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Topic: PhyloCode

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Molecular systematics

International Code of Botanical Nomenclature

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	PhyloCode - Wikipedia, the free encyclopedia
		The PhyloCode is a developing draft for a formal set of rules governing phylogenetic nomenclature.
		The PhyloCode grew out of a workshop at Harvard University in August 1998, where decisions were made about its scope and content.
		The number of supporters for official adoption of the PhyloCode is still small, and it is uncertain, as of 2006, when the code will be implemented and how widely it will be followed.
	en.wikipedia.org /wiki/PhyloCode (779 words)

	BZN 58(4) General Articles & Nomenclatural Notes
		Regarding similarities, the PhyloCode has the same general goals as the Zoological Code, namely, the provision of rules for naming taxa and applying existing names in new taxonomic contexts so that the names of taxa, and the application of names, will be unambiguous within a given taxonomic context.
		The PhyloCode is entirely neutral regarding the various measures of support that he lists (number of synapomorphies, Bremer support, bootstrap proportions, etc.); what is considered an adequate level of support is a taxonomic issue that is to be decided by the individual systematist.
		According to PhyloCode Article 11.8, when a clade name is a converted name derived from the stem of a genus name, the definition of the clade name must use the type species of the genus name as an internal specifier.
	www.iczn.org /BZNDec2001general_articles.htm (9338 words)

	Scientific American (Site not responding. Last check: 2007-10-08)
		Their proposed "PhyloCode" is a system for naming organisms based on evolutionary relationships (phylogeny), rather than grouping them by shared characteristics.
		Phylocode Members of a given rank are "diagnosed" by the rank's defining characteristics.
		As de Queiroz hurries to the PhyloCode meeting's final session along streets named for historic systematists--Linné, Jussieu, Buffon--he observes that future generations of scientists will be the ones to decide which code is most sensible.
	www.harding.edu /USER/plummer/WWW/morph/phylocode.htm (1193 words)

	John Hawks Anthropology Weblog : PhyloCode and human evolution
		PhyloCode is an attempt to address two simple problems with the Linnaean system.
		I think this is unfortunate, since the opportunity was there to establish a classification that would be at the same time unambiguous and maximally consistent with historic use of the term "hominid." To do so, a different term for the great ape and human clade would have to be invented or drawn from the literature.
		The PhyloCode is far from acceptance among taxonomists, but by providing a rank-free naming system for clades, it created the potential to avoid the issue.
	johnhawks.net /weblog/topics/phylogeny/phylocode_2005.html (4567 words)

	"Phylocode debate -- Mike Lee (for); Gary Nelson (against)" (Site not responding. Last check: 2007-10-08)
		Phylocode claims to be a new and alternative system of nomenclature for botany and zoology.
		It claims that Phylocode is fully sufficient for modern needs, achieved by abolishing ranks and binomial nomenclature, and by adopting a certain distinction between the ideas of definition and diagnosis. The distinction leads to an original proposal about types and their function.
		Phylocode is not yet operational. It remains to be adopted, imposed, or left to wither on the vine.
	www.systass.org /events_archive/phylocode-debate.html (2703 words)

	PhyloCode Preface (Site not responding. Last check: 2007-10-08)
		For example, under the PhyloCode, synonyms are names whose phylogenetic definitions specify the same clade, regardless of prior associations with particular ranks; in contrast, under the rank-based codes, synonyms are names of the same rank whose types are included within a single taxon at that rank, regardless of prior associations with particular clades.
		However, under both the PhyloCode and the rank-based codes, the primary purpose of a taxon name is to provide a means of referring unambiguously to a taxon, not to indicate its relationships.
		The theoretical foundation of the PhyloCode was developed in a series of papers by de Queiroz and Gauthier (1990, 1992, 1994), which was foreshadowed by earlier suggestions that a taxon name could be defined by reference to a part of a phylogenetic tree (e.g., Ghiselin, 1984).
	www.ohiou.edu /phylocode/preface.html (5585 words)

	BZN 58(2) General Articles & Nomenclatural Notes
		Since I was critical of the proposals of the PhyloCode I was happy to agree to this on the understanding that I could describe the aims and mechanics of the PhyloCode in as neutral a way as possible while allowing myself the opportunity of personal commentary.
		Advocates of the PhyloCode also claim that these gains are likely to be appreciated by those not interested in phylogeny or nomenclature (Cantino et al., 1999); it is clear that the intention is for the PhyloCode to be understood and used by non-systematists.
		The PhyloCode (Article 11.8) does insist that `when a clade name is converted from a preexisting genus name or is a new or converted name derived from the stem of a genus name, the definition of the clade name must use the type species of that genus as an internal specifier.'.
	www.iczn.org /BZNJun2001general_articles.htm (6868 words)

	American Scientist Online - Cracking the Code (Site not responding. Last check: 2007-10-08)
		The PhyloCode, however, is not based on evolutionary trees but on definitions that specify the references of taxon names in terms of common ancestry relationships.
		The PhyloCode represents a return to an approach more similar to that adopted by Linnaeus and other early naturalists in that names are more strongly tied to taxa (now conceptualized in evolutionary terms) than to ranks.
		Nevertheless, abandoning the Linnean hierarchical ranks is not a core proposition of the PhyloCode, which does not prohibit the use of ranks but only replaces their function in specifying the references of names with methods based on evolutionary principles.
	americanscientist.org /template/AssetDetail/assetid/46077;_ck2HPpoXIT (484 words)

	PhyloCode (Site not responding. Last check: 2007-10-08)
		An important decision made at the Yale workshop is that the rules governing clade names and those governing species names will be published in separate documents, and the timing of implementation of the two documents will be independent.
		The current version of the PhyloCode was posted in June 2006 and includes many substantive modifications of the previous version (see the last two paragraphs of the Preface for a summary of the changes).
		We are grateful to Richard Piccard, Academic Technology Manager in Computer Services at Ohio University, for technical support, and to Andy Anderson for preparing the downloadable MS-Word and PDF files for the April 2000 draft.
	www.ohiou.edu /phylocode (675 words)

	PhyloCode - EvoWiki (Site not responding. Last check: 2007-10-08)
		The PhyloCode, a formal set of rules governing phylogenetic nomenclature in the same way the ICZN and ICBN govern the Linnean, rank-based system (genus, family, order, class, etc).
		It is administered by the International Society for Phylogenetic Nomenclature, the first meeting of which is to be held in July 2004.
		Although not yet in effect, the PhyloCode is expected to begin early this decade.
	wiki.cotch.net /index.php?title=PhyloCode&printable=yes (73 words)

	Trochophores & Understanding the new PhyloCode
		Due to the frequent detection of new marine organisms, understanding and utilizing the PhyloCode is essential for all researchers.
		PhyloCode, the new code of taxonomic nomenclature, is due to begin in 2005—and this code will either replace the Linnean system of nomenclature or run in parallel.
		PhyloCode, the new code of taxonomic nomenclature, is due to begin in 2005—and this code will either replace the Linnean system of nomenclature or run in parallel.
	www.mbari.org /seminars/2003/summer2003/august4_rouse.html (448 words)

	biolrev
		In their agonizing over how to strip out all the inconsistencies in achieving that identity, they have progressively abandoned modifiable taxon definitions, Linnaean ranks, and the species binomen (some even abandon the notion of species as entities), and the next logical step is clearly to abandon classification.
		However, the PhyloCode provisions are even more draconian and authoritarian, although the decision-making process about which definition to accept, and which to reject, is made explicit and open.
		The PhyloCode team, and other reformers, are most welcome to continue the philosophical debate, and the rest of the world will observe their byzantine disquisitions at a distance.
	palaeo.gly.bris.ac.uk /Essays/phylocode/biolrev.html (10073 words)

	PhyloCode Discussion - Message 2001-06-0035: Re: [Re: Subscribers]
		The ICBN recommends the -opsida end= ing for metaphytes and the -mycetes ending for eumycotans, which I have sligh= tly modified (by one letter) to -opsidea and -mycetea, so that all classes in= all kingdoms of organisms would have a common -ea suffix.
		According to PhyloCode rules=, _Delta_ will be an alphacean, but under the ICBN, it will be a deltacean!= And, if _Deltaceae_ is ever cladistically defined, _Delta_ will belong to= both clades, which is absolutely impossible under traditional taxonomy, since they are of the same rank.
		I agree that until PhyloCode goes into effect things should probably be done, as much as possible, in accord with the current codes.
	phylocode.miketaylor.org.uk /archive/messages/2001-06-0035.html (670 words)

	New Scientist Breaking News - Linnean naming system faces challengers (Site not responding. Last check: 2007-10-08)
		Critics have slammed their proposal, arguing that it will be a waste of time and effort that will hinder the urgent task of cataloguing the thousands or even millions of as yet undiscovered species before they go extinct.
		The PhyloCode would eliminate the need for that by abolishing genera, families and every other rank above the level of species.
		At a meeting in Paris in July, PhyloCode proponents began the task of applying this code to the Earth's living things.
	www.newscientist.com /article.ns?id=dn6369 (1155 words)

	Etaerio - A Plant News Weblog: Will the PhyloCode Replace Taxonomic Nomenclature?
		PhyloCode organizes species into clades, groups of organisms with a common ancestor.
		Proponents of PhyloCode claim that the new method will generate fewer name changes as well as a more precise view of the relationships between species, as modern molecular methods allow for more accurate classification than that based on physical resemblance.
		PhyloCode the Phylocode website with a formal set of rules governing phylogenetic nomenclature
	www.ubcbotanicalgarden.org /weblog/000904.php (326 words)

	Why Benton should read the PhyloCode first (Site not responding. Last check: 2007-10-08)
		There is agreement that the PhyloCode will exist and will introduce priority, and it is likely that most debates will completely cease and that the rest will continue on a very low level, occasionally (remember Article 15.2) resulting in appeals to the Commission.
		Bryant (1997) explored this problem, and proposed that phylogenetic clade terms might include a statement of the 'designated phylogenetic context', in other words, the clade-term definition should refer to the included and excluded taxa, but also to the particular cladogram on which it is based.
		The idea of the companion volume, however, is older than that, as far as I recall; and the PhyloCode was never intended to be retroactive.
	www.unet.univie.ac.at /~a0000265/Benton-Phylocode.htm (8051 words)

	Pushing Phylocode - - science news articles online technology magazine articles Pushing Phylocode (Site not responding. Last check: 2007-10-08)
		Proponents of the PhyloCode say the old system, originally developed by Swedish botanist Carolus Linnaeus before Darwin discovered natural selection, is so archaic that every taxonomic grouping needs to be redefined.
		Under the PhyloCode, they might be defined as all creatures descended from the most recent common ancestor of Homo sapiens and the platypus.
		The new definition is the equivalent of pointing to the tips of two twigs on the tree of life, tracing the branches back to where they meet, and describing the taxonomic group as everything in between.
	www.discover.com /issues/apr-05/features/pushing-phylocode (1431 words)

	Cantino, Philip D.* and Michael J. Donoghue. (Site not responding. Last check: 2007-10-08)
		The PhyloCode, a code of phylogenetic nomenclature, has been in development since 1997.
		The PhyloCode will make it possible to name clades as they are discovered, without changing the names of other clades.
		The PhyloCode is designed for concurrent use with the ICBN, ICZN, etc. The first edition of the PhyloCode will govern only the naming of clades, but the intent is to add rules governing species names in the future.
	www.ou.edu /cas/botany-micro/botany2000/section13/abstracts/1.shtml (252 words)

	PhyloCode - Wikipedia, the free encyclopedia (Site not responding. Last check: 2007-10-08)
		Unlike conventional scientific nomenclature, the PhyloCode does not use set taxon ranks, and taxon names are given phylogenetic definitions.
		An apomorphy-based definition might read "the most inclusive clade exhibiting character M synapomorphic with that in species A"
		In conventional scientific nomenclature, it looks like this (note that this is the strict seven-level system in use for many years):
	www.encyclopedia-online.info /PhyloCode (192 words)

	American Scientist Online - Attacks on Taxonomy (Site not responding. Last check: 2007-10-08)
		But the publicity did little to unite two camps engaged in a debate that threatens the very foundations of the nomenclatural edifice upon which all of modern taxonomy is built.
		The PhyloCode would name and organize living things based on common ancestry and the branching of the evolutionary family tree.
		Although the clade concept is well defined, PhyloCode workers have not yet established rules for converting existing species names or for naming new species; at least a dozen proposed methods are on the table.
	www.americanscientist.org /template/AssetDetail/assetid/44520 (1001 words)

	phylocode (Site not responding. Last check: 2007-10-08)
		The PhyloCode is a proposal to register definitions of taxa.
		I have written a rebuttal to the PhyloCode concept, which was published in Biological Reviews in November 2000.
		This may be viewed in an html version, or downloaded as a pdf.
	palaeo.gly.bris.ac.uk /Essays/phylocode (93 words)

	The Systematics Association
		to follow the recent discussion of the Phylocode on Taxacom follow this link.
		Does the PhyloCode offer a viable alternative to traditional Linnaean taxonomy?' an essay by Jake Alexander.
		The official PhyloCode web site can be found here http://www.ohiou.edu/phylocode/.
	www.systass.org (534 words)

	PhyloCode, Nomenclature, Classification and Taxonomy
		PhyloCode stands in contrast to traditional Linnaean systems of nomenclature and classification by rejecting the use of categorical ranks, stipulating that phylogenetic analysis must underpin named taxa, and re-conceptualizing the diagnosis of named taxa.
		Issues to be discussed in this session include challenges facing PhyloCode from outside critics (both practical and conceptual), responses to those challenges, and foundational and practical issues that are generating debate and controversy within the PhyloCode community.
		Also to be discussed are more general issues in species and speciation and how this plays out with regard to classification.
	www.ishpssb.org /ocs/viewsessionabstract.php?id=85 (235 words)

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