Recent changes to the classification in the NCBI taxonomy database
The brachiopod section of the taxonomy database has been revised. The brachiopod classes Inarticulata and Articulata are no longer used in the classification because the Inarticulata are not recognized as monophyletic in recent cladistic analyses. A monophyletic Brachiopoda is recognized comprising four subphyla: Craniiformea, Linguliformea, Rhynchonelliformea, and Phoroniformea. Recognition of the new subphylum Phoroniformea within the Brachiopoda follows Cohen (2000) [Monophyly of brachiopods and phoronids: reconciliation of molecular evidence with Linnaean classification (the subphylum Phoroniformea nov.). Proc. R. Soc. Lond. B 267: 225-231]. Classification within the subfamilies Craniiformea, Linguliformea and Rhynchonelliformea is based on the system used in the Treatise on Invertebrate Paleontology Part H Brachiopoda, vol. 2 & 3 (2000), published by the University of Kansas and the Geological Society of America. Information from this publication is presented at: http://www.com.univ-mrs.fr/EuroBrachNet/CLASS/Class.htm.Back to top
The mosses (Musci) have recently been reorganized according to the classification of Buck and Goffinet (2000), in order to more accurately reflect our current understanding of moss phylogeny. Major features of the new classification include: the elevation of the moss clade to Bryophyta (NOT to be confused with 'bryophytes', referring to a paraphyletic group comprising mosses, liverworts and anthocerotes), and the recognition of three new major clades, Andreaeobryopsida, Takakiopsida and Polytrichopsida, of equal rank with Bryposida, Sphagnopsida, and Andreaeopsida. The 15 suborders of Bryales recognized by Vitt (1984) have been folded, for the most part, into four subclasses of Bryopsida (Bryidae, Dicranidae, Diphysciidae and Funariidae).
Buck, W.R. and B. Goffinet. 2000. Morphology and classification of mosses. In Shaw, A.J. and Goffinet, B. (Eds.) The Biology of Bryophytes. Cambridge University Press. In press.
Vitt, D.H. 1984. Classification of the Bryopsida. In R.M. Schuster (Ed.). New Manual of Bryology, vol 2, 266-759. Hattori Botanical Laboratory, Nichinan, Japan.Back to top
Takifugu and Fugu.
The pufferfish genus Fugu has recently been renamed Takifugu in the taxonomy database. This is based on the recommendation of: Matsuura, K. 1990. The pufferfish genus Fugu Abe, 1952, a junior subjective synonym of Takifugu Abe, 1949. Bull. Natn. Sci. Mus., Tokyo, Ser. A. 18(1):15-20. Takifugu includes the species Takifugu rubripes (formerly Fugu rubripes), which is a well known model organism for the vertebrate genome. Any sequence from Takifugu rubripes can still be retrieved by searching on 'Fugu rubripes', because Fugu rubripes is included in the database as a synonym of Takifugu rubripes.Back to top
What are the Euteleostomi ?
The name Euteleostomi was recently included in the taxonomy database for the monophyletic group comprising the the Sarcopterygii ('lobe-finned fishes' and tetrapods) plus the Actinopterygii ('ray-finned fishes'). The group was formerly named the 'bony vertebrates' in the database.
Previously, the name Osteichthyes has also been applied to the monophyletic euteleostomes or 'bony vertebrates.' However the name Osteichthyes has been traditionally applied to the 'bony fishes', a paraphyletic assemblage comprising Actinopterygii and Sarcopyterygii minus the tetrapods. For this reason, application of the name Osteichthyes to the monophyletic group of all Sarcopterygii and Actinopterygii was not well accepted. The name Euteleostomi was first proposed as an alternative, to overcome these problems, in:
Nelson, J.S. (1994). p.65, "Fishes of the World," 3rd edition. John Wiley and Sons, New York.Back to top
Sharks and rays.
The elasmobranch section (sharks and rays) of the taxonomy database has recently been revised. The Elasmobranchii is divided into two main clades: the Galeomorphi (comprising the clades Galeoidea and Heterodontidea), and the Squalea (comprising the Dalatioidei, Echinorhinoidea, Hypnosqualea, Notidanoidea and Squaloidei). The Hypnosqualea includes the Squatiniformes, Pristiophoriformes, and the Batoidea which was previously named the Rajiformes (the Rajiformes is currently restricted to the Rajidae [skates]). Batoid interrelationships have been revised, though they remain enigmatic. Thus, the classification and phylogeny presented here is not a definitive one. Nevertheless, it is intended to provide a practical and informative composite of the hypotheses presented in the following most recent overviews of elsamobranch interrelationships:
de Carvalho, M.R. (1996) Higher-level elasmobranch phylogeny, basal squaleans, and paraphyly. p.35-62 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.
McEachran, J.D., Dunn, K.A, and Miyake, T. (1996) Interrelationships of the batoid fishes (Chondrichthyes: Batoidea). p.63-84 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.
Shirai, S. (1996) Phylogenetic interrelationships of Neoselachians (Chondrichthyes: Euselachii). p.9-34 in: M.L.J. Stiassny, L.R. Parenti, and G.D. Johnson (eds), "Interrelationships of Fishes." Academic Press, San Diego and London.Back to top
An update on the classification of the Phaeophyceae.
By Akira F. Peters, Institut fuer Meereskunde, Kiel, Germany, 22-10-2000 email: email@example.com
last updated January 2001
Chordariales: Now treated as a family within Ectocarpales (cf. below), and Stereocladon (so far Chordariaceae) as a genus in the new order Scytothamnales (cf. below). All families disappear but all genera except Stereocladon remain in Chordariaceae
Desmarestiales: Himantothallus is classified within Desmarestiaceae (Peters et al. 1997).
Dictyosiphonales: This order disappears because it is now included in Ectocarpales (cf below). The families are removed and the genera included in Chordariaceae. However, Adenocystis (so far Punctariaceae) is moved to the new family Adenocystaceae within Ectocarpales (cf. below), Akkesiphycus (so far Punctariaceae) into "unclassified Laminariales", and Pogotrichum (so far Punctariaceae) into a new family, Pogotrichaceae, within Ectocarpales.
Durvillaeales: reduced to a family (Durvillaeaceae) in the Fucales (Rousseau & de Reviers 1999a).
Ectocarpales: The orders Chordariales, Dictyosiphonales, and Scytosiphonales are now included in Ectocarpales (Rousseau & de Reviers 1999b). Scytosiphonales is the easiest case, it is now ranked as a family (Scytosiphonaceae)(Kogame et al. 1999, Rousseau & de Reviers 1999b). The other orders were shown to be polyphyletic (Siemer 1998, Siemer et al. 1998) and more changes are necessary. The following five families appear to have a sound circumscription based on molecular, cytological, morphological and life-history characters (Peters & Ramirez 2000):
Adenocystaceae (Rousseau et al. 2000), containing Adenocystis, Utriculidium and Caepidium (Peters & Ramirez 2000). Strongly supported by molecular data.
Chordariaceae: The largest family, containing many genera. The following genera are included: Asperococcus, Chordaria, Corycus, Dictyosiphon, Elachista, Giraudia, Gononema, Haplogloia, Hecatonema, Hummia, Isthmoplea, Laminariocolax, Laminarionema, Leathesia, Leptonematella, Litosiphon, Myrionema, Myriotrichia, Punctaria, Sorocarpus, Sphaerotrichia, Stictyosiphon, Streblonema, Striaria (Siemer et al. 1998, Peters & Ramirez 2000). The circumscription of the family is potentially controversial as it includes several genera that were type species OF other families. However, molecular data from rbcL and nuclear ribosomal genes consistently suggest to merge them all in one large group. They share a heteromorphic life history and probably a single sex pheromone. Chordariaceae is the oldest family name available for this group.
Ectocarpaceae now includeS only the genera Ectocarpus and Kuckuckia. The family is well characterised by the possession of ribbon-shaped plastids (a synapomorphy) and sequence data (Siemer 1998, Peters & Ramirez 2000). Other genera included here are now classified as follows: Asterocladon, Asteronema, Bachelotia (unclassified Phaeophyceae), Feldmannia, Geminocarpus, Hincksia, Pylaiella (Pogotrichaceae), Gononema , Mikrosyphar, Streblonema (Chordariaceae) Phaeostroma (Unclassified Ectocarpales).
Acinetosporaceae, including the genera Acinetospora, Feldmannia, Geminocarpus, Hincksia, Pogotrichum, Pylaiella (NB: new spelling of Pylaiella, no longer Pilayella, Silva et al. 1999). Acinetosporaceae Hamel ex J. Feldmann 1937 has priority upon Pogotrichaceae Pedersen 1978 and Pilayellaceae Pedersen 1984. This group forms a well-supported clade in molecular trees based on rbcL data. So far, trees from nuclear ribosomal data do not reveal them as a well-supported group but are not contradictory to their recognition. Members in this group share discoid plastids, pedunculated pyrenoids, intercalaric meristems and an isomorphic life history. These characters might be considered plesiomorphic.
Scytosiphonaceae, containing the same genera as before.
Unclassified Ectocarpales: Coelocladia (Siemer et al. 1998)
Fucales (all changes according to Rousseau & Reviers 1999a): Inclusion of Durvillaeales (reduced from ordinal rank) as own family. Inclusion in Sargassaceae of all families currently in Cystoseiraceae. Xiphophora (so far in Fucaceae) should be in a group "unclassified Fucales"
Laminariales: Apart from the removal of Sporochnales (cf. below), Saccorhiza should be treated in the family Phyllariaceae (Henry & South 1987). Halosiphon (so far in Chordaceae) should go into unclassified Laminariales (Peters 1998). Akkesiphycus (so far Dictyosiphonales, Punctariaceae) should also be in the category "unclassified Laminariales" (Kawai 1986).
Scytosiphonales: reduced to familial rank within Ectocarpales (Kogame et al. 1999, Rousseau & de Reviers 1999b).
Scytothamnales: This is a new order (Peters & Clayton 1998, confirmed in de Reviers & Rousseau 1999b and Peters & RamĖrez 2000), containing the genera, Scytothamnus, Splachnidium (formerly unclassified Dictyosiphonales), and Stereocladon (formerly Chordariaceae).
Unclassified Phaeophyceae: Analipus (within Heterochordariaceae; Tan & Druehl 1994), Asterocladon (formerly Ectocarpaceae; M¸ller et al. 1998), Asteronema (formerly Ectocarpaceae; de Reviers & Rousseau 1999b), Bachelotia (formerly Ectocarpaceae; de Reviers & Rousseau 1999b), Ralfsia (within Ralfsiaceae; Tan & Druehl 1994).
The sister group of the Phaeophyceae is still uncertain. Bailey et al. (1998) have presented molecular data that suggest Phaeothamniophyceae as likely a sister group of the brown algae as Xanthophyceae.
Bailey, J. C., Bidigare, R. R., Christensen, S. J. & Andersen, R. A. 1998. Phaeothamniophyceae classis nova: a new lineage of chromophytes based upon photosynthetic pigments, rbcL sequence analysis and ultrastructure. Protist 149: 245-263.
Kawai, H. 1986. Life history and systematic position of Akkesiphycus lubricus (Phaeophyceae). Journal of Phycology 22: 286-291.
Kogame, K., Horiguchi, T. & Masuda, M. 1999. Phylogeny of the order Scytosiphonales (Phaeophyceae) based on DNA sequences of rbcL, partial rbcS and partial LSU nrDNA. Phycologia 38: 496-502.
Henry, E. C. & South, G. R. 1987. Phyllariopsis gen. nov. and a reappraisal of the Phyllariaceae Tilden 1935 (Laminariales, Phaeophyceae). Phycologia 26: 9-16.
Mueller, D. G., Parodi, E. R. & Peters, A. F. 1998. Asterocladon lobatum gen. et sp. nov., a new brown alga with stellate chloroplast arrangement, and its systematic position judged from nrDNA sequences. Phycologia 37: 425-432.
Peters, A. F. 1998. Ribosomal DNA sequences support taxonomic separation of the two species of Chorda: reinstatement of Halosiphon tomentosus (Lyngbye) Jaasund (Phaeophyceae, Laminariales). European Journal of Phycology 33: 65-71.
Peters, A. F. & Clayton, M. N. 1998. Molecular and morphological investigation of three brown algal genera with stellate plastids: evidence for Scytothamnales ord. nov. (Phaeophyceae). Phycologia 37: 106-113.
Peters, A. F. & Ramirez, M. E. 2000. Molecular phylogeny of small brown algae, with special reference to the systematic position of Caepidium antarcticum (Adenocystaceae, Ectocarpales). Cryptogamie, Algologie, accepted manuscript.
Peters, A. F., van Oppen, M. J. H., Wiencke, C., Stam, W. T. & Olsen, J. L. 1997. Phylogeny and historical ecology of the Desmarestiaceae (Phaeophyceae) support a southern hemisphere origin. Journal of Phycology 33: 294-309.
de Reviers, B. & Rousseau, F. 1999. Towards a new classification of the brown algae. Progress in Phycological Research 13: 107-201.
Rousseau, F. & de Reviers, B. 1999a. Phylogenetic relationships within the Fucales (Phaeophyceae) based on combined partial SSU + LSU rDNA sequence data. European Journal of Phycology 34: 53-64.
Rousseau, F. & de Reviers, B. 1999b. Circumscription of the order Ectocarpales (Phaeophyceae): bibliographical synthesis and molecular evidence. Cryptogamie, Algologie 20: 5-18.
Rousseau, F., de Reviers, B., Leclerc, M. C., Asensi, A. & Delepine, D. 2000. Adenocystaceae fam. nov. (Phaeophyceae), a new family based on morphological and molecular evidences. European Journal of Phycology 35: 35-43.
Siemer B.,L. 1998. Molecular phylogenetic studies in the simple brown algae. PhD Thesis, University of Copenhagen, 138 p.
Siemer, B.,L., Stam, W. T., Olsen, J. L. & Pedersen, P. M. 1998. Phylogenetic relationships of the brown algal orders Ectocarpales, Chordariales, Dictyosiphonales, and Tilopteridales (Phaeophyceae) based on Rubisco large subunit and spacer sequences. Journal of Phycology 34: 1038-1048.
Silva, P. C., Lamy, D., Loiseaux-De Goer, S. & de Reviers, B. 1999. Proposal to conserve the name Pylaiella (Phaeophyceae) with a conserved spelling. Taxon 48: 000-000.
Stache-Crain, B., Mueller, D. G. & Goff, L. J. 1997. Molecular systematics of Ectocarpus and Kuckuckia (Ectocarpales, Phaeophyceae) inferred from phylogenetic analysis of nuclear and plastid-encoded DNA sequences. Journal of Phycology 33: 152-168.
Tan, I. H. & Druehl, L. D. 1994. A molecular analysis of Analipus and Ralfsia (Phaeophyceae) suggests the order Ectocarpales is polyphyletic. Journal of Phycology 30: 721-729.Back to top
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