The trace fossil Thalassinoides from the Upper Ordovician of Tuva

Traces of Thalassinoides (the tunnels of unknown burrowing organisms) are described from carbonates of the Khondelensky layers of the Upper Ordovician of Tuva. Hitherto, this fossil was unknown in the Ordovician of the USSR. They demonstrate great similarity with Thalassinoides from coeval deposits of the Great Basin, USA. The traces are assumed to have been made in terrigenous-carbonate sediments deposited on the areas of a gently sloping shelf in quiet water, below wave base. □ Upper Ordovician, terrigenous-carbonate sediments, burrows.     

Isopodichnus in a trace fossil assemblage from the Old Red Sandstone

Isopodichnus stromnessi sp. nov. from the Lower Stromness Flags of Orkney is described in detail, and the range of variation in the traces ascribed to different habits of different sized individuals producing the traces. Activity diagrams illustrate scme of the burrowing habits of the organism. Isopodichnus is typical of non-marine strata, particularly those of shallow impermanent lacustrine environments, and can be distinguished from Cruziana on the basis of the shape of the trace ending. AsSociated burrows are briefly described and indicate the presence of a hitherto undescribed invertebrate fauna associated with the Orcadian flagstone sequence of the Middle Old Red Sandstone.     

Ethological analysis of the trace fossil Zoophycos: hints from the Arctic Ocean

Löwemark, L. 2011: Ethological analysis of the trace fossil Zoophycos: Hints from the Arctic Ocean. Lethaia, Vol. 45, pp. 290–298. The distribution of the trace fossil Zoophycos in Quaternary marine sediments from the Arctic Ocean was studied in twelve piston and gravity cores retrieved during the Swedish icebreaker expeditions YMER80, Arctic Ocean‐96 and LOMROG I & II. The sampled cores span an area from the Makarov Basin to the Fram Strait. Zoophycos was only found in two cores taken at more than 2 km water depth on the slope of the Lomonosov Ridge, but was absent in cores obtained at shallower depth, confirming earlier observations of the trace maker’s bathymetric preferences. The two cores containing Zoophycos are characterized by quiet sedimentation and slightly enhanced food flux compared with the general Arctic. The occurrence of Zoophycos in these cores in a setting that is characterized by extreme seasonal variations in food flux due to the total ice coverage during winters and high primary productivity during the long summer days, is interpreted to be a cache‐behaviour response to pulsed flux of food to the benthic realm. □Arctic Ocean, ethology, Quaternary, spreiten, trace fossils, Zoophycos.     

Behavioural interpretation of a rosetted spreite trace fossil: Dactyloidites ottoi (Geinitz)

Excellently preserved specimens of the trace fossil Haenrzschelinia onoi (Geinitz) allow its three-dimensional reconstruction and interpretation of the behaviour underlying the morphological pattern. H. onoi is a rosette-shaped endogenic trace fossil comprising central tube and branching incomplete radial protrusive spreiten. The basic behaviour pattern (rosetted vertical spreiten with central shaft) is the same as that of Brooksella Walcott 1896 and Dactyloidites Hall 1886. Haentzschelinia is therefore placed in synonymy with Dactyloidites , which has priority.     

Sinusichnus, a trace fossil from Antarctica and Venezuela: expanding the dataset of crustacean burrows

The sinusoidal decapod crustacean burrow Sinusichnus sinuosus is documented from the Upper Cretaceous Hidden Lake Formation of James Ross Island (Antarctica), the Upper Oligocene-Lower Miocene Naricual Formation of the Eastern Venezuela Basin, and the Middle Miocene Socorro Formation of the Falcón Basin of Western Venezuela, significantly expanding its geographical and palaeolatitudinal range. These burrows may have served for bacterial farming in relatively stressful settings characterized by deltaic progradation. Sinusichnus sinuosus seems to display a broad latitudinal range, from low latitude tropical settings (Venezuela) to intermediate latitude temperate areas (Spain and France), and high latitude cold waters (Antarctica). The appearance of S. sinuosus in the Cretaceous reveals the acquisition of more sophisticated feeding strategies by decapod crustaceans, reflecting the dominance of the Modern Evolutionary Fauna.     

The trace fossil Nummipera eocenica from the Tatra Mountains,Poland: morphology and palaeoenvironmental implications

Jach, R., Machaniec, E. & Uchman, A. 2011: The trace fossil Nummipera eocenica from the Tatra Mountains, Poland: morphology and palaeoenvironmental implications. Lethaia, Vol. 45, pp. 342–355. The tubular trace fossil Nummipera eocenica Hölder 1989 occurs in a single stratigraphical horizon in Eocene nummulitic limestones of the Tatra Mountains, Poland. The wall of N. eocenica is built of Discocyclina and Nummulities (larger foraminifera) tests, very rarely of the Ditrupa (Polychaeta) tube fragments, bivalve shell fragments, echinoid spines and coralline algae. Morphotype are distinguished on the basis of wall composition and structure. Morphotype A is dominated by fusiform Discocyclina tests, which were preferentially selected by the trace makers for construction of a well‐constructed and resistant wall. Morphotype B contains more robust tests of Nummulites, while morphotype C is dominated by saddle‐shaped tests of Discocyclina. Nummipera eocenica was produced during a period of seafloor stabilization caused by a deepening. The succession of the morphotypes B, A reflects diminishing energy and increasing water depth. Probably morphotype C represents even lower energy environment than morphotype A. The trace fossil is interpreted as a domichnion, which wall was constructed for protection. The trace maker can be considered between polychaetes and crustaceans; however, comparisons to the closest recent analogues, the polychaete Diopatra cuprea or alpheid shrimps, are not satisfactory. □Bartonian, burrow, Carpathians, large foraminifera, trace fossils.     

Hope springs eternal in the starfish gonad: preserved potential for sexual reproduction in a single-clone population of a fissiparous starfish

Among echinoderms, asexual reproduction by fission occurs in few species. This strategy is considered a temporary response to stressful conditions and usually alternates with sexual reproduction events; thus, monoclonal populations are extremely rare. The occurrence of a single-clone population of the starfish Coscinasterias tenuispina at Llançà (NW Mediterranean) allowed us to study intra-clonal variation of the reproductive cycle during a two-year study. The few developed gonads (all male) were found in winter months, coinciding with the minimum photoperiod (ρ = ?0.82; P < 0.001) and lowest temperatures (ρ = ?0.75; P < 0.001), only in best-fed individuals, indicating that food availability influences individual ability for gonad development. Fissiparity happened throughout all the sampled period, but its rate increased with warm temperatures (ρ = 0.68; P < 0.0001). In contrast to what has been reported in other species, no correlation between fission rates and population density was found. The population was maintained over time by asexual reproduction and remained monoclonal. Although sexual reproduction has probably not occurred in this all-male population for a long time, the ability to yearly produce mature gonads is retained by some individuals, indicating that potential to reproduce sexually may be preserved, even in the case of strictly asexual populations.     

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.     

Homologies in the fossil record: The middle ear as a test case

This paper examines the middle ear of fossil living animals in terms of the homologies which have been drawn between its parts in different vertebrate groups. Seven homologies are considered: 1, the middle ear cavity/spiracular pouch; 2, the stapes/hyomandibula; 3, the stapedial/hyomandibular processes; 4 the tympanic membrane; 5, the otic notch; 6, the fenestra ovalis; 7, and the stapedial/hyomandibular foramen. The reasons leading to assessments of homology are reviewed. Homologies 1 and 2, based largely on embryological evidence, are fairly robust, though there are arguments about the details. Homologies 3, 4 and 5 stem from ideas about early tetrapod evolution, and were influenced by contingent factors including the order and time of discovery of early fossil taxa, and perceptions of their phylogeny which resulted from this. They were also influenced by ideas of the evolution of terrestriality among tetrapods. Most of the conceptions have been overturned in recent years by new fossil discoveries and new ways of looking at old data. Homology 6 has been little considered. One possible hypothesis, placed in a strictly archetypal theoretical framework has been ignored but deserves consideration on other grounds. Homology 7 depends on how tetrapods are characterised, not a question which has posed difficulties until recently, but which is likely to with the discovery of intermediate fossil forms.     

A new earthworm trace fossil from paleosols: Aestivation chambers from the Late Pleistocene Sopas Formation of Uruguay

A new ichnotaxon, attributed to earthworm aestivation chambers, is described from paleosols of the Sopas Formation (Upper Pleistocene) of northern Uruguay. This ichnofossil consists of a spherical chamber with a constructed wall of imbricated faecal pellets and a filling of rounded to meniscate pellets arranged in winding strings. The strings may also be connected to specimens of Taenidium serpentinum in the paleosol, resulting in a compound trace fossil. Castrichnus incolumis igen. et isp. nov. is interpreted as an earthworm aestivation chamber based on its morphological similarity to the chambers produced by extant earthworms. As such, C. incolumis is considered an indicator of subaerial exposure, and also of seasonal climate. C. incolumis is the second trace fossil that can be attributed with certainty to earthworms. In addition, the Castrichnus–T. serpentinum compound specimens indicate that in paleosols, earthworms can be the producers of T. serpentinum. Aestivation chambers would represent a new ethological category.     

Global amphibian declines: a perspective from the Caribbean

Recent concern over the possibility of a global decline in amphibians prompted this assessment of the West Indian species. At the species level, the West Indian amphibian fauna (156 species, all frogs and toads) has not undergone a general decline, and no species is known to be extinct. However, one Puerto Rican species (Eleutherodactylus karlschmidti) has not been seen in over ten years despite considerable search effort. Seven other species, including the Puerto Rican livebearing frog (E. jasperi), have not been seen recently, although their present status cannot be determined until additional effort is made to locate them. Two stream-associated species on Hispaniola (E. semipalmatus and Hyla vasta) appear to have declined in recont years, probably due to the alteration of riparian habitats by deforestation. Other vertebrate groups in the West Indies, such as mammals, have been more affected by human-caused environmental degradation than have amphibians. Large-scale extinctions of frogs and other forest-dwelling species are not expected to occur until forest cover reaches very low levels. Haiti is on the brink of such extinctions with less than 1% of its forest cover remaining. Two recommendations are made to help curtail the expected loss of biodiversity: (i) import charcoal to replace that produced by burning native trees (used as cooking fuel), as an immediate measure, and (ii) control human population growth, as a long-term solution.     

A new tool for determining degrees of mineralization in fossil amphibian skeletons: The example of the Late Palaeozoic branchiosaurid Apateon from the Autun Basin,France

Studying ontogenetic features of fossil tetrapods is of major interest for investigating the adaptive strategies of early tetrapods to their palaeoenvironments. To determine the degree of calcification of skeletal elements, biologists have until now relied on X-ray radiographs of organisms or isolated bones, or on thin sections. An X-ray tomographic scan of Apateon, a Carboniferous – Permian branchiosaurid from the Autun Basin, France, reveals distinct density properties related to different mineralized tissues (calcified cartilage versus bone). The rendering of Apateon as a “test individual” provides a 3D map of the degrees of ossification of the axial and cranial elements. The combination of these anatomical observations with histological information from classical thin sections made in limb bones of several other specimens of the same locality allows the detailed determination of their ontogenetic stage. A comparison with the well-known specimens of the Saar-Nahe Basin, Germany, makes it possible to investigate the influence of different palaeoenvironments on ontogenetic features.