Carpozoan echinoderms from the Middle Cambrian (Mayaktakh Formation) of Siberia (lower reaches of the Lena River)

Two new monotypic genera and a new monotypic family Rozanovicystidae of the class Cincta are described from the Middle Cambrian (Mayaktakh Formation) of the northeastern part of the Siberian Platform. Based on data obtained by morphofunctional analysis, there is a possibility that these animals could move by jet propulsion by ejecting water from the opercular aperture. Probable homologies of the main skeletal parts are discussed.     

Palaeoecological significance of calcimicrobial communities during ramp evolution: An example from the Lower Cambrian of Germany

Summary The palaeoecology of calcimicrobial communities from the only Gondwana-related Lower Cambrian in Central Europe (eastern Germany, carbonates and siliciclastics) has been studied. Six morphological groups of calcimicrobes are described. Some of them show a significant ability for sediment stabilization and construction of biohermal reef mounds. Other types of calcimicrobes were more common in biostromal thickets. Some of them were capable of populating different environments, growing in different modes and on different substrates. AnEpiphyton-archaeocyathan reef mound is described, illustrating the importance of calcimicrobes for mound formation. The fossil communities together with a complex of sedimentary features allow a reconstruction of the depositional history of the environment. Based on comparison with similar Gondwanan Lower Cambrian successions (Sardinia/Italy, Spain) and facies development a model is proposed describing the sedimentary history. Three depositional stages are distinguished: (1) deep subtidal ramp, (2) shallow subtidal ramp, (3) shallow subtidal to intertidal mixed siliciclastic-carbonate ramp with migrating oolitic shoals. In spite of similarities with the deposits in southern Europe, some distinct differences exist with respect to the succession of facies, the completeness of the sections, the fossil spectrum, and the nature of the siliciclastic sediments. For the German Lower Cambrian, a facies development from a low energy deep environment to a high energy shallow environment (partly restricted and with some evaporites) can be reconstructed. As compared with Sardinia and Spain, the depositional environment of the eastern German Lower Cambrian successions was predominantly characterized by low-energy conditions.     

Anabarella australis (Mollusca, Helcionelloida) from the Lower Cambrian of Greenland

The Early Cambrian helcionelloid mollusc Anabarella australis is described from North-East Greenland, representing the second occurrence of the species outside of Australia. Other Australian molluscs of this age are known from many localities including North China, Siberia, Altai, Transbaikalia, southern Kazakhstan, Mongolia, eastern Germany and Spain. These records, supported now by A. australis, demonstrate the close proximity of continents in the Early Cambrian.     

Lunulichnus Tuberosus Ichnogen. and Ichnosp. Nov. from the Early Eocene Wasatch Formation,Fossil Butte National Monument,Wyoming: An Arthropod-Constructed Trace Fossil Associated with Alluvial Firmgrounds

A new trace fossil, Lunulichnus tuberosus, is described from fluvial deposits of the Wasatch Formation (early Eocene) at Fossil Butte National Monument, southwestern Wyoming, USA. L. tuberosus are straight, vertical to obliquely oriented, unlined cylindrical burrows with pronounced crescent-shaped wall sculptings. In situ examples of these trace fossils are most commonly preserved as sand-filled casts emanating from the erosional bases of fluvial channel sandstone bodies into underlying floodplain mudstone/siltstone beds. L. tuberosus is interpreted as the dwelling trace of a stream-dwelling decapod crustacean. Excellent preservation of fine detail, particularly their diagnostic crescent-shaped wall sculptings, support the hypothesis that L. tuberosus were excavated in firm substrata subjacent to fluvial erosional surfaces. As such, they are interpreted as constituents of alluvial Glossifungites trace fossil assemblages.     

Revision of the Cambrian discoidal animals Stellostomites eumorphus and Pararotadiscus guizhouensis from South China

The discoidal fossils identified as Stellostomites eumorphus Sun & Hou, Rotadiscus grandis Sun & Hou and Rotadiscus guizhouensis Zhao & Zhu are abundant in the Cambrian Chengjiang and Kaili Lagerstätten of southwest China. Reinvestigation of all available specimens of S. eumorphus and R. guizhouensis indicates that S. eumorphus has radiating lobe structures different from those of Eldonia ludwigi Walcott and has one additional set of dorsal radiating canals, and has a distinct central cavity, two characters that are not present in E. ludwigi. R. guizhouensis differs from R. grandis in the morphology of the disc, internal radiating lobes and tentacles. This supports the validity of the genus StellostomitesSun & Hou, 1987, and substantiates the erection of a new genus, Pararotadiscus nov. gen., to receive Rotadiscus guizhouensis Zhao Zhu, 1994. Anatomical and taphonomical analyses indicate that S. eumorphus and P. guizhouensis were gregarious pelagic animals. The new anatomical information emphasize close phylogenetic relations with lophophorates (U-shaped intestine, circumoral tentacles and ectodermal, marginal accreted disc), though some features (e.g. dendritic tentacles, ventral pustules that may relate to reduced podia) do not exclude affinitics with echinoderms.     

Oikozetetes from the early Cambrian of South Australia: implications for halkieriid affinities and functional morphology

Shells of Oikozetetes and isolated halkieriid sclerites from a section of the lower Cambrian Mernmerna Formation in the Flinders Ranges, South Australia, are tentatively considered as being derived from the same scleritome. Details of shell morphology and the possible combination of biomineralized shell and sclerites suggest that Oikozetetes , if interpreted correctly, is closely related to Halkieria . A new interpretation of Oikozetetes shell morphology, in addition to the first report of paired muscle scars on the interior surface, sheds new light on the possible functional morphology of halkieriid shells and the means of attaching the shell to the body. The occurrence of Oikozetetes in South Australia extends its biostratigraphic range to the lower Cambrian and biogeographic range to East Gondwana.     

Gill rays of primitive vertebrate Yunnanozoon from Early Cambrian: a first record

Yunnanozoans (including Yunnanozoon and Haikouella) are important representatives of the primitive vertebrates in the Early Cambrian Chengjiang fauna. For Yunnanozoans, we know less about Yunnanozoon than about Haikouella due to the poor preservation of Yunnanozoon. Up to now, there have been some reports that Haikouella had developed gill rays, while there have been no reports on Yunnanozoon. In this paper, we described our new findings of the distinct gill rays of Yunnanozoon lividum based on new well-preserved material collected from the Lower Cambrian Maotianshan Shale in Xiaolantian of Yunnan Province, China. This study provides new data on the evolutionary relationship of the primitive vertebrates and their early evolution. __________ Translated from Acta Palaeontologica Sinica, 2006, 45(3): 345–350 [译自: 古生物学报]     

Spirodesmos milanai n. isp.: A Shallow-Water Spiral Trace Fossil from the Cambrian of the Eastern Cordillera,Northwest Argentina

Abstract

A new ichnofossiliferous locality in Salta Province (northwest Argentina) contains an association with numerous irregular spiral traces assigned to Spirodesmos milanai n. isp., in mature sandstones and quartzites with rippled bedding surfaces, rare wavy lamination and cross-bedded stratification. This record of early spiral behavior is interpreted as a primitive grazing method formed on muddy laminae above sand layers, and is related to a feeding strategy of an annelid-type of organism. Associated traces are Cruziana cf. semiplicata, Diplocraterion isp., Monocraterion isp., Rusophycus isp., Skolithos linearis Haldeman and Skolithos magnus Howell. The ichnoassemblage is similar to a shallow-water ichnoassociation from the Permian Ecca Group of South Africa (Mason et al., 1983 Mason, T. R., Stanistreet, I. G. and Tavener-Smith, R. 1983. Spiral trace fossils from the Permian Ecca Group of Zululand. Lethaia, 16: 241–247. [Crossref], [Web of Science ®] , [Google Scholar]).     

The gnathobasic spine microstructure of recent and Silurian chelicerates and the Cambrian artiopodan Sidneyia: Functional and evolutionary implications

Gnathobasic spines are located on the protopodal segments of the appendages of various euarthropod taxa, notably chelicerates. Although they are used to crush shells and masticate soft food items, the microstructure of these spines are relatively poorly known in both extant and extinct forms. Here we compare the gnathobasic spine microstructures of the Silurian eurypterid Eurypterus tetragonophthalmus from Estonia and the Cambrian artiopodan Sidneyiainexpectans from Canada with those of the Recent xiphosuran chelicerate Limulus polyphemus to infer potential variations in functional morphology through time. The thickened fibrous exocuticle in L. polyphemus spine tips enables effective prey mastication and shell crushing, while also reducing pressure on nerve endings that fill the spine cavities. The spine cuticle of E. tetragonophthalmus has a laminate structure and lacks the fibrous layers seen in L. polyphemus spines, suggesting that E. tetragonophthalmus may not have been capable of crushing thick shells, but a durophagous habit cannot be precluded. Conversely, the cuticle of S. inexpectans spines has a similar fibrous microstructure to L. polyphemus, suggesting that S. inexpectans was a competent shell crusher. This conclusion is consistent with specimens showing preserved gut contents containing various shelly fragments. The shape and arrangement of the gnathobasic spines is similar for both L. polyphemus and S. inexpectans, with stouter spines in the posterior cephalothoracic or trunk appendages, respectively. This differentiation indicates that crushing occurs posteriorly, while the gnathobases on anterior appendages continue mastication and push food towards and into the mouth. The results of recent phylogenetic analyses that considered both modern and fossil euarthropod clades show that xiphosurans and eurypterids are united as crown-group euchelicerates, with S. inexpectans placed within more basal artiopodan clades. These relationships suggest that gnathobases with thickened fibrous exocuticle, if not homoplasious, may be plesiomorphic for chelicerates and deeper relatives within Arachnomorpha. This study shows that the gnathobasic spine microstructure best adapted for durophagy has remained remarkably constant since the Cambrian.     

Tardigrades as ‘Stem-Group Arthropods’: The Evidence from the Cambrian Fauna

The Cambrian fauna can now reasonably be seen as containing many taxa that lie in the stem-groups of the extant phyla. As such, these fossils suggest how both the ‘body plans’ of extant phyla were assembled, and also how various ‘minor’ phyla relate to the larger groupings of today such as the arthropods and annelids.

The various arthropod and lobopod taxa of the Cambrian faunas have been controversial and have generally been considered either as lying in the crown or (occasionally) stem groups of the euarthropods, onychophorans and tardigrades. However, phylogenetic analysis strongly suggests that many of even the most euarthropod-like taxa do not lie within the euarthropod crown-group but are more basal. Further, the commonly expressed view that Cambrian lobopods are in effect stem- or crown-group onychophorans also seems not to be well supported. Lobopods in the Cambrian appear to be diverse and not particularly closely related to one another, and certainly cannot be combined in a monophyletic clade.

Both these advances offer hope that the tardigrades (placed as the sister group to the euarthropods in many analyses of extant taxa, here collectively named the Tactopoda) may be more closely related to some of these Cambrian taxa than others. The challenge for both neontologists and palaeontologists is to refine the systematic analysis of both living and fossil taxa in order to maximise the usefulness of the (admittedly few) characters that unite tardigrades to their Cambrian forbears.     

Pædomorphic patterns of the Cambrian genus Alueva (Trilobita, Ellipsocephalidae) from the Iberian Chains (NE Spain)

Three hundred protaspid and meraspid specimens of the trilobite species Alueva undulata Sdzuy, 1961 from the uppermost Bilbilian limestones of the Valdemiedes Formation (Iberian Chains, NE Spain) have been released by the action of acid. A pædomorphocline is proposed embracing the different species of Alueva, based on the comparison of the ontogenic patterns of the species Alueva undulata Sdzuy, 1961, and the adult morphologies of Alueva moratrix (Sdzuy, 1958). This analysis suggests that the species Alueva? hastata (Sdzuy, 1958) is not related to the pædomorphocline, and provides an approach for evaluating the phylogenetic relationships between the species A. undulata and A. moratrix, which occur across the Lower-Middle Cambrian transition in the Iberian Chains, directly linked with the Valdemiedes event.     

First report of Gogia (Eocrinoidea, Echinodermata) from the Early-Middle Cambrian of Sonora (Mexico), with biostratigraphical and palaeoecological comments

The blastozoan echinoderm genus Gogia is reported for the first time in the Early and the Middle Cambrian of Mexico. Reports in different members of the section of San José de Gracia (Sonora State, northwestern Mexico) extend the palaeogeographical range of the genus to the South Laurentia, and the stratigraphic range of Gogia granulosa to the whole first half of middle Middle Cambrian. Isolated plates occur in rocks deposited in detrital inner platform and complete specimens, in carbonate outer platform, confirming their ability to live in diverse environments. Their presence in these different environments through the Early-Middle Cambrian on Laurentia agrees with the onshore-offshore expansion of echinoderms during Cambrian.     

Opportunistic exploitation of dinosaur dung: fossil snails in coprolites from the Upper Cretaceous Two Medicine Formation of Montana

Multiple associations of fossil snails with dinosaur coprolites demonstrate that snails and dinosaurs not only shared ancient habitats but were trophically linked via dinosaur dung. Over 130 fossil snails representing at least seven different taxa have been found on or within herbivorous dinosaur coprolites from the Upper Cretaceous Two Medicine Formation of Montana. The terrestrial snail Megomphix is the most common taxon, but three other terrestrial taxa (Prograngerella, Hendersonia and Polygyrella) and three aquatic snails (Lioplacodes, ?Viviparus and a physid) also occur in coprolites. At least 46% of the shells in the faeces are whole or nearly so, indicating that most (if not all) of the snails were not ingested by dinosaurs, but were post‐depositional visitors to the dung pats. The sizeable, moist and microbially enriched dinosaur faeces would have provided both food and roosting sites for the ancient snails, and the large number of snail–coprolite associations reflect recurring, opportunistic exploitation of dung. The terrestrial taxa in the coprolites suggest that this Late Cretaceous locality included sufficiently moist detrital or vegetative cover for snails when dinosaur dung was not present. The aquatic snails probably entered the faeces during flood events. Dinosaur dung would have provided an abundant but patchy influx of resources that was probably seasonally available in the ancient environment.     

Fish communities in temporarily open/closed estuaries from the warm- and cool-temperate regions of South Africa: A review

The majority of estuaries along the coastline of southern Africa are termed temporarily open/closed estuaries (TOCEs) and are closed off from the sea for varying periods by a sandbar which forms at the mouth. It is therefore important to understand the processes occurring within TOCEs and their importance to fishes in order to make sound management recommendations. Estuaries along the coast of South Africa and their associated fish assemblages are biogeographically distinct and occur in either a subtropical, warm-temperate or cool-temperate zone. There are 125 TOCEs found within the cool-temperate and warm-temperate zones. Most fish species found in TOCEs are the juveniles of marine taxa that breed at sea. Permanently open estuaries generally have a higher diversity of species than TOCEs, but TOCEs still provide important nursery areas for many marine species and numerically often have a higher proportion of estuarine resident species. Important taxa in terms of abundance and biomass in warm-temperate TOCEs include the sparids Rhabdosargus holubi and Lithognathus lithognathus, several mugilid species, estuarine residents (particularly Gilchristella aestuaria and Atherina breviceps) and the freshwater cichlid Oreochromis mossambicus. The diversity of fishes in cool-temperate TOCEs is low when compared with warm-temperate systems and Liza richardsonii tends to dominate catches by number and mass in most systems. Several species recorded in TOCEs show clear longitudinal distribution trends. For example Atherina breviceps is generally more abundant in the lower reaches of estuaries. Mouth state, particularly the frequency, timing and duration of mouth opening plays a key role in determining species richness, composition, diversity and abundance in TOCEs. Mouth state is directly linked to freshwater input. Reduced river inflow leads to prolonged mouth closure and shorter open phases, which inhibits immigration and emigration of marine fish species between estuaries and the sea. Understanding of the effects of various processes occurring within these systems, particularly variation in freshwater input, on the biota of these important systems facilitates the development of informed management recommendations.     

Early evolutionary relationships among known life forms inferred from elongation factor EF-2/EF-G sequences: Phylogenetic coherence and structure of the archaeal domain

Summary Phylogenies were inferred from both the gene and the protein sequences of the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria). All treeing methods used (distance-matrix, maximum likelihood, and parsimony), including evolutionary parsimony, support the archaeal tree and disprove the eocyte tree (i.e., the polyphyly and paraphyly of the Archaea). Distance-matrix trees derived from both the amino acid and the DNA sequence alignments (first and second codon positions) showed the Archaea to be a monophyletia-holophyletic grouping whose deepest bifurcation divides a Sulfolobus branch from a branch comprising Methanococcus, Halobacterium, and Thermoplasma. Bootstrapped distance-matrix treeing confirmed the monophyly-holophyly of Archaea in 100% of the samples and supported the bifurcation of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 97% of the samples. Similar phylogenies were inferred by maximum likelihood and by maximum (protein and DNA) parsimony. DNA parsimony trees essentially identical to those inferred from first and second codon positions were derived from alternative DNA data sets comprising either the first or the second position of each codon. Bootstrapped DNA parsimony supported the monophyly-holophyly of Archaea in 100% of the bootstrap samples and confirmed the division of Archaea into a Sulfolobus branch and a methanogen-halophile branch in 93% of the bootstrap samples. Distance-matrix and maximum likelihood treeing under the constraint that branch lengths must be consistent with a molecular clock placed the root of the universal tree between the Bacteria and the bifurcation of Archaea and Eukarya. The results support the division of Archaea into the kingdoms Crenarchaeota (corresponding to the Sulfolobus branch and Euryarchaeota). This division was not confirmed by evolutionary parsimony, which identified Halobacterium rather than Sulfolobus as the deepest offspring within the Archaea.Offprint requests to: P. Cammarano     

Molecular docking for substrate identification: the short-chain dehydrogenases/reductases

Protein ligand docking has recently been investigated as a tool for protein function identification, with some success in identifying both known and unknown substrates of proteins. However, identifying a protein's substrate when cross-docking a large number of enzymes and their cognate ligands remains a challenge. To explore a more limited yet practically important and timely problem in more detail, we have used docking for identifying the substrates of a single protein family with remarkable substrate diversity, the short-chain dehydrogenases/reductases.We examine different protocols for identifying candidate substrates for 27 short-chain dehydrogenase/reductase proteins of known catalytic function. We present the results of docking > 900 metabolites from the human metabolome to each of these proteins together with their known cognate substrates and products, and we investigate the ability of docking to (a) reproduce a viable binding mode for the substrate and (b) to rank the substrate highly amongst the dataset of other metabolites. In addition, we examine whether our docking results provide information about the nature of the substrate, based on the best-scoring metabolites in the dataset. We compare two different docking methods and two alternative scoring functions for one of the docking methods, and we attempt to rationalise both successes and failures.Finally, we introduce a new protocol, whereby we dock only a set of representative structures (medoids) to each of the proteins, in the hope of characterising each binding site in terms of its ligand preferences, with a reduced computational cost. We compare the results from this protocol with our original docking experiments, and we find that although the rank of the representatives correlates well with the mean rank of the clusters to which they belong, a simple structure-based clustering is too naïve for the purpose of substrate identification. Many clusters comprise ligands with widely varying affinities for the same protein; hence important candidates can be missed if a single representative is used.     

Cutmarked bones from Pliocene archaeological sites at Gona, Afar, Ethiopia: implications for the function of the world's oldest stone tools

Newly recorded archaeological sites at Gona (Afar, Ethiopia) preserve both stone tools and faunal remains. These sites have also yielded the largest sample of cutmarked bones known from the time interval 2.58-2.1 million years ago (Ma). Most of the cutmarks on the Gona fauna possess obvious macroscopic (e.g., deep V-shaped cross-sections) and microscopic (e.g., internal microstriations, Herzian cones, shoulder effects) features that allow us to identify them confidently as instances of stone tool-imparted damage caused by hominid butchery. In addition, preliminary observations of the anatomical placement of cutmarks on several of the recovered bone specimens suggest that Gona hominids may have eviscerated carcasses and defleshed the fully muscled upper and intermediate limb bones of ungulates--activities that further suggest that Late Pliocene hominids may have gained early access to large mammal carcasses. These observations support the hypothesis that the earliest stone artifacts functioned primarily as butchery tools and also imply that hunting and/or aggressive scavenging of large ungulate carcasses may have been part of the behavioral repertoire of hominids by c. 2.5 Ma, although a larger sample of cutmarked bone specimens is necessary to support the latter inference.     

A new member of the short-chain dehydrogenases/reductases superfamily: Purification, characterization and substrate specificity of a recombinant carbonyl reductase from Pichia stipitis

A novel short-chain dehydrogenases/reductases superfamily (SDRs) reductase (PsCR) from Pichia stipitis that produced ethyl (S)-4-chloro-3-hydroxybutanoate with greater than 99% enantiomeric excess, was purified to homogeneity using fractional ammonium sulfate precipitation followed by DEAE-Sepharose chromatography. The enzyme purified from recombinant Escherichia coli had a molecular mass of about 35 kDa on SDS–PAGE and only required NADPH as an electron donor. The K_m value of PsCR for ethyl 4-chloro-3-oxobutanoate was 4.9 mg/mL and the corresponding V_max was 337 μmol/mg protein/min. The catalytic efficiency value was the highest ever reported for reductases from yeasts. Moreover, PsCR exhibited a medium-range substrate spectrum toward various keto and aldehyde compounds, i.e., ethyl-3-oxobutanoate with a chlorine substitution at the 2 or 4-position, or α,β-diketones. In addition, the activity of the enzyme was strongly inhibited by SDS and β-mercaptoethanol, but not by ethylene diamine tetra acetic acid.     

The appendicular skeleton of Suuwasseaemilieae (Sauropoda: Flagellicaudata) from the Upper Jurassic Morrison Formation of Montana (USA)

Appendicular elements of the sauropod dinosaur Suuwasseaemilieae, from the Upper Jurassic Morrison Formation of Montana, USA, display a peculiar mix of autapomorphic and plesiomorphic features. While more similar in overall morphology to Apatosaurus than other flagellicaudatans, the coracoid of Suuwassea lacks the quadrangular shape of Apatosaurus. The humerus of Suuwassea bears a pronounced proximal tuberculum, a feature seen elsewhere only in saltasaurine titanosaurian sauropods. The rectangular proximal articular surface of the tibia is proportioned neither like Diplodocus nor Apatosaurus type specimens, although this region may be intraspecifically variable. The pes of Suuwassea possesses plesiomorphically elongate phalanges and a small, uncompressed ungual, unlike other flagellicaudatans except Dyslocosaurus. The localization of tooth marks on the pedal elements suggests that sauropod feet may have been singled out by scavengers, as has been noted for elephants.     

An alternative mechanism for the catalysis of peptide bond formation by L/F transferase: substrate binding and orientation

Eubacterial leucyl/phenylalanyl tRNA protein transferase (L/F transferase) catalyzes the transfer of a leucine or a phenylalanine from an aminoacyl-tRNA to the N-terminus of a protein substrate. This N-terminal addition of an amino acid is analogous to that of peptide synthesis by ribosomes. A previously proposed catalytic mechanism for Escherichia coli L/F transferase identified the conserved aspartate 186 (D186) and glutamine 188 (Q188) as key catalytic residues. We have reassessed the role of D186 and Q188 by investigating the enzymatic reactions and kinetics of enzymes possessing mutations to these active-site residues. Additionally three other amino acids proposed to be involved in aminoacyl-tRNA substrate binding are investigated for comparison. By quantitatively measuring product formation using a quantitative matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based assay, our results clearly demonstrate that, despite significant reduction in enzymatic activity as a result of different point mutations introduced into the active site of L/F transferase, the formation of product is still observed upon extended incubations. Our kinetic data and existing X-ray crystal structures result in a proposal that the critical roles of D186 and Q188, like the other amino acids in the active site, are for substrate binding and orientation and do not directly participate in the chemistry of peptide bond formation. Overall, we propose that L/F transferase does not directly participate in the chemistry of peptide bond formation but catalyzes the reaction by binding and orientating the substrates for reaction in an analogous mechanism that has been described for ribosomes.