Phylogenetic Interpretation Research Articles

Reassessment of Dolichopithecus (Kanagawapithecus) leptopostorbitalis, a colobine monkey from the Late Pliocene of Japan

In the original description of Dolichopithecus (Kanagawapithecus) leptopostorbitalis, Iwamoto, Hasegawa and Koizumi, 2005, a moderately large-sized colobine monkey from the Late Pliocene of central Japan, affinities to the European Dolichopithecus rather than to the Transbaikalian Parapresbytis were noted based on the similarities in cranial morphology. Computed tomography scans confirm the presence of the maxillary sinus in the holotype, whereas it is probably absent in specimens of the European Dolichopithecus ruscinensis, the type species of this genus. This feature is either present or absent homogeneously in any given genus of living anthropoids. Its presence or absence is unknown in Parapresbytis, but the distinct morphology of the maxillary incisors in this taxon suggests that this form had different feeding habits from the Japanese colobines. These findings suggest that the Japanese colobine should be referred to henceforth as Kanagawapithecus leptopostorbitalis. Kanagawapithecus shares many important facial and dental features with Dolichopithecus rather than with Parapresbytis, but this association depends largely on the limited availability of comparable materials for the latter. Among colobines, the presence of the maxillary sinus is recorded only in Libypithecus and Cercopithecoides. The maxillary sinus is absent in all modern Asian colobines, implying that Kanagawapithecus is an isolated form without any relationship to living forms. Nevertheless, such phylogenetic interpretations are largely dependent on the restricted fossil evidence from the Pliocene and Pleistocene of eastern Eurasia and will be reexamined when new findings are made.

Is the General Time-Reversible Model Bad for Molecular Phylogenetics?

The general time reversible model (GTR) is presently the most popular model used in phylogentic studies. However, GTR has an undesirable mathematical property that is potentially of significant concern. It is the purpose of this article to give examples that demonstrate why this deficit may pose a problem for phylogenetic analysis and interpretation.

A New Stalked Filter-Feeder from the Middle Cambrian Burgess Shale, British Columbia, Canada

Burgess Shale-type deposits provide invaluable insights into the early evolution of body plans and the ecological structure of Cambrian communities, but a number of species, continue to defy phylogenetic interpretations. Here we extend this list to include a new soft-bodied animal, Siphusauctum gregarium n. gen. and n. sp., from the Tulip Beds (Campsite Cliff Shale Member, Burgess Shale Formation) of Mount Stephen (Yoho National Park, British Columbia). With 1,133 specimens collected, S. gregarium is clearly the most abundant animal from this locality.This stalked animal (reaching at least 20 cm in length), has a large ovoid calyx connected to a narrow bilayered stem and a small flattened or bulb-like holdfast. The calyx is enclosed by a flexible sheath with six small openings at the base, and a central terminal anus near the top encircled by indistinct openings. A prominent organ, represented by six radially symmetrical segments with comb-like elements, surrounds an internal body cavity with a large stomach, conical median gut and straight intestine. Siphusauctum gregarium was probably an active filter-feeder, with water passing through the calyx openings, capturing food particles with its comb-like elements. It often occurs in large assemblages on single bedding planes suggesting a gregarious lifestyle, with the animal living in high tier clusters. These were probably buried en masse more or less in-situ by rapid mud flow events. Siphusauctum gregarium resembles Dinomischus, another Cambrian enigmatic stalked animal. Principal points of comparison include a long stem with a calyx containing a visceral mass and bract-like elements, and a similar lifestyle albeit occupying different tiering levels. The presence in both animals of a digestive tract with a potential stomach and anus suggest a grade of organization within bilaterians, but relationships with extant phyla are not straightforward. Thus, the broader affinities of S. gregarium remain largely unconstrained.

Guenon Radiation is Enriched by a New Species that Demonstrates an Evolutionary Complexity with Which we are yet to Become Familiar

th September described this discovery to the scientific community (1). As is becoming increasingly frequent these days, given the high number of scientific articles, the media news reached us faster than the scientific information. The area known as TL2, a few hundred km as the crow flies south- west from the city of Kisangani, famous for its manufacturing, and important port on the Zaire river, is still uncontaminated and houses several important endemisms. This new species, studied in the area since 2007, on the basis of first sightings by the inhabitants of the zone and local hunters, has been named Cercopithecus lomamiensis. C.lomamiensis (CLO) is a tree-dweller and has been described in secondary forest ecology but climbs down to the ground with a certain regularity, foraging for seasonal herbs, things which many tree dwelling guenons do, even daily. Guenon's tree dwelling habit is never complete and should be intended in a critical sense (this would avoid unsatisfactory scholastic phylogenetic interpretations). The discovery and description of this new species, which required this long study, including circumstantial evidences, in order to ascertain the exact specific status, are of extreme interest in the study of the evolution, biogeography and conservation of this varied and fascinating type of African arboreal primate (2) that remains still very uncertain. The article in PlosOne analyses in a very detailed way this new species which at first sight, comprises characteristics which are common for its type: slender postcranial structure, undifferentiated, and multicoloured pattern. While the colours of its mantle reminds one of C.mitis, or mona group, the distribution of fur on the borders of the face and ears (but not on the crown) and the intense sky blue colouration of the scrotal and perineal area are something it has in common with C.hamlyni (CHA). Among the facial characteristics of C. lomamiensis one can observe a resemblance to C. hamlyni, something in the profile, a streak of lighter fur along the nose (however, nothing in comparison to the intensity of that of the CHA). CLO can mainly be distinguished from C. hamlyni, apart from its complete geographical separation, by the colours of the mantle, and for its generally less robust body. Moreover, although the cranial morphology and the sagittal profile are similar with CHA, the morphometric investigation designates principle traits of two distinct morphologies. On the contrary, if the morphological analysis does not lean towards a satisfactory relationship, what these two species seem to have most in common are the genetic traits resulting from the analysis of the loci of sexual chromosomes (TSPY and Xq13.3) which, despite indicating different divergent chronologies, both interspecific and intraspecific, unite the two taxa and separates them from the complicate radiation of the guenons. On this base the monotypic C. hamlyni group (3) enriches now of another component, different indeed, but presumably related on a genetic base. Further, it is now necessary to revise the taxonomic key to the superspecies, as C. hamlyni (sp. g.), was since now included in the species with prevailing colour not greenish, as its pelage is very dark (greenish olive speckled heavily with black, and with pearl grey tips). It should be interesting to know if in previous studies this taxon has been never met and tentatively described. Museum collection are full of samples that have given, and can still give interesting surprises.Thomas and Wroughton (4) described a variant of C. hamlyni (Cercopithecus leucampix aurora), where the yellow was predominant in the coat. It was tentatively compared with samples belonging to the C. mitis group, but the sample was too incomplete for an exhaustive analysis. Long time passed without certainties and the C. hamlyni remained for one hundred years alone in its peculiar group (5).

The “rostrum”-problem in coleoid terminology – an attempt to clarify inconsistencies

In the coleoid literature, the terminology of shell elements that are deposited on the external surface of the primary shell wall is inconsistent and confusing. Morpho- and phylogenetic interpretations have been therefore controversial. A strict layer-by-layer comparison of seventeen species from seven coleoid subgroups suggests that the coleoid shell is covered by either one (Diplobelida, Spirulida, Sepiida, Vampyropoda) or two (Aulacocerida, Belemnitida, Belemnoteuthidida) outer shell formations. The confusion has been caused mainly by the often ignored presence of a primordial rostrum in the Aulacocerida, Belemnitida, and Belemnoteuthidida. The primordial rostrum is a secondary shell formation, which covers the entire primary shell and, which is itself enveloped by a tertiary shell formation, the rostrum proper. In the Diplobelida, Spirulida, and Sepiida, the primary shell is invested by a single outer formation, the sheath; a rostrum proper is absent in the latter groups. As a secondary shell formation, the aulacocerid, belemnitid and belemnoteuthidid primordial rostrum on the one hand, and the diplobelid, spirulid and sepiid sheath on the other hand are considered to represent homologues. Accordingly, the rostrum proper of the Aulacocerida, Belemnitida, and Belemnoteuthidida are homologues as tertiary shell formations. Outer shell formations in gladius-bearing vampyropods (and teuthids?) might be represented by a single layer. The clarification of the homology of secondary and tertiary shell formations, however, cannot resolve phylogenetic relationships within the Coleoidea.

Mitochondrial diversity in Amerindian Kichwa and Mestizo populations from Ecuador

This study presents mitochondrial DNA (mtDNA) data from 107 unrelated individuals from two of the major ethnic groups in Ecuador: Amerindian Kichwas (n = 65) and Mestizos (n = 42). We characterized the diversity of the matrilineal lineages of these Ecuadorian groups by analyzing the entire mtDNA control region. Different patterns of diversity were observed in the two groups as result of the unique historical and demographic events which have occurred in each population. Higher genetic diversity values were obtained for the Mestizo group than for the Amerindian group. Interestingly, only Native American lineages were detected in the two population samples, but with differences in the haplogroup distribution: Kichwa (A, 49%; B, 3%; C, 8%; and D, 40%) and Mestizo (A, 33%; B, 33%; C, 10%; and D, 24%). Analysis of the complete mtDNA control region proved to be useful to increase the discrimination power between individuals who showed common haplotypes in HVSI and HVSII segments; and added valuable information to the phylogenetic interpretation of mtDNA haplotypes.

On some surface structures of potential taxonomic importance in families of the suborders Polydesmidea and Dalodesmidea (Polydesmida, Diplopoda).

Surface structures have rarely been the subject of a comprehensive study in Polydesmida despite their tremendous variety within this order. A number of these peripheral structures are here studied in most families of the suborders Polydesmidea and Dalodesmidea (sensu Hoffman 1980), using scanning electron microscopy. An illustrated description of the surface sculpture of the prozonite, the limbus and the intercalary cuticular micro-scutes on the metazonite is given for the first time for the studied families, together with an account of some other poorly known surface structures. Taken together, these characters allow us to recognize two main groupings of families. The families Ammodesmidae, Cryptodesmidae, Cyrtodesmidae, Haplodesmidae, Oniscodesmidae and Pyrgodesmidae have knobs on the posterior part of the prozonites, a toothed to lobed limbus, and no micro-scutes on the metazonites, wheras the families Fuhrmannodesmidae, Polydesmidae, Dalodesmidae, Macrosternodesmidae, Nearctodesmidae, Opisotretidae and Trichopolydesmidae have no knobs on the posterior part of the prozonites, a spiky or reduced limbus, and intercalary micro-scutes on the metazonites. The results are complemented with literature records and compared with current taxonomic and phylogenetic interpretations of the group.

Specific limits and emerging diversity patterns in East African populations of laminate-toothed rats, genus Otomys (Muridae: Murinae: Otomyini): Revision of the Otomys typus complex

We combined evidence from biogeography, craniodental traits, linear and geometric morphometrics (233 skulls), cytogenetics (karyotypes of 18 individuals) and mitochondrial DNA sequences (44 cytochrome b and 21 12S rRNA sequences) to test species limits within Otomys typus s.l. (Muridae: Murinae: Otomyini), a complex that is patchily distributed across alpine zones of Ethiopia and East Africa. Our results confirm the specific validity of O. dartmouthi, O. jacksoni, O. orestes, and O. uzungwensis, forms recently removed from synonymy under typus s.l.; support elevation of four other alpine forms to species (O. fortior, O. helleri, O. thomasi, and O. zinki); identify three additional new species (O. cheesmani sp. nov., O. simiensis sp. nov., O. yaldeni sp. nov.); and enable redefinition of O. typus s.s. as a species restricted to certain mountains west of the Great Rift Valley in Ethiopia (Simien and Guna Mountains in the north, extending to the highlands of the western rim of the Rift Valley). Phylogenetic interpretation of the cytochrome b data clearly demonstrates that the alpine morphotype once united under O. typus s.l. has originated independently at high elevations on several mountain ranges in eastern and northeastern Africa; although generally adapted to high-elevation vegetation, such alpine species are ecologically segregated from one another. Patterns of morphometric, genetic, and ecological differentiation among populations once misassigned to nominal O. tropicalis and O. typus more parsimoniously reflect regional cladogenesis along elevational gradients, rather than multiple, successive colonization by different ancestral forms from southern Africa as earlier supposed. Although incomplete and preliminary, information gathered for O. tropicalis indicates that it too is a species composite; several lines of research are discussed to redress its polyphyletic content. Our results, together with other recent taxonomic studies of Otomys, appreciably elevate the level of endemism within eastern Africa and underscore the significance of Africa's eastern highlands to the continental diversification of Otomyini.

Two new plioplatecarpine (Squamata, Mosasauridae) genera from the Upper Cretaceous of North America, and a global phylogenetic analysis of plioplatecarpines

ABSTRACT A new plioplatecarpine taxon, Latoplatecarpus, gen. nov., is proposed here to incorporate two species, L. willistoni, sp. nov., and L. nichollsae (comb. nov.). The new genus is currently restricted in distribution to the lower middle Campanian of North America. Phylogenetic analysis incorporating 97 morphological characters and 17 ingroup taxa indicates that (1) Ectenosaurus clidastoides is the basal-most member within the Plioplatecarpinae; (2) Platecarpus planifrons is generically distinct from P. tympaniticus; (3) Latoplatecarpus willistoni, gen. et sp. nov., constitutes the basal-most member within the clade that is sister to Platecarpus tympaniticus; and (4) as many as 17 unequivocal character changes support the clade comprising the three post-middle Campanian Plioplatecarpus species. Plesioplatecarpus, gen. nov., is erected to establish Plesioplatecarpus planifrons (comb. nov.). Further, we propose that the North American specimens referred to Platecarpus somenensis pertain to Latoplatecarpus nichollsae, based on the available phylogenetic, ontogenetic, biostratigraphic, and paleobiogeographic data and interpretations. Consequently, the current study recognizes 11 species within seven genera to constitute the Plioplatecarpinae. Of anatomical note, we suggest that quadrates in most plioplatecarpine taxa including Latoplatecarpus were tilted anteriorly in life, as a result of the suspensorial articulation forming along the distomedial portion of the long suprastapedial process that typifies quadrates in plioplatecarpine mosasaurs.

Why the phylogenetic regression appears robust to tree misspecification.

The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confounding similarities due to identity by descent. Because the true phylogeny is unknowable, an estimate must be used, introducing a source of error into phylogenetic comparative analysis that can be difficult to quantify. This manuscript aims to elucidate how tree misspecification is propagated through a comparative analysis. I focus on the phylogenetic regression under a Brownian motion model of evolution and consider the effect of local phylogenetic perturbations on the regression fit. Motivated by Felsenstein's method of independent contrasts, I derive a matrix square root of the phylogenetic covariance matrix that has an obvious phylogenetic interpretation. I use this result to transform the perturbed phylogenetic regression model into an ordinary linear regression in which one interpretable point has been affected. The simplicity of this formulation allows the contributions of data and phylogeny to be disentangled when studying the effect of tree misspecification. Consequentially, I find that branch length misspecification can be easily explained in terms of the reweighting of contrast scores between subtrees. An analytical consideration of this and other perturbations helps to explain why the phylogenetic regression appears generally to be robust to tree misspecification, and I am able to identify conditions under which the regression may not yield robust results. I discuss why soft polytomies do not meet these problematic conditions, leading to the conclusion that unresolved bifurcations should have only modest effects on the regression fit.

Evidence for Dietary Niche Separation Based on Infraorbital Foramen Size Variation among Subfossil Lemurs

The size of the infraorbital foramen (IOF) has been used in drawing both phylogenetic and ecological inferences regarding fossil taxa. Within the order Primates, frugivores have relatively larger IOFs than folivores or insectivores. This study uses relative IOF size in lemurs to test prior trophic inferences for subfossil lemurs and to explore the pattern of variation within and across lemur families. The IOFs of individuals belonging to 12 extinct lemur species were measured and compared to those of extant Malagasy strepsirhines. Observations matched expectations drawn from more traditional approaches (e.g. dental morphology and microwear, stable isotope analysis) remarkably well. We confirm that extinct lemurs belonging to the families Megaladapidae and Palaeopropithecidae were predominantly folivorous and that species belonging to the genus Pachylemur (Lemuridae) were frugivores. Very high values for relative IOF area in Archaeolemur support frugivory but are also consistent with omnivory, as certain omnivores use facial touch cues while feeding. These results provide additional evidence that the IOF can be used as an informative osteological feature in both phylogenetic and paleoecological interpretations of the fossil record.

Cretaceous diplodocids in Asia? Re‐evaluating the phylogenetic affinities of a fragmentary specimen

Abstract: The recent description of an anterior caudal vertebra purportedly belonging to a diplodocid sauropod from the Early Cretaceous of China has the potential to drastically alter our interpretation of the evolution and timing of geographical dispersal of a major dinosaur lineage. However, comparison with a wider taxonomic sample points more strongly towards titanosauriform affinities for this specimen, which is in keeping with the affinities of all other sauropods known from the Cretaceous of Asia. We explain the disparity in phylogenetic interpretation of this isolated vertebra as a by‐product of scoring differences and analysis of fragmentary material using repurposed data matrices. Rescoring the isolated vertebra based on our interpretation of the anatomy and rerunning the original analyses removes the specimen from Diplodocoidea but does not place it within Titanosauriformes, because of inadequacy in taxon and character sampling inherited from the repurposed data matrices. We suggest that phylogenetic analysis must begin with an initial hypothesis of affinity, based on comparative anatomy and spatiotemporal distributions, that must be adequately tested by the data matrix employed – i.e. data matrices should be tailored to sample anatomically, geographically and temporally relevant clades, and new characters should be added in tandem with new taxa so that the potential synapomorphy pool is not diluted. This is especially important for analyses of fragmentary specimens, which are likely to return coarse phylogenetic results with general evolutionary and palaeobiogeographical implications.

The mesothoracic intercoxal perforation in Chrysomelinae and its evolutionary significance (Insecta: Coleoptera: Chrysomelidae)

In the thorax of many beetles the posterior parts of the mesoventrite and anterior parts of the metaventrite are flexed inward to form mesocoxal cavities laterally and a transverse double-walled infolding medially. This study focuses on the structure of the median part of the infolding in Chrysomelinae (=Timarchini + Chrysomelini; 42 species studied). Whereas the infolding is intact in Timarchini and very few Chrysomelini, it is almost always perforated in Chrysomelini. The perforation connects the body cavity anterior and posterior to it. It is usually small or absent in wingless Chrysomelinae, but there are exceptions. The phylogenetic interpretation of the intercoxal perforation in the entire Cucujiformia is unclear: among Chrysomelidae, the perforation was found in a representative of Hispinae, but was absent in the cryptocephaline and criocerine species examined; among non-chrysomelid Cucujiformia the perforation was found in an anthribid, but was absent in the examined tenebrionid and erotylid species. From a functional perspective, the perforation likely reduces the movability of the intercoxal area. The origin of this perforation appears as an unusual type of evolutionary structural transformation where ± widely separated (but opposed) parts of the body wall belonging either to two external projections or to a single infolding (depending on the point of view) became attached to each other along their external surfaces, and then dissolved. As a result, the parts of the body cavity on both sides of the perforated walls came to communicate in a new place.

The male postabdomen of the “ancestral” archostematan beetle Tetraphalerus bruchi Heller, 1913 (Ommatidae) and its phylogenetic significance

External and internal features of the male postabdomen of Tetraphalerus bruchi were examined with a broad spectrum of morphological techniques and are described in detail. The conditions found in males of Tetraphalerus are compared to those in other archostematan beetles and members of other coleopteran suborders. The far-reaching reduction of the sternite I, structural modifications of sternite II, the retracted condition of the terminal segments, and ventromedially fused apodemes arising from the anterior margin of tergite IX are likely autapomorphies of Coleoptera. The male postabdomen of Tetraphalerus is less derived than in most other groups of Coleoptera. The sclerotized elements are symmetrical. In contrast to earlier statements on the archostematan male genital apparatus a distinctly developed, sclerotized basal piece is present. The aedeagus is trilobed and all elements of the copulatory apparatus are distinct. The muscular equipment is simple and moderately developed. All muscles (except the transverse muscles 61 and 62) occur pairwise and symmetrically. The distinct increase of the number of postabdominal muscles in representatives of the higher lineages of Coleoptera is likely linked with a torsion of the copulatory apparatus, which also results in asymmetries of the sclerotised parts. The testes of Tetraphalerus are long, multi-coiled tubes like in other archostematans, Myxophaga (Torridincola) and Adephaga. The presence of a deep notch on the parameres is a synapomorphy of Tetraphalerus and Omma. Curved parameres, a shortened distal portion, and a distinctly shortented penis are potential synapomorphies of Omma rutherfordi and Omma mastersi. The large size of the sclerotized part of the phallobase (‘basal piece’) and the division of the sclerotization of sternum IX are potential groundplan autapomorphies of Archostemata, with secondary modification of the latter feature in Cupedidae. The reduced condition of the sclerotization of sternum VIII is an apomorphic condition which has likely evolved independently in Tetraphalerus and Paracupes. Further anatomical investigation of the male genital apparatus of Coleoptera and holometabolous insects in general is required for a reliable morphological and phylogenetic interpretation. Concerning the presence or absence of particular sclerotizations (e.g., ‘basal piece’ of phallobase) histological section series and Confocal Laser Scanning Microscopy can add more precise information to what can be observed using permanent preparations of macerated specimens.

The importance of microscopic examinations of eggshells: Discrimination of bioalteration and diagenetic overprints from biological features

Although fossilization usually favors the preservation of calcium carbonate biominerals, diagenetic alterations might still produce erratic patterns that overprint the original biological structures. This investigation tries to discriminate in the fossil record “pathological” eggshells from diagenetic induced features as well as determine their origin, and aims, when possible, to provide alternative parsimonious interpretations to the origin of some of these rare and erratic features. In the past, most dinosaur eggshell studies failed to combine cathodoluminescence, scanning electron microscopy, transmitted and polarized light microscopic observations and were limited to only one or several of these examinations, which might have contributed to misinterpretations by lack of thorough observations. Sauropod eggshells from Faidella (Spain) and Auca Mahuevo (Argentina) provide ideal proxies to perform this research, as they display aberrant crystallographic features that have been or could be considered pathological. Under cathodoluminescence, the specimens fluoresce tremendously, indicating a strong diagenetic component in their make up. Guide by this information, further transmitted and polarized light microscopic examinations reveal microscopic dissolution fronts, which otherwise would have been left unnoted. The proposed hypothesis for the Faidella specimens in that organic filaments, which represent up to 2% of the shell composition, were exposed on the internal wall surfaces of pore canals where the calcium carbonate had been dissolved during a first diagenetic event. As such, the exposed extremities of the organic filaments likely triggered the formation of pseudo cores that mimic those in the membrana testacea during oogenesis. Observations based on the Argentinean specimens indicate that an added extra external structural layer is also separated from the original biological eggshell by a dissolution and recrystallization front. In addition to this abiotic process, artifact formations induced by bacterial mediation, a topic treated in an earlier publication, was also common at Auca Mahuevo. Without combined microscopic and cathodoluminiscence observations, the Faidella and Auca Mahuevo megaloolithid eggshells could be easily considered pathological eggshells. This would bias ensuing phylogenetic, paleobiological, and paleoenvironmental interpretations.

Systemic foundering

Systemic foundering

A comparative analysis of vibrissa count and infraorbital foramen area in primates and other mammals

Vibrissae are specialized sensory “hairs” that respond to mechanical stimuli. Sensory information from vibrissae is transmitted to the brain via the infraorbital nerve, which passes through the infraorbital foramen (IOF). Several analyses have documented that primates have smaller IOFs than non-primate mammals, and that haplorhines have smaller IOFs than strepsirrhines. These grade shifts in IOF area were attributed to differences in “vibrissa development.” Following earlier analyses, IOF area has been used to derive a general estimate of “whiskeredness” in extinct primates, and consequently, IOF area has been used in phylogenetic and paleoecological interpretations. Yet, the relationship between IOF area and vibrissa count has not been tested, and little is known about how IOF area and vibrissa counts vary among mammals. This study explores how relative IOF area and vibrissa count differ among 25 mammalian orders, and tests for a correlation between IOF area and vibrissa count. Results indicate that primates and dermopterans (Primatomorpha) have smaller IOFs than most non-primate mammals, but they do not have fewer vibrissae. In addition, strepsirrhines and haplorhines do not differ from one another in relative IOF area or vibrissa counts. Despite different patterns documented for IOF area and vibrissa count variation across mammals, results from this study do confirm that vibrissa count and IOF area are significantly and positively correlated ( p < 0.0001). However, there is considerable scatter in the data, suggesting that vibrissa counts cannot be predicted from IOF area. There are three implications of these finding. First, IOF area reflects all mechanoreceptors in the maxillary region, not just vibrissae. Second, IOF area may be an informative feature in interpretations of the fossil record. Third, paleoecological interpretations based on vibrissae are not recommended.

Azadinium obesum (Dinophyceae), a new nontoxic species in the genus that can produce azaspiracid toxins

Tillmann U., Elbrächter M., John U., Krock B. and Cembella A. 2010. Azadinium obesum (Dinophyceae), a new nontoxic species in the genus that can produce azaspiracid toxins. Phycologia 49: 169–182. DOI: 10.2216/09-35.1The novel dinoflagellate taxon we describe here as Azadinium obesum sp. nov. was isolated as clone 2E10 from the North Sea along the Scottish east coast, the same locality as for Azadinium spinosum Elbrächter et Tillmann, the type and formerly only species for this genus. In contrast to A. spinosum, a known producer of azaspiracid (AZA) toxins, the isolate of A. obesum produces no known AZA analogues detectable by liquid chromatography coupled with tandem mass spectrometry. Azadinium obesum is a small (13–18 µm length; 10–14 µm width) photosynthetic dinoflagellate with a thin theca exhibiting the Kofoidean plate tabulation: Po, cp, X, 4′, 3a, 6″, 6C, 5?S, 6′″, 2″″. This species is morphologically distinguished from A. spinosum by slightly larger mean cell size, consistent absence of an antapical spine, the lack of a stalked pyrenoid and several details of the plate configuration. Among these thecal features, the first precingular (1″) plate of A. obesum does not touch the first epithecal intercalary plate and is four sided rather than five sided as in A. spinosum. Furthermore, in A. obesum the lower half of the first apical (1′) plate is very narrow and tongue-like, and precingular plates 1″ and 6″ are very close together, whereas these diverge in A. spinosum. DNA sequence and phylogenetic analysis elucidates and supports the separation (but close affinity) of A. obesum and A. spinosum, as well as the description of the former as a distinct species. Phylogenetic interpretation of the four genes analysed – internal transcribed spacer, 18S rDNA, 28S rDNA (D1/D2) and cytochrome oxidase I – further validates the recently erected genus Azadinium Elbrächer et Tillmann but does not clarify the position of the genus with respect to higher taxonomic levels within the subclass Peridiniphycidae.

The importance of microscopic examinations of eggshells: Discrimination of bioalteration and diagenetic overprints from biological features

Although fossilization usually favors the preservation of calcium carbonate biominerals, diagenetic alterations might still produce erratic patterns that overprint the original biological structures. This investigation tries to discriminate in the fossil record “pathological” eggshells from diagenetic induced features as well as determine their origin, and aims, when possible, to provide alternative parsimonious interpretations to the origin of some of these rare and erratic features. In the past, most dinosaur eggshell studies failed to combine cathodoluminescence, scanning electron microscopy, transmitted and polarized light microscopic observations and were limited to only one or several of these examinations, which might have contributed to misinterpretations by lack of thorough observations. Sauropod eggshells from Faidella (Spain) and Auca Mahuevo (Argentina) provide ideal proxies to perform this research, as they display aberrant crystallographic features that have been or could be considered pathological. Under cathodoluminescence, the specimens fluoresce tremendously, indicating a strong diagenetic component in their make up. Guide by this information, further transmitted and polarized light microscopic examinations reveal microscopic dissolution fronts, which otherwise would have been left unnoted. The proposed hypothesis for the Faidella specimens in that organic filaments, which represent up to 2% of the shell composition, were exposed on the internal wall surfaces of pore canals where the calcium carbonate had been dissolved during a first diagenetic event. As such, the exposed extremities of the organic filaments likely triggered the formation of pseudo cores that mimic those in the membrana testacea during oogenesis. Observations based on the Argentinean specimens indicate that an added extra external structural layer is also separated from the original biological eggshell by a dissolution and recrystallization front. In addition to this abiotic process, artifact formations induced by bacterial mediation, a topic treated in an earlier publication, was also common at Auca Mahuevo. Without combined microscopic and cathodoluminiscence observations, the Faidella and Auca Mahuevo megaloolithid eggshells could be easily considered pathological eggshells. This would bias ensuing phylogenetic, paleobiological, and paleoenvironmental interpretations.

Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B′ (rpoB′) gene

A considerable number of species of the Halobacteriaceae possess multiple copies of the 16S rRNA gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. Two additional problems have been pointed out: (i) the genera Haloterrigena and Natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus Natrialba form definitely separate clusters in neighbour-joining trees, suggesting that these two clusters could be separated into two genera. In an attempt to solve these problems, the RNA polymerase B' subunit has been used as an additional target molecule for phylogenetic analysis, using partial sequences of 1305 bp. In this work, a primer set was designed that consistently amplified the full-length RNA polymerase B' subunit gene (rpoB') (1827-1842 bp) from 85 strains in 27 genera of the Halobacteriaceae. Differences in sequence length were found within the first 15 to 31 nt, and their downstream sequences (1812 bp) were aligned unambiguously without any gaps or deletions. Phylogenetic trees reconstructed from nucleotide sequences and deduced amino acid sequences by the maximum-likelihood method demonstrated that multiple species/strains in most genera individually formed cohesive clusters. Two discrepancies were observed: (i) the two species of Natronolimnobius were placed in definitely different positions, in that Natronolimnobius innermongolicus was placed in the Haloterrigena/Natrinema cluster, while Natronolimnobius baerhuensis was closely related to Halostagnicola larsenii, and (ii) Natronorubrum tibetense was segregated from the three other Natronorubrum species in the protein tree, while all four species formed a cluster in the gene tree, although supported by a bootstrap value of less than 50 %. The six Haloterrigena species/strains and the five species of Natrinema formed a large cluster in both trees, with Halopiger xanaduensis and Nln. innermongolicus located in the cluster in the protein tree and Nln. innermongolicus in the gene tree. Hpg. xanaduensis broke into the cluster of the genus Halobiforma, instead of the Haloterrigena/Natrinema cluster, in the gene tree. The six Natrialba species formed a tight cluster with two subclusters, of neutrophilic species and alkaliphilic species, in both trees. Overall, our data strongly suggest that (i) Nln. innermongolicus is a member of Haloterrigena/Natrinema, (ii) Nrr. tibetense might represent a new genus and (iii) the two genera Haloterrigena and Natrinema might constitute a single genus. As more and more novel species and genera are proposed in the family Halobacteriaceae, the full sequence of the rpoB' gene may provide a supplementary tool for determining the phylogenetic position of new isolates.