Biology subjects

Jaric, I.

Publications and source records attributed to Jaric, I..

14 recordsLinked to original sources

bioRxiv2024

Hungry catfish - effect of prey availability on movement dynamics of a top predator

O_LIThe availability and spatial distribution of prey determines the energetic costs of predators foraging and largely drives their space use, activity level and foraging timing. Consequently, predators in ecosystems with different prey availability and distribution should adjust their movement patterns to optimise their foraging success in order to maximise efficiency. C_LIO_LIThe aim of this study was to investigate the ability of a top predator, European catfish (Silurus glanis), to adapt its space use, temporal activity and diet patterns in environments with varying prey density and distribution, and to examine the consequences for the catfishs body growth. C_LIO_LICatfish activity, tracked with high-resolution acoustic telemetry positioning systems deployed in two oligotrophic lakes with limited fish prey and one eutrophic reservoir with abundant fish prey, showed clear differences in their spatial and foraging behaviour. In oligotrophic, prey-poor lakes, catfish showed larger space use, altered diurnal activity patterns, reduced use of the open water, increased variability in inter- and intra-individual space use and had a more diverse diet compared to their conspecifics in the eutrophic, prey-rich reservoir. However, despite these behavioural alterations the reduced food availability in prey-poor lakes ultimately led to a reduced catfish growth, as these behavioural changes could not fully compensate for the lower prey fish abundance. C_LIO_LIThe study showed that top predators can combine different behavioural mechanisms and individual strategies to adapt to different ecological contexts. The observed ability of catfish to optimize activity, space use and diet highlights the evolutionary need to maximise foraging efficiency and overall fitness in different habitats, giving catfish a significant competitive advantage. Such competitive abilities are prerequisites for the actual catfish success as an invasive species within a Europe. C_LI

ecology↗

bioRxiv2023

Predicting the timing of ecological phenomena across regions using citizen science data

Spatial predictions of intra-annual ecological variation enhance ecological understanding and inform decision-making. Unfortunately, it is often challenging to use statistical or machine learning techniques to make such predictions, due to the scarcity of systematic, long-term observational data. Conversely, opportunistic time-stamped observation records, supported by highly informative data such as photographs, are increasingly available for diverse ecological phenomena in many regions. However, a general framework for predicting such phenomena using opportunistic data remains elusive. Here, we introduce a novel framework that leverages the concept of relative phenological niche to model observation records as a sample of temporal environmental conditions in which the represented ecological phenomenon occurs. We demonstrate its application using two distinct, management-relevant, ecological events: the emergence of the adult stage of the invasive Japanese beetle (Popillia japonica), and of fruiting bodies of the winter chanterelle mushroom (Craterellus tubaeformis). The framework accounts for spatial and temporal biases in observation data, and it contrasts the temporal environmental conditions (e.g., in temperature, precipitation, wind speed, etc.) associated with the observation of these events to those available in their occurrence locations. To discriminate between the two sets of conditions, we employ machine-learning algorithms (boosted regression trees and random forests). The proposed approach can accurately predict the temporal dynamics of ecological events across large geographical scales. Specifically, it successfully predicted the intra-annual timing of occurrence of adult Japanese beetles and of winter chanterelle mushrooms across Europe and North America. We further validate the approach by successfully predicting the timing of occurrence of adult Japanese beetles in Northern Italy, a recent hotspot of invasion in continental Europe, and the winter chanterelle mushroom in Denmark, a country with a high number of records of this mushroom. These results were also largely insensitive to temporal bias in recording effort. Our results highlight the potential of opportunistic observation data to predict the temporal variation of a wide range of ecological phenomena in near real-time. Furthermore, the conceptual and methodological framework is intuitive and easily applicable for the large number of ecologists already using machine-learning and statistical-based predictive approaches.

ecology↗

bioRxiv2023

Early-life stress and ovarian hormones alter transcriptional regulation in the nucleus accumbens resulting in sex-specific responses to cocaine

Early-life stress and ovarian hormones contribute to increased female vulnerability to cocaine addiction. Here we reveal molecular substrates in the key reward area, the nucleus accumbens, through which these female-specific factors affect immediate and conditioning responses to cocaine in mice. We find shared involvement of X chromosome and estrogen signaling gene regulation in enhanced conditioning responses seen after early-life stress and during the low-estrogenic state in females. During the low-estrogenic state, females respond to acute cocaine exposure by increasing the accessibility of neuronal chromatin enriched for the binding sites of {Delta}FosB, a transcription factor implicated in chronic cocaine response and addiction. Conversely, high-estrogenic females respond to cocaine by preferential closing of neuronal chromatin, providing a mechanism for limiting cocaine-driven chromatin and synaptic plasticity. We find that physiological estrogen withdrawal, exposure to early-life stress, and absence of the second X chromosome all nullify the protective effect of high-estrogenic state on cocaine conditioning in females. Our findings offer a molecular framework to understand sex-specific neuronal mechanisms underlying cocaine use disorder.

neuroscience↗

bioRxiv2022

Rearing environment persistently modulates the phenotype of mice

The phenotype of an organism results from its genotype and the influence of the environment throughout development. Even when using animals of the same genotype, independent studies may test animals of different phenotypes, resulting in poor replicability due to genotype-by-environment interactions 1-4. Thus, genetically defined strains of mice may respond differently to experimental treatments depending on their rearing environment 5. However, the extent of such phenotypic plasticity and its implications for the replicability of research findings have remained unknown. Here, we examined the extent to which common environmental differences between rearing facilities modulate the phenotype of genetically homogeneous (inbred) mice. We conducted a comprehensive multi-center study, where inbred mice from the same breeding stock were reared in five different facilities throughout early life and adolescence, before being transported to a single test laboratory. We found persistent effects of rearing facility on the composition and heterogeneity of the gut microbial community. These effects were paralleled by persistent differences in body weight and in the behavioural phenotype of the mice. Furthermore, we show that common variation among rearing facilities is strong enough to influence epigenetic patterns in neurons at the level of chromatin organization. We detected changes in chromatin organization in the regulatory regions of genes involved in nucleosome assembly, neuronal differentiation, synaptic plasticity and regulation of behavior. Our findings demonstrate that common environmental differences between rearing facilities may produce facility-specific phenotypes, from the molecular to the behavioural level. We expect our findings to stimulate further research into the mechanisms and drivers of these epigenetic changes mediated by the laboratory environment. Furthermore, they highlight an important limitation of inferences from single-laboratory studies and a need to account for the animals environmental background in study design to produce robust and replicable findings.

neuroscience↗

bioRxiv2021

Dynamics of the habitat use of three predatory freshwater fish in a lentic ecosystem

To understand the conditions of coexistence in multiple-species predator community, we studied longitudinal and vertical movement of pike (Esox lucius), pikeperch (Sander lucioperca) and catfish (Silurus glanis) in the [R]imov Reservoir, using an autonomous telemetry system for 11 months. We found significant differences among these three species in movement and depth that varied considerably in time, with the greatest differences between warm (late spring and early autumn) and cold season (late autumn to early spring). Preference for different sections of the reservoir was stable for pike, while pikeperch and catfish frequently visited tributary during the warm season, and moved closer to the dam during the cold season. Pike longitudinal activity was highest in the cold season, pikeperch in the warm season, and catfish activity peaked in both the warm and cold seasons. Overlap in the depth used among species was higher in the warm season, when all species used the upper layer of the water column, and lower in cold season, when pikeperch and catfish used deeper areas. These results demonstrated ability of predators to actively inspect a large portion of the reservoir in both longitudinal and vertical dimensions, although differing in the timing of their habitat use and activity.

ecology↗

bioRxiv2021

Influence of internal seiche dynamics on vertical movement of fish

O_LIInternal seiches are common in stratified lakes, with significant effects on stratification patterns, hydrodynamics and vertical nutrient transport. In particular, seiche can change the vertical distribution of the thermocline and the cold hypolimnetic and warm epilimnetic water masses by several meters on a timescale of a few hours. The results are rapid and strong changes in temperature profiles and oxygen availability that can have profound effects on vagrant and sessile organisms. Internal seiche dynamics could therefore affect fish communities directly through physiological stress and elevated mortality, and indirectly through prey distribution. C_LIO_LIThe aim of this study was to analyze the effects of internal seiche dynamics on lacustrine fish behaviour, and to characterize fish reaction patterns, with the main focus on vertical movement of fish in the vicinity of a shifting thermocline, and avoidance of cold hypolimnetic water. C_LIO_LIThe analysis was based on acoustic telemetry data from Lake Milada, a post-mining lake in the Czech Republic, with a total of 55 tracked individuals of four species: northern pike (Esox lucius), wels catfish (Silurus glanis), tench (Tinca tinca) and rudd (Scardinius erythropthalmus). C_LIO_LIThe effects of seiche dynamics on the four species studied were weak but significant during the day, but only on rudd during the night. Upward seiche produced stronger reactions in fish than downward seiche, and the effects were manifested only during the strongest seiche events. C_LIO_LIThermocline shifting during seiche events may induce a transient reduction in habitat for seiche-reacting species, thus potentially affecting predation and other inter- and intra-specific interactions, and probably affecting fish community dynamics. C_LI Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

ecology↗

bioRxiv2021

Reliability of Mouse Behavioural Tests of Anxiety: a Systematic Review and Meta-Analysis on the Effects of Anxiolytics.

Animal research on anxiety and anxiety disorders relies on valid animal models of anxiety. However, the validity of widely used rodent behavioural tests of anxiety has repeatedly been questioned, as they often fail to produce consistent results across independent replicate studies using different study populations or different anxiolytic compounds. In this study, we assessed the sensitivity of behavioural tests of anxiety in mice to detect anxiolytic effects of drugs prescribed to treat anxiety in humans. To this end, we conducted a pre-registered systematic review of studies reporting tests of anxiolytic compounds against a control treatment using common behavioural tests of anxiety in mice. PubMed and EMBASE were searched on August 21st 2019 for studies published in English and 814 papers were identified for inclusion. Risk of bias was assessed based on Syrcles risk of bias tool and the Camarades study quality checklist on a randomly selected subsample of 180 papers. Meta-analyses on effect sizes of treatments using standardized mean differences (Hedges g) showed that only two of 17 test measures reliably detected effects of anxiolytic compounds other than diazepam. Further, we report considerable variation in both direction and size of effects of most anxiolytics on most outcome variables, indicating poor replicability of test results. This was corroborated by high heterogeneity in most test measures. Finally, we found an overall high risk of bias. Our findings indicate a general lack of sensitivity of common behavioural tests of anxiety in mice to anxiolytic compounds and cast serious doubt on both construct and predictive validity of most of those tests. The use of animals to model human conditions can be justified only if the expected results are informative, reproducible, and translatable. In view of scientifically valid and ethically responsible research, we call for a revision of behavioural tests of anxiety in mice and the development of more predictive tests.

neuroscience↗

bioRxiv2021

Extinction of the Thylacine

Like the Dodo and Passenger Pigeon before it, the predatory marsupial Thylacine (Thylacinus cynocephalus), or Tasmanian tiger, has become an iconic symbol of human-caused extinction. The last captive animal died in 1936, but even today reports of the Thylacines possible ongoing survival in remote regions of Tasmania are newsworthy and capture the publics imagination. Extirpated from mainland Australia in the mid-Holocene, the large island of Tasmania became the species final stronghold. Following European settlement in the 1800s, the Thylacine was heavily persecuted and pushed to the margins of its range, although many sightings were reported thereafter--even well beyond the 1930s. To gain a new depth of insight into the extinction of the Thylacine, we assembled an exhaustive database of 1,237 observational records from Tasmania (from 1910 onwards), quantified their uncertainty, and charted the patterns these revealed. We also developed a new method to visualize the species 20th-century spatio-temporal dynamics, to map potential post-bounty refugia and pinpoint the most-likely location of the final persisting subpopulation. A direct reading of the high-quality records (confirmed kills and captures, in combination with sightings by past Thylacine hunters and trappers, wildlife professionals and experienced bushmen) implies a most-likely extinction date within four decades following the last capture (i.e., 1940s to 1970s). However, uncertainty modelling of the entire sighting record, where each observation is assigned a probability and the whole dataset is then subject to a sensitivity analysis, suggests that extinction might have been as recent as the late 1980s to early 2000s, with a small chance of persistence in the remote south-western wilderness areas. Beyond the intrinsically fascinating problem of reconstructing the final fate of the Thylacine, the new spatio-temporal mapping of extirpation developed herein would also be useful for conservation prioritization and search efforts for other rare taxa of uncertain status.

zoology↗

bioRxiv2020

How moral values influence conservation: a framework to capture different management perspectives

Perspectives in conservation are based on a variety of value systems. Such differences in how people value nature and its components lead to different evaluations of the morality of conservation goals and approaches, and often underlie disagreements in the formulation and implementation of environmental management policies. Specifically, whether a conservation action (e.g. killing feral cats to reduce predation on bird species threatened with extinction) is viewed as appropriate or not can vary among people with different value systems. Here, we present a conceptual, mathematical framework intended as a tool to systematically explore and clarify core value statements in conservation approaches. Its purpose is to highlight how fundamental differences between these value systems can lead to different prioritizations of available management options and offer a common ground for discourse. The proposed equations decompose the question underlying many controversies around management decisions in conservation: what or who is valued, how, and to what extent? We compare how management decisions would likely be viewed under three different idealised value systems: ecocentric conservation, which aims to preserve biodiversity; new conservation, which considers that biodiversity can only be preserved if it benefits humans; and sentientist conservation, which aims at minimising suffering for sentient beings. We illustrate the utility of the framework by applying it to case studies involving invasive alien species, rewilding, and trophy hunting. By making value systems and their consequences in practice explicit, the framework facilitates debates on contested conservation issues, and complements philosophical discursive approaches about moral reasoning. We believe dissecting the core value statements on which conservation decisions are based will provide an additional tool to understand and address conservation conflicts.

ecology↗

bioRxiv2020

Cell Type-Specific Chromatin Accessibility Analysis in the Mouse and Human Brain

The Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) is becoming increasingly popular in the neuroscience field where chromatin regulation is thought to be involved in neurodevelopment, activity-dependent gene regulation, hormonal and environmental responses, and the pathophysiology of neuropsychiatric disorders. The advantages of using this assay include a small amount of material needed, relatively simple and fast protocol, and the ability to capture a range of gene regulatory elements with a single assay. However, with increasing interest in chromatin research, it is an imperative to have feasible, reliable assays that are compatible with a range of neuroscience study designs in both animals and humans. Here we tested three different protocols for neuronal chromatin accessibility analysis, including a varying brain tissue freezing method followed by fluorescent-activated nuclei sorting (FANS) and the ATAC-seq analysis. Our study shows that the cryopreservation method impacts the number of open chromatin regions that can be identified from frozen brain tissue using the cell-type specific ATAC-seq assay. However, we show that all three protocols generate consistent and robust data and enable the identification of functional regulatory elements, promoters and enhancers, in neuronal cells. Our study also implies that the broad biological interpretation of chromatin accessibility data is not significantly affected by the freezing condition. In comparison to the mouse brain analysis, we reveal the additional challenges of doing chromatin analysis on post mortem human brain tissue. However, we also show that these studies are revealing important cell type-specific information about gene regulation in the human brain. Overall, the ATAC-seq coupled with FANS is a powerful method to capture cell-type specific chromatin accessibility information in the mouse and human brain. Our study provides alternative brain preservation methods that generate high quality ATAC-seq data while fitting in different study designs, and further encourages the use of this method to uncover the role of epigenetic (dys)regulation in healthy and malfunctioning brain.

neuroscience↗

bioRxiv2019

Societal attention toward extinction threats

Public attention and interest in the fate of endangered species is a crucial prerequisite for effective conservation programs. Societal awareness and values will largely determine whether conservation initiatives receive necessary support and lead to adequate policy change. Using text data mining, we assessed general public attention toward climate change and biological invasions, which represent two key threats for endangered amphibian, reptile, bird and mammal species in three European countries (France, Germany and the United Kingdom). Our analysis revealed that public attention patterns differed among species groups and countries but was globally higher for climate change than for biological invasions. Both threats received better recognition in threatened than in non-threatened species, as well as in native species than in species from other countries and regions. The relative level of attention toward the two threats corresponded well with the listing of the threats and their severity within the IUCN Red List. We conclude that more efficient communication regarding the threat from biological invasions should be developed, and that conservation practitioners should take advantage of the existing attention toward the threat of climate change.

ecology↗

bioRxiv2019

Sex and Estrous Cycle Effects on Anxiety- and Depression-related Phenotypes in Two-hit Developmental Stress Model

Stress during sensitive developmental periods can adversely affect physical and psychological development and contribute to later-life mental disorders. In particular, adverse experiences during childhood dramatically increase the risk for the development of depression and anxiety disorders. Although women of reproductive age are twice as likely to develop anxiety and depression than men of the corresponding age, little is known about sex-specific factors that promote or protect against the development of psychopathology. To examine potential developmental mechanisms driving sex disparity in risk for anxiety and depression, we established a two-hit developmental stress model including maternal separation in early life followed by social isolation in adolescence. Our study shows complex interactions between early-life and adolescent stress, between stress and sex, and between stress and female estrogen status in shaping behavioral phenotypes of adult animals. In general, increased locomotor activity and body weight reduction were the only two phenotypes where two stressors showed synergistic activity. In terms of anxiety- and depression-related phenotypes, single exposure to early-life stress had the most significant impact and was female-specific. We show that early-life stress disrupts the protective role of estrogen in females, and promotes female vulnerability to anxiety- and depression-related phenotypes associated with the low-estrogenic state. We found plausible transcriptional and epigenetic alterations in psychiatric risk genes, Nr3c1 and Cacna1c, that likely contributed to the stress-induced behavioral effects. In addition, two general transcriptional regulators, Egr1 and Dnmt1, were found to be dysregulated in maternally-separated females and in animals exposed to both stressors, respectively, providing insights into possible transcriptional mechanisms that underlie behavioral phenotypes. Our findings provide a novel insight into developmental risk factors and biological mechanisms driving sex differences in depression and anxiety disorders, facilitating the search for more effective, sex-specific treatments for these disorders.

neuroscience↗

bioRxiv2018

Susceptibility of European freshwater fish to climate change: species profiling based on life-history and environmental characteristics

Climate change is expected to strongly affect freshwater fish communities. Combined with other anthropogenic impacts, the impacts will alter species distributions and contribute to population declines and local extinctions. To provide timely management and conservation of fishes, it is relevant to identify species that will be most impacted by climate change and those that will be resilient. Species traits are considered a promising source of information on characteristics that influence resilience to various environmental conditions and impacts. We collated life history traits and climatic niches of 443 European freshwater fish species and compared those identified as susceptible to climate change to those that are considered to be resilient. Significant differences were observed between the two groups in their distribution, life-history and climatic niches, with climate-change susceptible species being distributed more southwardly within Europe, and being characterized by higher threat levels, lower commercial relevance, lower vulnerability to fishing, smaller body size and warmer thermal envelopes. We establish a list of species revealed to be of highest priority for further research and monitoring regarding climate change susceptibility within Europe. The presented approach represents a promising tool, to quickly assess large groups of species regarding their susceptibility to climate change and other threats, and to identify research and management priorities.

ecology↗

bioRxiv2018

On the overlap between scientific and societal taxonomic attention - insights for conservation

Attention directed at different species by society and science is particularly relevant within the field of conservation, as societal preferences will strongly impact support for conservation initiatives and their success. Here, we assess the association between societal and research interests in four charismatic and threatened species groups, derived from a range of different online sources and social media platforms as well as scientific publications. We found a high level of concordance between scientific and societal taxonomic attention, which was consistent among assessed species groups and media sources. Results indicate that research is apparently not as disconnected from the interests of society as it is often reproached, and that societal support for current research objectives should be adequate. While the high degree of similarity between scientific and societal interest is both striking and satisfying, the dissimilarities are also interesting, as new scientific findings may constitute a constant source of novel interest for the society.

ecology↗