Occupancy in dynamic systems: accounting for multiple scales and false positives using environmental DNA to inform monitoring

Occupancy is an important metric to understand current and future trends in populations that have declined globally. In addition, occupancy can be an efficient tool for conducting landscape-scale and long-term monitoring. A challenge for occupancy monitoring programs is to determine the appropriate spatial scale of analysis and to obtain precise occupancy estimates for elusive species. We used a multi-scale occupancy model to assess occupancy of Columbia spotted frogs in the Great Basin, USA, based on environmental DNA (eDNA) detections. We collected three replicate eDNA samples at 220 sites across the Great Basin. We estimated and modeled ecological factors that described watershed and site occupancy at multiple spatial scales simultaneously while accounting for imperfect detection. Additionally, we conducted visual and dipnet surveys at all sites and used our paired detections to estimate the probability of a false positive detection for our eDNA sampling. We applied the estimated false positive rate to our multi-scale occupancy dataset and assessed changes in model selection. We had higher naïve occupancy estimates for eDNA (0.37) than for traditional survey methods (0.20). We estimated our false positive detection rate per qPCR replicate at 0.023 (95% CI: 0.016–0.033). When the false positive rate was applied to the multi-scale dataset, we did not observe substantial changes in model selection or parameter estimates. Conservation and resource managers have an increasing need to understand species occupancy in highly variable landscapes where the spatial distribution of habitat changes significantly over time due to climate change and human impact. A multi-scale occupancy approach can be used to obtain regional occupancy estimates that can account for spatially dynamic differences in availability over time, especially when assessing potential declines. Additionally, this study demonstrates how eDNA can be used as an effective tool for improved occupancy estimates across broad geographic scales for long-term monitoring.     

Present and future needs for algae and algal products

A review of the present needs, mainly for production of phycocolloids and food condiments, is given. Supply and demand vary from balanced, in some, to disproportionate in other fields. World-wide shortage of agarophytes contrasts with huge, unexploited beds of brown seaweeds.In future, partly conflicting trends will decide the needs for algae and algal products. Growth in the human population, pollution, overexploitation of land and lack of freshwater will encourage use of seaweeds. Modern biotechnology will favour this development, but will also be a serious threat to industrial exploitation of seaweeds. Future uses of marine algae will be decisively influenced by the effort put into and the results coming out of seaweed research.     

Distribution of Fusarium wilt of Bambara nut (Vigna subterranea (L.) Verdc.) in farmers’ fields’ of Busia County in Western Kenya and its management using farmyard manure

A study was carried out to determine Fusarium wilt distribution in Bambara nut farmers’ fields and its management using farm yard manure (FYM). Four villages in Busia County were purposively sampled for the study. The data generated were subjected to analysis of variance and treatment means separated by least significant difference test. Fusarium wilt incidence in the fields ranged from 14.63 to 43.56%. In the greenhouse, FYM reduced the disease incidence by 10.2% and severity by 9.5% on the black landrace and 1.9 and 12.8%, respectively, on the red landrace. In the field, FYM reduced disease incidence by 9.1% and severity by 6.9% on the black landrace and 10.4 and 10.4%, respectively, on the red landrace. Farm yard manure had the lowest area under disease progress curve irrespective of the landrace. The study confirmed the presence of the pathogen in the fields and the ability to manage the disease using FYM.     

Ants adjust their pheromone deposition to a changing environment and their probability of making errors

Animals must contend with an ever-changing environment. Social animals, especially eusocial insects such as ants and bees, rely heavily on communication for their success. However, in a changing environment, communicated information can become rapidly outdated. This is a particular problem for pheromone trail using ants, as once deposited pheromones cannot be removed. Here, we study the response of ant foragers to an environmental change. Ants were trained to one feeder location, and the feeder was then moved to a different location. We found that ants responded to an environmental change by strongly upregulating pheromone deposition immediately after experiencing the change. This may help maintain the colony''s foraging flexibility, and allow multiple food locations to be exploited simultaneously. Our treatment also caused uncertainty in the foragers, by making their memories less reliable. Ants which had made an error but eventually found the food source upregulated pheromone deposition when returning to the nest. Intriguingly, ants on their way towards the food source downregulated pheromone deposition if they were going to make an error. This may suggest that individual ants can measure the reliability of their own memories and respond appropriately.     

EVOLUTION AND EXTINCTION IN A CHANGING ENVIRONMENT: A QUANTITATIVE-GENETIC ANALYSIS

Because of the ubiquity of genetic variation for quantitative traits, virtually all populations have some capacity to respond evolutionarily to selective challenges. However, natural selection imposes demographic costs on a population, and if these costs are sufficiently large, the likelihood of extinction will be high. We consider how the mean time to extinction depends on selective pressures (rate and stochasticity of environmental change, and strength of selection), population parameters (carrying capacity, and reproductive capacity), and genetics (rate of polygenic mutation). We assume that in a randomly mating, finite population subject to density-dependent population growth, individual fitness is determined by a single quantitative-genetic character under Gaussian stabilizing selection with the optimum phenotype exhibiting directional change, or random fluctuations, or both. The quantitative trait is determined by a finite number of freely recombining, mutationally equivalent, additive loci. The dynamics of evolution and extinction are investigated, assuming that the population is initially under mutation-selection-drift balance. Under this model, in a directionally changing environment, the mean phenotype lags behind the optimum, but on the average evolves parallel to it. The magnitude of the lag determines the vulnerability to extinction. In finite populations, stochastic variation in the genetic variance can be quite pronounced, and bottlenecks in the genetic variance temporarily can impair the population's adaptive capacity enough to cause extinction when it would otherwise be unlikely in an effectively infinite population. We find that maximum sustainable rates of evolution or, equivalently, critical rates of environmental change, may be considerably less than 10% of a phenotypic standard deviation per generation.     

Scale-dependent interactions between intrinsic and extrinsic processes reduce variability in protist populations

Interactions between intrinsic processes and extrinsic fluctuations can positively impact population persistence in ways often not predicted by classic ecological models. These interactions only arise when the intrinsic and extrinsic processes operate on the proper relative scales in time or space. Both metapopulation theory and resonance/attenuation theory suggest that interactions which lower population variability will occur when the intrinsic and extrinsic process occur on similar time scales. I performed an aquatic protist microcosm experiment to investigate how the relative frequencies of extrinsic density perturbations and intrinsic resource pulses impacted population variability. Population variability was lowest in the treatments of intermediate frequency, in which the extrinsic fluctuations and intrinsic processes were on the same time scale. This result is consistent with general theoretical predictions, and empirically documents the importance of considering scale in interactions between intrinsic and extrinsic processes that positively impact population persistence.     

Environmental factors influencing the vertical migration of planktonic rotifers in a hypereutrophic tarn

The diel vertical migration of planktonic rotifers in a small, hypereutrophic tarn was investigated on four occasions in 1983. When the tarn was isothermal the rotifers were distributed throughout the water column. After stratification, the rotifers were confined to the top 1–2 m of oxygenated water. On all four dates the rotifers were aggregated at specific depths in the water column. On some occasions, the pattern of aggregation changed as the animals performed distinct diurnal migrations. Keratella cochlearis, K. quadrata and Polyarthra vulgaris usually followed the reverse migrations of the phytoplankton. In contrast, the movements of Anuraeopsis fissa were less pronounced and were associated with variations in the depth of the oxycline.     

Environmental factors influencing the occurrence of juvenile fish in the mangroves of Pagbilao,Philippines

128 fish species belonging to 54 families were collected from the mangroves of Pagbilao. Ambassis kopsi (Ambassidae) was the most abundant species.Fourteen environmental factors were correlated to the catch per unit time for some species. The occurrence of A. kopsi was positively correlated to nitrate in the water, carbon in the sediments and litter fall. Out of the 8 species investigated, 6 were positively correlated to litter fall. Three species showed positive correlation to phosphate in the water, two to organic carbon in the sediments, nitrate, silicate and pH, and one to salinity and carotenoids in water. The biomass of the total catch was correlated to carbon in the sediments and litter fall.     

Effect of short-and long-term exposure to low environmental temperature on brain regional GABA metabolism

Single exposure of adult male rats to low environmental temperature (LET, 12 ± 0.5°C) for 2 h significantly increased the hypothalamic and striatal GABA levels without affecting those in other regions of brain. The activity of glutamate decarboxylase (GAD) was elevated in hypothalamus (H) and corpus striatum (CS) under these conditions. GABA accumulation rate (measured with ethanolamine-O-sulfate, an inhibitor of GABA-transaminase) was also increased in both H and CS of rats exposed to LET for 2 h. Unlike after a single exposure, the repeated exposure (2 h/day) for 7, 15, and 30 onsecutive days did not change the hypothalamic GABA metabolism. No change in GABA metabolism was observed in CS when rats were repeatedly exposed to LET for 7 consecutive days. Prolongation of repeated exposure to LET (2 h/day) for 15 and 30 consecutive days decreased the striatal GABA level and increased the activity of GABA-transaminase, although GAD activity was not altered under these conditions. These results suggest that single exposure to LET accelerates GABA synthesis and may reduce the GABAergic activity in both H and CS; whereas repeated exposure to LET for 15 or 30 consecutive days enhances GABAergic activity with the stimulation of GABA utilization only in CS without affecting its synthesizing process. Thus, it may be suggested that the hypothalamic and striatal GABA system may play a characteristic role in response to short-and long-term exposure to LET.