Occurrence of Isocitrate Lyase in a Thermophilic Bacillus Species

A thermophilic, sporeforming bacterium has been isolated from soil on a medium containing acetate as a carbon source. This organism is similar to Bacillus stearothermophilus in most respects but differs in its inability to hydrolyze starch. Isocitrate lyase is present in cell-free extracts of organisms grown in a medium with acetate as a carbon source. The specific activity was 400 times lower in extracts of organisms utilizing glucose as a carbon source. With crude extracts, enzyme activity was strongly stimulated by Mg(++), but cysteine and ethylenediaminetetraacetate had little effect. It appeared to be more heat-stable than the pure isocitrate lyase from Pseudomonas indigofera.     

Determining Occurrence Dynamics when False Positives Occur: Estimating the Range Dynamics of Wolves from Public Survey Data

Large-scale presence-absence monitoring programs have great promise for many conservation applications. Their value can be limited by potential incorrect inferences owing to observational errors, especially when data are collected by the public. To combat this, previous analytical methods have focused on addressing non-detection from public survey data. Misclassification errors have received less attention but are also likely to be a common component of public surveys, as well as many other data types. We derive estimators for dynamic occupancy parameters (extinction and colonization), focusing on the case where certainty can be assumed for a subset of detections. We demonstrate how to simultaneously account for non-detection (false negatives) and misclassification (false positives) when estimating occurrence parameters for gray wolves in northern Montana from 2007–2010. Our primary data source for the analysis was observations by deer and elk hunters, reported as part of the state’s annual hunter survey. This data was supplemented with data from known locations of radio-collared wolves. We found that occupancy was relatively stable during the years of the study and wolves were largely restricted to the highest quality habitats in the study area. Transitions in the occupancy status of sites were rare, as occupied sites almost always remained occupied and unoccupied sites remained unoccupied. Failing to account for false positives led to over estimation of both the area inhabited by wolves and the frequency of turnover. The ability to properly account for both false negatives and false positives is an important step to improve inferences for conservation from large-scale public surveys. The approach we propose will improve our understanding of the status of wolf populations and is relevant to many other data types where false positives are a component of observations.     

Rapidly Shifting Sex Ratio across a Species Range

Sex ratios are subject to distortion by a range of inherited parasites [1]. Although it has been predicted that the presence of these elements will result in spatial and temporal variation in host sex ratio [2], [3] and [4], testing of this hypothesis has been constrained by availability of historical data. We here determine spatial and temporal variation in sex ratio in a interaction between a butterfly and male-killing Wolbachia bacteria [5] by assaying infection presence in museum specimens, and from this inferring infection prevalence and phenotype in historical populations. Comparison of contemporary and museum samples revealed profound change in four of five populations examined. Two populations become extremely female biased, associated with spread of the male-killer bacterium. One evolved from extremely female biased to a sex ratio near parity, resulting from the infection losing male-killing activity. The final population fluctuated widely in sex ratio, associated with varying frequency of the male killer. We conclude that asynchronous invasion and decline of sex-ratio distorters combines with the evolution of host suppressors to produce a rapidly changing mosaic of sex ratio. As a consequence, the reproductive ecology of the host species is likely to be fundamentally altered over short time scales [6]. Further, the study demonstrates the utility of museum specimens as “silent witnesses” of evolutionary change.     

Effects of Metals on a Range of Streptomyces Species

A plate diffusion method was used to assess the tolerance of 28 mesophilic and 4 thermophilic species of streptomycetes to eight metals. This method allowed a qualitative screen of the effects of the metals on growth, on sporulation, and in some cases, on secondary metabolite production. Tolerant and sensitive species were identified, some of which exhibited the same response (i.e., tolerance or sensitivity) to a number of metals. Experiments in liquid culture were used to quantify the precise concentration ranges of the metals at which the most tolerant or sensitive species could grow. Distribution profiles of the sensitivities of all species examined toward different metals revealed that the order of toxicity was Hg > Cd > Co > Zn > Ni > Cu > Cr > Mn.     

Behavioral Isolation Based on Visual Signals in a Sympatric Pair of Darter Species

Elaborate visual communication signals characterize many animal lineages. Often sex‐limited, these signals are generally assumed to result from sexual selection, and in many cases, their evolution is thought to play a central role in speciation. The co‐evolution of male visual signals and female preferences is hypothesized to result in behavioral isolation between divergent lineages; however, for many lineages characterized by elaborate visual signals, the importance of visual differences in behavioral isolation is not well established. Darters (fish genus Etheostoma) are particularly appropriate for examining the role of visual signals in behavioral isolation. They comprise one of the most diverse groups of North American freshwater fish, and nearly every species is characterized by unique nuptial coloration. Multiple darter species co‐exist in sympatric populations, indicating that reproductive barriers are central to maintaining these extraordinarily diverse color patterns. This study demonstrates the presence of behavioral isolation between a pair of distinctly colored sympatric darter species, Etheostoma barrenense and Etheostoma zonale, through experimental observations using an artificial stream. In addition, a series of dichotomous mate‐choice trials indicate that females prefer conspecific males over heterospecifics based on visual differences alone. We therefore provide the first evidence that visual signals are a critical trait maintaining behavioral isolation in darters, a lineage of fishes with spectacular diversification in visual communication.     

Searching for a Needle in a Haystack: Evaluating Survey Methods for Non-indigenous Plant Species

The control and management of non-indigenous plant species (NIS) can be conceptually divided into three phases: inventory/survey, monitoring and management. Here we focus on phase one, determining which species are present and where they are located within the environment. Sampling for NIS is inherently time-consuming and thus costly. Many management areas are large and therefore can only be surveyed (partial observation of the total area by sampling) and not inventoried (total observation of area). Survey data should reflect the spatial distribution of the target species populations over the landscape. Such data can then be used in combination with environmental data, to create probability maps of target species occurrence for the entire area of interest. We used a GIS model to evaluate seven different survey methods for consistency and reliability of intersecting NIS species’ patches and producing samples which reflect the spatial distribution of the population, and which can be performed in a cost and time-efficient manner. The GIS model was developed to create NIS populations which were then sampled using the different survey methods, and the results recorded. To improve the applicability of the model, four patch sizes and levels of occurrence were used, along with random and weighted distribution patterns in relation to patch proximity to roads and trails. Grid and random points, and targeted (stratified continuous) transects (starting on a road or trail (rights of way (RoW)) and finishing 2 km from any RoW) methods provided the most consistent samples of the population. Logistically, point methods required an unrealistic distance and time commitment in comparison with transect methods. The importance of collecting information on the size of NIS patches was demonstrated as more small patches were intersected than larger ones when the area infested was held constant. Thus, if frequency of patches is used to explain the results of a survey then comparisons between species and methods are difficult to interpret thus leading to erroneous conclusions. However, use of percentage of area infested estimates provides for easier comparison between species and sample methods. The targeted transect method provided the most reliable, efficient and consistent sample with the expected spatial distribution.     

Predictive Occurrence Models for Bat Species in California

Abstract: The ability to accurately predict the potential occurrence of species of management concern is useful for wildlife managers, particularly for those whose management activities involve large areas where sampling is difficult due to logistical or financial constraints. During the summers of 2002 and 2003, we used mist nets to capture bats (Myotis yumanensis, M. californicus, M. evotis, M. thysanodes, Eptesicus fuscus, Lasionycteris noctivagans, Tadarida brasiliensis, Antrozous pallidus, Lasiurus borealis, and Lasiurus cinereus) in Whiskeytown National Recreation Area in north-central California, USA. We used landscape-scale variables, logistic regression, and Akaike's Information Criterion (AIC_c) to model species distributions and produce spatially discerning predictive occurrence maps. We developed a priori models that we used to determine which landscape-scale variables best discriminated between capture sites and non-capture sites. The odds of capturing a bat were 3.3 greater when total edge increased by 10,000 m, whereas for Yuma myotis (Myotis yumanensis), the odds of predicting presence were 0.2 greater when distance to lakes and ponds decreased by 2,000 m. Elevation was important in predicting the distribution of silver-haired bats (Lasionycteris noctivagans) and big brown bats (Eptesicus fuscus). Increasing elevation by 400 m decreased the odds of capturing a silver-haired bat by 0.1 and a big brown bat by 0.4. Classification accuracy for our models ranged from 80.9% for all bat species combined to 72.3% for Yuma myotis and silver-haired bats. Predictive occurrence models can be valuable to bat conservation efforts because they provide spatial data important for evaluating the effects of management activities on species distributions.     

Occurrence and Pathogenicity of Fusarium Species in Banana Fruits

Banana fruits were studied over a six-month period in order to determine the incidence of species of the Fusarium genus and assess their potential pathogenicity. The 72 samples studied were commercially available in Italy and Spain, where they were brought from Panama, Ecuador and Canary Islands. Among the species detected in the fruits, Fusarium semitectum var. majus Wollenw. was predominant, followed by F. moniliforme Sheld., F. solani (Mart.) Appel & WoUenw., F. oxysporum Schlecht., F. proliferatum (Matsushima) Nirenberg, F. graminearum Schw., F. camptoceras WoUenw. &C Reinking, F. subglutinans (WoUenw. & Reinking) Nelson et al., F. dimerum Penzig in Sacc, F. acuminatum EU. & Ev., and F. equiseti (Corda) Sacc. Fusarium proliferatum had never been reported to occur as contaminating fungi in banana fruits to date. Fusarium subglutinans, F. acuminatum and F. graminearum were found to be the most markedly pathogenic of all. The lack of noticeable differences in relation to the incidence of the different species isolated from the samples indicates that the mycoflora found is typical of this fruit and does not depend on its origin.     

Geographical Range and Local Abundance of Tree Species in China

Most studies on the geographical distribution of species have utilized a few well-known taxa in Europe and North America, with little research in China and its wide range of climate and forest types. We assembled large datasets to quantify the geographic ranges of tree species in China and to test several biogeographic hypotheses: 1) whether locally abundant species tend to be geographically widespread; 2) whether species are more abundant towards their range-centers; and 3) how abundances are correlated between sites. Local abundances of 651 species were derived from four tree plots of 20–25 ha where all individuals ≥1 cm in stem diameter were mapped and identified taxonomically. Range sizes of these species across China were then estimated from over 460,000 geo-referenced records; a Bayesian approach was used, allowing careful measures of error of each range estimate. The log-transformed range sizes had a bell-shaped distribution with a median of 703,000 km², and >90% of 651 species had ranges >10⁵ km². There was no relationship between local abundance and range size, and no evidence for species being more abundant towards their range-centers. Finally, species’ abundances were positively correlated between sites. The widespread nature of most tree species in China suggests few are vulnerable to global extinction, and there is no indication of the double-peril that would result if rare species also had narrow ranges.     

Temporal Patterns of Species Accumulation in a Survey of Lepidoptera in a Beech-Maple Forest

One of the most significant challenges to insect conservation is lack of information concerning species diversity and distribution. Because a complete inventory of all species in an area is virtually impossible, interest has turned to developing statistical techniques to guide sampling design and to estimate total species richness within a site. We used two such techniques, diversity partitioning and non-parametric richness estimation, to determine how variation in sampling effort over time affected species accumulation for a survey of Lepidoptera in an old-growth beech-maple forest. Temporal scaling of sampling effort had significant effects on two measures of species diversity. Increases in species richness were primarily driven by changes in species occurrences with season, while Shannon diversity was largely determined at the scale of individual sampling units (i.e. by spatial effects). Variation in sampling effort affected the values of the two most widely regarded richness estimators (ICE and Chao 2); neither diversity estimator achieved stable values across a range of sampling efforts. Even after 52 trap-nights and accounting for seasonality, rare species (singletons and uniques) remained a significant component of the moth community. To the extent that moth communities in other forest systems are similarly comprised of many rare species, non-parametric richness estimators should be expected to yield variable estimates with increased effort and should only be used to provide a minimum benchmark for predicting the number of species remaining to be sampled. Our results suggest the best strategy for a short-term survey of forest Lepidoptera should emphasize spreading sampling intervals throughout a given year rather than focusing on intensive sampling during a short time period or prolonged sampling over many years.     

Diurnal Human Activity and Introduced Species Affect Occurrence of Carnivores in a Human-Dominated Landscape

Diurnal human activity and domestic dogs in agro-forestry mosaics should theoretically modify the diurnal habitat use patterns of native carnivores, with these effects being scale-dependent. We combined intensive camera trapping data with Bayesian occurrence probability models to evaluate both diurnal and nocturnal patterns of space use by carnivores in a mosaic of land-use types in southern Chile. A total of eight carnivores species were recorded, including human-introduced dogs. During the day the most frequently detected species were the culpeo fox and the cougar. Conversely, during the night, the kodkod and chilla fox were the most detected species. The best supported models showed that native carnivores responded differently to landscape attributes and dogs depending on both the time of day as well as the spatial scale of landscape attributes. The positive effect of native forest cover at 250m and 500 m radius buffers was stronger during the night for the Darwin''s fox and cougar. Road density at 250m scale negatively affected the diurnal occurrence of Darwin´s fox, whereas at 500m scale roads had a stronger negative effect on the diurnal occurrence of Darwin´s foxes and cougars. A positive effect of road density on dog occurrence was evidenced during both night and day. Patch size had a positive effect on cougar occurrence during night whereas it affected negatively the occurrence of culpeo foxes and skunks during day. Dog occurrence had a negative effect on Darwin''s fox occurrence during day-time and night-time, whereas its negative effect on the occurrence of cougar was evidenced only during day-time. Carnivore occurrences were not influenced by the proximity to a conservation area. Our results provided support for the hypothesis that diurnal changes to carnivore occurrence were associated with human and dog activity. Landscape planning in our study area should be focused in reducing both the levels of diurnal human activity in native forest remnants and the dispersion rates of dogs into these habitats.     

SDMdata: A Web-Based Software Tool for Collecting Species Occurrence Records

It is important to easily and efficiently obtain high quality species distribution data for predicting the potential distribution of species using species distribution models (SDMs). There is a need for a powerful software tool to automatically or semi-automatically assist in identifying and correcting errors. Here, we use Python to develop a web-based software tool (SDMdata) to easily collect occurrence data from the Global Biodiversity Information Facility (GBIF) and check species names and the accuracy of coordinates (latitude and longitude). It is an open source software (GNU Affero General Public License/AGPL licensed) allowing anyone to access and manipulate the source code. SDMdata is available online free of charge from <http://www.sdmserialsoftware.org/sdmdata/>.     

Occurrence of Sable (Martes zibellina,Carnivora, Mustelidae) beyond the Boundaries of the Species Range in the Middle Urals: Facts from 2014–2016

Biology Bulletin - Eleven sables were captured in Sverdlovsk oblast, at distances of 133 to 203 km from the southwestern boundary of the species range, in 2014–2016. The capture sites were...     

Home Range Size of Sympatric Squirrel Species Inhabiting a Lowland Dipterocarp Forest in Malaysia1

Home range sizes and spatial overlap of four sympatric squirrel species were investigated in a lowland dipterocarp forest in Malaysia using a radio‐tracking method. The population density of Callosciurus caniceps was highest and C. notatus was next highest, while C. nigrovittatus and Lariscus insignis were scarce. C. caniceps was larger than C. nigrovittatus and C. notatus while L. insignis was extremely small. For females, home range size was smaller in L. insignis than Callosciurus spp., which may support the body weight hypothesis: larger species have larger home ranges. Among the three Callosciurus species, female C. caniceps had the smallest home range. These differences were accounted for by habitat characteristics rather than by density or body weight; C. caniceps was dominant in bushy areas and used crowded small trees while C. notatus and C. nigrovittatus used large trees in the forest. In this study, home range size did not change seasonally; this differs from studies in temperate regions, possibly because food availability is much less variable among seasons in tropical rain forest. Home range overlap among heterospecific individuals was common but different species seemed to partition space by using different vertical levels of the forest. Consequently, the home range size and spatial overlap of sympatric squirrel species may be affected by habitat diversity in tropical rain forest.     

Some but not All Tetrahymena Species Destroy Monolayer Cultures of Cells from a Wide Range of Tissues and Species

The activities of Tetrahymena corlissi, Tetrahymena thermophila, and Tetrahymena canadensis were studied in coculture with cell lines of insects, fish, amphibians, and mammals. These ciliates remained viable regardless of the animal cell line partner. All three species could engulf animal cells in suspension. However, if the animal cells were monolayer cultures, the monolayers were obliterated by T. corlissi and T. thermophila. Both fibroblast and epithelial monolayers were destroyed but the destruction of human cell monolayers was done more effectively by T. thermophila. By contrast, T. canadensis was unable to destroy any monolayer. At 4 °C T. thermophila and T. corlissi did not carryout phagocytosis and did not destroy monolayers, whereas T. canadensis was able to carryout phagocytosis but still could not destroy monolayers. Therefore, monolayer destruction appeared to require phagocytosis, but by itself this was insufficient. In addition, the ciliates expressed a unique swimming behavior. Tetrahymena corlissi and T. thermophila swam vigorously and repeatedly into the monolayer, which seemed to loosen or dislodge cells, whereas T. canadensis swam above the monolayer. Therefore, differences in swimming behavior might explain why T. corlissi has been reported to be a pathogen but T. canadensis has not.     

Non-radioactive in situ Hybridization Protocol Applicable for Norway Spruce and a Range of Plant Species

The high-throughput expression analysis technologies available today give scientists an overflow of expression profiles but their resolution in terms of tissue specific expression is limited because of problems in dissecting individual tissues. Expression data needs to be confirmed and complemented with expression patterns using e.g. in situ hybridization, a technique used to localize cell specific mRNA expression. The in situ hybridization method is laborious, time-consuming and often requires extensive optimization depending on species and tissue. In situ experiments are relatively more difficult to perform in woody species such as the conifer Norway spruce (Picea abies). Here we present a modified DIG in situ hybridization protocol, which is fast and applicable on a wide range of plant species including P. abies. With just a few adjustments, including altered RNase treatment and proteinase K concentration, we could use the protocol to study tissue specific expression of homologous genes in male reproductive organs of one gymnosperm and two angiosperm species; P. abies, Arabidopsis thaliana and Brassica napus. The protocol worked equally well for the species and genes studied. AtAP3 and BnAP3 were observed in second and third whorl floral organs in A. thaliana and B. napus and DAL13 in microsporophylls of male cones from P. abies. For P. abies the proteinase K concentration, used to permeablize the tissues, had to be increased to 3 g/ml instead of 1 g/ml, possibly due to more compact tissues and higher levels of phenolics and polysaccharides. For all species the RNase treatment was removed due to reduced signal strength without a corresponding increase in specificity. By comparing tissue specific expression patterns of homologous genes from both flowering plants and a coniferous tree we demonstrate that the DIG in situ protocol presented here, with only minute adjustments, can be applied to a wide range of plant species. Hence, the protocol avoids both extensive species specific optimization and the laborious use of radioactively labeled probes in favor of DIG labeled probes. We have chosen to illustrate the technically demanding steps of the protocol in our film.Anna Karlgren and Jenny Carlsson contributed equally to this study.Corresponding authors: Anna Karlgren at Anna.Karlgren@ebc.uu.se and Jens F. Sundström at Jens.Sundstrom@vbsg.slu.se     

Climate-Induced Elevational Range Shifts and Increase in Plant Species Richness in a Himalayan Biodiversity Epicentre

Global average temperature increase during the last century has induced species geographic range shifts and extinctions. Montane floras, in particular, are highly sensitive to climate change and mountains serve as suitable observation sites for tracing climate-induced biological response. The Himalaya constitute an important global biodiversity hotspot, yet studies on species’ response to climate change from this region are lacking. Here we use historical (1849–50) and the recent (2007–2010) data on temperature and endemic species’ elevational ranges to perform a correlative study in the two alpine valleys of Sikkim. We show that the ongoing warming in the alpine Sikkim Himalaya has transformed the plant assemblages. This study lends support to the hypothesis that changing climate is causing species distribution changes. We provide first evidence of warmer winters in the region compared to the last two centuries, with mean temperatures of the warmest and the coldest months may have increased by 0.76±0.25°C and 3.65±2°C, respectively. Warming-driven geographical range shifts were recorded in 87% of 124 endemic plant species studied in the region; upper range extensions of species have resulted in increased species richness in the upper alpine zone, compared to the 19^th century. We recorded a shift of 23–998 m in species’ upper elevation limit and a mean upward displacement rate of 27.53±22.04 m/decade in the present study. We infer that the present-day plant assemblages and community structure in the Himalaya is substantially different from the last century and is, therefore, in a state of flux under the impact of warming. The continued trend of warming is likely to result in ongoing elevational range contractions and eventually, species extinctions, particularly at mountaintops.