Using Artificial Rocks to Restore Nonrenewable Shelter Sites in Human‐Degraded Systems: Colonization by Fauna

Many animals spend much of their time within retreat sites underneath loose surface rocks and may be highly selective in terms of the physical characteristics of the sites that they use. If such shelters are eliminated by anthropogenic activities, such as rock removal for landscaping, the only way to restore these nonrenewable habitats may be to replace them with artificial rocks. To construct artificial rock habitats, we need to understand which rock attributes are important for faunal use and develop methods to mimic these important natural retreat site characteristics. Based on our prior understanding of rocky retreat sites used by reptiles in sandstone outcrops of southeastern Australia, we constructed realistic‐looking artificial rocks from fiber‐reinforced cement and evaluated (1) the degree to which they mimicked natural retreat sites in both thermal regime and three‐dimensional crevice structure and (2) their colonization by fauna after deployment in the field. Our results demonstrate that thermal regimes and crevice structures beneath the artificial rocks were similar to those beneath natural rocks. In addition, 100% of the artificial rocks were colonized (by 45 invertebrate, six lizard, and two snake species, including the endangered Broad‐headed snake, Hoplocephalus bungaroides) after only 40 weeks. Together, these results suggest that restoring degraded habitats for rock‐dwelling species is feasible and can provide a rapid means of enhancing shelter‐site availability for such species.     

Reef fish assemblages in north-western Sri Lanka: distribution patterns and influences of fishing practises

The distribution and abundance of reef fishes in relation to habitat structure were studied within Bar Reef Marine Sanctuary (BRMS) and on an adjacent reef, disturbed by destructive fishing techniques, in north-western Sri Lanka, by visually censusing 135 species groups using fifty metre belt-transects. Two types of continental shelf patch-reefs are found in the study area: coral reefs and sandstone reefs, which are divided into distinct habitats, four for the coral reef (shallow reef flat, shallow patch reef, deep reef flat and Porites domes) and two for the sandstone reef (structured sandstone-reef and flat sandstone-reef). Fish assemblages varied in structure between reef types and among habitats within reef types. Functional aspects of habitat structure and composition, such as available food and shelter, seemed to be important factors influencing distribution patterns. The strongest separation in the organisation of fish assemblages in BRMS was between reef types: 19% of all species were confined to the coral-reef patches while 22% were restricted to the sandstone reef patches and 59% were represented on both reef types. In terms of distribution among habitats, 21% of all species were restricted to one habitat while only 1.5% were present in all. The highest density of fish was in the coral reef habitats while highest species diversity was found in the most structurally complex habitat: the structured sandstone-reef. This habitat also had the highest proportion of species with restricted distribution. Planktivores were the most abundant trophic group in BRMS, and the species composition of the group varied among habitats. The comparison of the disturbed reef with BRMS suggested that habitat alteration caused by destructive fishing methods has strongly influenced the fish community. Within the fished area the structure of the fish assemblages was more heterogeneous, fish abundance was lower by an order of magnitude and species numbers were lower than in BRMS.     

Gymnemopsis phuwuaensis (Apocynaceae,Asclepiadoideae), a new species from northeastern Thailand

A new species, Gymnemopsis phuwuaensis A. Kidyoo, has been discovered in northeastern Thailand and is here described and illustrated. An identification key to all species of the genus is provided. Photographs and a diagnostic comparison with the morphologically similar species G. calcicola Kerr, are also provided. Gymnemopsis phuwuaensis displays clear differences in form and color of the corolla as well as in size of bract and flower. A lectotype for Gymnemopsis pierrei is also designated.     

Seed Dispersal Modes of the Sandstone Plateau Vegetation of the Middle Caquetá River Region,Colombian Amazonia1

We characterized the dispersal spectra and phenology of 298 vascular plant species of the sandstone plateaus of Colombian Amazonia. Dispersal modes were determined by the morphology of dispersion units, personal observations on fruit consumption, and an extensive literature review. We obtained the number of species per dispersal mode for the sandstone plateaus and for two recognized vegetation types: open‐herbaceous vegetation and low forest‐shrub vegetation. Dispersal modes were assigned to 295 plant species. Animals dispersed the highest percentage of species (46.6%), while the percentage of autochorous and anemochorous species was 29.4 and 23 percent, respectively. The dispersal spectrum of the low forest‐shrub vegetation type, based on the coverage of every species, showed that percentages of anemochorous (40.2%) and zoochorous species (37.8%) were similar. Autochory was the most important seed dispersal mode of the open‐herbaceous vegetation (60%). Birds were the principal group of potential dispersers (58.9%) of zoochorous species and reptiles the least important. We found two marked fruiting peaks, one from the end of the dry season to the beginning of the wet season and the second one from the beginning to the middle of the dry season. Our results showed that besides the differences in the vegetation structure and floristic composition between the sandstone plateaus and the adjacent tall forest, there also exist differences in the dispersal spectra and the fruiting rhythms.     

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Light sheet fluorescence microscopy (LSFM) is gaining more and more popularity as a method to image embryonic development. The main advantages of LSFM compared to confocal systems are its low phototoxicity, gentle mounting strategies, fast acquisition with high signal to noise ratio and the possibility of imaging samples from various angles (views) for long periods of time. Imaging from multiple views unleashes the full potential of LSFM, but at the same time it can create terabyte-sized datasets. Processing such datasets is the biggest challenge of using LSFM. In this protocol we outline some solutions to this problem. Until recently, LSFM was mostly performed in laboratories that had the expertise to build and operate their own light sheet microscopes. However, in the last three years several commercial implementations of LSFM became available, which are multipurpose and easy to use for any developmental biologist. This article is primarily directed to those researchers, who are not LSFM technology developers, but want to employ LSFM as a tool to answer specific developmental biology questions. Here, we use imaging of zebrafish eye development as an example to introduce the reader to LSFM technology and we demonstrate applications of LSFM across multiple spatial and temporal scales. This article describes a complete experimental protocol starting with the mounting of zebrafish embryos for LSFM. We then outline the options for imaging using the commercially available light sheet microscope. Importantly, we also explain a pipeline for subsequent registration and fusion of multiview datasets using an open source solution implemented as a Fiji plugin. While this protocol focuses on imaging the developing zebrafish eye and processing data from a particular imaging setup, most of the insights and troubleshooting suggestions presented here are of general use and the protocol can be adapted to a variety of light sheet microscopy experiments.     

Nonmarine aspects of the Cambrian Tonto Group of the Grand Canyon, USA, and broader implications

A re-examination of the classic time-transgressive model of the Cambrian Tonto Group of the Grand Canyon challenges some of the basic assumptions regarding strandline migration during the Sauk transgression, the applicability of sequence stratigraphy to epicratonic deposits, and the criteria by which siliciclastic deposits of the North American Cambrian system are categorized as marine. Indicators for high short-term depositional rates, coupled with the complex splay and coalescence of meter-scale parasequence architectures, detract from the shoreline migration and deepening seas model that has held sway for over 60 years. Ostensibly marine signatures, represented by sparse and fragmentary trilobite fossils and abundant bedding plane trace fossils, are closely associated with nonmarine signatures, represented by nonmarine palynoflora and clay mineral assemblages, and highly oxidized paleoweathering profiles. The vast extent of three-dimensional exposure of the Cambrian section in the Grand Canyon shows a paleogeography not of a single discrete shoreline translated laterally with rising and falling sea-level, but of a single mosaic setting of emergent shoals and rocky peaks, broad fluvial and tidal channels, and shallow pools and interchannel flats. Much detail concerning sediment dynamics and paleoenvironment is lost or overlooked when summary terms like “marginal marine” or “nearshore” are applied to such settings. It is suggested here that the Tonto Group, with its mixed marine and nonmarine attributes, and considering its historic role as a teaching model, be viewed not as an exceptional Cambrian deposit, but as an exemplar of epicratonic deposits on a pre-vegetated landscape.     

An enigmatic,diminutive theropod footprint in the shallow marine Pliensbachian Hasle Formation,Bornholm, Denmark

A well‐preserved three‐toed footprint, measuring 34 mm in length from a very small predatory dinosaur with an estimated hip height of 153 mm and a total body length around 50 cm including tail, is reported from the type section of the marine Lower Jurassic (Pliensbachian), Hasle Formation on the Danish island of Bornholm in the Baltic Sea. The morphology of the footprint is similar to the ichnogenus Stenonyx Lull 1904 from the contemporaneous Pliensbachian Szydlowek site in Poland. Apart from the Polish material, footprints from diminutive dinosaurs are rare and reported from few other localities around the world. The occurrence of a diminutive dinosaur footprint in a shallow marine sandstone is enigmatic. The well‐defined morphology of the footprint, together with the very small size of the trackmaker, excludes the possibility that the track was emplaced by a swimming or wading animal. At the type locality where the footprint was found the formation consists of ferruginous coarse siltstone and very fine‐grained sandstone, showing hummocky and swaley cross‐stratification and rare large‐scale trough cross‐bedding and planar lamination. Deposition took place mainly in the upper shoreface in a storm‐dominated environment 1 km west of the N?S‐oriented faulted coastline. The formation becomes thinner and finer grained with heterolithic intercalations towards the south, indicating coast‐parallel transport in this direction. The extreme uniformity in sedimentary facies as seen in two nearby fully cored boreholes shows that the accommodation space created by rapid subsidence along the fault was continuously filled in to upper shoreface level by rapid longshore sediment influx from the north. In quiet periods with easterly winds and extreme low‐water low tide, the small dinosaur creating the newly found footprint is interpreted to have walked in shallow beach pools, thus explaining the strange occurrence of the footprint in a marine deposit.     

Cryptoendolithic actinomycetes from antarctic sandstone rock samples: Micromonospora endolithica sp. nov. and two isolates related to Micromonospora coerulea Jensen 1932

Three cryptoendolithic, aerobic actinomycetes (AA-459T, AA-319 and AA-321) from antarctic sandstone were characterised phenotypically and by molecular taxonomic methods. The isolates had single spores on substrate mycelium, meso-diaminopimelic acid (m-DAP) and glycine (cell wall type II), a whole cell sugar pattern D (galactose, xylose, arabinose, glucose or rhamnose) and phospholipids of type PII (diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol). Their predominant fatty acids were iso-16:0 and iso-15:0 or 17:1omega8c, the menaquinone profile was complex with mainly MK10 (H4) and MK10 (H6). A wide variety of sugars and several acids were utilised for growth. The isolates were sensitive to a few antibiotics, but formation and excretion of antibiotics was not observed. Phenotypically, isolates AA-319 and AA-321 were similar. Phylogenetic analysis of 16S rRNA gene sequences revealed close relationship of strains AA-319 and AA-321 with each other (99.5%) and clustering (98.5%) with Micromonospora coerulea DSM 43143T. DNA-DNA hybridisation showed both strains to be genomically highly similar to strain DSM 43143T. Phenotypically they could be viewed as separate taxa, but presently they will be considered as strains of Micromonospora coerulea. Strain AA-459T was phylogenetically close to Micromonospora chersina DSM 44151T (99.1%) and to Micromonospora rosaria DSM 803T, but DNA-DNA similarity with M. chersina DSM 44151T was low with 28.9/33.5 %, indicating the presence of a different and new species. Consequently, isolate AA-459T (DSM 44398T NRRL B-24248T) is described as the type strain of Micromonospora endolithica sp. nov.     

The cation status of some indigenous plants from a Cango valley limestone-sandstone transition,South Africa

Leaf tissue of four representative species from a limestone-sandstone transition, together with their respective soils, were analysed for cations. The species studied comprisedLeucospermum cuneiforme (Proteaceae) from the acid sandstone,Indigofera sp. nov. (Fabaceae) from the base-rich limestone,Elytropappus rhinocerotis (Asteraceae) from the transition zone andDodonaea angustifolia (Sapindaceae) which occured on all three substrates. The sandstone substrate is low in cations, particularly K and it is suggested that the Leucospermum may supplement its K nutrition with Na. Despite growing on soils of differing cation content, Dodonaea maintained a constant leaf cation content over the three substrates.