Mapping functional traits: comparing abundance and presence-absence estimates at large spatial scales

Efforts to quantify the composition of biological communities increasingly focus on functional traits. The composition of communities in terms of traits can be summarized in several ways. Ecologists are beginning to map the geographic distribution of trait-based metrics from various sources of data, but the maps have not been tested against independent data. Using data for birds of the Western Hemisphere, we test for the first time the most commonly used method for mapping community trait composition – overlaying range maps, which assumes that the local abundance of a given species is unrelated to the traits in question – and three new methods that as well as the range maps include varying degrees of information about interspecific and geographic variation in abundance. For each method, and for four traits (body mass, generation length, migratory behaviour, diet) we calculated community-weighted mean of trait values, functional richness and functional divergence. The maps based on species ranges and limited abundance data were compared with independent data on community species composition from the American Christmas Bird Count (CBC) scheme coupled with data on traits. The correspondence with observed community composition at the CBC sites was mostly positive (62/73 correlations) but varied widely depending on the metric of community composition and method used (R2: 5.6×10−7 to 0.82, with a median of 0.12). Importantly, the commonly-used range-overlap method resulted in the best fit (21/22 correlations positive; R2: 0.004 to 0.8, with a median of 0.33). Given the paucity of data on the local abundance of species, overlaying range maps appears to be the best available method for estimating patterns of community composition, but the poor fit for some metrics suggests that local abundance data are urgently needed to allow more accurate estimates of the composition of communities

Nitrogen fixation by caucasian clover and white clover in irrigated ryegrass pastures

The N₂ fixation ability of caucasian clover was compared with that of white clover in irrigated ryegrass pastures over years 2 and 3 of a grazing experiment, using the ¹⁵N enrichment technique. ‘Endura’ caucasian clover was inoculated with the specific Rhizobium strain ICC148. The N concentration in clover herbage and the proportion of clover N derived from N₂ fixation (PN) were similar for both clovers at averages of 4.6%N and 50–60% respectively over the 2 years. The amount of N₂ fixed per hectare was directly related to the amount of clover dry matter (DM) produced by the two clover species. Caucasian clover produced four times the DM yield of white clover in year 2 (5400 cf. 1450 kg DM/ha) and four times the amount of N₂ fixed in herbage (136 cf. 36 kg N/ ha). In year 3, caucasian clover produced 50% more clover DM (3450 cf. 2370 kg DM/ha) and N₂ fixed (98 cf. 66 kg N/ha) than white clover. The increased N input from caucasian clover increased grass %N and N uptake from soil in caucasian clover pastures resulting in higher total pasture production compared with white clover pastures (15.7 cf. 14.2 t DM/ha) by year 3. In this study, caucasian clover demonstrated greater potential than white clover to meet the N demands of high-yielding perennial ryegrass in an intensive pastoral system.The authors acknowledge funding from the Struthers Trust for the development of the grazing experiment at Lincoln University and FRST funding for provision of ¹⁶N and N analyses. We thank the C. Alma Baker and Struthers Trusts for providing A.D. Black with financial support from post-graduate scholarships

Exploring the seismic expression of fault zones in 3D seismic volumes

Acknowledgments The seismic interpretation and image processing has been run in the SeisLab facilty at the University of Aberdeen (sponsored by BG, BP and Chevron) Seismic imaging analysis was performed in GeoTeric (ffA), and Mathematica (Wolfram research). Interpretation of seismic amplitudes was performed Petrel 2014 (Schlumberger). We thank Gaynor Paton (Geoteric) for in depth discussion on the facies analysis methodology and significant suggestions to improve the current paper. We thank the New Zealand government (Petroleum and Minerals ministry) and CGG for sharing the seismic dataset utilized in this research paper. Seismic images used here are available through the Virtual Seismic Atlas (www.seismicatlas.org). Nestor Cardozo and an anonymous reviewer are thanked for their constructive comments and suggestions that strongly improved the quality and organization of this paper.Peer reviewedPostprin

A conceptual framework for studying collective reactions to events in location-based social media

Events are a core concept of spatial information, but location-based social media (LBSM) provide information on reactions to events. Individuals have varied degrees of agency in initiating, reacting to or modifying the course of events, and reactions include observations of occurrence, expressions containing sentiment or emotions, or a call to action. Key characteristics of reactions include referent events and information about who reacted, when, where and how. Collective reactions are composed of multiple individual reactions sharing common referents. They can be characterized according to the following dimensions: spatial, temporal, social, thematic and interlinkage. We present a conceptual framework, which allows characterization and comparison of collective reactions. For a thematically well-defined class of event such as storms, we can explore differences and similarities in collective attribution of meaning across space and time. Other events may have very complex spatio-temporal signatures (e.g. political processes such as Brexit or elections), which can be decomposed into series of individual events (e.g. a temporal window around the result of a vote). The purpose of our framework is to explore ways in which collective reactions to events in LBSM can be described and underpin the development of methods for analysing and understanding collective reactions to events

The use of tumour markers CEA, CA-195 and CA-242 in evaluating the response to chemotherapy in patients with advanced colorectal cancer.

Tumour markers CEA, CA-195 and CA-242 were measured in 33 patients undergoing chemotherapy for advanced colorectal cancer. The aim was to determine whether they could be used to accurately monitor the course of the disease, and reduce the need for imaging. Treatment with a 5-fluorouracil based regimen resulted in a partial response in nine patients (27%), whereas the remainder either had disease stabilisation or suffered from progression. Before treatment the CEA was elevated in 85% of patients and the CA-195 and CA-242 in 78%. All three markers were elevated in 70% and at least one elevated in 93%. CA-195 and CA-242 appeared to be co-expressed, by contrast with the CEA. When compared to the results of serial CT scanning the CEA correlated best with the course of the disease, the positive predictive value being 54% for a partial response, 77% for minor and partial responses combined and 100% for progressive disease. The corresponding values for CA-195 were 46%, 62% and 100% respectively and for CA-242, 50%, 67% and 100% respectively. Thus, although falling levels of markers overestimate the number of responses demonstrated by imaging, rising tumour markers invariably herald progressive disease. This was often evident up to 16 weeks before progression was observed on scanning. CEA is the most useful of the three markers in the monitoring of patients being treated for advanced colorectal cancer, but other markers may prove valuable if the CEA is normal. The use of tumour markers should reduce the need for regular scanning

Using molecular networking for microbial secondary metabolite bioprospecting

The oceans represent an understudied resource for the isolation of bacteria with the potential to produce novel secondary metabolites. In particular, actinomyces are well known to produce chemically diverse metabolites with a wide range of biological activities. This study characterised spore-forming bacteria from both Scottish and Antarctic sediments to assess the influence of isolation location on secondary metabolite production. Due to the selective isolation method used, all 85 isolates belonged to the phyla Firmicutes and Actinobacteria, with the majority of isolates belonging to the genera Bacillus and Streptomyces. Based on morphology, thirty-eight isolates were chosen for chemical investigation. Molecular networking based on chemical profiles (HR-MS/MS) of fermentation extracts was used to compare complex metabolite extracts. The results revealed 40% and 42% of parent ions were produced by Antarctic and Scottish isolated bacteria, respectively, and only 8% of networked metabolites were shared between these locations, implying a high degree of biogeographic influence upon secondary metabolite production. The resulting molecular network contained over 3500 parent ions with a mass range of m/z 149-2558 illustrating the wealth of metabolites produced. Furthermore, seven fermentation extracts showed bioactivity against epithelial colon adenocarcinoma cells, demonstrating the potential for the discovery of novel bioactive compounds from these understudied locations