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.     

From oocyte maturation to the in vitro cell cycle: the history of discoveries of Maturation-Promoting Factor (MPF) and Cytostatic Factor (CSF)

This article briefly reviews the classical cell cycle studies using oocytes and zygotes of mainly amphibians in the past century. The discussions are focused on the investigations into the cytoplasmic factors that regulate meiosis during oocyte maturation and the initiation of mitosis during fertilisation, which were carried out in the author's lab between 1967 and 1987. This chronicle traces the development of the problems and the direction in which their solutions were attempted in the course of these investigations. The author tries to answer the following questions: why he decided to study oocyte maturation, how he discovered progesterone as a maturation-inducing hormone, how he discovered and characterised the cytoplasmic regulators of the cell cycle, Maturation-Promoting Factor (MPF) and Cyto-Static Factor (CSF), and how he invented the method of observing cell cycle processes in a cytoplasmic extract in vitro.     

Ecology and biogeography of plant communities associated with the post Plio-Pleistocene relict Rhododendron ponticum subsp. baeticum in southern Spain

Aims Rhododendron ponticum L. is reputed to be a post Plio‐Pleistocene relict plant species with a disjunct distribution that comprises the Iberian Peninsula to the west and the Euxinian region plus some restricted Mediterranean areas to the east. We analysed the ecological range (of subsp. baeticum) in the western area (Aljibe Mountains, north of the Strait of Gibraltar) to understand the factors determining the present area limitation. Location Sierra del Aljibe, north of the Strait of Gibraltar (Iberian Peninsula). Methods We selected 20 riparian sites where R. ponticum is common, and compiled data on the ecological diversity of associated woody species and ferns. We established a 500‐m main transect in each site, along the stream or river course, in which we placed five 20‐m‐long plots at regular intervals. We recorded physiographic habitat features, woody plants and fern abundance, and the number of R. ponticum individuals. Results Rhododendron ponticum in southern Spain is restricted to riparian forests in acidic soils (pH 4.0–6.4), and is mainly found on the banks of inclined and enclosed streams. In our inventory we recorded 59 woody taxa and 12 ferns, with R. ponticum being the dominant species of the understorey (mean abundance 78.6%). The communities are characterized by a high incidence of the humid warm temperate element, both in number of species (18.8 ± 3.7 per site) and abundance; meanwhile, the presence of the modern Mediterranean element (mean number of species 3.4 ± 3.8 per site) appears to be favoured by disturbance. These ecological–historical groups of taxa also show distinct patterns of typological habit, frequency of endemism, infrageneric diversity and geographical range. Populations of R. ponticum are characterized by a very variable density of seedlings in many sites, and the virtual lack of juveniles. Main conclusions Riparian forests of the Aljibe Mountains constitute a refuge for R. ponticum where the species persists, but populations appear to be in decline. The narrow ecological range of R. ponticum in the area strongly contrasts with its wide amplitude in the eastern natural area, mainly the Euxinian region, where R. ponticum probably finds better conditions due to the environmental heterogeneity of the region, and the lack of a hot dry season.     

Seasonal changes in the pigments, carbohydrates and growth of red spruce as affected by ozone

Two-year-old red spruce seedlings were exposed to various levels ot ozone, from 0.4 to 3 times ambient levels, in open-top chambers in Ithaca, NY, USA. Exposures, which varied with changes in day length, commenced on May 30, 1987 and continued until December 14, 1987. Seedling biomass, carbohydrate contents, pigment contents, and rate of electron transport were assessed twice monthly during the fumigation period. Orthogonal quadratic or cubic polynomials were used to model the response through time each variable measured. A one-way analysis of variance model was fitted to every regression coefficient in each polynomial model to test for ozone effects on seasonal physiological patterns. Ozone did not influence growth, foliar pigment content, foliar starch content, root carbohydrate content, or rate of electron transport. The seasonal change of needle raffinose content differed between exposed to low (0.4 ×, 1×) and high (2×, 3×) ozone levels. There was also a trend towards reduced total soluble sugar content foliage during late autumn in higher ozone treatments.     

Effects of N-immissions on nutrient status and vitality ofPinus sylvestris near a hen-house

Near a hen house (50–600 m), vitality ofPinus sylvestris, N-, P-, K-, Ca-, Mg-contents of the needles, N-, Mg-, K-, Ca- and Al-contents in soil extracts and NH₃/NH ₄ ⁺ -contents of the air were determined. Damage symptoms occurred when N-immissions hit the canopy directly. In contrast no visible decline of the above ground plant could be observed if N was mainly deposited on the soil.     

An empirical analysis of the factors contributing to 20-year decrease in soil pH in an old-field plantation of loblolly pine

The pH of weak-acid solutions is controlled by acid concentration (HA + A^–), the degree of acid dissociation (A^–/HA), and the strength of the acids present (pK_a). We developed an empirical approach that allows the relative importance of each of these factors to be estimated for soils. This empirical model was applied to soils collected from an old-field plantation of loblolly pine (Pinus taeda L.) at 5 and 25 years of age. During this period, soil pH dropped by 0.3 to 0.8 units, and extractable calcium, magnesium and potassium declined by 20 to 80%. The empirical model indicates that the decline in pH resulted largely from the reduction in base saturation of the exchange complex. However, the average acid strength of the exchange complex decreased during the 20 years, preventing a greater decline of perhaps 0.1 to 0.2 units in the observed pH. The rate of decrease in the acid neutralizing capacity to pH 3.5 was about 1.3 kmol_c/ha annually, while the increase in base neutralizing capacity was about 2.7 and 1.6 kmol_c/ha annually to pH 5.5 and 8.2, respectively. Extractable alkali and alkaline earth cations declined by about 2.2 kmol_c/ha annually, matched by the rate of increase in aluminium. These changes demonstrated the dynamic nature of poorly buffered soils, and indicated that changes in soil acidity may be expected over a period of decades (especially following changes in land-use).     

Forest-level analysis of stability under exploitation: depensation responses and catastrophe theory

Stability analysis of whole forests is proposed as a qualitative tool for the study of forest responses to partial or patchy harvests or mortality. Instead of modeling every tree or stand, aggregate tree biomass is modeled. In order to aggregate stands, spatial effects must be incorporated. It is shown that depensation growth responses (reduced growth at low biomass) are common because forests often modify harch environments to be more suitable for their growth. Depensation can result from thinning, partial mortality, patchy cutting, or clearcutting, depending on forest type and abiotic factors. Examples of these types of behaviors are given. Stability analysis of different growth regimes under exploitation are related to catastrophe theory and to optimal harvesting policies. Such qualitative analysis is shown to be applicable to data-poor regions such as the tropics where there is great concern over responses of forests to exploitation.     

Distribution of catecholaminergic and serotoninergic systems in forebrain and midbrain of the newt,Triturus alpestris (Urodela)

Summary Mapping of monoaminergic systems in the brain of the newt Triturus alpestris was achieved with antisera against (1) thyrosine hydroxylase (TH), (2) formaldehyde-conjugated dopamine (DA), and (3) formaldehyde-conjugated serotonin (5-HT). In the telencephalon, the striatum was densely innervated by a large number of 5-HT-, DA-and TH-immunoreactive (IR) fibers; IR fibers were more scattered in the amygdala, the medial and lateral forebrain bundles, and the anterior commissure. In the anterior and medial diencephalon, TH-IR perikarya contacting the cerebrospinal fluid (CSF-C perikarya) were located in the preoptic recess organ (PRO), the organum vasculosum laminae terminalis and the suprachiasmatic nucleus. Numerous TH-IR perikarya, not contacting the CSF, were present in the posterior preoptic nucleus and the ventral thalamus. At this level, DA-IR CSF-C neurons were only located in the PRO. In the posterior diencephalon, large populations of 5-HT-IR and DA-IR CSF-C perikarya were found in the paraventricular organ (PVO) and the nucleus infundibularis dorsalis (NID); the dorsal part of the NID additionally presented TH-IR CSF-C perikarya. Most regions of the diencephalon showed an intense monoaminergic innervation. In addition, numerous TH-IR, DA-IR and 5-HT-IR fibers, orginating from the anterior and posterior hypothalamic nuclei, extended ventrally and reached the median eminence and the pars intermedia of the pituitary gland. In the midbrain, TH-IR perikarya were located dorsally in the pretectal area. Ventrally, a large group of TH-IR cell bodies and some weakly stained DA-IR and 5-HT-IR neurons were observed in the posterior tuberculum. No dopaminergic system equivalent to the substantia nigra was revealed. The possible significance of the differences in the distribution of TH-IR and DA-IR neurons is discussed, with special reference to the CSF-C neurons.Abbreviations AM amygdala - CAnt commissura anterior - CH commissura hippocampi - CP commissura posterior - Ctm commissura tecti mesencephali - DH dorsal hypothalamus - DTh dorsal thalamus - FLM fasciculus longitudinalis medialis - Fsol fasciculus solitarius - H habenula - LFB lateral forebrain bundle - ME median eminence - MFB medial forebrain bundle - NID nucleus infundibularis dorsalis - nIP neuropil of nucleus interpeduncularis - NPOP nucleus preopticus posterior - NS nucleus septi - OVLT organum vasculosum laminae terminalis - PD pars distalis - Pdo dorsal pallium - PHi primordium hippocampi - PI pars intermedia - Pl lateral pallium - PN pars nervosa - PRO preoptic recess organ - Ptec pretectal area - PVO paraventricular organ - Ra nucleus raphe - Rm nucleus reticularis medius - SCO subcommisural organ - ST striatum; strm stria medullaris thalami - strt stria terminalis thalami - TM tegmentum mesencephali - TO tectum opticum - TP tuberculum posterius - trch tractus cortico-habenularis - trmp tractus mamillopeduncularis - VH ventral hypothalamus - Vm nucleus motorius nervi trigemini - VTh ventral thalamus - II optic nerve     

Carbon and nitrogen isotope ratios in different compartments of a healthy and a declining Picea abies forest in the Fichtelgebirge,NE Bavaria

Summary Natural carbon and nitrogen isotope ratios were measured in different compartments (needles and twigs of different ages and crown positions, litter, understorey vegetation, roots and soils of different horizons) on 5 plots of a healthy and on 8 plots of a declining Norway spruce (Picea abies (L.) Karst.) forest in the Fichtelgebirge (NE Bavaria, Germany), which has recently been described in detail (Oren et al. 1988a; Schulze et al. 1989). The ¹³C values of needles did not differ between sites or change consistently with needle age, but did decrease from the sun-to the shade-crown. This result confirms earlier conclusions from gas exchange measurements that gaseous air pollutants did no long-lasting damage in an area where such damage was expected. Twigs (¹³C between-25.3 and-27.8) were significantly less depleted in ¹³C than needles (¹³C between-27.3 and-29.1), and ¹³C in twigs increased consistently with age. The ¹⁵N values of needles ranged between-2.5 and-4.1 and varied according to stand and age. In young needles ¹⁵N decreased with needle age, but remained constant or increased in needles that were 2 or 3 years old. Needles from the healthy site were more depleted in ¹⁵N than those from the declining site. The difference between sites was greater in old needles than in young ones. This differentiation presumably reflects an earlier onset of nitrogen reallocation in needles of the declining stand. ¹⁵N values in twigs were more negative than in needles (-3.5 to-5.2) and showed age- and stand-dependent trends that were similar to the needles. ¹⁵N values of roots and soil samples increased at both stands with soil depth from-3.5 in the organic layer to +4 in the mineral soil. The ¹⁵N values of roots from the mineral soil were different from those of twigs and needles. Roots from the shallower organic layer had values similar to twigs and needles. Thus, the bulk of the assimilated nitrogen was presumably taken up by the roots from the organic layer. The problem of separation of ammonium or nitrate use by roots from different soil horizons is discussed.