; Winsor, 2006, 2009; Rieppel, 2010), which dismisses evidence in favour of causal theories as its philosophical foundation. Without data, there is no difference between the explanation of biological diversity as the Plan of Creation and as a result of ancestors and evolution. A system of nomenclature for clades that do not change over time, touted by its advocates to be based on unknowable truths (as Ghiselin said, “irrespective of evidence or belief”) is fundamentalism, not science. An advantage of the PhyloCode over rank-based codes is that it applies at all levels of the taxonomic hierarchy (p.xii). This statement is patently false. Early iterations of the PhyloCode attempted to provide uninomina and rules to govern species (Cantino et al., 1999), but after further consideration (Dayrat et al., 2008; Cellinese et al., 2012), Cantino, de Queiroz and their acolytes abandoned that as unworkable: All taxa named under this code are clades (p. x). This code does not govern the establishment or precedence of species names or names associated with ranks below the species under the rank-based codes. … the name of a species or infraspecific taxon must satisfy the provisions of the appropriate rank-based code. (Art. 21.1, p. 97). Because most named taxa are species-level taxa and most names are specific binomina, this ceding of authority over those names to the traditional Codes entails, among other things, that the PhyloCode does not even attempt to govern the names of most biological entities. Perhaps its advocates do not see universality and consistency as important aspects of a nomenclatural system––after all, the project was conceived as a grandiose solution to some rather particular, higher-level nomenclatural ambiguities in angiosperms and reptiles, levels of inclusiveness at which the traditional rules of nomenclature generally do not apply. However, the corollary of excluding governance over species names is that anyone choosing to adopt the PhyloCode also will need to maintain a familiarity with the traditional rules of nomenclature for their taxa, in order to accommodate the preponderance of namable entities, as well as to refer to “specifiers” (see below). Thus, charitably conceding the unlikely prospect that the systematic community will adopt the PhyloCode, the resulting compendium of biological nomenclature would be a chimera of rank-based and clade-based names for the foreseeable future (see Strickland’s epigram at the start of this review). The PhyloCode retains the familiar and venerable principle of priority (which, apparently to promote as a new idea, Cantino and de Queiroz have renamed “precedence”) as the rule for rejecting junior synonyms and homonyms: Precedence is based on the date of establishment, with earlier names having precedence over later ones … (Art. 12.2, p. 67). This has interesting implications for the names of species. Because this code is independent of categorical ranks (Art. 3.1), the first part of a species binomen is not interpreted as a genus name but simply as the name of a taxon that includes that species. (Art. 21.2, p. 97). So PhyloCode generic names and their implied circumscriptions do not mean anything––they are just the first half of the species name. And, when a type specimen is used as a specifier, the species name that it typifies and the author and publication year of that species name must be cited (Art. 11.5, p. 52). Remember, under the Codes, a species name is a binomen. Therefore, the PhyloCode’s lack of circumscriptive signification of the generic name, plus the principle of priority, together imply that the species name with “precedence” is the combination of genus and species names published by the author who originally described the species under the cognizant Code. Thus, for example under the PhyloCode, the butterfly clade Heliconius would include the species Papilio doris L., Nereis aoede Hübner, Migonitis burneyi Hübner, Heliconia cydno Doubleday, and Eueides eratosignis Joicey & Talbot, among others. No doubt readers can envision many comparable instances of obsolete combinations infesting their own pet groups. Of course, the PhyloCode empowers its own “Committee of Phylogenetic Nomenclature” to suppress and emend names, but because the PhyloCode does not govern species names (Art. 21.1), they seem to be hamstrung by such issues. No matter how one defines the clades Iguanidae or Caudata, under the PhyloCode’s rules, the green iguana is going to be Lacerta iguana L., and the fire salamander is going to be Lacerta salamandra L. In such cases, ignoring the revisionary taxonomic efforts and resultant modifications of generic circumscriptions of the past two centuries promotes nothing but conflict and confusion. Given the aforementioned exclusion of the species category and specific names from consideration in the PhyloCode, and its Art. 1.1 (p. 5), which states, (t)he only taxa whose names are governed by this code are clades, it is astounding to read, on the same page, Art. 2.1 (repeated in the glossary, p. 112): In this code, a clade is an ancestor (organism, population or species) and all of its descendants. Wait. What? Clades are taxa (Art. 1.1). Groups of individual organisms are clades (Art. 2.1). If the PhyloCode does not deal with species, why are Cantino and de Queiroz making pronouncements about population-level variation? But there’s more! The Phylocode’s glossary definition of monophyletic is: a set3 consisting of an ancestor and all of its descendants; usually used for groups the members of which share a more recent common ancestor with one another than with any non-members, though monophyletic groups of organisms within sexually reproducing species/populations may not have this property (p. 116). The first part of this definition is the same as the definition of “clade”, and most systematists would likely agree that clades are monophyletic. The statements “an ancestor and all of its descendants” and “share a more recent common ancestor with one another than with any non-member” circumscribe the same “set” and are synonymous. If, as the PhyloCode urges, we entertain parts of tokogenetic lineages as “clades,” then members of a paternal lineage, for example, still share a more recent common ancestor with one another than with any nonmember. So what “property” are Cantino and de Queiroz talking about here? Monophyletic groups may not have the property of monophyly? Of course, every systematist is well aware that populations or even species might not be “monophyletic,” in the sense that all of the individuals in said unit are more closely related to one another than they are to any other individual. The conceptual difference between tokogenetic and phylogenetic relationships was clearly delineated by Hennig (1966) and has been a mainstay of cladistic epistemology ever since. Nevertheless, Cantino and de Queiroz’ definitions conflate the two. Only when we consider biparental inheritance, hybridization and other nonphylogenetic processes do any of their pronouncements about nonmonophyletic “clades” make any sense at all, and that is not because individual organisms don’t have common ancestors––it is because they have multiple common ancestors. Thus, Hennig’s clear distinctions: tokogeny is not phylogeny, clades are not groups of individual organisms, and monophyly is a property of groups of taxa, not groups of organisms. Failure to recognize these critical epistemological differences is a sloppy “tree-thinking” category-error that not only sows chaos within systematics, but also spills over and muddies the waters for biology teachers (Brower, 2006, 2016). The Phylocode’s glossary entry for “species” says: the term is used both for a kind of biological entity (for example, a population lineage segment) and for the lowest primary rank in traditional nomenclature. … (p. 119). This also is semantically confusing, given that “kinds” and “ranks” are classes, and a “population lineage segment” is an individual (the term is from de Queiroz’, 2005 “General Lineage Species Concept,” a retread of Simpson’s (1951) Evolutionary Species Concept), unless one bears in mind Mayr’s (1976) distinction between the species category and particular species. If the Phylocode is constrained to address nomenclature pertaining to taxonomic groups more inclus" @default.
W3087554614 created "2020-09-25" @default.
W3087554614 creator A5024238141 @default.
W3087554614 date "2020-09-15" @default.
W3087554614 modified "2023-09-26" @default.
W3087554614 title "Dead on arrival: a postmortem assessment of “phylogenetic nomenclature”, 20+ years on" @default.
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