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.     

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     

Lectin binding sites in the vitelline envelope of Bufo arenarum oocytes: Role in fertilization

Incubation of dejellied spawned oocytes from Bufo arenarum with different lectins results in a decrease of oocyte fertility. Concanavalin A was the most effective lectin; phytohem-agglutinin P and wheat germ lectin were less effective. Agglutinin from soybean was scarcely active. These lectin effects could be ascribed to a hindering of specific sites for some proteases, since the same treatment renders the oocyte vitelline envelope insensitive to spermatolysin (an essential requisite for fertilization) and to trypsin. Also in this case concanavalin A was the most effective lectin. Univalent concanavalin A was also effective in blocking the fertility of dejellied oocytes. These results indicate that the residues of α-D-glucose and α-D-mannose present in the vitelline envelope are involved in gamete interactions in Bufo arenarum. This idea is also supported by the finding that dejellied oocytes (fertilizables) have a number of binding sites for concanavalin A that is three or four orders of magnitude higher than coelomic or fertilized oocytes (both not penetrable by spermatozoa).     

Influence of wetland hydroperiod on diversity and abundance of metamorphosing juvenile amphibians

Numbers of successfully metamorphosing juvenile amphibians were tabulated at three wetlands in South Carolina, U.S.A. using terrestrial drift fences with pitfall traps. A relatively undisturbed Carolina bay was studied for eight years, a partially drained Carolina bay for four years, and a man-made borrow pit for three years. Annual production of juveniles at the undisturbed Carolina bay ranged from zero to 75,644 individuals of 15 species. Fewer individuals of fewer species typically metamorphosed at the borrow pit than at the undisturbed bay, with the least numbers at the partially drained Carolina bay. Both total number and species diversity of metamorphosing juveniles at each site each year showed a strong positive correlation with hydroperiod, i.e., the number of days a site contained standing water that year. Data for one common anuran species and the most common salamander species were analyzed separately by multiple regression, in addition to the community analyses. For the mole salamander, Ambystoma talpoideum, hydroperiod was a significant predictor of the number of metamorphosing juveniles, but the number of breeding females was not. For the ornate chorus frog, Pseudacris ornata, the number of breeding females was a significant predictor of the number of metamorphosing juveniles, but hydroperiod was not. Variation in the dates of wetland filling and drying interacts with other factors to determine amphibian community structure and diversity. Either increasing or decreasing the number of days a wetland holds water could increase or decrease the number and species diversity of amphibians in and around a wetland.     

Carryover effects from environmental change in early life: An overlooked driver of the amphibian extinction crisis?

Ecological carryover effects, or delayed effects of the environment on an organism's phenotype, are central predictors of individual fitness and a key issue in conservation biology. Climate change imposes increasingly variable environmental conditions that may be challenging to early life-history stages in animals with complex life histories, leading to detrimental physiological and fitness effects in later life. Yet, the latent nature of carryover effects, combined with the long temporal scales over which they can manifest, means that this phenomenon remains understudied and is often overlooked in short-term studies limited to single life-history stages. Herein, we review evidence for the physiological carryover effects induced by elevated ultraviolet radiation (UVR; 280–400 nm) as a potential contributor to recent amphibian population declines. UVR exposure causes a suite of molecular, cellular and physiological consequences known to underpin carryover effects in other taxa, but there is a lack of research linking embryonic and larval UVR exposures to fitness consequences post-metamorphosis in amphibians. We propose that the key impacts of UVR on disease-related amphibian declines are facilitated through carryover effects that bridge embryonic and larval UVR exposure with potential increased disease susceptibility post-metamorphosis. We conclude by identifying a practical direction for the study of ecological carryover effects in amphibians that could guide future ecological research in the broader field of conservation physiology. Only by addressing carryover effects can many of the mechanistic links between environmental change and population declines be elucidated.     

Environmental influences on local amphibian diversity: the role of floods on river basins

We tested two hypotheses about boundary units and seven about environmental control of species diversity in order to explain geographical trends in the richness of amphibian species in the Mediterranean watershed of the southern coast of the Iberian Peninsula. The number of amphibian species tends to decrease from west to east. The longitudinal trend in the richness of amphibian species actually occurs on passing from one basin to another, but there is not any longitudinal trend within the basins. Multivariate analyses confirmed that the disturbances of episodic river-basin floodings were the principal factor which controls the richness of amphibian species. They explained 94.8% of the observed variations in the richness of amphibian species in this area, according to the intermediate disturbance hypothesis.We propose hydrographic basins as suitable geographical units for further biogeographical analysis and for considering the role of disturbances produced by floods in the environmental control of species diversity.     

Immunoneutralization of insulin partially modifies dorsoventral patterning in developing frog embryos

Determination of anteroposterior and dorsoventral axes is an important early event in the development of vertebrates involving extensive cellular interactions including inductive events. Recently we showed that insulin plays an essential role in prepancreatic development of the frogMicrohyla ornata. In the present study we have investigated the effects of immunoneutralization of endogenous insulin on the process of pattern formation. Treatment of neurulating embryos with antiserum to insulin caused abnormal pattern formation. The defects included loss of normal architecture of the neural tube, reduction in the size of the neural tube and, most conspicuously, rotation of the dorsoventral axis of the neural tube, notochord and adjoining mesodermal elements. The effects could be alleviated partially by pretreatment of embryos with exogenous insulin. This supports our belief that insulin plays an important role in induction and pattern formation of the amphibian nervous system. In addition, using 2-deoxy-α-D-glucose, an inhibitor of glucose metabolism, it is shown that the stimulatory effects of exogenous insulin on developing frog embryos are, at least partially, through the glucose metabolism pathway. Preliminary results of this study were presented at the National Symposium on Genes and Human Environment, held at Hyderabad, February 1994 and DAE Symposium on Stress and Adaptive Responses in Biological Systems, held at Vadodara, March 1994.     

Miniature Ag−AgCl electrode for voltage clamping of theAmbystoma collecting duct

Summary We have developed a miniature silver-silver chloride electrode. The outer diameter of the electrodes averaged 22 m and the input resistance 8.8 k. Since the core of the electrode is a glass fiber, the problem of the extreme malleability of a small diameter silver fiber is circumvented. The properties of the electrode permit us to insert it into short (600 m) fragments of the amphibian collecting duct while they are being perfusedin vitro. The passage of currents in the range of 0 to 6×10^–8 amperes allowed us to voltage clamp the nephron fragment between +20 and –20 mV. The current-voltage plots are linear over this range. Two lines of evidence suggest that the voltage clamp is homogeneous. First, the voltage measured at the perfusion end during a voltage-clamp experiment of the tubule is not significantly different from that measured at the collecting end. Secondly, the specific resistance of collecting ducts estimated from the core conductor analysis is 3.3±0.8×10⁴ cm, a value not significantly different from that computed from the current-voltage plots as determined with the Ag–AgCl electrode, 3.0±0.5×10⁴ cm. This method permits precise control of both the ionic and electrical gradients across fragments of the amphibian collecting duct.     

Spatial variation in breeding phenology at small spatial scales: A stochastic effect of population size

Spatial variation in phenology can occur at small spatial scales over which individuals can disperse or forage within one generation. Previous studies have assumed that variations in phenological peaks are caused by differences in abiotic environmental characteristics. However, environments should generally be similar among local habitats over small spatial scales. When the local population size is small, the phenological peak of the local population should be strongly affected by the variation in timing expressed by individuals. If a regional population consists of small local subpopulations (e.g., a metapopulation), the stochastic processes regulated by population sizes may explain the spatial variation in phenology. In this study, we quantitatively evaluated the extent of the spatial and annual variations in the breeding phenology of the forest green tree frog, Rhacophorus arboreus habiting a small area (<10 km²). The spatial variation in phenological peaks among 25 breeding sites was large over 6 years. This spatial variation was not explained by differences in air temperature or water depth. Randomization tests revealed that a large portion of the spatial variation could be explained by differences in population size, without considering site-specific factors. Annual variations in phenological peaks tended to be greater for smaller populations. These results imply that the stochastic process might have caused the spatial and annual variations in the phenological peaks of R. arboreus observed in the study region. Understanding spatiotemporal variation in phenology determined by stochastic process would be important to better predict interspecific interactions and (meta)population dynamics at small spatial scales.