Towards a management hierarchy (classification) for the Catalogue of Life
Draft Discussion Document
Dr. Dennis P. Gordon FLS
Member of Species2000 Team and Taxonomy Group
Principal Scientist, Aquatic Biodiversity and Biosecutity
National Institute of Water & Atmospheric Research
Private Bag 14-901, Kilbirnie
Wellington, New Zealand
Elected Life Member, New Zealand Marine Sciences Society
Past President, International Bryozoology Association
Immediate Past-Chairman, Royal Society of New Zealand Committee on Biodiversity
Immediate Past-Chairman, Species 2000 Asia-Oceania Working Group
Member, Ocean Biogeographic Information System (OBIS) Editorial Board
Member of Steering Committee, World Register of Marine Organisms
You may cite this as:
Gordon DP (2009). Towards a management hierarchy (classification) for the Catalogue of Life: Draft Discussion Document. In Species 2000 & ITIS Catalogue of Life: 2009 Annual Checklist (Bisby FA, Roskov YR, Orrell TM, Nicolson D, Paglinawan LE, Bailly N, Kirk PM, Bourgoin T, Baillargeon G., eds). CD-ROM; Species 2000: Reading, UK.
The Catalogue of Life partnership, comprising Species 2000 and ITIS (Integrated Taxonomic Information System), has the goal of achieving a comprehensive catalogue of all known species on Earth. The actual number of described species (after correction for synonyms) is not presently known but estimates suggest about 1.8 million species.
The collaborative teams behind the Catalogue of Life need an agreed standard classification for these 1.8 million species, i.e. a working hierarchy for management purposes. This discussion document is intended to highlight some of the issues that need clarifying in order to achieve this goal beyond what we presently have.
Life's diversity is classified into a hierarchy of categories. The best-known of these is the Kingdom. When Carl Linnaeus introduced his new "system of nature" in the 1750s (Systema Naturae per Regna tria naturae, secundum Classes, Ordines, Genera, Species ...) he recognised three kingdoms, viz Plantae, Animalia, and a third kingdom for minerals that has long since been abandoned. As is evident from the title of his work, he introduced lower-level taxonomic categories, each successively nested in the other, named Class, Order, Genus, and Species. The most useful and innovative aspect of his system (which gave rise to the scientific discipline of Systematics) was the use of the binominal, comprising genus and species, that uniquely identified each species of organism.
Linnaeus's system has proven to be robust for some 250 years. The starting point for botanical names is his Species Plantarum, published in 1753, and that for zoological names is the tenth edition of the Systema Naturae published in 1758. Since that time the expansion of knowledge and increase in the number of described species has required the expansion of the number of hierarchical levels within the system. The ranks of Family and Phylum were introduced in the early 1800s and many super- and sub-categories have been added since then. The kingdom itself is today nested in a category called Domain, although Superkingdom is a better name.
There is currently no consensus among the world's taxonomists concerning which of the many classification schemes to use for the hierarchy of life, in part because of the confusion resulting from Hennig's (1966) redefinition of existing terminology of classification and the separate goals of cladification and classification (Mayr & Bock (2002). One solution is to offer more than one classification scheme (as in the Encyclopedia of Life). Discussions at the June 2008 conference of the World Register of Marine Species (WoRMS) at the Flanders Marine Institute (VLIZ), Ostend, indicated a preference among the officers of both the Catalogue of Life and WoRMS for a single management classification. On a more practical basis, writers of botanical and zoological textbooks find it easier to organise contents according to a single schema.
Purposes of a classification
At this point, it is probably useful to consider what is most needed in a classification, which is a system of ordering information. In recent years much has been written about biological classification and some viewpoints have been heatedly expressed. Linnaeus's utilitarian system has itself come under attack (see for example Ereshefshy 2001; Moore 2002), with a number of critics demanding an end to the use of ranks. "Ranks are irrelevant to phylogenetic insights and, being a source of confusion, are excluded" (Patterson 1993), but this viewpoint has been justifiably criticised (e.g. Benton 2000; Dyke 2002). Given the plethora of clade and taxon names in use, ranks at least relativise unfamiliar taxa and convey information about where in a tree they occur.
It is not the purpose here to summarise the various viewpoints but a need to consider what we want from a classification is inescapable. Cavalier-Smith (1998) has given a useful discussion. One bone of contention in recent decades has been whether or not to allow the use of paraphyletic taxa in classification. A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group. One of the best-known examples is that of Reptilia, nominally a class of Chordata. Since it is agreed that birds (nominally class Aves) have a reptilian ancestor, and Reptilia by convention does not include Aves, then Reptilia is a paraphyletic group. But paraphyletic groups potentially abound at all levels of the taxonomic hierarchy. Indeed, there are many thousands of taxa where it is not yet known if they are paraphyletic (including some of the descendants) or holophyletic (including all of the descendants). Cavalier-Smith's classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic.
He writes: "Theoretically, the Hennigian attempt to restrict taxa to clades, and forbid paraphyletic groups is incompatible with the basic purpose of phylogenetic classification, even though it misleadingly masquerades under that name. What a biological classification aims to do is to arrange organisms in a hierarchical series of nested taxa, in which each more-inclusive higher-level taxon is subdivided comprehensively into less-inclusive taxa at the next level below. ... Cladists have long accepted that the inability to classify ancestral and many fossil taxa is the Achilles heel of Hennigian classificatory principles, and refer to it as a problem; it is not a problem at all for systematics, but merely a defect in the Hennigian ideas on classification. Obviously, if you assert that you must not make paraphyletic groups then you cannot properly classify ancestral species excluded from a particular clade. No comprehensive phylogenetic classification is even theoretically possible unless one accepts paraphyletic as well as holophyletic taxa. The dogma against paraphyletic taxa is logically incompatible with the ... goal of taxonomy as the creation of a comprehensive classification of all organisms, both extant and extinct."
An example of a modern classification that attempts to meld cladification with classification is that of birds (treated as infraclass Aves), but in which some sequentially paraphyletic taxa are allowed (Livezey & Zusi 2007). By nesting birds in Reptilia, unnecessary in a traditional Darwinian classification in the view of Mayr and Bock (2002), and in order to reflect the number of branching points to arrive at Neornithes, the new classification introduces a plethora of subcategories. It remains to be seen how successful (widely accepted) this classification will be.
"The purpose of a classification is to provide a simplified reference system that is biologically sound and widely useful. It should be compatible with the phylogeny, but it cannot serve its central simplifying purpose unless it leaves out some of the fine detail about relationships that are essential for some phylogenetic purposes. One can use a phylogeny as a basis for making a classification, but one cannot logically deduce a fully detailed phylogeny from a classification. Nor is a phylogeny sufficient to give a classification. A phylogeny and a classification must be congruent (i.e. not contradictory) but they are different ways of abstracting from and representing biological relationships" (Cavalier-Smith 1998).
Mayr and Bock (2002) have taken the same view. Their stated goal was a traditional "Darwinian classification", in their terminology. Such a classification is based on "a balanced consideration of both genealogical branching (cladogenesis) and similarity (amount of phyletic evolutionary change = anagenesis). ..."A Darwinian classification is as genealogical as a cladification, only it is a genealogy of groups (classes) and not of clades."
The above material, including that in quotes, was presented at the VLIZ meeting. The feedback from participants was that paraphyly was to be avoided where possible unless current uncertainty precluded any firm decision as to relationship. Uncertainty definitely exists at all taxonomic levels. For example, the notion of six eukaryote supergroups has recently gained some acceptance (as indicated by biology textbooks) but there are problems with most of them (cf. Baldauf et al. 2000; Wegener Parfrey et al. 2006; Lane & Archibald 2008). These are, as defined:
Amoebozoa - composed of lineages of unicellular organisms, generally well supported in molecular phylogenies; without clear-cut morphological apomorphies, although most lineages produce pseudopodia that are broad (lobose).
Opisthokonta - includes animals, fungi, and their unicellular relatives (such as Capsaspora and collar flagellates), which share (or are derived from organisms with) a single posterior cilium and are strongly supported by sequence data.
Rhizaria - a group united only by molecular phylogenies; members include ecologically important and abundant organisms such as foraminiferans and cercozoans, which are largely understudied.
Excavata - unicellular eukaryotes that share an array of cytoskeletal features and a distinctive ventral 'excavation' that is a feeding groove, plus forms lacking some of these features that have been identified as relatives by molecular means; the common ancestry of the group as a whole is, at best, weakly supported by published molecular data.
Chromalveolata - predominantly unicellular assemblage of photosynthetic and non-photosynthetic organisms united by the 'chromalveolate hypothesis', which states that the plastids of chromists and alveolates are the product of a single secondary endosymbiosis in the common ancestry of the two groups; support for this group is largely based on plastid-related characters between subsets of its component lineages, with no single character or phylogeny that has been shown to unite all of its hypothesised members.
Archaeplastida - includes all primary plastid-containing lineages, and is well supported in both plastid and phylogenomic-scale nuclear gene phylogenies; molecular evidence for the single origin of red-algal, green-algal, and glaucophyte plastids is supported by the structure of plastid genomes and the light-harvesting complex.
As pointed out by Wegener Parfey et al. (2006), while Opisthokonta is supported by most studies, support for the other supergroups is less consistent. This situation raises the question of what may be construed to constitute a kingdom. Cavalier-Smith (1998), who introduced the name Opisthokonta, remarked that at least one cladist urged him to establish a kingdom-level taxon with this name, but "A kingdom Opisthokonta would be much less useful than the existing kingdoms Animalia, Fungi and Protozoa as a way of subdividing the living world into manageable groups of similar organisms, i.e. a classification as opposed to a phylogeny" (Cavalier-Smith 1998).
Major kingdom-level classifications
Margulis and Schwartz (1998) have given a useful summary of the history of classification. Their popular textbook Five Kingdoms (in three editions) is based on Whittaker's (1959) five-kingdom scheme (bacteria, protoctists, plants, animals, fungi), itself a development of Copeland's (1956) four-kingdom scheme (in which Fungi is not a kingdom). Cavalier-Smith (1981) argued that the minimum number of kingdoms suitable for general purposes was six. In that year he introduced the Chromista, defined then as now on both ultrastructural and molecular grounds. This kingdom is now widely accepted, including by the Catalogue of Life, although the scope and content of the Chromista are still being refined. Cavalier-Smith (1987) circumscribed and raised a putatively basal protozoan group, Archaezoa, to kingdom rank, at the same time raising both Eubacteria and Archaebacteria to kingdom rank, effectively creating an eight-kingdom scheme. Subsequently it was discovered that the "Archaezoa" were not, as thought, primitively amitochondriate, their condition being derived, and this kingdom was abandoned. Cavalier-Smith currently treats Bacteria as a single prokaryote kingdom and his system remains at six kingdoms (Cavalier-Smith 2004a).
Cavalier-Smith (1998, 2002a, 2006) rejects the three-domains scheme (Archaea, Bacteria, Eucarya) of Woese et al. (1990), as do Margulis and Schwartz (1998). Instead these authors argue the case for two superkingdoms, the one prokaryote (synonymous with Bacteria), the other eukaryote. Archaebacteria (Archaea) is treated as a subkingdom by Margulis and Schwarz (1998) and as a phylum by Cavalier-Smith (1998, 2002a).
Viruses are not considered in the above-mentioned popular-level accounts. Cavalier-Smith (1998) regarded viruses as "laterally transmissible parasitic genetic elements", not living organisms.
Criteria for a Management Classification:
What does the Catalogue of Life require of a management classification? In the booklet accompanying the 2008 Annual checklist (Bisby et al. 2008), it is mentioned that a GSD aspires to "have an explicit mechanism for seeking at least one responsible/consensus taxonomy, and for applying it consistently." It further states that the classification employed in the checklist "has been agreed by Species 2000 and ITIS as a practical management tool to provide access to the Catalogue, the Catalogue of Life Taxonomic Classification Edition 1. This top level classification has remained unchanged in 2005-2008."
The high-level classification currently in use is clearly evolving. In part it reflects traditional concepts; in part, certain groups like prokaryotes and Fungi reflect consensus views among an authoritative body of experts; in the case of ITIS the classification of invertebrates partly reflects one or more textbooks that have been influential (and remain so) in the North American context (e.g. Brusca & Brusca 2003).
To serve the needs of the Catalogue of Life and its broad user community, a case can be made for re-evaluating the existing high-level classification. Arguably, we need a fairly robust classification scheme that (a) reflects current expert opinion in such a way that it is neither geographically not personality-biased, (b) is likely to be stable for the next five years, and (c) is neither so new that it is untested nor so out of date as to be misleading or unhelpful. What follows is a discussion of selected taxa that either advances an opinion or leaves the question open for consideration. An expert panel could be asked to vote in order to achieve a decision that can be adopted by the Catalogue of Life. In any event, the consideration here is mainly that of higher-level taxa, viz phylum level and above; authors of GSDs are expected to provide a consensus classification for their specialist taxon (mostly below phylum level).
Pragmatically, the eight major categories used in the Catalogue of life, being unequal, are not assigned the rank of kingdom.
A Discussion of the Major Categories and Selected Higher Taxa
Regardless of whether or not these important biological entities are life forms, their inclusion in the Catalogue of Life is pragmatic and utilitarian. As stripped-down parasites, viruses appear to polyphyletic and ancient in origin. RNA viruses may have originated in the nucleoprotein world by escape or reduction from RNA-cells, whereas DNA viruses (at least some of them) might have evolved directly from RNA viruses. The antiquity of viruses can explain why most viral proteins have no cellular homologues or only distantly related ones. Viruses may have played a critical role in major evolutionary transitions, such as the invention of DNA and DNA replication mechanisms, the formation of the major superkingdoms of life, and even the origin of the eukaryotic nucleus (Forterre 2006). In the event, what was then the largest-known virus - a mimivirus - was recently discovered in amoebae (La Scola et al. 2003), with a 600-nm particle size comparable to mycoplasma. It is a double-stranded DNA virus of which the >1.1 million base pair genome sequence exhibits a similarity to proteins of known functions. The size and complexity of the mimivirus genome challenges the established frontier between viruses and parasitic cellular organisms. A second giant virus, called a mamavirus, has recently been discovered that is even larger and it is infected by a newly discovered virophage, suggesting that the mamavirus is in some sense 'alive' (Pearson 2008).
Viral classification is based on a consensus of the International Committee on Taxonomy of Viruses (ICTV).
Recommendation: Continue with the status quo.
The objections of Cavalier-Smith (1998, 2002a) and Mayr and Bock (2002) (see also Rivera and Lake 2004) to the concept of three domains, two of which are prokaryotic, have not been widely accepted by bacteriologists and the Catalogue of Life provisionally follows the consensus of the majority even if the question is still open. Currently the Catalogue uses the BIOS system developed by a team based at the National Institute for Environmental Studies (Japan) and is part of a collaborative effort that includes contributions by J. Euzéby and B. Tindall. The taxonomy is based on Release 7.4 of the nomenclatural taxonomy of G.M. Garrity, T.G. Lilburn and J.R. Cole.
Recommendation: Continue with the status quo in the interim.
Conceivably, the Protozoa (a kingdom in the 1998 scheme of Cavalier-Smith) could be divided into three or several kingdoms but, as indicated above, the circumscription and relative ranking of protozoan (and higher) groupings is still unclear (Lane & Archibald 2008). In any case, Protozoa is arguably monophyletic (Cavalier-Smith 2002b).
With the segregation of a kingdom Chromista (see below) from the "Protista" or "Protoctista" (see Margulis & Schwartz 1998), Protozoa is the most appropriate name for the balance of organisms remaining (Cavalier-Smith 1998). The most comprehensive illustrated treatments of protozoan taxa are those published as the Illustrated Guide to the Protozoa, but whereas the first (single-volume) edition of this compendium (Lee et al. 1985) was accompanied by a full classification, the recent two-volume edition (Lee et al. 2000) is less definitive. An introductory essay on changing views of protistan systematics (Patterson 2000) lists five hierarchical systems in abbreviated form to phylum or class level, including that of Cavalier-Smith (1998) before settling on a rankless alphabetical list of 72 taxon names/vernacular names (genus and higher). The first taxonomic chapter in volume one deals with "Order Choanoflagellida", which is not listed as such among the 72 names; it is hiding in the list among the "Opisthokonts (chytrids, fungi, collar flagellates, metazoa)". Though honest in treatment, this isn't very helpful for those seeking a pragmatic interim classification.
Cavalier-Smith is acknowledged by Patterson (2000) as "one of the major architects of contemporary schemes of classification and is influential on the constructs of others" but is criticised on the grounds that "Unlike most contemporary workers, Cavalier-Smith endorses the inclusion of... paraphyletic groups of organisms. ... This makes it unpalatable to the mainstream of taxonomic philosophy". But where protozoans are concerned a good case can be made for a paraphyletic kingdom, especially for the time-being (e.g. Schlegel & Hülsmann 2007).
Cavalier-Smith has been studying cellular ultrastructure since the late 1970s and has a long history of publication integrating the results of molecular sequencing with ultrastructure to achieve an evolving classification scheme. Critics object to the many new taxon names introduced by Cavalier-Smith during the past quarter-century and the fact that his classification is constantly being modified, but this is only to be expected as it is refined by new information. Cavalier-Smith 2002b, 2003a) published a definitive classification of Protozoa that has been modified as more detailed work has been carried out on different clades and taxa within the kingdom by himself, coworkers, and peers, e.g. the Amoebozoa (Cavalier-Smith et al. 2004; Berney & Pawlowski 2005; Kudryavtsev et al. 2005; Nikolaev et al. 2005; Smirnov et al. 2005, 2007, 2008; Tekle et al. 2008), Cercozoa (Cavalier-Smith & Chao 2003a; Vickerman et al. 2005; Karpov et al. 2006; Hoppenrath & Leander 2006; Cavalier-Smith et al. 2008; Bass et al. 2009), Choanozoa and Apusozoa (Cavalier-Smith & Chao 2003b; Cavalier-Smith et al. 2008), Metamonada and Loukozoa (Cavalier-Smith 2003b), Phaeodaria (Radiozoa) (Polet et al. 2004), Percolozoa (Cavalier-Smith & Nikolaev 2008), Myzozoa (Dinozoa [including Perkinsozoa] and Apicomplexa) (Cavalier-Smith & Chao 2004; Stelter et al. 2007), Euglenozoa (von der Heyden et al. 2004), and Rhizaria (Bass et al. 2005). We have the choice of using a synthesis classification resulting from this body of work or assigning rank names to the rankless categories in other sources.
Recommendations: 1) That we choose a ranked classification scheme for an interim paraphyletic kingdom Protozoa. 2) That we choose an interim synthesis derived from that developed by Cavalier-Smith, his research partners, and peers. At present, the classification scheme in the 2008 Annual Checklist is an uncritical mix of taxon names, some of which can be attributed to Cavalier-Smith; a large number are unplaced. AlgaeBase is the source of algal taxon names for the Catalogue of Life; a scheme is needed that integrates algal and non-algal taxa.
The most recent detailed classifications of this kingdom, by Cavalier-Smith (2000, 2004b), Cavalier-Smith and Chao (2006), and Cavalier-Smith and von der Heyden (2007), include six phyla in two subkingdoms. Subkingdom Cryptista includes the photosynthetic cryptophytes and the colourless kathablepharids. As an example of the differences in treatment of these constituent groups, whereas Cavalier-Smith (2004b) has three cryptistan classes (Cryptophyceae and Goniomonadea in subphylum Cryptomonada and Leucocryptea in subphylum Leucocrypta), the compendious The Illustrated Guide to the Protozoa, published by the Society of Protozoologists (Lee et al. 2000), has an entry for order Cryptomonadida (containing both Cryptomonas and Goniomonas, with neither assigned to family) (Kugrens et al. 2000) and, widely separated in the same volume under the heading "Residual free-living and heterotrophic flagellates", a family Kathablepharidae that contains, inter alia, the genus Leucocryptos (Patterson et al. 2000). Okamoto and Inouye (2005) proposed a new phylum, Kathablepharida, for Leucocryptos and Katablepharis, but this is effectively the same in content as the earlier established subphylum Leucocryptea. In the 2008 annual Checklist, the cryptophyte/cryptomonad "algal" taxa seem to have been covered thanks to AlgaeBase, but not the non-photosynthetic forms; a scheme is needed that integrates algal and non-algal taxa.
Recommendation: Provisionally follow the classification of Cavalier-Smith and Chao (2006) for subkingdom Cryptista, with sole phylum Cryptista and constituent subphyla Cryptomonada and Leucocrypta.
Cavalier-Smith and Chao (2006) recognise only three heterokont (stramenopile) phyla - the predominantly photosynthetic Ochrophyta (containing a number of algal classes), the non-photosynthetic Pseudofungi, and the Bigyra (now comprising subphyla Opalozoa, Bicoecia, and Sagenista). In some schemes, all three phyla are lumped together as phylum Heterokontophyta (e.g. Cavalier-Smith 1995a; Hoek et al. 1995). Cavalier-Smith (1986) first introduced the taxon Heterokonta. It has been widely accepted and it seems logical that his current use of the taxon (an infrakingdom that includes subordinate phyla) should prevail. The 2008 Annual Checklist has an inconsistent treatment and needs correcting. For example, diatoms appear in three places and it appears that two classification systems are in simultaneous use (one from AlgaeBase and one from ITIS?); two diatom classes - Coscinodiscophyceae and Fragilariophyceae - are listed under phylum Ochrophyta in kingdom Chromista, whereas class Bacillariophyceae is listed as a phylum-rank entry under kingdom Plantae. Without detailed checking, it is not clear how much overlap there is; certainly order Rhizosoleniales occurs twice in the 2008 Checklist, in both the Chromista and the Plantae.
The number of classes in phylum Ochrophyta varies according to author preference - Synurophyceae is sometimes segregated from Chrysophyceae and Phaeothamniophyceae and Schizocladiophyceae from Phaeophyceae, for example. Two new classes of Ochrophyta - Synchromophyceae and Aurearenophyceae - have been recognised in the past two years (Horn et al. 2007; Kai et al. 2008).
Recommendation: Provisionally follow the classification of Cavalier-Smith (2004b) and Cavalier-Smith and Chao (2006) for infrakingdom Heterokonta, with the addition of new classes recognised since that time.
There are two classes of Haptophyta - Pavlovophyceae and Prymnesiophyceae - both of which have been accepted by Andersen (2004). The 2008 Annual Checklist, however, includes the Pavlovales in the Prymnesiophyceae.
Recommendation: Provisionally follow the higher classification of Cavalier-Smith (2000) and Andersen (2004) for Haptophyta.
The traditional Heliozoa (sun protists) has long been recognised to be polyphyletic (Patterson 1993). Recent work (Cavalier-Smith & Chao 2003, 2006) has shown that some, like the well-known genus Actinophrys, are related to opalozoans in the phylum Bigyra; others belong among the protozoan phylum Cercozoa (Nikolaev et al. 2004). The core remaining group that now defines phylum Heliozoa comprises only the order Centrohelida, within which two new suborders have been recognised (Cavalier-Smith & von der Heyden, 2007). Owing to a weak grouping of centrohelids with haptophytes on 18S rRNA trees, the Heliozoa is provisionally considered to be chromistan not protozoan, but the question remains open (Sakaguchi et al. 2007).
Recommendation: Provisionally follow the classification of Cavalier-Smith and von der Heyden (2007) for phylum Heliozoa.
A new chromistan phylum, Telonemia (Shalchian-Tabrizi et al. 2006, 2007) was recently established for two named species of Telonema, a marine heterotrophic flagellate, and some unidentified forms. A protozoan class Telonemea was first recognised by Cavalier-Smith (1993). Initially allied with the then protozoan phylum Opalozoa, Telonemea was subsequently transferred to the phylum Apusozoa (Cavalier-Smith 2003a). Its present placement among the chromalveolates seems secure but it is likely to require its own chromistan subkingdom (Shalchian-Tabrizi et al. 2006).
Recommendation: That the phylum Telonemia be included in future Annual Checklists.
As with the other kingdoms, Plantae is classified in a variety of ways. Fundamentally, there are algal phyla (red and green) and embryophytes (land plants). The ancestral embryophyte is thought to be among the Charales (stoneworts) or Coleochaetales. Bremer (1985), a cladist, erected a phylum Streptophyta to include the ancestral algal embryophyte and all descendent groups (bryophytes, pteridophytes, and seed plants). At the other extreme, each of the main bryophyte, pteridophyte, and spermatophyte subdivisions has been accorded phylum (or Division) status. This latter treatment is exemplified in the 2008 Annual Checklist, which lists three bryophyte phyla, four pteridophyte phyla, and five seed-plant phyla. This treatment is terribly anachronistic and must be abandoned. [On what grounds can one possibly justify a separate phylum for Gingko, or for gnetophytes (which appear to be nested among the Pinales according to the latest molecular studies)?] A sensible middle approach, found in Cavalier-Smith (1998) but not restricted to him, is to recognise just two embryophyte phyla - Bryophyta (comprising liverworts, hornworts, and mosses) and Tracheophyta, all species of which are characterised by a diploid phase that has xylem and phloem. The treatment of Plantae adopted for the Species 2000 New Zealand project and accepted by all authors additionally comprises four algal phyla - Glaucophyta, Cyanidiophyta, Rhodophyta, and Chlorophyta. [Cyanidiophyta is not in Cavalier-Smith (1998) but work since then has shown that cyanidiophytes have the smallest known genomes of any phototrophic eukaryotes (Muravenko et al. 2001); additional studies of cytomorphology, biochemistry, and molecular-sequence data (e.g. Pinto et al. 2003) support the segregation of the Cyanidiophyta from the Rhodophyta at the level of phylum. Indeed, Cyanidiophyta is in the 2008 Annual Checklist].
Recommendation: That the Catalogue of Life adopts a pragmatic phylum-level plant classification similar to or modified after that in Cavalier-Smith (1998).
Animalia in the 2008 Annual Checklist comprises 31 phyla. The number of phyla in Brusca and Brusca (2003), presumably favoured by ITIS, is 34. The differences are accounted for as follows: (1) Monoblastozoa (in Brusca & Brusca) - comprises a single poorly known taxon, Salina salve , found only once in a saline culture (Frenzel 1892). Not in Checklist but may as well be included. (2) Rhombozoa and Orthonectida (in Brusca & Brusca) - combined as Mesozoa in the Checklist. (3) Kinorhyncha, Loricifera, and Priapul(id)a (in Brusca & Brusca) - combined as Cephalorhyncha in Checklist. (4) Myxozoa (in Checklist) is not a phylum in Brusca and Brusca. Today there is a great deal of consensus concerning the phyla of Animalia but some questions remain. These are discussed below, alphabetically, under the phylum names presently used in the Checklist.
(i) Phylum Gnathifera or phyla Acanthocephala, Gnathostomulida, Rotifera?
Each of these is commonly treated by biologists as a separate phylum (e.g. Ruppert & Barnes 1994; Margulis & Schwartz 1998; Brusca & Brusca 2003). However, some molecular data (e.g. Garey et al. 1996; Garcia-Varela & Nadler 2006) and morphological features suggest that Acanthocephala is nested in Rotifera. A syncytial epidermis links rotifers, Seison (a marine rotifer-like organism found on nebaliid crustaceans), and Acanthocephala, moving Ahlrichs (1995, 1997) to propose the name Syndermata for this grouping. As revealed by transmission (Rieger & Tyler 1995) and scanning electron microscopy (Sørensen 2003), the jaw apparatus of gnathostomulids and rotifers is remarkably similar. That of Seison is less obviously homologous (Segers & Malone 1998), and the Seisonidea may have diverged from rotifers at an early stage of their evolution. On the other hand, Seison has similar sperm to acanthocephalans and the epidermis of both groups contains bundles of filaments. For those who wish to treat these major groups as phyla, the cat among the pigeons was the discovery of Limnognathia maerski, representing a new class of organism (Micrognathozoa) from cold fresh waters in Greenland and the Crozet Islands (Kristensen & Funch 2000; De Smet 2002). It has a remarkable jaw apparatus (the most complicated known among invertebrates) that has clear homologies, in both the jaw elements and the musculature, with both the trophi in Rotifera and the jaws in Gnathostomulida. [The jaw apparatus appears to have significance for these groups as the radula does for Mollusca.] Accordingly, these three groups have been considered to be closely related and were united by Kristensen and Funch (2000) in the Gnathifera, a phylum first introduced by Alrichs in 1995. A morphological cladistic analysis supports this association (Jenner 2006). It is still an open question whether the Rotifera is paraphyletic. Nielsen (1995) considers it a sister taxon of Acanthocephala. The solution used in the Species 2000 New Zealand project was to treat Acanthocephala as a class of Gnathifera and not a subclass of Rotifera, hence a phylum Gnathifera that includes classes Gnathostomulida, Micrognathozoa, Rotifera, and Acanthocephala. But these classes could be treated as subphyla.
This approach was discussed with Hendrik Segers (rotifer specialist) and Wolfgang Sterrer (gnathostomulid specialist) at Ostend. Hendrik's current opinion (expressed in an email dated 28 August 2008 ) is:
"As for the position of Micrognathozoa, the taxon was proposed at Class level (within Gnathifera), and is generally recognized as representing a more or less independent lineage from Gnathostomulida and Rotifera, with unclear affiliation (see Giribet et al., 2004: Cladistics 20: 1-13). Taking into account that pragmatism plays an important role in establishing the CoL hierarchy, and considering that you treat both Rotifera and Gnathostomulida as separate phylum-level taxa (and also Acanthocephala, which is a group of parasitic rotifers, phylogenetically speaking), then I would suggest treating Micrognathozoa at the same level as rotifers and gnathostomulids. The alternative, treating those groups as subtaxa of Gnathifera doesn't solve any problem (you still end up with three taxa at the same level), and raises other problems (e.g., position of Cycliophora, to name one), in my humble opinion."
Wolfgang Sterrer likewise prefers to treat Rotifera and Gnathostomulida as phyla but the preferred status of Micrognathozoa remains a critical issue. When erected, it was as a class of Gnathifera. I/we cannot unilaterally treat it as a phylum and in any case I think the jaw apparatus has been established as homologous with other gnathiferan groups. So this leaves things as unresolved in my opinion.
Recommendation: That we canvass a range of specialists who have morphological and molecular familiarity with the gnathiferan groups including Reinhardt Kristensen and his Danish colleagues.
As a general comment, most GSDs will be accompanied by a standard classification that is favoured by the GSD author and his/her colleagues, hence the Catalogue of Life management teams don't have to decide what hierarchy to use for that GSD. Often, however, a GSD will comprise just part of a phylum and not be accompanied by a comprehensive phylum-level classification. The Arthropoda, generally regarded as monophyletic, is a case in point, and arriving at such a classification will be a challenge, particularly as so many internal relationships are constantly being clarified in each of the constituent subphyla and classes. For the Crustacea, for example, a good start was made by Martin and Davis (2001). This comprehensive classification covers the entire group. It is widely used, though not universally insofar as specialists of various crustacean taxa modify or adapt parts of it according to their preference and/or new knowledge. Boxshall (2007) has highlighted several ongoing controversies and unresolved taxonomic problems within Crustacea.
Recommendation: That we seek a synthesis for the Arthropoda by amalgamation of the most highly regarded schemes for each of the constituent subphyla and classes.
Adrianov and Malakhov (1995) erected this phylum for Kinorhyncha, Loricifera, Priapulida, and Nematomorpha so it is inconsistent for the 2008 Annual Checklist to list Nematomorpha separately if Cephalorhyncha is chosen. On the other hand, the first three of these phyla have in common an eversible snout (introvert) with scalid-spines and inner and outer retractor muscles, a similar excretory filter (protonephridium), and similar sense organs and there is some justification for uniting them in a single group, the Scalidophora (Lemburg 1995). On the other hand, Kinorhyncha has internal and external body segmentation, lacking in the other groups. Neuhaus and Higgins (2002) have noted that conflicting evidence exists for every one of the possible sister-group relationships among these phyla and prefer to keep them separate in a superphylum Scalidophora (which has priority over Cephalorhyncha).
Recommendation: That the Catalogue of Life abandons Cephalorhyncha and treats each of these phyla separately (as in Brusca & Brusca 2003). However, Priapulida should be spelled thus, not Priapula. This has been thoroughly discussed on http://wwwuser.gwdg.de/~clembur/priapufr.htm, where the author points out that Priapulida has been in use for more than a century, is the name favoured by all experts of the group, is abundantly found in a Google search (compared to Priapula), and that the latter is used mainly only in a few textbooks and by some molecular workers.
(iv) Cnidaria, Myxozoa
Recently, a classification of Cnidaria was published (Daly et al. 2007) that provides a way of checking the completeness of the existing arrangement in the 2008 Annual Checklist (an amalgam of the Hexacorallia GSD and the balance of taxa contributed by ITIS). The family Tetraplatiidae, unplaced in the 2008 Checklist, is included in the Narcomedusae. Interestingly, this new classification makes no mention of the Myxozoa, conclusively demonstrated last July to be cnidarian (Jiménez-Guri et al. 2007). The Myxozoa are treated as a cnidarian class in the Sp2000NZ project.
Recommendations: That the existing 2008 Checklist be compared with the new classification published by Daly et al. (2007) and that the Myxozoa be subsumed in Cnidaria.
The 2008 Checklist has a class-level taxon Somasteroidea, a group that is somewhat anachronistic in the recent context (dating from Fell 1962). In fact it has no living species and the included genus Platasterias is nowadays classified as an asteroid.
Recommendation: That Chris Mah be approached to check the asteroid classification.
(vi) Ectoprocta and Entoprocta
The earliest available name for these unrelated creatures was Polyzoa, introduced in 1830, followed by Bryozoa one year later. Polyzoa was popular in Britain and Australasia, Bryozoa in Europe and North America. Ectoprocta and Entoprocta were introduced as subphyla of Bryozoa in 1869. Libbie Hyman raised the subphylum names to phylum in the 1950s, in her magisterial series on the invertebrates, and since then they have been popularised in North American textbooks on invertebrates. This is unfortunate. No publishing member of the International Bryozoology Association, established in 1965, uses Ectoprocta, and the opinion of this body should prevail. Kamptozoa (coined as a phylum name in 1929) is increasingly used in contradistinction to Entoprocta.
Recommendation: That Ectoprocta and Entoprocta be abandoned in favour of Bryozoa and Kamptozoa, respectively.
Pawlowski et al. (1996) and Hanelt et al. (1996), respectively using 18S ribosomal RNA and DNA sequences, inferred that the Rhombozoa and Orthonectida are not each other's closest relatives. Ribosomal DNA and Hox gene sequences indicate that rhombozoans may be lophotrochozoans that have secondarily lost many morphological characters (Katayama et al. 1995; Kobayashi et al. 1999). The presence of cuticle and muscle fibres in orthonectids is in marked contrast to dicyemids, in which they are absent (Slyusarev 2000, 2003).
Recommendation:That the annual Checklist abandon Mesozoa in favour of the phylum names Dicyemida (or Rhombozoa) and Orthonectida, as in Margulis and Schwartz (1998) and Brusca and Brusca (2003). [Note that specialist F.G. Hochberg (Santa Barbara Museum of Natural History) advocates the use of Dicyemida over Rhombozoa as a phylum name. Dicyemida is used in the Sp2000NZ project.]
Why is this spelling used instead of Nematoda, which is standard in most sources? A classification of Nematoda is provided by Hodda (2007) in which there are five classes (compared to two in the 2008 Checklist).
Recommendation: That Nematoda be used as the phylum-level name.
The classification scheme used in the 2008 Annual Checklist would be considered conservative by some, not reflecting the results of recent research. Many textbooks retain the economically important parasitic flukes (Digenea and Monogenea) and tapeworms (Cestoda) as classes parallel to Turbellaria, mostly for practical reasons, and the view of Mayr and Bock (2002) would be that this is appropriate. Ehlers (1986) has shown there are three distinct groups within Platyhelminthes (which may itself be monophyletic), viz Acoelomorpha (Acoela and Nemertodermatida), Catenulida, and Rhabditophora. In some molecular treatments (e.g. Wallberg et al 2007) the two acoelomorph orders come out as separate groups of basal Bilateria. Tyler (2004), on the other hand, has pointed out the morphological characters that unite acoelomorphs with the balance of Platyhelminthes. Following Tyler (2004), the Sp2000NZ project treats each of the three major groups discerned by Ehlers as subphyla. Thus Rhabditophora contains two classes - Archoophora and Neoophora. Archoophora includes, inter alia, the turbellarian orders Macrostomorpha, Polycladida, and Lecithoepitheliata; Neoophora contains not only the balance of turbellarian orders but also the parasitic flukes and tapeworms as subinfraclasses under infraclass Neodermata. This treatment loses the traditional class ranks of flukes and cestodes but retains the orders. The classification of Lockyer et al. (2003) is helpful in reflecting these relationships but, as indicated in the introductory material, there are problems inherent in trying to translate, too far, a cladogram into a classification.
Recommendation: That a panel of experts advise the Catalogue of Life concerning an appropriate classification for Platyhelminthes.
This phylum is not listed as such in either Brusca and Brusca (2003) or in the 2008 Annual Checklist - not surprising, since it has only recently been recognised. Xenoturbella, a flatworm-like genus with only two described marine species (Israelsson 1999), is arguably the most primitive deuterostome (Bourlat et al. 2003, 2006; Stach et al. 2005).
Recommendation: That the phylum Xenoturbellida be included in the next Checklist.
A new tree of life has been developed for the Fungi that will no doubt inform the Index Fungorum (Bruns 2006; James et al. 2006). Inter alia, the Microsporidia is not listed in the 2008 Annual Checklist classification.
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