Characterization of <Emphasis Type="Italic">target</Emphasis> nuclear DNA from faeces reduces technical issues associated with the assumptions of low-quality and quantity template

Faecal material has increasingly become an important non-invasive source of DNA for wildlife population genetics. However, DNA from faecal sources can have issues associated with quantity (low-template and/or low target-to-total DNA ratio) and quality (degradation and/or low DNA-to-inhibitor ratio). A number of studies utilizing faecal material assume and compensate for the above properties with minimal characterization of quantity or quality of target DNA, which can unnecessarily increase the risk of downstream technical problems. Here, we present a protocol which quantifies faecal DNA using a two step approach: (1) estimating total DNA concentration using a Picogreen^TM fluorescence assay and (2) estimating target nuclear DNA concentration by comparing amplification products of field samples at suspected concentrations to those of control DNA at known concentrations. We applied this protocol to faecal material collected in the field from two species: woodland caribou (Rangifer tarandus) and swift fox (Vulpes velox). Total DNA estimates ranged from 6.5 ng/μl to 28.6 ng/μl (X = 16.2 ng/μl) for the caribou extracts and 1.0–26.1 ng/μl (X = 7.5 ng/μl) for the swift fox extracts. Our results showed high concordance between total and target DNA estimates from woodland caribou faecal extracts, with only 10% of the samples showing relatively lower target-to-total DNA ratios. In contrast, DNA extracts from swift fox scat exhibited low target DNA yields, with only 38% (19 of 50) of the samples showing comparative target DNA amplification of at least 0.1 ng. With this information, we were able to estimate the amount of target DNA entered into PCR amplifications, and identify samples having target DNA below a lower threshold of 0.2 ng and requiring modification to genotyping protocols such as multiple tube amplification. Our results here also show that this approach can easily be adapted to other species where faeces are the primary source of DNA template.     

Tree species diversity in small, tropical riparian forest fragments in Belize, Central America

Tree species diversity was measured in a network of very small galleryforests within the Mountain Pine Ridge savanna in Belize. Research focussed onforest patches smaller than 1 ha in size (micro-forests) and linearstrips of trees along creeks lacking interior core zones with low understoreylight levels (tree thickets). Twenty-five micro-forests and 51 tree thicketsites were sampled throughout the savanna. A total of 144 morphospecies 5cm dbh (106 in micro-forests and 117 in tree thickets) werefound, which represents 1/5 of the approximately 700 native tree species in Belize.Most (85.3%) of the species encountered are typically found in tropical rainforests and few are restricted to savanna or riparian environments. Speciesaccumulated at a much faster rate in micro-forests than in tree thickets. Onlyone species, the palm Acoelorraphe wrightii, was extremelyabundant, accounting for almost 30% of all stems. Many of the species werepresent in very low densities: 19% of all species found in micro-forests and 42%of those found in tree thickets had on average one or fewer stems per hectare. Alarge proportion of species were also found infrequently across the landscape,being present in only 36% of micro-forests and at 52% of tree thicket sites. Theresults indicate that networks of very small forest patches can contain highnumbers of species and could therefore contribute to the maintenance of regionalbiodiversity.     

Climate tolerance and interspecific variation in geographic range size

The fact that climate influences the continental-scale distributions of species is one of the central tenets of ecology and biogeography. Equally elemental is that species exhibit enormous variation in geographic range size, with most occupying comparatively small areas. The degree to which climate can account for this variation remains unclear. Here, I test three alternative climate-based hypotheses for variation in range size using a large sample of tree and shrub species native to North America north of Mexico. I show that the lowest value of January average daily minimum temperature encompassed by a species' geographic range (T(MIN)), representing the 'climate extremes hypothesis', explains almost 80% of the variation in range size. Hypotheses based on seasonality and climate optima find substantially less support. The relationship between range size and T(MIN) does not change across the breadth of latitudes examined, and is general for conifers and hardwoods, and growth form (tree versus shrub). Differential freezing resistance gains support as the mechanism underlying interspecific variation in range size: using 35 species for which data were available, both T(MIN) and range size are shown to be strongly correlated with measures of freezing resistance.     

Mapping of B-cell epitopes on the polypeptide chain of the Epstein-Barr virus major envelope glycoprotein and candidate vaccine molecule gp340.

The Epstein-Barr virus (EBV) major envelope glycoprotein gp340 is the subject of current efforts to develop an EBV subunit vaccine. The importance of gp340-specific humoral immunity has been highlighted by studies of natural infection in humans and gp340 immunization of experimental animals. The former studies have demonstrated the presence of gp340-specific serum antibodies which mediate EBV neutralization, complement fixation, and antibody-dependent cellular cytotoxicity. The latter studies have often shown a correlation between the induction of gp340-specific EBV-neutralizing antibodies and protection from virus challenge. We have used a series of bacterial beta-galactosidase-gp340 fusion proteins and overlapping synthetic peptides from the gp340 open reading frame to map the positions of B-cell epitopes within the gp340 primary amino acid sequence. The data reported here indicate the presence of B-cell epitopes within the carboxy-terminal third of the gp340 polypeptide chain. These epitopes could not be detected with a peptide enzyme-linked immunosorbent assay, thereby suggesting that they are discontinuous. Affinity purification of antibodies with a gp340 fusion protein from the carboxy terminus of the gp340 polypeptide chain has been used to show that these antibodies are not EBV neutralizing in vitro. The consequences of these findings for future EBV vaccine development are considered.     

The biogeography and filtering of woody plant functional diversity in North and South America

Aim In recent years evidence has accumulated that plant species are differentially sorted from regional assemblages into local assemblages along local‐scale environmental gradients on the basis of their function and abiotic filtering. The favourability hypothesis in biogeography proposes that in climatically difficult regions abiotic filtering should produce a regional assemblage that is less functionally diverse than that expected given the species richness and the global pool of traits. Thus it seems likely that differential filtering of plant traits along local‐scale gradients may scale up to explain the distribution, diversity and filtering of plant traits in regional‐scale assemblages across continents. The present work aims to address this prediction. Location North and South America. Methods We combine a dataset comprising over 5.5 million georeferenced plant occurrence records with several large plant functional trait databases in order to: (1) quantify how several critical traits associated with plant performance and ecology vary across environmental gradients; and (2) provide the first test of whether the woody plants found within 1° and 5° map grid cells are more or less functionally diverse than expected, given their species richness, across broad gradients. Results The results show that, for many of the traits studied, the overall distribution of functional traits in tropical regions often exceeds the expectations of random sampling given the species richness. Conversely, temperate regions often had narrower functional trait distributions than their smaller species pools would suggest. Main conclusion The results show that the overall distribution of function does increase towards the equator, but the functional diversity within regional‐scale tropical assemblages is higher than that expected given their species richness. These results are consistent with the hypothesis that abiotic filtering constrains the overall distribution of function in temperate assemblages, but tropical assemblages are not as tightly constrained.     

Habitat selection by Canada lynx: making do in heavily fragmented landscapes

Habitat loss and fragmentation result in landscapes where high quality habitat patches are surrounded by matrix habitats of low and variable quality. For mobile species to persist in such landscapes, individual animals often rely on the high quality habitats but also use matrix habitats for supplemental resources or while moving between higher quality patches. Determining what habitat features animals select when in these matrix areas is important, as retaining desirable features in lower quality habitats may enable species persistence. We examine a population of US federally threatened Canada lynx (Lynx canadensis) in northcentral Washington, near the southwestern range limit, where lynx habitat is fragmented by topography, wildfires, and human impacts. We used Global Positioning System radio-collar data from 17 lynx in the North Cascade Mountains during 2007–2013 to explore lynx habitat use. We used Random Forest models to analyze core hunting, resting, and denning habitat, and the habitats lynx select while between patches of core habitat. While selecting core habitat, lynx used spruce (Picea engelmannii)-fir (Abies lasiocarpa), lodgepole pine (Pinus contorta), and mixed sub-boreal-Douglas fir (Pseudotsuga menziesii) forests, and avoided dry forests and forest openings including new burns. When not in core habitat, lynx used a wider range of habitats, including new burns where fire skips and residual trees offered cover. Our results show clearly that Canada lynx tolerate a wider range of habitats where they occupy fragmented landscapes. Consequently, maintaining animals in fragmented landscapes requires that we identify and conserve not only the core habitats a particular species selects, but also the habitat features animals use while in less suitable environments.     

Modeling the potential North American distribution of Russian olive,an invader of riparian ecosystems

Russian olive (Elaeagnus angustifolia L., Elaeagnaceae) has gained notoriety as an invasive tree in the United States (US), particularly owing to its impacts within western riparian ecosystems. In Canada, its potential for range expansion has yet to be assessed, despite alarming infestations in parts of southern British Columbia (BC). Existing niche model predictions are of limited utility because they are restricted to the US, were constructed in the absence of higher latitude records in Canada, and did not consider potentially important soil-related predictors. Here, we address these gaps, and include more than 1400 new occurrence records for Canada, most of which were collected using Google Street View. Our Maxent niche models achieved excellent performance (AUC > 0.9), and identified mean temperature of the coldest quarter and topsoil pH as the first and second-most important predictor variables, respectively, neither of which was included in previously published niche models. High habitat suitability is predicted in areas of western Canada that presently lack occurrence records, including along several major rivers in south-central BC. Our findings should prove valuable to nascent detection and management efforts in western Canada, and also highlight the benefits of basing niche model predictions on occurrence records encompassing as much of the invaded range as possible.     

The evolutionary species pool hypothesis and patterns of freshwater diatom diversity along a pH gradient

Aim To interpret the unimodal relationship between diatom species richness and lake pH within the context of the evolutionary species pool hypothesis (SPH). We test the following primary prediction arising from the SPH: the size of the potential species pool (PSP) will increase along a gradient representing the historical commonness of different pH environments (pH commonness). To do this we assume that the present‐day spatial dominance of near‐neutral pH conditions compared with acidic and alkaline conditions reliably mimics the relative spatial availabilities of historical pH conditions among freshwater lakes. We also determine whether local richness represents a constant proportion of PSP size along the pH commonness gradient. Location Two hundred and thirty‐four lakes distributed over a 405,000 km² region of the north‐eastern United States of America. Methods Sediment diatom morphospecies lists and pH data were acquired from the US Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) website. Using 248 morphospecies that occurred in at least 10 of the 234 lakes, four different measures of PSPs were calculated along the pH gradient. Local species richness was equated with the number of species occurring within the lake. Alpha diversity was equated with the average species richness of lakes with similar pH values. A combination of statistical methods were employed, including correlations, quadratic regression and piecewise regression. Results PSP size increased significantly with pH commonness for all four measures of PSP size, thus supporting the primary prediction of the evolutionary SPH. Local richness comprised a larger proportion of the PSP within acidic lakes than within circumneutral lakes. Alpha diversity and lake species richness both increased significantly with pH commonness, but the former did so in a two‐step fashion. We test and reject several alternative contemporary time‐scale explanations for our findings. Main Conclusions Our findings are consistent with the hypothesis that diatom taxonomic richness is presently lower within acidic and highly alkaline lakes than in circumneutral lakes owing to the limited opportunity in space and/or time for the evolution of suitably adapted species. Whereas ecological processes can explain why certain species are excluded from particular habitats, e.g. acidic lakes, they cannot account for why so few species are adapted to those habitats in the first place.