Undersampled Areas Research Articles

Broadening Student Perceptions of Science through Participatory Data Collection & Research-Education Partnerships

We present results from the first year of a three-year extramurally funded project involving a partnership between an ethnically diverse urban high school and professional research botanists. The goals are to provide students exposure to real-world science, broaden interest in scientific fields of study, and increase floristic data and herbarium specimen collections in under-sampled areas of Solano County, California. A floristic survey was conducted in a 425-acre, open-space public park in Vacaville, California, that is actively grazed by cattle and characterized by grasses, forbs, and oaks. A total of 77 students were enrolled in the course associated with the partnership, and 47 participated in four visits to the collection site. Twenty-five unique plant specimens were collected, including 14 native and 11 introduced species. Results of a student perception survey suggest that the partnership has had a positive impact on students’ understanding of scientific methodology and interest in pursuing a science career. Perception survey results were disaggregated by ethnicity; Hispanic students, more than any other group, indicated that they feel more confident in scientific research and writing skills. There was no significant difference between male and female students’ responses.

Assessing coastal carbon variability in two Delaware tidal marshes

Coastal wetlands provide numerous ecosystem services, including the ability to sequester and store carbon. Recent initiatives, such as the U.S. Climate Alliance’s National Working Lands Challenge, have sought to better understand and quantify this ‘blue carbon’ storage as a land management approach to maintain, or potentially offset, atmospheric carbon emissions. To build on this effort locally, loss on ignition and elemental analyses were used to assess sediment organic matter, dry bulk density, and carbon density variability within the root zone of a mesohaline and oligohaline tidal marsh in Delaware. Additionally, we assessed sediment carbon variability at depth greater than one meter and quantified the black carbon fraction in the mesohaline tidal marsh. Organic matter concentrations ranged between 11.85 ± 1.19% and 23.12 ± 6.15% and sediment carbon density ranged from 0.03 ± 0.01 g cm−3 to 0.06 ± 0.02 g cm−3 with both found to significantly differ between the mesohaline and oligohaline tidal marsh systems. Significant differences between dominant vegetation types were also found. We used these data to further estimate and valuate the carbon stock at the mesohaline tidal marsh to be 350 ± 310 metric tons of soil carbon accumulation per year with a social carbon value of $40,000 ± $35,000. This work improves our knowledge of Delaware-specific carbon stocks, and it may further facilitate broad estimates of carbon storage in under-sampled areas, and thereby enable better quantification of economic and natural benefits of tidal wetland systems by land managers.

DNA Barcoding and geographical scale effect: The problems of undersampling genetic diversity hotspots.

DNA barcoding identification needs a good characterization of intraspecific genetic divergence to establish the limits between species. Yet, the number of barcodes per species is many times low and geographically restricted. A poor coverage of the species distribution range may hamper identification, especially when undersampled areas host genetically distinct lineages. If so, the genetic distance between some query sequences and reference barcodes may exceed the maximum intraspecific threshold for unequivocal species assignation. Taking a group of Quercus herbivores (moths) in Europe as model system, we found that the number of DNA barcodes from southern Europe is proportionally very low in the Barcoding of Life Data Systems. This geographical bias complicates the identification of southern query sequences, due to their high intraspecific genetic distance with respect to barcodes from higher latitudes. Pairwise intraspecific genetic divergence increased along with spatial distance, but was higher when at least one of the sampling sites was in southern Europe. Accordingly, GMYC (General Mixed Yule Coalescent) single‐threshold model retrieved clusters constituted exclusively by Iberian haplotypes, some of which could correspond to cryptic species. The number of putative species retrieved was more reliable than that of multiple‐threshold GMYC but very similar to results from ABGD and jMOTU. Our results support GMYC as a key resource for species delimitation within poorly inventoried biogeographic regions in Europe, where historical factors (e.g., glaciations) have promoted genetic diversity and singularity. Future European DNA barcoding initiatives should be preferentially performed along latitudinal gradients, with special focus on southern peninsulas.

Spatial structure of boreal woodland caribou populations in northwest Canada

Local population units (LPUs) were delineated in Canada’s recovery strategy for threatened boreal woodland caribou (Rangifer tarandus caribou). Population viability analyses central to contemporary integrated risk assessments of LPUs implicitly assume geographic closure. Several LPUs in northwest Canada, however, were in part delineated by geopolitical boundaries and/or included large areas in the absence of evidence of more finely resolved population spatial structure. We pooled >1.2 million locations from >1200 GPS or VHF-collared caribou from northeast British Columbia, northwest Alberta and southwestern Northwest Territories. Bayesian cluster analysis generated 10 alternative candidate LPUs based on a spatial cluster graph of the extent of pairwise co-occurrence of collared caribou. Up to four groups may be artifacts in as yet under-sampled areas. Four were mapped LPUs that were conserved (Prophet, Parker, Chinchaga and Red Earth). One small group between Parker and Snake-Sahtaneh known locally as the “Fort Nelson core,” and outside any mapped LPU, was also conserved. Finally, one large group, at >136000 km2, spanned all three jurisdictions and subsumed all of six delineated LPUs (Maxhamish, Snake-Sahtaneh, Calendar, Bistcho, Yates, Caribou Mountains) and part of southern Northwest Territories. These results suggest less geographic closure of LPUs than those currently delineated, but further analyses will be required to better reconcile various sources of knowledge about local population structure in this region.

Morphological and molecular identification of specimens in the genus Euseius (Acari: Phytoseiidae) from the Republic of Congo.

The purpose of this study was to identify the taxonomic status of several individuals belonging to the genus Euseius, collected from three host plants (cassava, okra, and chilli) in the Republic of the Congo, using morphometric and molecular analysis. For this, hierarchical ascending classification on principal component analysis was performed using morphological measurements from 21 and 22 individuals of E. fustis and Euseius sp., respectively, with the original description of Euseius neodossei considered. For molecular analysis, two DNA fragments were amplified and sequenced: the mitochondrial 12S rRNA and the nuclear ribosomal region ITSS. This integrative approach found that (1) morphological differences existed between the Euseius sp. and both E. neodossei and E. fustis, and (2) both mitochondrial DNA fragments showed a clear delineation between Euseius sp. and E. fustis. The results obtained highlight the value of using integrative taxonomy to improve the identification of species in under-sampled areas and the need to increase the number of DNA sequences deposited in GenBank database from this region. This is the first time that DNA sequences of mites from the Congo (Brazzaville) have been deposited in this database.

Fungi of French Guiana gathered in a taxonomic, environmental and molecular dataset

In Amazonia, the knowledge about Fungi remains patchy and biased towards accessible sites. This is particularly the case in French Guiana where the existing collections have been confined to few coastal localities. Here, we aimed at filling the gaps of knowledge in undersampled areas of this region, particularly focusing on the Basidiomycota. From 2011, we comprehensively collected fruiting-bodies with a stratified and reproducible sampling scheme in 126 plots. Sites of sampling reflected the main forest habitats of French Guiana in terms of soil fertility and topography. The dataset of 5219 specimens gathers 245 genera belonging to 75 families, 642 specimens are barcoded. The dataset is not a checklist as only 27% of the specimens are identified at the species level but 96% are identified at the genus level. We found an extraordinary diversity distributed across forest habitats. The dataset is an unprecedented and original collection of Basidiomycota for the region, making specimens available for taxonomists and ecologists. The database is publicly available in the GBIF repository (https://doi.org/10.15468/ymvlrp).

Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges Bank.

Atlantic cod (Gadus morhua) populations in the Gulf of Maine (GoM) are at a fraction of their historical abundance, creating economic hardships for fishermen and putting at risk the genetic diversity of the remaining populations. An understanding of the biocomplexity among GoM populations will allow for adaptive genetic diversity to be conserved to maximize the evolutionary potential and resilience of the fishery in a rapidly changing environment. We used restriction-site-associated DNA sequencing (RADseq) to characterize the population structure and adaptive genetic diversity of five spawning aggregations from the western GoM and Georges Bank. We also analyzed cod caught in the eastern GoM, an under-sampled area where spawning aggregations have been extirpated. Using 3,128 single nucleotide polymorphisms (SNPs), we confirmed the existence of three genetically separable spawning groups: (1) winter spawning cod from the western GoM, (2) spring spawning cod, also from the western GoM, and (3) Georges Bank cod. Non-spawning cod from the eastern GoM could not be decisively linked to either of the three spawning groups and may represent a unique component of the resource, a mixed sample, or cod from other unsampled source populations. The genetic differentiation among the three major spawning groups was primarily driven by loci putatively under selection, particularly loci in regions known to contain genomic inversions on linkage groups (LG) 7 and 12. These LGs have been found to be linked to thermal regime in cod across the Atlantic, and so it is possible that variation in timing of spawning in western GoM cod has resulted in temperature-driven adaptive divergence. This complex population structure and adaptive genetic differentiation could be crucial to ensuring the long-term productivity and resilience of the cod fishery, and so it should be considered in future management plans.

Submesoscale ocean fronts act as biological hotspot for southern elephant seal

The area west of the Kerguelen Islands (20–70°E/45–60°S) is characterized by a weak mesoscale activity except for a standing meander region of the Antarctic Circumpolar Current (ACC) localized between 20 and 40°E. A unique bio-physical dataset at high-resolution collected by a southern elephant seal (Mirounga leonina) reveals a conspicuous increase in foraging activity at the standing meander site up to 5 times larger than during the rest of her three-month trip west of the Kerguelen Islands. Here, we propose a physical explanation for such high biological activity based on the study of small-scale fronts with scales of 5 to 20 km, also called submesoscales. The standing meander is associated with intensified frontal dynamics at submesoscale, not observed in the rest of the region. Results shed new light on the spatial distribution of submesoscale fronts in the under-sampled area west of the Kerguelen plateau and emphasize their importance for upper trophic levels. Despite that most elephant seals target foraging grounds east of the Kerguelen Plateau, our findings suggest that excursions to the west are not accidental, and may be explained by the recurrently elevated physical and biological activity of the site. As such, other standing meanders of the ACC may also act as biological hotspots where trophic interactions are stimulated by submesoscale turbulence.

A spatially-explicit model of alien plant richness in Tenerife (Canary Islands)

Biological invasions are one of the major threats to biodiversity, especially in oceanic islands. In the Canary Islands, the relationships between plant Alien Species Richness (ASR) and their environmental and anthropogenic determinants were thoroughly investigated using ecological models. However, previous predictive models rarely accounted for spatial autocorrelation (SAC) and uncertainty of predictions, thus missing crucial information related to model accuracy and predictions reliability. In this study, we propose a Generalized Linear Spatial Model (GLSM) for ASR under a Bayesian framework on Tenerife Island. Our aim is to test whether the inclusion of SAC into the modelling framework could improve model performance resulting in more reliable predictions. Results demonstrated as accounting for SAC dramatically reduced the model's AIC (ΔAIC = 4423) and error magnitudes, showing also better performances in terms of goodness of fit. Calculation of uncertainty related to predicted values pointed out those areas where either the number of observations (e.g. under-sampled areas) or the reliability of the environmental predictors was lower (e.g. low spatial resolution in highly heterogeneous environments). Although our results confirmed what was already observed in other ecological studies, such as the important role of roads in ASR spread, methodological considerations on the applied modelling approach point out the importance of considering spatial autocorrelation and researcher's prior knowledge to increase the predictive power of statistical models as well as the correctness in terms of coefficients estimates. The proposed approach may serve as an essential management tools highlighting those portions of territory that will be more prone to biological invasions and where monitoring efforts should be addressed.

Some methods to improve the utility of conditioned Latin hypercube sampling.

The conditioned Latin hypercube sampling (cLHS) algorithm is popularly used for planning field sampling surveys in order to understand the spatial behavior of natural phenomena such as soils. This technical note collates, summarizes, and extends existing solutions to problems that field scientists face when using cLHS. These problems include optimizing the sample size, re-locating sites when an original site is deemed inaccessible, and how to account for existing sample data, so that under-sampled areas can be prioritized for sampling. These solutions, which we also share as individual R scripts, will facilitate much wider application of what has been a very useful sampling algorithm for scientific investigation of soil spatial variation.

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci.

Streptococcus pneumoniae serotype 3 remains a significant cause of morbidity and mortality worldwide, despite inclusion in the 13-valent pneumococcal conjugate vaccine (PCV13). Serotype 3 increased in carriage since the implementation of PCV13 in the USA, while invasive disease rates remain unchanged. We investigated the persistence of serotype 3 in carriage and disease, through genomic analyses of a global sample of 301 serotype 3 isolates of the Netherlands3–31 (PMEN31) clone CC180, combined with associated patient data and PCV utilization among countries of isolate collection. We assessed phenotypic variation between dominant clades in capsule charge (zeta potential), capsular polysaccharide shedding, and susceptibility to opsonophagocytic killing, which have previously been associated with carriage duration, invasiveness, and vaccine escape. We identified a recent shift in the CC180 population attributed to a lineage termed Clade II, which was estimated by Bayesian coalescent analysis to have first appeared in 1968 [95% HPD: 1939–1989] and increased in prevalence and effective population size thereafter. Clade II isolates are divergent from the pre-PCV13 serotype 3 population in non-capsular antigenic composition, competence, and antibiotic susceptibility, the last of which resulting from the acquisition of a Tn916-like conjugative transposon. Differences in recombination rates among clades correlated with variations in the ATP-binding subunit of Clp protease, as well as amino acid substitutions in the comCDE operon. Opsonophagocytic killing assays elucidated the low observed efficacy of PCV13 against serotype 3. Variation in PCV13 use among sampled countries was not independently correlated with the CC180 population shift; therefore, genotypic and phenotypic differences in protein antigens and, in particular, antibiotic resistance may have contributed to the increase of Clade II. Our analysis emphasizes the need for routine, representative sampling of isolates from disperse geographic regions, including historically under-sampled areas. We also highlight the value of genomics in resolving antigenic and epidemiological variations within a serotype, which may have implications for future vaccine development.

Joint simulation of compositional and categorical data via direct sampling technique – Application to improve mineral resource confidence

Ore deposits usually consist of ore materials with different discrete (e.g. rock and alteration types) and continuous (e.g. geochemical and mineral composition) features. Financial feasibility studies are highly dependent on the modelling of these features and their associated joint uncertainties. Few geostatistical techniques have been developed for the joint modelling of high-dimensional mixed data (continuous and categorical) or constrained data, such as compositional data. The compositional nature of the mineral and geochemical data induces several challenges for multivariate geostatistical techniques, because such data carry relative information and are known for spurious statistical and spatial correlation effects. This paper investigates the application of the direct sampling algorithm for joint modelling of compositional and categorical data. In some mining projects the amount of available data may be enormous in some parts of the deposit and if the density of measurements is sufficient, multivariate geospatial patterns can be derived from that data and be simulated (without model inference) at other undersampled areas of the deposit with similar characteristics. In this context, the direct sampling multiple-point simulation method can be implemented for this reconstruction process. The compositional nature of the data is addressed via implementing an isometric log-ratio transformation. The approach is illustrated through two case studies, one synthetic and one real. The accuracy of the results is checked against a set of validation data, revealing the potential of the proposed methodology for joint modelling of compositional and categorical information. The direct sampling technique can be considered as a smart move to assess the future risk and uncertainty of a resource by making use of all the information hidden within the early data.

Progress in the discovery of amphipod crustaceans

At present, amphipod crustaceans comprise 9,980 species, 1,664 genera, 444 subfamilies, and 221 families. Of these, 1,940 species (almost 20%) have been discovered within the last decade, including 18 fossil records for amphipods, which mostly occurred in Miocene amber and are probably all freshwater species. There have been more authors describing species since the 1950s and fewer species described per author since the 1860s, implying greater taxonomic effort and that it might be harder to find new amphipod species, respectively. There was no evidence of any change in papers per author or publication life-times of taxonomists over time that might have biased apparent effort. Using a nonhomogeneous renewal process model, we predicted that by the year 2100, 5,600 to 6,600 new amphipod species will be discovered. This indicates that about two-thirds of amphipods remain to be discovered which is twice the proportion than for species overall. Amphipods thus rank amongst the least well described taxa. To increase the prospect of discovering new amphipod species, studying undersampled areas and benthic microhabitats are recommended.

Seawater acidification and anthropogenic carbon distribution on the continental shelf and slope of the western South Atlantic Ocean

Abstract Increases in atmospheric carbon dioxide (CO2) concentrations since the beginning of the Industrial Revolution have led to increases in the flux of CO2 into the oceans. A large fraction of this increased flux occurs due to anthropogenic carbon (Cant), i.e., the excess carbon released by human activities. The oceans take up large amounts of Cant, and this process likely affects calcifying organisms and the formation and dissolution of calcium carbonate. In this study, we measured hydrographic and carbonate system parameters in the western South Atlantic Ocean. This region is key for understanding climate issues; however, it remains understudied, especially regarding the drivers of ocean acidification and its effects on marine organisms and ecosystems. Using novel data collected in this undersampled area of the global ocean, we (i) determined values of the marine carbonate system parameters and (ii) characterized the seawater acidification state along the western boundary current off the southeastern and southern coasts of Brazil. Specifically, we measured total alkalinity (AT) and pH and applied the TrOCA approach (to derive the Cant storage in the water masses) in the study area. Our results show that (i) AT and the dissolved inorganic carbon distribution in the study region are governed by calcification/dissolution and dilution/evaporation processes and that (ii) Cant is present in the central and intermediate water masses at an average concentration (± method precision) of 75.0 ± 6.6 μmol kg−1 and at depths of up to ~1000 m. The highest concentrations are observed in the lower levels of the Tropical Water, although we cannot exclude an overestimated Cant concentration in this layer, and the South Atlantic Central Water (SACW). These findings suggest that cross-shelf processes likely contribute to increased Cant along western boundary current systems. The storage of Cant in the SACW and the Antarctic Intermediate Water has led to long-term pH decreases of −0.17 ± 0.07 and −0.10 ± 0.06 pH units, respectively.

Four new Licmophora species (Licmophorales), with a review of valve characters and exploration of cingulum characters, including a new septum type

Licmophora species are common epiphytes, with new species being discovered in under-sampled areas, and a need for a larger morphological character set for all species. In the rich flora of Guam, there are several distinctive new species, four of which we describe here, with a reconsideration and expansion of their useful taxonomic characters. Licmophora attenuata n. sp. formed large colonies on long mucilage stalks; narrowly cuneate valves, 209–339 µm long, were notable for a large, possibly hollow, spine, and the head-pole rimoportulae set back along the sternum. Licmophora bulbosa n. sp. was solitary or on short, branched mucilage stalks, with broadly cuneate valves, 95–122 µm long, with slightly inflated apices giving it a ‘turkey baster’ shape; valvocopulae bore a novel perforated silica ingrowth along the entire midrib, which we call a Tharngan strip. Licmophora curvata n. sp. attached by mucilage pads, the 87–170 µm long cells were distinctive by their curvature and 21–30 µm broad valves. Licmophora labianatis n. sp. was found in large colonies on long branched stalks, with 311–365 µm long valves that were distinctive for a delicate section mid-way along the valve where vimines were absent. Licmophora cells are heterovalvar and we define the ‘back’ frustule as the one with the basal rimoportula. Frustules are also heteropolar and thus have a left and right side. These terms do not correspond to epivalve/hypovalve and primary/secondary sides of valves and are useful for specifying locations of features. The Licmophora epitheca (i.e., the mature half of the frustule) has a cingulum comprising five copulae (a valvocopula + four pleurae) that differ from each other and between species; we describe their morphology in detail. Copular striae were often denser than valvar striae. Midribs were positioned symmetrically along the midline of the band, or asymmetrically, closer to one margin. Advalvar and abvalvar copular striae consisted of single slits or a series of pores (rimate vs porate) and the type often changed along the band. Midribs on valvocopulae transitioned in distinctive ways from the abvalvar side at the cell apex to the advalvar side. The 2nd and 4th pleurae (closed at the apex of the frustule, like the valvocopula) were sometimes very similar to one another but in other species the 4th pleura was reduced to an apical cap with a very narrow band. The 1st and 3rd pleurae, closed at the base, were usually distinct from one another in the size and shape of the open tips. The expanded set of valve + copula characters will be useful in resolving the taxonomy of the majority of short, straight Licmophora species, but studies of additional species are needed to narrow the list to the most useful copula characters.

V12-10 EVALUATING THE DIAGNOSTIC ROLE OF IN-BORE MAGNETIC RESONANCE IMAGING GUIDED PROSTATE BIOPSY

You have accessJournal of UrologyImaging Based Techniques & Uroradiology1 Apr 2018V12-10 EVALUATING THE DIAGNOSTIC ROLE OF IN-BORE MAGNETIC RESONANCE IMAGING GUIDED PROSTATE BIOPSY Tiffany Cherry, Diarmaid Moran, Paul Simkin, Richard Dowling, Stefan Heinze, and Homayoun Zargar Tiffany CherryTiffany Cherry More articles by this author , Diarmaid MoranDiarmaid Moran More articles by this author , Paul SimkinPaul Simkin More articles by this author , Richard DowlingRichard Dowling More articles by this author , Stefan HeinzeStefan Heinze More articles by this author , and Homayoun ZargarHomayoun Zargar More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2018.02.3018AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookTwitterLinked InEmail INTRODUCTION AND OBJECTIVES With the increasing role of magnetic resonance imaging (MRI) in prostate cancer diagnosis, in-bore MRI (IB-MRI) guided biopsy has become a feasible method of sampling suspicious lesions with real-time guidance. This may allow a focus on otherwise under-sampled areas while also reducing the diagnosis of clinically insignificant cancers. We aim to report the diagnostic role that IB-MRI guided biopsies have played in our initial cohort. METHODS All patients intended for IB-MRI guided prostate biopsy at our institution are included. Retrospectively recorded data includes indication, previous biopsy results, PIRADS score of targeted lesion, histological results and complications. We also assessed the impact on clinical management. RESULTS 31 patients with identified lesions attempted to undergo IB-MRI guided biopsy. A median number of 5 cores were taken (range 3-11). 19 patients had previously undergone a prostate biopsy (14 transperineal, 5 TRUS), 9 of whom were on active surveillance. Outcomes are summarised in Table 1 with results categorised according to the PIRADS score of the targeted lesion. Any grade of prostate cancer was considered a positive result. Two significant complications occurred (urinary sepsis and rectal bleeding), and 2 intended biopsies did not proceed (1 patient intolerability, 1 target lesion no longer seen). See Table 1: Summary of MRI guided biopsy resultsOf the 10 patients with no previous biopsy, 5 were offered radical therapy for clinically significant prostate cancer (Gleason grade greater than or equal to 7) and 1 was placed onto active surveillance for Gleason 6 disease. Excluding biopsy naïve patients, undergoing an IB-MRI changed the preferred clinical management in 10 out of 19 patients, 9 of whom have chosen to undergo definitive therapy. CONCLUSIONS IB-MRI guided biopsy appears to offer a reliable and acceptable method to accurately target identified lesions. Overall in our cohort, this method led to definitive therapy being offered to 52% of those patients biopsied. Its ongoing role in the prostate cancer diagnostic pathway should continue to be evaluated. © 2018FiguresReferencesRelatedDetails Volume 199Issue 4SApril 2018Page: e1239-e1240 Advertisement Copyright & Permissions© 2018MetricsAuthor Information Tiffany Cherry More articles by this author Diarmaid Moran More articles by this author Paul Simkin More articles by this author Richard Dowling More articles by this author Stefan Heinze More articles by this author Homayoun Zargar More articles by this author Expand All Advertisement Advertisement PDF downloadLoading ...

Novel 3D geometry and models of the lower regions of large trees for use in carbon accounting of primary forests.

There is high uncertainty in the contribution of land-use change to anthropogenic climate change, especially pertaining to below-ground carbon loss resulting from conversion of primary-to-secondary forest. Soil organic carbon (SOC) and coarse roots are concentrated close to tree trunks, a region usually unmeasured during soil carbon sampling. Soil carbon estimates and their variation with land-use change have not been correspondingly adjusted. Our aim was to deduce allometric equations that will allow improvement of SOC estimates and tree trunk carbon estimates, for primary forest stands that include large trees in rugged terrain. Terrestrial digital photography, photogrammetry and GIS software were used to produce 3D models of the buttresses, roots and humus mounds of large trees in primary forests dominated by Eucalyptus regnans in Tasmania. Models of 29, in situ eucalypts were made and analysed. 3D models of example eucalypt roots, logging debris, rainforest tree species, fallen trees, branches, root and trunk slices, and soil profiles were also derived. Measurements in 2D, from earlier work, of three buttress 'logs' were added to the data set. The 3D models had high spatial resolution. The modelling allowed checking and correction of field measurements. Tree anatomical detail was formulated, such as buttress shape, humus volume, root volume in the under-sampled zone and trunk hollow area. The allometric relationships developed link diameter at breast height and ground slope, to SOC and tree trunk carbon, the latter including a correction for senescence. These formulae can be applied to stand-level carbon accounting. The formulae allow the typically measured, inter-tree SOC to be corrected for not sampling near large trees. The 3D models developed are irreplaceable, being for increasingly rare, large trees, and they could be useful to other scientific endeavours.

Dimethylsulfoniopropionate (DMSP) and dimethyl sulfide (DMS) cycling across contrasting biological hotspots of the New Zealand subtropical front

Abstract. The oceanic frontal region above the Chatham Rise east of New Zealand was investigated during the late austral summer season in February and March 2012. Despite its potential importance as a source of marine-originating and climate-relevant compounds, such as dimethyl sulfide (DMS) and its algal precursor dimethylsulfoniopropionate (DMSP), little is known of the processes fuelling the reservoirs of these sulfur (S) compounds in the water masses bordering the subtropical front (STF). This study focused on two opposing short-term fates of DMSP-S following its uptake by microbial organisms (either its conversion into DMS or its assimilation into bacterial biomass) and has not considered dissolved non-volatile degradation products. Sampling took place in three phytoplankton blooms (B1, B2, and B3) with B1 and B3 occurring in relatively nitrate-rich, dinoflagellate-dominated subantarctic waters, and B2 occurring in nitrate-poor subtropical waters dominated by coccolithophores. Concentrations of total DMSP (DMSPt) and DMS were high across the region, up to 160 and 14.5 nmol L−1, respectively. Pools of DMSPt showed a strong association with overall phytoplankton biomass proxied by chlorophyll a (rs = 0.83) likely because of the persistent dominance of dinoflagellates and coccolithophores, both DMSP-rich taxa. Heterotrophic microbes displayed low S assimilation from DMSP (less than 5 %) likely because their S requirements were fulfilled by high DMSP availability. Rates of bacterial protein synthesis were significantly correlated with concentrations of dissolved DMSP (DMSPd, rs = 0.86) as well as with the microbial conversion efficiency of DMSPd into DMS (DMS yield, rs = 0.84). Estimates of the potential contribution of microbially mediated rates of DMS production (0.1–27 nmol L−1 day−1) to the near-surface concentrations of DMS suggest that bacteria alone could not have sustained DMS pools at most stations, indicating an important role for phytoplankton-mediated DMS production. The findings from this study provide crucial information on the distribution and cycling of DMS and DMSP in a critically under-sampled area of the global ocean, and they highlight the importance of oceanic fronts as hotspots of the production of marine biogenic S compounds.

Why choose Random Forest to predict rare species distribution with few samples in large undersampled areas? Three Asian crane species models provide supporting evidence.

Species distribution models (SDMs) have become an essential tool in ecology, biogeography, evolution and, more recently, in conservation biology. How to generalize species distributions in large undersampled areas, especially with few samples, is a fundamental issue of SDMs. In order to explore this issue, we used the best available presence records for the Hooded Crane (Grus monacha, n = 33), White-naped Crane (Grus vipio, n = 40), and Black-necked Crane (Grus nigricollis, n = 75) in China as three case studies, employing four powerful and commonly used machine learning algorithms to map the breeding distributions of the three species: TreeNet (Stochastic Gradient Boosting, Boosted Regression Tree Model), Random Forest, CART (Classification and Regression Tree) and Maxent (Maximum Entropy Models). In addition, we developed an ensemble forecast by averaging predicted probability of the above four models results. Commonly used model performance metrics (Area under ROC (AUC) and true skill statistic (TSS)) were employed to evaluate model accuracy. The latest satellite tracking data and compiled literature data were used as two independent testing datasets to confront model predictions. We found Random Forest demonstrated the best performance for the most assessment method, provided a better model fit to the testing data, and achieved better species range maps for each crane species in undersampled areas. Random Forest has been generally available for more than 20 years and has been known to perform extremely well in ecological predictions. However, while increasingly on the rise, its potential is still widely underused in conservation, (spatial) ecological applications and for inference. Our results show that it informs ecological and biogeographical theories as well as being suitable for conservation applications, specifically when the study area is undersampled. This method helps to save model-selection time and effort, and allows robust and rapid assessments and decisions for efficient conservation.

Holocene paleoenvironmental change in southeastern Africa (Makwe Rockshelter, Zambia): Implications for the spread of pastoralism

Abstract The paleoenvironmental conditions surrounding the origins of pastoralism and the movement of herders from eastern to southern Africa sometime between ∼4000 and 2000 ybp have been much debated. We lack, however, detailed paleoenvironmental data from sites sampling the hunter-to-herder transition in southeastern Africa, the likely corridor from eastern to southern Africa for early pastoralists. Here we report on new paleoenvironmental data from a site in the under-sampled area of eastern Zambia, Makwe Rockshelter, which has two aggregates of archaeological horizons representing the mid-Holocene (∼5700-5000 ybp) and the late Holocene (∼1600-800 ybp). The mid-Holocene sediments at Makwe document a foraging society, whereas the late Holocene sediments include both wild game and domestic livestock. Using stable carbon isotopes (δ13C) of herbivore enamel (n = 107), we show that the shift from mid-Holocene to late Holocene paleoenvironments was characterized by an increase in C4 vegetation. These data are complemented by paleoenvironmental records from Lake Malawi that show that C4 vegetation peaked after ∼2000 ybp and was coincident with the onset of cooler, more arid climates. This combined paleoenvironmental record has implications for the spread of pastoralism across southeastern Africa between ∼3000 and 2000 ybp and potential ‘animal disease barriers’ these early herders may have faced.