Landscape and forest structure at moose mortality sites on Isle Royale National Park. A LiDAR based assessment

Landscape structure and heterogeneity play a potentially important, but little understood role in predator-prey interactions and behaviourally-mediated habitat selection. For example, habitat complexity may either reduce or enhance the efficiency of a predator's efforts to search, track, capture, kill and consume prey. For prey, structural heterogeneity may affect predator detection, avoidance and defense, escape tactics, and the ability to exploit refuges. This study, investigates whether and how vegetation and topographic structure influence the spatial patterns and distribution of moose (Alces alces) mortality due to predation and malnutrition at the local and landscape levels on Isle Royale National Park. 230 locations where wolves (Canis lupus) killed moose during the winters between 2002 and 2010, and 182 moose starvation death sites for the period 1996-2010, were selected from the extensive Isle Royale Wolf-Moose Project carcass database. A variety of LiDAR-derived metrics were generated and used in an algorithm model (Random Forest) to identify, characterize, and classify three-dimensional variables significant to each of the mortality classes. Furthermore, spatial models to predict and assess the likelihood at the landscape scale of moose mortality were developed. This research found that the patterns of moose mortality by predation and malnutrition across the landscape are non-random, have a high degree of spatial variability, and that both mechanisms operate in contexts of comparable physiographic and vegetation structure. Wolf winter hunting locations on Isle Royale are more likely to be a result of its prey habitat selection, although they seem to prioritize the overall areas with higher moose density in the winter. Furthermore, the findings suggest that the distribution of moose mortality by predation is habitat-specific to moose, and not to wolves. In addition, moose sex, age, and health condition also affect mortality site selection, as revealed by subtle differences between sites in vegetation heights, vegetation density, and topography. Vegetation density in particular appears to differentiate mortality locations for distinct classes of moose. The results also emphasize the significance of fine-scale landscape and habitat features when addressing predator-prey interactions. These finer scale findings would be easily missed if analyses were limited to the broader landscape scale alone.

The role of landuse and natural determinants for grassland vegetation composition in the Swiss Alps

The Alps provide a high habitat diversity for plant species, structured by broad- and fine-scale abiotic site conditions. In man-made grasslands, vegetation composition is additionally affected by the type of landuse. We recorded vegetation composition in 216 parcels of grassland in 12 municipalities representing an area of 170 x 70 km in the south-eastern part of the Swiss Alps. Each parcel was characterized by a combination of altitudinal level (valley, intermediate, alp). traditional landuse (mown. grazed), current management (mown, grazed, abandoned). and Fertilization (unfertilized, fertilized). For each parcel we also assessed the abiotic factors aspect, slope, pH value, and geographic coordinates, and for each municipality annual precipitation and its cultural tradition. We analysed vegetation composition using (i) variation partitioning in RDA. (ii) cover of graminoids. non-legume forbs, and legumes, and (iii) dominance and frequency of species. Species composition was determined by, in decreasing order of variation explained. landuse, broad-scale abiotic factors, fine-scale abiotic factors. and cultural tradition. Current socio-economically motivated landuse changes, such as grazing of unfertilized former meadows or their abandonment, strongly affect vegetation composition. In our study, the frequency of characteristic meadow species was significantly smaller in grazed and even smaller in abandoned parcels than in still mown ones, suggesting less severe consequences of grazing for vegetation composition than of abandonment. Therefore. low-intensity grazing and mowing every few years should be considered valuable conservation alternatives to abandonment. Furthermore. because each landuse type was characterized by different species. a high variety of landuse types should be promoted to preserve plant species diversity in Alpine grasslands. (C) 2007 Gesellschaft fur Okologie. Published by Elsevier GmbH. All rights reserved.

On the detection of dynamic responses in a drought-perturbed tropical rainforest in Borneo

The dynamics of aseasonal lowland dipterocarp forest in Borneo is influenced by perturbation from droughts. These events might be increasing in frequency and intensity in the future. This paper describes drought-affected dynamics between 1986 and 2001 in Sabah, Malaysia, and considers how it is possible, reliably and accurately, to measure both coarse- and fine-scale responses of the forest. Some fundamental concerns about methodology and data analysis emerge. In two plots forming 8 ha, mortality, recruitment, and stem growth rates of trees ≥10 cm gbh (girth at breast height) were measured in a ‘pre-drought’ period (1986–1996), and in a period (1996–2001) including the 1997–1998 ENSO-drought. For 2.56 ha of subplots, mortality and growth rates of small trees (10–<50 cm gbh) were found also for two sub-periods (1996–1999, 1999–2001). A total of c. 19 K trees were recorded. Mortality rate increased by 25% while both recruitment and relative growth rates increased by 12% for all trees at the coarse scale. For small trees, at the fine scale, mortality increased by 6% and 9% from pre-drought to drought and on to ‘post-drought’ sub-periods. Relative growth rates correspondingly decreased by 38% and increased by 98%. Tree size and topography interacted in a complex manner with between-plot differences. The forest appears to have been sustained by off-setting elevated tree mortality by highly resilient stem growth. This last is seen as the key integrating tree variable which links the external driver (drought causing water stress) and population dynamics recorded as mortality and recruitment. Suitably sound measurements of stem girth, leading to valid growth rates, are needed to understand and model tree dynamic responses to perturbations. The proportion of sound data, however, is in part determined by the drought itself.

Isolation and characterization of nine polymorphic microsatellite markers for the deep-sea shrimp Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea)

Background: The shrimp Nematocarcinus lanceopes Bate, 1888 is found in the deep sea around Antarctica and sub-Antarctic islands. Previous studies on mitochondrial data and species distribution models provided evidence for a homogenous circum-Antarctic population of N. lanceopes. However, to analyze the fine-scale population genetic structure and to examine influences of abiotic environmental conditions on population composition and genetic diversity, a set of fast evolving nuclear microsatellite markers is required. Findings: We report the isolation and characterization of nine polymorphic microsatellite markers from the Antarctic deep-sea shrimp species Nematocarcinus lanceopes (Crustacea: Decapoda: Caridea). Microsatellite markers were screened in 55 individuals from different locations around the Antarctic continent. All markers were polymorphic with 9 to 25 alleles per locus. The observed heterozygosity ranged from 0.545 to 0.927 and the expected heterozygosity from 0.549 to 0.934. Conclusions: The reported markers provide a novel tool to study genetic structure and diversity in Nematocarcinus lanceopes populations in the Southern Ocean and monitor effects of ongoing climate change in the region on the populations inhabiting these.

Tools for better SLM knowledge management and informed decision-making in addressing land degradation at different scales: the WOCAT–LADA–DESIRE methodology

Desertification research conventionally focuses on the problem – that is, degradation – while neglecting the appraisal of successful conservation practices. Based on the premise that Sustainable Land Management (SLM) experiences are not sufficiently or comprehensively documented, evaluated, and shared, the World Overview of Conservation Approaches and Technologies (WOCAT) initiative (www.wocat.net), in collaboration with FAO’s Land Degradation Assessment in Drylands (LADA) project (www.fao.org/nr/lada/) and the EU’s DESIRE project (http://www.desire-project.eu/), has developed standardised tools and methods for compiling and evaluating the biophysical and socio-economic knowledge available about SLM. The tools allow SLM specialists to share their knowledge and assess the impact of SLM at the local, national, and global levels. As a whole, the WOCAT–LADA–DESIRE methodology comprises tools for documenting, self-evaluating, and assessing the impact of SLM practices, as well as for knowledge sharing and decision support in the field, at the planning level, and in scaling up identified good practices. SLM depends on flexibility and responsiveness to changing complex ecological and socioeconomic causes of land degradation. The WOCAT tools are designed to reflect and capture this capacity of SLM. In order to take account of new challenges and meet emerging needs of WOCAT users, the tools are constantly further developed and adapted. Recent enhancements include tools for improved data analysis (impact and cost/benefit), cross-scale mapping, climate change adaptation and disaster risk management, and easier reporting on SLM best practices to UNCCD and other national and international partners. Moreover, WOCAT has begun to give land users a voice by backing conventional documentation with video clips straight from the field. To promote the scaling up of SLM, WOCAT works with key institutions and partners at the local and national level, for example advisory services and implementation projects. Keywords: Sustainable Land Management (SLM), knowledge management, decision-making, WOCAT–LADA–DESIRE methodology.

Climate refugia: joint inference from fossil records, species distribution models and phylogeography

Climate refugia, locations where taxa survive periods of regionally adverse climate, are thought to be critical for maintaining biodiversity through the glacial–interglacial climate changes of the Quaternary. A critical research need is to better integrate and reconcile the three major lines of evidence used to infer the existence of past refugia – fossil records, species distribution models and phylogeographic surveys – in order to characterize the complex spatiotemporal trajectories of species and populations in and out of refugia. Here we review the complementary strengths, limitations and new advances for these three approaches. We provide case studies to illustrate their combined application, and point the way towards new opportunities for synthesizing these disparate lines of evidence. Case studies with European beech, Qinghai spruce and Douglas-fir illustrate how the combination of these three approaches successfully resolves complex species histories not attainable from any one approach. Promising new statistical techniques can capitalize on the strengths of each method and provide a robust quantitative reconstruction of species history. Studying past refugia can help identify contemporary refugia and clarify their conservation significance, in particular by elucidating the fine-scale processes and the particular geographic locations that buffer species against rapidly changing climate.

Manganiferous minerals of the epidote group from the Archaean basement of West Greenland

The chemical compositions and crystal structures of Mn3+-containing minerals from the epidote group in Greenland rocks are investigated and described in detail. They occur in hydrothermally altered Archaean mafic sequences within the gneissic complex of the North Atlantic craton of West Greenland. The Mn-containing minerals have a characteristic red to pink colour. A detailed microchemical study shows a significant inter- and intra-sample variation in Mn content. The samples from different parageneses can be classified as Mn-bearing epidote and Mn-bearing clinozoisite. The intra-sample variation in the content of Al, Fe and Mn is on a very fine scale, but still allows for identification of a negative correlation between Mn and Fe. Textures indicate different stages of growth. Crystal chemical data are compared with literature data and illustrate the basic systematic differences between the influence of Fe and Mn on the crystal structure of the epidote group minerals.

Gene flow and the maintenance of species boundaries

Hybrid zones are regions where individuals from genetically differentiated populations meet and mate, resulting in at least some offspring of mixed ancestry. Patterns of gene flow (introgression) in hybrid zones vary across the genome, allowing assessment of the role of individual genes or genome regions in reproductive isolation. Here, we document patterns of introgression between two recently diverged species of field crickets. We sampled at a very fine spatial scale and genotyped crickets for 110 highly differentiated single nucleotide polymorphisms (SNPs) identified through transcriptome scans. Using both genomic and geographic cline analysis, we document remarkably abrupt transitions (<100 m) in allele frequencies for 50 loci, despite high levels of gene flow at other loci. These are among the steepest clines documented for any hybridizing taxa. Furthermore, the cricket hybrid zone provides one of the clearest examples of the semi-permeability of species boundaries. Comparisons between data from the fine-scale transect and data (for the same set of markers) from sampling a much larger area in a different region of the cricket hybrid zone reveal consistent patterns of introgression for individual loci. The consistency in patterns of introgression between these two distant and distinct regions of the hybrid zone suggests that strong selection is acting to maintain abrupt discontinuities within the hybrid zone and that genomic regions with restricted introgression likely include genes that contribute to nonecological prezygotic barriers.

Matching Social and Ecological Systems in Complex Ocean Fisheries

This paper considers ocean fisheries as complex adaptive systems and addresses the question of how human institutions might be best matched to their structure and function. Ocean ecosystems operate at multiple scales, but the management of fisheries tends to be aimed at a single species considered at a single broad scale. The paper argues that this mismatch of ecological and management scale makes it difficult to address the fine-scale aspects of ocean ecosystems, and leads to fishing rights and strategies that tend to erode the underlying structure of populations and the system itself. A successful transition to ecosystem-based management will require institutions better able to economize on the acquisition of feedback about the impact of human activities. This is likely to be achieved by multiscale institutions whose organization mirrors the spatial organization of the ecosystem and whose communications occur through a polycentric network. Better feedback will allow the exploration of fine-scale science and the employment of fine-scale fishing restraints, better adapted to the behavior of fish and habitat. The scale and scope of individual fishing rights also needs to be congruent with the spatial structure of the ecosystem. Place-based rights can be expected to create a longer private planning horizon as well as stronger incentives for the private and public acquisition of system relevant knowledge.

Targeted Deletion Of Functionally Validated Enhancers Defines Their Role in Mouse Limb Development

Transcriptional enhancers are genomic DNA sequences that contain clustered transcription factor (TF) binding sites. When combinations of TFs bind to enhancer sequences they act together with basal transcriptional machinery to regulate the timing, location and quantity of gene transcription. Elucidating the genetic mechanisms responsible for differential gene expression, including the role of enhancers, during embryological and postnatal development is essential to an understanding of evolutionary processes and disease etiology. Numerous methods are in use to identify and characterize enhancers. Several high-throughput methods generate large datasets of enhancer sequences with putative roles in embryonic development. However, few enhancers have been deleted from the genome to determine their roles in the development of specific structures, such as the limb. Manipulation of enhancers at their endogenous loci, such as the deletion of such elements, leads to a better understanding of the regulatory interactions, rules and complexities that contribute to faithful and variant gene transcription – the molecular genetic substrate of evolution and disease. To understand the endogenous roles of two distinct enhancers known to be active in the mouse embryo limb bud we deleted them from the mouse genome. I hypothesized that deletion of these enhancers would lead to aberrant limb development. The enhancers were selected because of their association with p300, a protein associated with active transcription, and because the human enhancer sequences drive distinct lacZ expression patterns in limb buds of embryonic day (E) 11.5 transgenic mice. To confirm that the orthologous mouse enhancers, mouse 280 and 1442 (M280 and M1442, respectively), regulate expression in the developing limb we generated stable transgenic lines, and examined lacZ expression. In M280-lacZ mice, expression was detected in E11.5 fore- and hindlimbs in a region that corresponds to digits II-IV. M1442-lacZ mice exhibited lacZ expression in posterior and anterior margins of the fore- and hindlimbs that overlapped with digits I and V and several wrist bones. We generated mice lacking the M280 and M1442 enhancers by gene targeting. Intercrosses between M280 -/+ and M1442 -/+, respectively, generated M280 and M1442 null mice, which are born at expected Mendelian ratios and manifest no gross limb malformations. Quantitative real-time PCR of mutant E11.5 limb buds indicated that significant changes in transcriptional output of enhancer-proximal genes accompanied the deletion of both M280 and M1442. In neonatal null mice we observed that all limb bones are present in their expected positions, an observation also confirmed by histology of E18.5 distal limbs. Fine-scale measurement of E18.5 digit bone lengths found no differences between mutant and control embryos. Furthermore, when the developmental progression of cartilaginous elements was analyzed in M280 and M1442 embryos from E13.5-E15.5, transient development defects were not detected. These results demonstrate that M280 and M1442 are not required for mouse limb development. Though M280 is not required for embryonic limb development it is required for the development and/or maintenance of body size – adult M280 mice are significantly smaller than control littermates. These studies highlight the importance of experiments that manipulate enhancers in situ to understand their contribution to development.

Description and chemical composition of ferromanganese encrustations and deposits in the Atlantic Ocean from R/V Atlantis II cruises 20, 42, 60, 85; R/V Chain cruise 35; R/V Knorr cruise 61 and RRS Shackleton cruise 75/1 stations

Chemical and mineralogical compositions of ferromanganese oxide coatings on rocks dredged from the New England Seamounts, the Sierra Leone Rise and the Mid-Atlantic Ridge near the Equator have been determined in an investigation of regional differences in Atlantic ferromanganese deposits. Most encrustations are clearly of hydrogenous origin, consisting mainly of todorokite and delta MnO2, but several recovered from the equatorial fracture zones may be hydrothermal accumulations. Differences in the chemistry of the water column and in growth rates of the ferromanganese coatings may be important in producing this regional contrast in composition. Fine-scale changes in element abundances within the encrustations indicate that the nature of the substrate has little influence on compositional variations.

Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

Geochemistry of minerals from lavas of ODP Leg 135 holes

We use Nomarski differential interference contrast imaging to reveal the wealth of complex detail in plagioclase zoning for selected samples from Sites 834, 839, and 841. All sites contain some plagioclase with the very complex internal core zoning, convolute zoning, or very fine-scale euhedral oscillatory zoning of the sort generally considered typical of island-arc volcanic rocks. Plagioclase with contrasted zoning styles may coexist within a single lithologic unit or even within a single thin section. Especially notable is the presence of scattered plagioclase phenocrysts with complex zoning throughout Unit 7 in Hole 834B, which in other respects is relatively uniform in composition and appears to have had little or no differential sorting of crystals and liquid. Although our study is by no means comprehensive, it is sufficient to indicate that magmatic conditions have been variable during crystallization of these rocks, and mixing or at least minor contamination may be required to explain some of the relations observed. By analogy with experimental studies, it is possible that variations in water content, either over time or within different parts of a chamber or conduit system, have contributed to the observed contrasts in zoning.

Reefs shift from net accretion to net erosion along a natural environmental gradient

Coral reefs persist in an accretion-erosion balance and ocean acidification resulting from anthropogenic CO2 emissions threatens to shift this balance in favor of net reef erosion. Corals and calcifying algae, largely responsible for reef accretion, are vulnerable to environmental changes associated with ocean acidification, but the direct effects of lower pH on reef erosion has received less attention, particularly in the context of known drivers of bioerosion and natural variability. This study examines the balance between reef accretion and erosion along a well-characterized natural environmental gradient in Kane'ohe Bay, Hawai'i using experimental blocks of coral skeleton. Comparing before and after micro-computed tomography (µCT) scans to quantify net accretion and erosion, we show that, at the small spatial scale of this study (tens of meters), pH was a better predictor of the accretion-erosion balance than environmental drivers suggested by prior studies, including resource availability, temperature, distance from shore, or depth. In addition, this study highlights the fine-scale variation of pH in coastal systems and the importance of microhabitat variation for reef accretion and erosion processes. We demonstrate significant changes in both the mean and variance of pH on the order of meters, providing a local perspective on global increases in pCO2. Our findings suggest that increases in reef erosion, combined with expected decreases in calcification, will accelerate the shift of coral reefs to an erosion-dominated system in a high-CO2 world. This shift will make reefs increasingly susceptible to storm damage and sea-level rise, threatening the maintenance of the ecosystem services that coral reefs provide.

Geochemical composition of gabbroic rocks from ODP Hole 179-1105A, southwest Indian Ridge

Oxide-free olivine gabbro and gabbro, and oxide olivine gabbro and gabbro make up the bulk of the gabbroic suite recovered from Ocean Drilling Program (ODP) Leg 179 Hole 1105A, which lies 1.2 km away from Hole 735B on the eastern transverse ridge of the Atlantis II Fracture Zone, Southwest Indian Ridge. The rocks recovered during Leg 179 show striking similarities to rocks recovered from the uppermost 500 m of Hole 735B during ODP Leg 118. The rocks of the Atlantis platform were likely unroofed as part of the footwall block of a large detachment fault on the inside corner of the intersection of the Southwest Indian Ridge and the Atlantis II Transform at ~11.5 Ma. We analyzed the lithologic, geochemical, and structural stratigraphy of the section. Downhole lithologic variation allowed division of the core into 141 lithologic intervals and 4 main units subdivided on the basis of predominance of oxide gabbroic vs. oxide-free gabbroic rocks. Detailed analyses of whole-rock chemistry, mineral chemistry, microstructure, and modes of 147 samples are presented and clearly show that the gabbroic rocks are of cumulate origin. These studies also indicate that geochemistry results correlate well with downhole magnetic susceptibility and Formation MicroScanner (FMS) resistivity measurements and images. FMS images show rocks with a well-layered structure and significant numbers of mappable layer contacts or compositional contrasts. Downhole cryptic mineral and whole-rock chemical variations depict both "normal" and inverse fine-scale variations on a scale of 10 m to <2 m with significant compositional variation over a short distance within the 143-m section sampled. A Mg# shift in whole-rock or Fo contents of olivine of as much as 20-30 units over a few meters of section is not atypical of the extreme variation in downhole plots. The products of the earliest stages of basaltic differentiation are not represented by any cumulates, as the maximum Fo content was Fo78. Similarly, the extent of fractionation represented by the gabbroic rocks and scarce granophyres in the section is much greater than that represented in the Atlantis II basalts. The abundance of oxide gabbros is similar to that in Hole 735B, Unit IV, which is tentatively correlated as a similar unit or facies with the oxide gabbroic units of Hole 1105A. Oxide phases are generally present in the most fractionated gabbroic rocks and lacking in more primitive gabbroic rocks, and there is a definite progression of oxide abundance as, for example, the Mg# of clinopyroxene falls below 73-75. Coprecipitation of oxide at such early Mg#s cannot be modeled by perfect fractional crystallization. In situ boundary layer fractionation may offer a more plausible explanation for the complex juxtaposition of oxide- and nonoxide-bearing more primitive gabbroic rocks. The geochemical signal may, in part, be disrupted by the presence of mylonitic shear zones, which strike east-west and dip both to the south and north, but predominantly to the south away from the northern rift valley where they formed. Downhole deformation textures indicate increasing average strain and crystal-plastic deformation in units that contain oxides. Oxide-rich zones may represent zones of rheologic weakness in the cumulate section along which mylonitic and foliated gabbroic shear zones nucleate in the solid state at high temperature, or the oxide may be a symptom of former melt-rich zones and hypersolidus flow, as predicted during study of Hole 735B.