Inclusive Taxon Research Articles

First record of abelisaurid theropods and a peirosaurid crocodyliform from the Upper Cretaceous of Precordillera of La Rioja, NW Argentina

Extra-Patagonian records of Cretaceous theropod dinosaurs in Argentina are limited. When it comes to the Northwest of Argentina, most of the records come from the Cretaceous rocks of Salta Province, which yielded ceratosaurian abelisauroids like Noasaurus and Guemesia. Preliminary studies of the Los Llanos Formation at Eastern La Rioja Province recognized bone remains of Upper Cretaceous undetermined Abelisauridae and Coelurosauria. Recent surveys in the Northwest of the same province, in the outcrops of the Upper Cretaceous Ciénaga del Río Huaco Formation, at Quebrada Santo Domingo (Precordillera), resulted in the discovery of six isolated shed tooth crowns of putative abelisaurid theropods and crocodyliforms. They were found in association with partial skeletons of titanosaurid sauropod dinosaurs from two quarry sites, in the lower and upper sections of the same unit. Here we corroborate the taxonomic assignment of these specimens and their phylogenetic relationships. Five out of six teeth were assigned to Abelisauridae, whereas the remaining is considered to belong to a peirosaurid crocodyliform. Thus, the first occurrence of abelisaurid theropods and peirosaurid crocodyliforms in the Upper Cretaceous of the Precordillera of La Rioja is confirmed. Even though the teeth cannot be assigned to a less inclusive taxon, the difference in their stratigraphic position might indicate the presence of more than a single abelisaurid species in this region. The new results offer an optimistic perspective for future expeditions in this area, which intend to recover more skeletal elements.

Patterns of diversification and phylogenetic structure in the dorsolateral head musculature of Neotropical electric eels (Ostariophysi: Gymnotiformes), with a myological synonymy

Abstract The present study offers a broad comparative analysis of the dorsolateral head musculature in the Gymnotiformes, with detailed descriptions and illustrations of the dorsolateral head muscles of 83 species representing combined all valid genera. Results permit a detailed assessment of primary homologies and taxonomically-relevant variation across the order. This provides the basis for a myological synonymy, which organizes 33 previously proposed names for 15 recognized muscles. Morphological variation derived from dorsolateral head musculature was coded into 56 characters. When analyzed in isolation, that set of characters results in Gymnotidae as the sister group of remaining gymnotiforms, and all other currently recognized families as monophyletic groups. In a second analysis, myological characters were concatenated with other previously proposed characters into a phenotypic matrix. Results of that analysis reveal new myological synapomorphies for nearly all taxonomic categories within Gymnotiformes. A Partitioned Bremer Support (PBS) was used to asses the significance of comparative myology in elucidating phylogenetic relationships. PBS values show strongly non-uniform distributions on the tree, with positive scores skewed towards more inclusive taxa, and negative PBS values concentrated on less inclusive clades. Our results provide background for future studies on biomechanical constraints evolved in the early stages of gymnotiform evolution.

Postcranial osteology of Beipiaosaurus inexpectus (Theropoda: Therizinosauria).

Beipiaosaurus inexpectus, from the Lower Cretaceous Yixian Formation (Sihetun locality, near Beipiao), Liaoning, China, is a key taxon for understanding the early evolution of therizinosaurians. Since initial publication in 1999, only the cranial elements of this taxon have been described in detail. Here we present a detailed description of the postcranial skeletal anatomy of the holotype specimen of B. inexpectus, including two never before described dorsal vertebrae from the anterior half of the series. Based on these observations, and comparisons with the postcranial skeleton of therizinosaurian taxa named since the most recent diagnosis, we revised the diagnostic features for B. inexpectus adding three new possible autapomorphies (PII-3 shorter than PIII-4, subequal length of the pre- and postacetabular portions of the ilium, and equidimensional pubic peduncle of ilium). Additionally, we also propose three possible synapomorphies for more inclusive taxa (Therizinosauroidea and Therizinosauridae) and discuss implications for evolutionary trends within Therizinosauria. The newly acquired data from the postcranial osteology of the holotype specimen of B. inexpectus sheds light on our understanding of postcranial skeletal evolution and identification of therizinosaurians.

Analysis of the oral microbiome on the surface of modified dental polymers

ObjectivesThis study characterized the microbial diversity of formed biofilm on the surface of acrylic resins modified with nanostructured silver vanadate decorated with silver nanoparticles (AgVO3) after incubation in human saliva. DesignResin specimens prepared with AgVO3 at concentrations 0%, 1%, 2.5%, and 5% by either vacuum mixing or polymer solubilization were characterized by scanning electron microscopy (SEM) and X-ray diffraction (XRD). After 24 h and 7 days of saliva incubation, biofilm samples were collected from the surface of the specimens. The 16S rDNA genes were amplified, sequenced with the 454-Roche next-generation sequencing platform and analyzed to identify the Operational Taxonomic Units at the genus or higher level. ResultsSignificant differences in the dispersion pattern of the nanoparticles were observed among the two different methods of AgVO3 incorporation. In the microbiological analysis, a total of 103 genera and 7 more inclusive taxa, representing the phyla Bacteroidetes, Firmicutes and Proteobacteria were identified colonizing resin surfaces. The incorporation method of the AgVO3 had little to no significant effect on the microbiota of samples. Significant time and concentration-dependent responses to AgVO3 caused changes in the taxonomic profile at the phylum and genus level. ConclusionsThe results show differences in relation to the microbial diversity of modified resins during the initial phase of biofilm maturation. The incorporation of AgVO3 seems to significantly affect the colonizing microbiota.

Distribution patterns of Kielmeyera (Calophyllaceae): the Rio Doce basin emerges as a confluent area between the northern and southern Atlantic Forest

The Atlantic Forest is one of the most diverse and threatened tropical forests in the world, and the Rio Doce valley seems to represent a limit between biotas from its southern and northern portions. In the present study, we investigated the distribution of Kielmeyera (Calophyllaceae), a woody, typically wind-dispersed genus, with a high endemism rate in the Atlantic Forest. The 351 specimens analysed, representing 21 of 22 species of Kielmeyera from the Atlantic Forest, pointed to a complete dissimilarity between species composition in the southern (Rio de Janeiro state) and northern (Bahia state) portions of the forest. However, the Rio Doce valley in Espírito Santo state, rather than being a limit between these two portions, appear to represent a confluent area. The northern boundary of species from the southern portion is the São Mateus basin, whereas the southern boundary of species from the northern portion is at the Litorânea do Espírito Santo basin. Most specimens of Kielmeyera were collected in areas that currently are not remnants of original vegetation and that are not within any conservation unit, suggesting that an imminent loss of biodiversity is taking place. Studies comprising a broad range of functionally and phylogenetically distinct taxa make individual patterns of distribution obscure and overlook the conservation needs for specific groups. Therefore, our study on the distribution of Kielmeyera in the Atlantic forest highlights the importance of biogeographic analyses of less inclusive taxa of a flora.

A re-evaluation of the historical ‘dinosaur’ remains from the Middle-Upper Triassic of Poland

The so-called historical Polish discoveries of Triassic ‘dinosaurs’ have been repeatedly cited in papers and popular science books. Here, we re-evaluate each historical and purported Triassic dinosaur find from Poland. Additionaly, we describe several supposed ‘dinosaur’ bones collected by Polish geologists but only briefly mentioned: in regional geological journals, on collection labels, or in field notes. We attempt to assign all investigated specimens to the least inclusive taxon possible. Our revision indicates that part of this material represents non-dinosaur archosauromorph taxa. Most of the analysed specimens are fragmentary bones or isolated teeth and are indistinguishable from skeletal elements described from other well-known Triassic archosauromorph taxa. We conclude that fossils of dinosauriforms are present in the Upper Triassic of Silesia and Holy Cross Mountains. New analysis of Velocipes guerichi von Huene, 1932 holotype specimen from Kocury shows that it is the proximal part of fibula of a medium-sized theropod (or even neotheropod). Formally undescribed part of dinosauriform limb bone from the Holy Cross Mountains and V. guerichi from Silesia are the only identifiable dinosauromorph skeletal remains recognised in the Polish Triassic discovered prior to the description of Silesaurus opolensis Dzik, 2003 from the Upper Carnian of Krasiejów.

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing.

To characterize the profile of microbial communities colonizing titanium implants with different surface treatments after exposure to the oral environment at the genus or higher taxonomic level. Sixteen titanium disks, machined or sandblasted large-grit and acid-etched (SLA), were mounted on removable intraoral splints worn by four patients. After 24h of intraoral exposure, biofilm samples were collected from disks and supra/subgingival teeth areas. The 16S rDNA genes from each sample were amplified, sequenced with the Miseq Illumina instrument and analyzed. A total of 29 genera and seven more inclusive taxa, representing the phyla Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria and candidate division TM7 were identified in both titanium surfaces and teeth. No differences were found in relation to the operational taxonomic units (OTUs) and microbial diversity, assessed by Chao 1 and Shannon indices, when comparing SLA and machined titanium surfaces. Machined and SLA surfaces are colonized by similar numbers of prokaryotic OTUs after 24h of exposure to the oral environment. Higher complexity of the titanium surface topography in the initial phase of biofilm maturation does not seem to significantly influence the colonizing microbiota.

Alessioporus and Pulchroboletus (Boletaceae, Boletineae), two novel genera for Xerocomus ichnusanus and X. roseoalbidus from the European Mediterranean basin: molecular and morphological evidence

Alessioporus and Pulchroboletus are proposed as new monotypic genera to accommodate the thermo-xerophilic European species Xerocomus ichnusanus and X. roseoalbidus respectively. The present research focused on both morphological features and multigene molecular phylogeny (nrITS, nrLSU, tef-1α datasets) to elucidate the taxonomic status of these two rare Mediterranean boletes and delineate a natural classification within the family Boletaceae. Macro- and microscopic descriptions of the two species based on inclusive taxon sampling are provided and supported by line drawings of the main anatomical features. Phylogenetic relationships, ecology, geographical distribution and delimitation from the most closely allied taxa also are highlighted. In addition, epitype specimens are selected for both species.

Are black flies of the subgenusWilhelmia(Diptera: Simuliidae) multiple species or a single geographical generalist? Insights from the macrogenome

Organisms with vast distributions often represent geographical mosaics of cryptic species. The black fly Simulium (Wilhelmia) lineatum is among the most widely distributed members of the family Simuliidae, ranging from the British Isles to eastern China. Rather than viewing S. lineatum as a possible aggregate of multiple species, taxonomists have suggested a more inclusive taxon with additional synonyms. Accordingly, S. lineatum is an ideal candidate for testing the hypothesis that a wide geographical distribution signals the presence of more than one species. A cytogenetic approach was used to probe the macrogenome of S. lineatum and other taxa proposed by taxonomists as conspecific. The banding patterns in the polytene chromosomes of 480 larvae from 15 countries across the Palearctic Region revealed 128 rearrangements of the complement. All rearrangements were autosomal and 89% were inversions nonrandomly distributed among species and among chromosome arms. The analyses clarify long-standing confusion over previously proposed names and reveal a longitudinal succession of four species sequentially replacing one another from west to east: Simulium lineatum s.s., Simulium balcanicum, Simulium turgaicum, and Simulium takahasii. Thus, S. turgaicum is recalled from synonymy and the other three species are validated. Within the most-represented species, S. balcanicum, the frequency of inversions follows a longitudinal gradient with a north–south bias; as the distance between the sites increases along this north-west–south-east axis, the similarity of inversion frequencies between sites decreases. Validation of the concept that broadly distributed black flies are composites of structurally similar species provides a framework for guiding discovery of additional biodiversity.

Pterodactylus scolopaciceps Meyer, 1860 (Pterosauria, Pterodactyloidea) from the Upper Jurassic of Bavaria, Germany: the problem of cryptic pterosaur taxa in early ontogeny.

The taxonomy of the Late Jurassic pterodactyloid pterosaur Pterodactylus scolopaciceps Meyer, 1860 from the Solnhofen Limestone Formation of Bavaria, Germany is reviewed. Its nomenclatural history is long and complex, having been synonymised with both P. kochi (Wagner, 1837), and P. antiquus (Sömmerring, 1812). The majority of pterosaur species from the Solnhofen Limestone, including P. scolopaciceps are represented by juveniles. Consequently, specimens can appear remarkably similar due to juvenile characteristics detracting from taxonomic differences that are exaggerated in later ontogeny. Previous morphological and morphometric analyses have failed to separate species or even genera due to this problem, and as a result many species have been subsumed into a single taxon. A hypodigm for P. scolopaciceps, comprising of the holotype (BSP AS V 29 a/b) and material Broili referred to the taxon is described. P. scolopaciceps is found to be a valid taxon, but placement within Pterodactylus is inappropriate. Consequently, the new genus Aerodactylus is erected to accommodate it. Aerodactylus can be diagnosed on account of a unique suite of characters including jaws containing 16 teeth per-jaw, per-side, which are more sparsely distributed caudally and terminate rostral to the nasoantorbital fenestra; dorsal surface of the skull is subtly depressed rostral of the cranial table; rostrum very elongate (RI = ∼7), terminating in a point; orbits correspondingly low and elongate; elongate cervical vertebrae (approximately three times the length of their width); wing-metacarpal elongate, but still shorter than the ulna and first wing-phalanx; and pteroid approximately 65% of the total length of the ulna, straight and extremely thin (less than one third the width of the ulna). A cladistic analysis demonstrates that Aerodactylus is distinct from Pterodactylus, but close to Cycnorhamphus Seeley, 1870, Ardeadactylus Bennett, 2013a and Aurorazhdarcho Frey, Meyer and Tischlinger, 2011, consequently we erect the inclusive taxon Aurorazhdarchidae for their reception.

SimbirskiasaurusandPervushovisaurusreassessed: implications for the taxonomy and cranial osteology of Cretaceous platypterygiine ichthyosaurs

The ichthyosaur fossil record is interspersed by several hiatuses, notably during the Cretaceous. This hampers our understanding of the evolution and extinction of this group of marine reptiles during the last 50 million years of its history. Several Cretaceous ichthyosaur taxa named in the past have subsequently been dismissed and referred to the highly inclusive taxon Platypterygius, a trend that has created the impression of low Cretaceous ichthyosaur diversity. Here, we describe the cranial osteology, reassess the stratigraphic age, and evaluate the taxonomy and phylogenetic relationships of two Cretaceous ichthyosaurs from western Russia: Simbirskiasaurus birjukovi from the early Barremian and Pervushovisaurus bannovkensis from the middle Cenomanian, both formerly regarded as nomina dubia, and allocated to Platypterygius sp. and Platypterygius campylodon, respectively. We show that Simbirskiasaurus birjukovi and Pervushovisaurus bannovkensis are valid platypterygiine ophthalmosaurids, notably characterized by a peculiar narial aperture. The cranial anatomy and phylogenetic relationships of these taxa illuminate the evolution of narial aperture anatomy in Cretaceous ichthyosaurs, clarify the phylogenetic relationships among platypterygiines, and provide further arguments for a thorough revision of Platypterygius.

Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes

Ectolecithality is a form of oogenesis unique within Metazoa but common in Platyhelminthes, in which almost yolkless oocytes and tightly associated yolk cells are deposited together in egg capsules. Despite profound impacts on the embryogenesis and morphology of its beneficiaries, the origins of this developmental phenomenon remain obscure. Traditionally, all ectolecithal flatworms were grouped in a clade called Neoophora. However, there are also morphological arguments for multiple origins of ectolecithality and, to date, Neoophora has seen little support from molecular phylogenetic research, largely as a result of gaps in taxon sampling. Accordingly, we present a molecular phylogeny focused on resolving the deepest divergences among the free-living Platyhelminthes. Species were chosen to completely span the diversity of all major endo- and ectolecithal clades, including several aberrant species of uncertain systematic affinity and, additionally, a thorough sampling of the ‘lecithoepitheliate’ higher taxa Prorhynchida and Gnosonesimida, respectively, under- and unrepresented in phylogenies to date. Our analyses validate the monophyly of all classical higher platyhelminth taxa, and also resolve a clade possessing distinct yolk-cell and oocyte generating organs (which we name Euneoophora new taxon). Furthermore, implied-weights parsimony and Bayesian mixture model analyses suggest common ancestry of this clade with the lecithoepitheliates, implying that these taxa may retain a primitive form of ectolecithality. This topology thus corroborates the classical hypothesis of homology between yolk cells and oocytes in all Neoophora, and should serve to guide future evolutionary research on this unique developmental innovation in Platyhelminthes. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 570–588.

Homology and errors.

A recent review of the homology concept in cladistics is critiqued in light of the historical literature. Homology as a notion relevant to the recognition of clades remains equivalent to synapomorphy. Some symplesiomorphies are "homologies" inasmuch as they represent synapomorphies of more inclusive taxa; others are complementary character states that do not imply any shared evolutionary history among the taxa that exhibit the state. Undirected character-state change (as characters optimized on an unrooted tree) is a necessary but not sufficient test of homology, because the addition of a root may alter parsimonious reconstructions. Primary and secondary homology are defended as realistic representations of discovery procedures in comparative biology, recognizable even in Direct Optimization. The epistemological relationship between homology as evidence and common ancestry as explanation is again emphasized. An alternative definition of homology is proposed. © The Willi Hennig Society 2012.

Evolution of the bomolochiform superfamily complex (Copepoda: Cyclopoida): New insights from ssrDNA and morphology, and origin of umazuracolids from polychaete-infesting ancestors rejected

Poecilostome cyclopoids are among the most morphologically diverse copepods, having established symbiotic relationships with teleosts, elasmobranchs and invertebrate hosts belonging to no fewer than 14 marine phyla. Many parasitic lineages display radically divergent body plans and on that basis have traditionally been placed at higher taxonomic rank than they deserve. The most recent example is the monotypic family Umazuracolidae, established for a derived fish parasite with bomolochiform affinities. Phylogenetic analysis of complete ssrDNA (18S) sequences of 44 species belonging to 21 families of cyclopoid copepods shows that there is no support for the familial distinctiveness of the Umazuracolidae. Both maximum parsimony tree reconstruction and Bayesian inference, operating under the GTR + I + Γ model of nucleotide substitution, unambiguously placed Umazuracola elongatus in the Taeniacanthidae within the predominantly fish parasitic bomolochiform complex, refuting the original suggestion of a shared most recent common ancestry with polychaete symbionts. The phylogenies also revealed that the bomolochiform families and the Clausidiidae (and allies) form a monophyletic group, the clausidiiform complex, with high nodal support under both methods. Bayesian inference suggested a diphyletic origin of the “Poecilostomatoida” with the clausidiiform family-group holding a basal position while the traditional cyclopoid families form a monophyletic group in apposition to a second poecilostomatoid clade; however, maximum parsimony results were equivocal, depending on outgroup selection. Scrutiny of the morphological characters diagnosing the monotypic families Tegobomolochidae and Tuccidae demonstrated that they merely represent derived lineages within more inclusive taxa, the former being related to a group of nostril-inhabiting genera within the Bomolochidae, the latter forming the sistergroup of Taeniacanthodes within the Taeniacanthidae. The taeniacanthid genus Makrostrotos occupies a position at the base of the bomolochiform complex and is fixed as the type of a new family, Makrostrotidae. Although both morphological and molecular evidence hint that the Bomolochidae is nested within a paraphyletic Taeniacanthidae, the status quo of maintaining both families is favoured here pending additional molecular data. The bomolochiform complex, comprising the Bomolochidae, Taeniacanthidae, Telsidae and Makrostrotidae, is attributed superfamilial rank as the Bomolochoidea. A recent controversial phylogenetic analysis of the poecilostomatoid families is shown to be flawed, being based on a dataset containing imperfect or misleading information, and characters whose states were wrongly assessed.

Fossil gaps inferred from phylogenies alter the apparent nature of diversification in dragonflies and their relatives.

BackgroundThe fossil record has suggested that clade growth may differ in marine and terrestrial taxa, supporting equilibrial models in the former and expansionist models in the latter. However, incomplete sampling may bias findings based on fossil data alone. To attempt to correct for such bias, we assemble phylogenetic supertrees on one of the oldest clades of insects, the Odonatoidea (dragonflies, damselflies and their extinct relatives), using MRP and MRC. We use the trees to determine when, and in what clades, changes in taxonomic richness have occurred. We then test whether equilibrial or expansionist models are supported by fossil data alone, and whether findings differ when phylogenetic information is used to infer gaps in the fossil record.ResultsThere is broad agreement in family-level relationships between both supertrees, though with some uncertainty along the backbone of the tree regarding dragonflies (Anisoptera). "Anisozygoptera" are shown to be paraphyletic when fossil information is taken into account. In both trees, decreases in net diversification are associated with species-poor extant families (Neopetaliidae, Hemiphlebiidae), and an upshift is associated with Calopterygidae + Polythoridae. When ghost ranges are inferred from the fossil record, many families are shown to have much earlier origination dates. In a phylogenetic context, the number of family-level lineages is shown to be up to twice as high as the fossil record alone suggests through the Cretaceous and Cenozoic, and a logistic increase in richness is detected in contrast to an exponential increase indicated by fossils alone.ConclusionsOur analysis supports the notion that taxa, which appear to have diversified exponentially using fossil data, may in fact have diversified more logistically. This in turn suggests that one of the major apparent differences between the marine and terrestrial fossil record may simply be an artifact of incomplete sampling. Our results also support previous notions that adult colouration plays an important role in odonate radiation, and that Anisozygoptera should be grouped in a single inclusive taxon with Anisoptera, separate from Zygoptera.

Formal taxa, species groups, and perception of the genus Diplodactylus (Reptilia: Gekkonidae)

Genera with large numbers of species present particular difficulties; the analysis of relationships, of included taxa may be roblematic. One attempt to aproach this problem involves the reco of clusters of species tIat may be informally assembgd into species groups. The problems tE:g the recognition of such assemblages may induce are exlored. It is not that the species groups, as originail formulated, are problematic as they are initiafy erected to demarcate clusters withm an imperfectly known phylogeny of a supposedly monophyletic group. These species groups, however, tend to become recognized as “taxa” rather than operationaf clusters and as such tend to influence the approach to the inclusive taxon taken by subsequent workers. Rather than testing the concept of the species grous, there is a tendency to retain them and to insert other groups between them that do not exactly fit the original scheme. The establishment of species groups, first used to clarify a complex situation, has teen a source of problems for subseuent workers. The history of this aproach is traced for the gekkonid genus Diplodactylus and the problems that have arisen are outlined.

Defining the healthy "core microbiome" of oral microbial communities

BackgroundMost studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).ResultsWe sampled and sequenced microbiomes from several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy individuals. Within an individual oral cavity, we found over 3600 unique sequences, over 500 different OTUs or "species-level" phylotypes (sequences that clustered at 3% genetic difference) and 88 - 104 higher taxa (genus or more inclusive taxon). The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas) and Fusobacteria (genus Fusobacterium).Each individual sample harboured on average 266 "species-level" phylotypes (SD 67; range 123 - 326) with cheek samples being the least diverse and the dental samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate) from the samples that were obtained from solid surfaces (teeth).There was a large overlap in the higher taxa, "species-level" phylotypes and unique sequences among the three microbiomes: 84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the "core microbiome") contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads, while nearly all reads (99.8%) belonged to the shared higher taxa.ConclusionsWe obtained the first insight into the diversity and uniqueness of individual oral microbiomes at a resolution of next-generation sequencing. We showed that a major proportion of bacterial sequences of unrelated healthy individuals is identical, supporting the concept of a core microbiome at health.

Propositions for a character‐state‐based biological taxonomy

A new procedure for defining taxa upon a single character state is developed. It is centred on the designation of two specimens, belonging to two distinct species, exhibiting the same given character state, as type material, and referred to as ‘cladotypes’. A taxon name/definition designates a monophyletic group until one of the following assumptions is falsified: (1) the character state typified by cladotypes is homologous in individuals that are designated as cladotypes, and (2) cohesion mechanisms isolated individuals exhibiting the type‐character‐state from those that do not. A taxon defined by a character state that is found to be a combination of several character states is to be redefined upon a character state shared by its cladotypes. If several character states are available, the character state that makes the taxon the least inclusive taxon including cladotypic species (i.e., species to which belong cladotypes) is to be preferred. Taxon names designate obsolete phylogenetic hypotheses if the first assumption is falsified (such names are to be kept for this purpose, i.e., they are not to be recycled in another definition). Rules governing adaptation of previously erected names are proposed. Main cases of taxa synonymy involve definitions based on different pairs of cladotypes but referring to the same type‐character‐state; and definitions based on the same character‐state initially hypothesised as acquired by convergence in cladotypic species pairs, but later demonstrated as originating from a unique ancestor. Taxa could be synonyms if a permanent splitting event did not segregate individuals exhibiting a new character state, qualified as type‐character‐state, from individuals already assigned to a previously erected taxon. This procedure accommodates potentially any species concept, but is not tied to any; it is an extension of the composite species concept. Species are treated in a different way than other taxa: they are defined as sets of individuals belonging to the same evolving (segments of) metapopulation lineages as a holotype specimen, and do not need a defining character state.

Rank-Free Monography: A Practical Example From the Moss Clade <I>Leucophanella</I> (Calymperaceae)

Abstract Here I present a cladistically based monograph of a group of closely related mosses known as the Syrrhopodon involutus complex. Monographs remain a critical and indispensable component of systematics, but traditional monographic practices require some revisions if modern monographs are to truly reflect and incorporate phylogenetic understanding. I summarize the methods used to address issues relating to sampling and the formation of OTUs for this monograph, and emphasize the importance of incorporating morphological character data in a total evidence phylogenetic analysis. In addition to a traditional Linnaean taxonomic treatment, I provide rank-free definitions of the terminal taxa in the S. involutus complex. Following the PhyloCode recommendations for the designation and naming of more inclusive taxa, I present a novel method for naming terminal taxa as least-inclusive clades. This monographic treatment represents a first attempt at applying the PhyloCode at the terminal level in any plant gro...

A new species of Stenhelia (Copepoda, Harpacticoida) from a hydrothermal, active, submarine volcano in the New Ireland Fore-Arc system (Papua New Guinea) with notes on deep sea colonization within the Stenheliinae

A new species of harpacticoid copepod, Stenhelia gundulae (Stenheliinae), is described from Edison seamount, a hydrothermal active submarine volcano in the New Ireland Fore-Arc system (Papua New Guinea). Some species groups are identified within the genus Stenhelia. The new species is assigned to the ‘S. normani group’, which is characterized within a more inclusive taxon by the male P5 exp being fused to the basis and lacking two outer spines. The species most closely related to S. gundulae s.n. appear to be S. giesbrechti T. and A. Scott, 1896, S. tethysensis Monard, 1928 and S. normani T. Scott, 1905 including its former subspecies S. polluta Monard, 1928 and S. acutirostris Willey, 1935. The other known deep sea species of Stenhelia, S. noodti Schriever, 1982, S. islandico Schriever, 1982, S. lima Becker and Schriever, 1979 and S. diegensis Thistle and Coull, 1979, on the other hand belong to a different lineage, the ‘S. longicaudata group’ which is characterized by the apomorphic shape of the P1. It is hypothesized that deep sea colonization within the Stenheliinae occurred independently at least twice in two different lineages.