Consensus and Confusion in Molluscan Trees: Evaluating Morphological and Molecular Phylogenies

Mollusks are the most morphologically disparate living animal phylum, they have diversified into all habitats, and have a deep fossil record. Monophyly and identity of their eight living classes is undisputed, but relationships between these groups and patterns of their early radiation have remained elusive. Arguments about traditional morphological phylogeny focus on a small number of topological concepts but often without regard to proximity of the individual classes. In contrast, molecular studies have proposed a number of radically different, inherently contradictory, and controversial sister relationships. Here, we assembled a dataset of 42 unique published trees describing molluscan interrelationships. We used these data to ask several questions about the state of resolution of molluscan phylogeny compared to a null model of the variation possible in random trees constructed from a monophyletic assemblage of eight terminals. Although 27 different unique trees have been proposed from morphological inference, the majority of these are not statistically different from each other. Within the available molecular topologies, only four studies to date have included the deep-sea class Monoplacophora; but 36.4% of all trees are not significantly different. We also present supertrees derived from 2 data partitions and 3 methods, including all available molecular molluscan phylogenies, which will form the basis for future hypothesis testing. The supertrees presented here were not constructed to provide yet another hypothesis of molluscan relationships, but rather to algorithmically evaluate the relationships present in the disparate published topologies. Based on the totality of available evidence, certain patterns of relatedness among constituent taxa become clear. The internodal distance is consistently short between a few taxon pairs, particularly supporting the relatedness of Monoplacophora and the chitons, Polyplacophora. Other taxon pairs are rarely or never found in close proximity, such as the vermiform Caudofoveata and Bivalvia. Our results have specific utility for guiding constructive research planning in order to better test relationships in Mollusca as well as other problematic groups. Taxa with consistently proximate relationships should be the focus of a combined approach in a concerted assessment of potential genetic and anatomical homology, while unequivocally distant taxa will make the most constructive choices for exemplar selection in higher-level phylogenomic analyses.

Late Bronze Age casting debris and other base metal finds from Haughey’s Fort

This paper provides a full overview of base metal finds from the excavations conducted at Haughey's Fort between 1987 and 1995. Most of the assemblage consists of waste metal from casting activities relating to the Late Bronze Age occupation of the site. A small minority of objects are of a later date, mostly Iron Age. Both the latter and the vast majority of Late Bronze metal items were recovered from a specific sector of the inner enclosure. Typological parallels, context and chronology of the finds are discussed, and a tentative interpretation of the evidence proposed.

Distinguishing Species of Geoemyclid and Trionychid Turtles from Shell Fragments:Evidence from the Pleistocene at Niah Caves, Sarawak

Fragments of chelonian carapace and plastral dermal plates are well-represented from archaeological sites in the world's dry and wet tropics. However, although these bones are easily identified at an element level, few archaeological reports have explored the potential of using features of form and surface sculpturing as a way to refine that identification to genus or species. The ability to achieve such a refinement would benefit environmental and human subsistence strategy models alike. The objective of the current paper was to isolate recurrent and readily visible surface characteristics on the dermal plates from a selection of commonly occurring Southeast Asian hard- and soft-shelled turtles. Using these criteria, analysis is made of the chelonian assemblage from pre- and post-Last Glacial Maximum (LGM) cultural deposits in the West Mouth of Niah Cave. Copyright (C) 2009 John Wiley & Sons, Ltd.

Are there latitudinal gradients in species turnover?

Aim To examine the effect on the observed relationship betw een spatial turnover and latitude of both the measure of beta diversity used and the method of analysis.

Location The empirical analyses presented herein are for the New World.

Methods We take the spatial distributions of the owls of the New World as an exemplar data set to investigate the patterns of beta diversity across latitudes revealed by different analytical methods. To illustrate the strengths and weaknesses of alternative measures of beta diversity and different analytical approaches, we also use a simple random distribution model, focusing in particular on the influence of richness gradients and landmass geometry.

Results Our simple spatial model of turnover demonstrates that different combinations of analytical approach and measure of beta diversity can give rise to strikingly different relationships between turnover and latitude. The analyses of the bird data for the owls of the New World demonstrate that this observation extends to real data.

Conclusions For the particular assemblage considered, we present strong evidence that species richness declines at higher latitudes, and there is also some evidence that species turnover is greater nearer the equator, despite conceptual and practical difficulties involved in analysing spatial patterns of species turnover. We suggest some ways of overcoming these difficulties.

Fractal species distributions do not produce power-law species-area relationships

We derive the species-area relationship (SAR) expected from an assemblage of fractally distributed species. If species have truly fractal spatial distributions with different fractal dimensions, we show that the expected SAR is not the classical power-law function, as suggested recently in the literature. This analytically derived SAR has a distinctive shape that is not commonly observed in nature: upward-accelerating richness with increasing area (when plotted on log-log axes). This suggests that, in reality, most species depart from true fractal spatial structure. We demonstrate the fitting of a fractal SAR using two plant assemblages (Alaskan trees and British grasses). We show that in both cases, when modelled as fractal patterns, the modelled SAR departs from the observed SAR in the same way, in accord with the theory developed here. The challenge is to identify how species depart from fractality, either individually or within assemblages, and more importantly to suggest reasons why species distributions are not self-similar and what, if anything, this can tell us about the spatial processes involved in their generation.

Deglacial mesophotic reef demise on the Great Barrier Reef

Submerged reefs are important recorders of palaeo-environments and sea-level change, and provide a substrate for modern mesophotic (deep-water, light-dependent) coral communities. Mesophotic reefs are rarely, if ever, described from the fossil record and nothing is known of their long-term record on Great Barrier Reef (GBR). Sedimentological and palaeo-ecological analyses coupled with 67 14C AMS and U–Th radiometric dates from dredged coral, algae and bryozoan specimens, recovered from depths of 45 to 130 m, reveal two distinct generations of fossil mesophotic coral community development on the submerged shelf edge reefs of the GBR. They occurred from 13 to 10 ka and 8 ka to present. We identified eleven sedimentary facies representing both autochthonous (in situ) and allochthonous (detrital) genesis, and their palaeo-environmental settings have been interpreted based on their sedimentological characteristics, biological assemblages, and the distribution of similar modern biota within the dredges. Facies on the shelf edge represent deep sedimentary environments, primarily forereef slope and open platform settings in palaeo-water depths of 45–95 m. Two coral–algal assemblages and one non-coral encruster assemblage were identified: 1) Massive and tabular corals including Porites, Montipora and faviids associated with Lithophylloids and minor Mastophoroids, 2) platy and encrusting corals including Porites, Montipora and Pachyseris associated with melobesioids and Sporolithon, and 3) Melobesiods and Sporolithon with acervulinids (foraminifera) and bryozoans. Based on their modern occurrence on the GBR and Coral Sea and modern specimens collected in dredges, these are interpreted as representing palaeo-water depths of < 60 m, < 80–100 m and > 100 m respectively. The first mesophotic generation developed at modern depths of 85–130 m from 13 to 10.2 ka and exhibit a deepening succession of < 60 to > 100 m palaeo-water depth through time. The second generation developed at depths of 45–70 m on the shelf edge from 7.8 ka to present and exhibit stable environmental conditions through time. The apparent hiatus that interrupted the mesophotic coral communities coincided with the timing of modern reef initiation on the GBR as well as a wide-spread flux of siliciclastic sediments from the shelf to the basin. For the first time we have observed the response of mesophotic reef communities to millennial scale environmental perturbations, within the context of global sea-level rise and environmental changes.

Not all jellyfish are equal: isotopic evidence for inter- and intraspecific variation in jellyfish trophic ecology

Jellyfish are highly topical within studies of pelagic food-webs and there is a growing realisation that their role is more complex than once thought. Efforts being made to include jellyfish within fisheries and ecosystem models are an important step forward, but our present understanding of their underlying trophic ecology can lead to their oversimplification in these models. Gelatinous zooplankton represent a polyphyletic assemblage spanning >2,000 species that inhabit coastal seas to the deep-ocean and employ a wide variety of foraging strategies. Despite this diversity, many contemporary modelling approaches include jellyfish as a single functional group feeding at one or two trophic levels at most. Recent reviews have drawn attention to this issue and highlighted the need for improved communication between biologists and theoreticians if this problem is to be overcome. We used stable isotopes to investigate the trophic ecology of three co-occurring scyphozoan jellyfish species (Aurelia aurita, Cyanea lamarckii and C. capillata) within a temperate, coastal food-web in the NE Atlantic. Using information on individual size, time of year and ;delta C-13 and delta N-15 stable isotope values, we examined: (1) whether all jellyfish could be considered as a single functional group, or showed distinct inter-specific differences in trophic ecology; (2) Were size-based shifts in trophic position, found previously in A. aurita, a common trait across species?; (3) When considered collectively, did the trophic position of three sympatric species remain constant over time? Differences in delta N-15 (trophic position) were evident between all three species, with size-based and temporal shifts in delta N-15 apparent in A. aurita and C. capillata. The isotopic niche width for all species combined increased throughout the season, reflecting temporal shifts in trophic position and seasonal succession in these gelatinous species. Taken together, these findings support previous assertions that jellyfish require more robust inclusion in marine fisheries or ecosystem models.

Size-balanced community reorganization in response to nutrients and warming

It is widely accepted that global warming will adversely affect ecological communities. As ecosystems are simultaneously exposed to other anthropogenic influences, it is important to address the effects of climate change in the context of many stressors. Nutrient enrichment might offset some of the energy demands that warming can exert on organisms by stimulating growth at the base of the food web. It is important to know whether indirect effects of warming will be as ecologically significant as direct physiological effects. Declining body size is increasingly viewed as a universal response to warming, with the potential to alter trophic interactions. To address these issues, we used an outdoor array of marine mesocosms to examine the impacts of warming, nutrient enrichment and altered top-predator body size on a community comprised of the predator (shore crab Carcinus maenas), various grazing detritivores (amphipods) and algal resources. Warming increased mortality rates of crabs, but had no effect on their moulting rates. Nutrient enrichment and warming had near diametrically opposed effects on the assemblage, confirming that the ecological effects of these two stressors can cancel each other out. This suggests that nutrient-enriched systems might act as an energy refuge to populations of species under metabolic constraints due to warming. While there was a strong difference in assemblages between mesocosms containing crabs compared to mesocosms without crabs, decreasing crab size had no detectable effect on the amphipod or algal assemblages. This suggests that in allometrically balanced communities, the expected long-term effect of warming (declining body size) is not of similar ecological consequence to the direct physiological effects of warming, at least not over the six week duration of the experiment described here. More research is needed to determine the long-term effects of declining body size on the bioenergetic balance of natural communities.

Mining Money: the generative capacities of scientific and legal knowledge practices in the making of resource economies

In 1997 a scandal associated with Bre-X, a junior mining firm, and its prospecting activities in Indonesia, exposed to public scrutiny the ways in which mineral exploration firms acquire, assess and report on scientific claims about the natural environment. At stake here was not just how investors understood the provisional nature of scientific knowledge, but also evidence of fraud. Contemporaneous mining scandals not only included the salting of cores, but also unreliable proprietary sample preparation and assay methods, mis-representations of visual field estimates as drilling results and ‘overly optimistic’ geological reports. This paper reports on initiatives taken in the wake of these scandals and prompted by the Mining Standards Task Force (TSE/OSC 1999). For regulators, mandated to increase investor confidence in Canada’s leading role within the global mining industry, efforts focused first and foremost upon identifying and removing sources of error and wilfulness within the production and circulation of scientific knowledge claims. A common goal cross-cutting these initiatives was ‘a faithful representation of nature’ (Daston and Galison 2010), however, as the paper argues, this was manifest in an assemblage of practices governed by distinct and rival regulative visions of science and the making of markets in claims about ‘nature’. These ‘practices of fidelity’, it is argued, can be consequential in shaping the spatial and temporal dynamics of the marketization of nature.

Fate of organo-mineral particles in streams: Microbial degradation by streamwater & biofilm assemblages

Inland waters are of global biogeochemical importance. They receive carbon inputs of ~ 4.8 Pg C/ y of which, 12 % is buried, 18 % transported to the oceans, and 70 % supports aquatic secondary production. However, the mechanisms that determine the fate of organic matter (OM) in these systems are poorly defined. One aspect of this is the formation of organo-mineral complexes in aquatic systems and their potential as a route for OM transport and burial vs. their use as carbon (C) and nitrogen (N) sources within aquatic systems. Organo-mineral particles form by sorption of dissolved OM to freshly eroded mineral surfaces and may contribute to ecosystem-scale particulate OM fluxes. We experimentally tested the availability of mineral-sorbed OM as a C & N source for streamwater microbial assemblages and streambed biofilms. Organo-mineral particles were constructed in vitro by sorption of ¹³C:¹⁵N-labelled amino acids to hydrated kaolin particles, and microbial degradation of these particles compared with equivalent doses of ¹³C:¹⁵N-labelled free amino acids. Experiments were conducted in 120 ml mesocosms over 7 days using biofilms and water sampled from the Oberer Seebach stream (Austria). Each incubation experienced a 16:8 light:dark regime, with metabolism monitored via changes in oxygen concentrations between photoperiods. The relative fate of the organo-mineral particles was quantified by tracing the mineralization of the ¹³C and ¹⁵N labels and their incorporation into microbial biomass. Here we present the initial results of ¹³C-label mineralization, incorporation and retention within dissolved organic carbon pool. The results indicate that 514 (± 219) μmol/ mmol of the ¹³:¹⁵N labeled free amino acids were mineralized over the 7-day incubations. By contrast, 186 (± 97) μmol/ mmol of the mineral-sorbed amino acids were mineralized over a similar period. Thus, organo-mineral complexation reduced amino acid mineralization by ~ 60 %, with no differences observed between the streamwater and biofilm assemblages. Throughout the incubations, biofilms were observed to leach dissolved organic carbon (DOC). However, within the streamwater assemblage the presence of both organo-mineral particles and kaolin particles was associated with significant DOC removal (-1.7 % and -7.5 % respectively). Consequently, the study demonstrates that mineral and organo-mineral particles can limit the availability of DOC in aquatic systems, providing nucleation sites for flocculation and fresh mineral surfaces, which facilitate OM-sorption. The formation of these organo-mineral particles subsequently restricts microbial OM degradation, potentially altering the transport and facilitating the burial of OM within streams.

To fasten words again to visible – and invisible – things

In this extended introductory essay, Catherine Gander and Sarah Garland suggest new ways of looking at the correspondences between visual and verbal practices to consider their material and conceptual connections in a specifically American set of histories, contexts and interpretive traditions. Tracing a lineage of experiential philosophy that is grounded in the overturning of a Cartesian mind/body split, the authors argue for pluralistic perspectives on intermedial innovations that situate embodied and imaginative reader-viewer response as vital to the life of the artwork. Gander and Garland chart two main strands to this approach: the pragmatist strain of American aesthetics and social politics, rooted in the essays of transcendentalist Ralph Waldo Emerson and emanating from the writings of John Dewey and William James; and the conceptualist strain of French-American Marcel Duchamp, whose ground-breaking ideas both positioned the artwork as a phenomenological construction and liberated the artist from established methods of practice and discourse. The ‘imagetext’ (after W. J. T. Mitchell) is therefore, argue Gander and Garland, a site consisting of far more than word and image – but a living assemblage of language, idea, thing, cognition, affect and shared experience.

Estimating biomass, fishing mortality, and "total allowable discards" for surveyed non-target fish

Demersal fisheries targeting a few high-value species often catch and discard other "non-target" species. It is difficult to quantify the impact of this incidental mortality when population biomass of a non-target species is unknown. We calculate biomass for 14 demersal fish species in ICES Area VIIg (Celtic Sea) by applying species-and length-based catchability corrections to catch records from the Irish Groundfish Survey (IGFS). We then combine these biomass estimates with records of commercial discards (and landings for marketable non-target species) to calculate annual harvesting rates (HR) for each study species. Uncertainty is incorporated into estimates of both biomass andHR. Our survey-based HR estimates for cod and whiting compared well with HR-converted fishing mortality (F) estimates from analytical assessments for these two stocks. Of the non-target species tested, red gurnard (Chelidonichthys cuculus) recorded some annual HRs greater than those for cod or whiting; challenging "Pope's postulate" that F on non-target stocks in an assemblage will not exceed that on target stocks. We relate HR for each species to two corresponding maximum sustainable yield (MSY) reference levels; six non-target species (including three ray species) show annual HRs >= HRMSY. This result suggests that it may not be possible to conserve vulnerable non-target species when F is coupled to that of target species. Based on biomass, HR, and HRMSY, we estimate "total allowable catch" for each non-target species.

Radiocarbon chronology for the Early Gravettian of northern Europe : new AMS determinations for Maisieres-Canal, Belgium

The authors explore the arrival of the earliest Gravettian in north-west Europe, using new high precision radiocarbon dates for bone excavated at Maisieres-Canal in Belgium to define a short-lit^ed occupation around 33 000 years ago. The tanged points in that assemblage have parallels in British sites, including Goat's Hole (Paviland). This is the site of the famous ochred burial of a young adult male, confiisingly known as the 'Red Lady', notv dated to around 34 000 BP. The new results demonstrate that this British 'rich burial' and the Gravettian with tanged points may bebng to two different occupation horizons separated by a cold spell.

The dynamics of murid gammaherpesvirus 4 within wild, sympatric populations of bank voles and wood mice

Murid gammaherpesvirus 4 (MuHV-4) is widely used as a small animal model for understanding gammaherpesvirus infections in man. However, there have been no epidemiological studies of the virus in wild populations of small mammals. As MuHV-4 both infects cells associated with the respiratory and immune systems and attempts to evade immune control via various molecular mechanisms, infection may reduce immunocompetence with potentially serious fitness consequences for individuals. Here we report a longitudinal study of antibody to MuHV-4 in a mixed assemblage of bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus) in the UK. The study was conducted between April 2001 and March 2004. Seroprevalence was higher in wood mice than bank voles, supporting earlier work that suggested wood mice were the major host even though the virus was originally isolated from a bank vole. Analyses of both the probability of having antibodies and the probability of initial seroconversion indicated no clear seasonal pattern or relationship with host density. Instead, infection risk was most closely associated with individual characteristics, with heavier males having the highest risk. This may reflect individual variation in susceptibility, potentially related to variability in the ability to mount an effective immune response.

Carbon and nitrogen uptake of calcareous benthic foraminifera along a depth-related oxygen gradient in the OMZ of the Arabian Sea

Foraminifera are an important faunal element of the benthos in oxygen-depleted settings such as Oxygen Minimum Zones (OMZs) where they can play a relevant role in the processing of phytodetritus. We investigated the uptake of phytodetritus (labeled with 13C and 15N) by cal-careous foraminifera in the 0-1 cm sediment horizon under different oxygen concentrations within the OMZ in the eastern Arabian Sea. The in situ tracer experiments were carried out along a depth transect on the Indian margin over a period of 4 to 10 days. The uptake of phy-todetrital carbon within 4 days by all investigated species shows that phytodetritus is a rele-vant food source for foraminifera in OMZ sediments. The decrease of total carbon uptake from 540 to 1100 m suggests a higher demand for carbon by species in the low-oxygen core region of the OMZ or less food competition with macrofauna. Especially Uvigerinids showed high uptake of phytodetrital carbon at the lowest oxygenated site. Variation in the ratio of phytodetrital carbon to nitrogen between species and sites indicates that foraminiferal carbon and nitrogen use can be decoupled and different nutritional demands are found between spe-cies. Lower ratio of phytodetrital carbon and nitrogen at 540 m could hint for greater demand or storage of food-based nitrogen, ingestion or hosting of bacteria under almost anoxic condi-tions. Shifts in the foraminiferal assemblage structure (controlled by oxygen or food availabil-ity) and in the presence of other benthic organisms account for observed changes in the pro-cessing of phytodetritus in the different OMZ habitats. Foraminifera dominate the short-term processing of phytodetritus in the OMZ core but are less important in the lower OMZ bounda-ry region of the Indian margin as biological interactions and species distribution of foraminifera change with depth and oxygen levels.