Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Position and Delineation of Chrysopetalidae and Hesionidae (Annelida,Polychaeta, Phyllodocida)

Previous studies suggest that the polychaete taxa Hesionidae and Chrysopetalidae may not represent separate groups, that Pilargidae constitute a subgroup within Hesionidae, and that Hesionides and Microphthalmus are highly derived hesionids. Phylogenetic systematic analyses of Phyllodocida and the subgroup Nereidiformia are presented in order to clarify the position and delineation of these taxa. The phyllodocida analysis includes 18 families representing the majority of the taxa in the group, is rooted with Onuphidae, and is based on 42 absent/present coded morphological characters, obtained mainly from literature. All 69 resulting shortest trees include the clade (Chrysopetalidae, Nereididae, Hesionidae), but with either Syllidae, Nautiliniellidae, Pilargidae or (Aphroditiformia, Pisionidae) as sister. In- and outgroup taxon selection for the Nereidiformia study is dictated by the outcome of Phyllodocida analysis, with scores based on examined species of two chrysopetalids, four hesionids, one nereid, one pilargid, one pisionid, one syllid, plus the putative hesionids Hesionides arenaria and Microphthalmus sp. It is based on 46 absent/present coded morphological characters. Two equally parsimonious trees indicate that chrysopetalids and hesionids are well delineated, that pilargids and hesionids are non-overlapping, and that Microphthalmus and Hesionides are not hesionids.     

Phylogeny of Hesionidae (Aciculata, Polychaeta), assessed from morphology, 18S rDNA, 28S rDNA, 16S rDNA and COI

We assess phylogenetic relationships within the polychaete family Hesionidae from morphological data combined with nucleotide data from 18S rDNA, 28S rDNA, 16S rDNA and COI. Parsimony and Bayesian analyses were performed on two data sets; the first was based on a more restricted set of terminals with both morphological and molecular data (17 ingroup terminals), while the second included additional taxa with morphological data only (25 ingroup terminals). The different sets of terminals yielded fully congruent results, as did the parsimony and the Bayesian analyses. Our results indicate high levels of homoplasy in traditionally used morphological characters in the group, and that Hesioninae, Gyptini and Gyptis are nonmonophyletic. Hesionini (mainly Hesione and Leocrates ), Psamathini (mainly Hesiospina , Micropodarke , Nereimyra , Psamathe and Syllidia ), Ophiodrominae (Gyptini and Ophiodromini) and Ophiodromini (mainly Heteropodarke , Ophiodromus and Podarkeopsis ) are monophyletic and agree with previous classifications, and Hesionini is probably the sister to all other hesionids. The placements of the small hesionids capricornia and Lizardia , the hydrothermal vent taxa Hesiodeira and Hesiolyra , and the newly described Hesiobranchia , remain uncertain.     

A taxonomic revision of Paradoris sea slugs (Mollusca, Gastropoda, Nudibranchia, Doridina)

Paradoris , traditionally a generic taxon of discodorid sea slugs, is revised for the first time. One hundred and thirty specimens were examined, including all types and most of the nontype specimens available. New records for Paradoris are provided: South Africa, Tanzania, Seychelles, Western Australia, Thailand, Philippines, shallow waters of New Caledonia, southern Japan, and Hawaii. The individual variation of all taxonomic characters is thoroughly evaluated. Prior to the present study, Paradoris included 15 nominal species: 12 valid names and three synonyms. Three additional names, Discodoris erythraeensis , D. lora , and D. cavernae , are re-allocated to Paradoris , based on phylogenetic analysis. A phylogenetic diagnosis is provided for Paradoris : in particular, two new synapomorphies are described. Eight species names are regarded as valid: P. araneosa , P. dubia , P. erythraeensis , P. indecora , P. liturata , P. lopezi , P. mulciber , and P. tsurugensis . However, most of these species are poorly known, i.e. from very few specimens, and their taxonomic status might change when more individuals are available. P. lora is regarded as a nomen dubium . Six new synonymies are proposed, and explained by the fact that: (1) species names were created for one or a few specimens, without considering individual variation; (2) authors have not worked within a phylogenetic framework and have created new species names without considering all the existing species names already available within Paradoris . Three new morphospecies are described, but not formally named because their taxonomic status is still uncertain for several reasons (e.g. lack of knowledge of individual variation for some critical features).  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 125–238.     

Larval development of Euphausia superba Dana, 1852 and a phylogenetic analysis of the Euphausiacea

Literature data and new investigations by SEM of selected ontogenetic stages of the Antarctic Krill, Euphausia superba Dana, 1852 revealed morphological characters that are either missing in, or significantly changed towards, the adult. Besides adult features, such ontogenetic characters enabled us to propose a hypothesis of the phylogenetic relationships of and within the Euphausiacea on the basis of a computer aided cladistic analysis. These are of the form (Bentheuphausia amblyops + Euphausiidae = ('Thysanopoda' + Nematobrachion + Euphausiinae = (Meganyctiphanes norvegica + Euphausiini, new name + Nematoscelini, new name = (Nyctiphanes + Nematoscelina, new name)))). From this analysis the taxon names 'Euphausiina', 'Nematoscelini', and 'Nematoscelina' are introduced for in-groups of the taxon Euphausiacea as representing monophyletic units. The position of a set of ontogenetic characters remains relatively uncertain due to the still unknown larval development of Bentheuphausia amblyops (G. O. Sars, 1883).     

Reproductive biology of a new hesionid polychaete from the Great Barrier Reef

We describe Lizardia hirschi, a new hesionid genus and species, from shallow water on the Great Barrier Reef. It is characterized by small size (maximally around 2 mm long) and by males with paired penes on the last segment or the pygidium. The sperm are elongated, with a conical acrosome; extended, cylindrical nucleus; and three mitochondria. The females have three to four pairs of eggs in segments 10-13, up to 150 microm in diameter. The female reproductive system consists of spermathecae, situated in the notopodia of segments 10-12, and oviducts opening ventrally on segment 11. Fertilization may be internal. The female (but not the male) reproductive system appears to be homologous to that in another small hesionid, capricornia. The phylogenetic position of L. hirschi within Hesionidae is currently uncertain due to the retention of many apparently larval features in the adults.     

Phenotypic and genetic differentiation of two major phylogeographical lineages of arctic grayling Thymallus arcticus in the Lena River, and surrounding Arctic drainages

Two phylogeographical lineages of arctic grayling, Thymallus arcticus , in Siberia are extensively characterized based on both molecular genetic (mtDNA control region sequences) and phenotypic (12 meristic characters) data. One lineage, occurring in the delta region of the Lena River as well as all other Arctic draining rivers sampled, corresponds to the subspecific taxon Thymallus arcticus pallasii , whose type locality is the Kolyma River. This taxon is proposed to be a postglacial colonizer of the Lena delta. The second lineage occurs throughout the rest of the Lena basin and is proposed to have survived in a glacial refugium in the middle reaches of the Lena. These lineages form reciprocally monophyletic groups based on mtDNA sequences (net divergence 3.2%), a relationship that is concordant with phenotypic data, and thus reflects distinct taxa. The upper Lena taxon is given the preliminary name of Thymallus arcticus lenensis . Phylogenetic analysis, together with previously published data from North America, reveals that mtDNA sequences from North American populations group within the diverse clade corresponding to T. a. pallasii in Siberia. Despite the relatively close genetic relationship of most North American haplotypes with those in northern Siberia, inferences of fragmentation between the continents are supported, but bidirectional movements between the two continents are seen as likely. Despite inclusion in the clade representing T. a. pallasii in Siberia, the source of the relatively divergent Nahanni refuge haplotypes in North America is not resolved. Otherwise, inferences of postglacial expansion across several thousand kilometres are well supported within North America, but only smaller-scale colonization events among drainages are supported in Siberia.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 511–525.     

On the osteology and phylogenetic affinities of the Pseudasturidae – Lower Eocene stem-group representatives of parrots (Aves, Psittaciformes)

The osteology of the early Eocene (about 50 mya) avian taxon Pseudasturidae Mayr, 1998 is revised and its phylogenetic affinities are analysed. Members of the Pseudasturidae are known from abundant and excellently preserved skeletal material, both complete skeletons on slabs as well as isolated, three-dimensional bones. Although this taxon is thus among the best represented of all small early Tertiary birds, its systematic affinities were unknown so far. Derived osteological characters which are visible in newly recognized specimens from the Lower Eocene London Clay of England most convincingly support classification of the Pseudasturidae into the Psittaciformes (parrots). Both, in overall morphology and in terms of derived characters, the tarsometatarsus of the Pseudasturidae closely resembles that of the Eocene Quercypsittidae, which were assigned to the Psittaciformes by Mourer-Chauviré (1992 ). The Pseudasturidae are considered to be stem-group representatives of the Psittaciformes and the sister taxon of all other known psittaciform birds. The Eocene taxon lacks the specialized bill morphology of crown-group Psittaciformes of the Psittacidae. Several other osteological differences between the Pseudasturidae and the Psittacidae probably are also functionally correlated with the specialized feeding technique of the latter.  © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 136 , 715–729.     

Perissothallus, a new genus for Late Pennsylvanian–Early Permian noncalcareous algae conventionally assigned to Schizopteris (aphleboid foliage)

The morphogenus Schizopteris was established in the early 19th century for late Palaeozoic aphleboid foliage of uncertain affinities, and numerous specimens have subsequently been assigned to this taxon. Some of these fossils do not represent foliage, but rather noncalcareous algae. Although this inconsistency has been noted, an attempt to exclude the algae from Schizopteris has not yet been undertaken. Here we propose the new genus Perissothallus to accommodate those fossils conventionally assigned to Schizopteris that represent algae. The name P. versiformis is introduced for the type species from the Upper Pennsylvanian of Kansas (USA). Specimens from the Lower Permian of Germany are interpreted as a second species of Perissothallus , and the name P. densus is proposed. Perissothallus consists of erect cylindrical branches that radiate from a small holdfast and dichotomize repeatedly. Vegetative reproduction occurs in the form of daughter thalli produced on prostrate branches. Similarities in basic structure exist between Perissothallus and members of the extant algal genera Codium (Chlorophyta), Dictyota (Phaeophyta), and Scinaia (Rhodophyta).  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 477–488.     

A new chinchilloid (Rodentia,Hystricognathi) from the early Miocene of the localities of Bryn Gwyn and Gran Barranca (Patagonia,Argentina)

A new genus and species of chinchilloid rodent is described here. It was found in Colhuehuapian levels (early Miocene) of the localities of Bryn Gwyn and Gran Barranca, Chubut Province, Argentina. The new taxon shows a unique combination of characters (e.g., protohypsodont teeth, upper molars trilophodont, m1 and m2 tri- or tetralophodont with the second crest in position of variable development, and m3 trilophodont, cement absent) that make it different from any other known chinchilloids. We performed a phylogenetic analysis to corroborate the relationships of the new taxon within the Chinchilloidea. Our results indicate that the new taxon is best classified as Chinchilloidea incertae sedis, together with Incamys, Garridomys, and Scotamys. These species form the basal stock that leads to the modern lineage Chinchillidae (chinchillas and viscachas). The presence of the new taxon in these localities increases the diversity of chinchilloids during the early Miocene and reduces the dissimilarity between the faunas found in Bryn Gwyn and Gran Barranca.     

A NEW PARASEMIONOTID-LIKE FISH FROM THE LOWER TRIASSIC OF JURONG, JIANGSU PROVINCE, SOUTH CHINA

Abstract:  Based on a well-preserved specimen from the Early Triassic Lower Qinglong Formation exposed at Qingshan Quarry, Jurong, Jiangsu Province of China, the new taxon Peia jurongensis gen. et sp. nov. is named and described with anatomical details of its dermal skull, neurocranium and postcranial skeleton. The new taxon is characterized by the following set of characters: shallow V-shaped, tuber-like rostral; anterior part of frontal widened to roughly same width as its posterior part; roughly squared parietal; supraorbital absent; wide and slightly posteriorly inclined preopercle; five small ossifications present in dorsal half of preopercle; preopercular canal shifting anteriorly in ventral half of the preopercle, and reaching the anteroventral corner of this bone; dermosphenotic joining the skull roof and with a descending lamina; numerous branchiostegal rays. Comparisons are made between the new taxon and several parasemionotids from the same locality; a discussion is carried out on the distribution and evolution of several characters in halecomorphs and other closely related neopterygians.     

A new annual species of Bellium (Asteraceae) from the Balearic Islands

A new species, Bellium artrutxensis (Asteraceae: Astereae), is described from the therophytic pastures of southern Minorca (Balearic Islands). The analysis of nuclear ribosomal internal transcribed spacer (ITS) sequences showed that the new taxon was closely related to Bellium bellidioides , but differed with regard to the annual lifespan, the absence of epigeal stolons, and the presence of a patent eglandular indumentum on the leaves. The new taxon shows morphological features that are well suited for the colonization of dry environments with a marked summer drought, and may be of adaptive significance. The new species is diploid (2 n  = 18) and shows up to two accessory chromosomes in root tissues. B chromosomes have not been reported previously in other species of Bellium .  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 65–77.     

A new trirachodontid cynodont from the lower levels of the Burgersdorp Formation (Lower Triassic) of the Beaufort Group, South Africa and the cladistic relationships of Gondwanan gomphodonts

We describe a new trirachodontid cynodont from the base of the Burgersdorp Formation (Subzone A fauna of the Cynognathus Assemblage Zone), of the South African Karoo Basin. Langbergia modisei gen. et sp. nov. is characterized by circular to ovoid in outline upper postcanines and the absence of a maxillary platform lateral to the postcanine series. Apart from the new taxon, we recognize two other species of this family in the Cynognathus Assemblage Zone: Trirachodon berryi and Cricodon metabolus , the latter also represented in the Tanzanian Manda Formation. A phylogenetic analysis of gomphodont cynodonts was conducted using a data matrix of 43 craniodental characters and 18 terminals. Trirachodontidae appears as a monophyletic assemblage, with Langbergia appearing as the sister taxon of Cricodon . The monophyly of trirachodontids is weakly supported, however, with one extra step breaking it. Traversodontid cynodont relationships were also inspected and compared with a recent phylogeny proposed for this group. Considering the resulting phylogeny and the sudden appearance and diversification of Cynognathia representatives, the origin of basal Cynognathia (i.e. Cynognathus , Diademodon , and trirachodontids) is suggested to predate their first appearance in the fossil record.  © 2006 The Linnean Society of London, Zoological Journal of the Linnean Society , 2006, 147 , 383–413.     

Pindamoraria boraceiae, a new genus and species of freshwater Canthocamptidae (Copepoda, Harpacticoida) from Brazil

Members of a new genus and species of harpacticoid copepod crustacean appeared in samples from semi-terrestrial (moist arboreal mosses, wet soil) and aquatic (bromeliad tanks, Sphagnum moss, rock pools, stream) habitats in a remnant of the Atlantic Forest in south-eastern Brazil. The new taxon, for which we propose the name Pindamoraria boraceiae sp. nov. , is distinguished by a unique combination of characters, in particular the segmentation and setation pattern of legs 1–4 in both sexes, the structure of leg 5 in the female, and the strongly modified claw of the maxilliped in the male. It most resembles the canthocamptid genera Moraria , Pseudomoraria , Morariopsis and Paramorariopsis . Both previous records of species of Moraria from South America refer to members of Antarctobiotus , which is not considered a member of the Moraria group: Moraria (Kuehneltiella) neotropica Löffler has previously been transferred to Antarctobiotus ; and we propose herein the transfer of Moraria kummeroworum Ebert & Noodt to Antarctobiotus as well. In the New World, the genus Moraria extends only as far south as Honduras; and Pseudomoraria , Morariopsis and Paramorariopsis are Old World genera. The new species from Brazil is therefore the only member of the Moraria group known from South America.  © 2003 The Linnean Society of London, Zoological Journal of the Linnean Society , 2003, 139, 81–92.