Resampling-based methods for biologists

Regional microbial biogeography linked to soil respiration

The relationships between α-diversity and ecosystem functioning (BEF) have been extensively examined. However, it remains unknown how spatial heterogeneity of microbial community, i.e., microbial β-diversity within a region, shapes ecosystem functioning. Here, we examined microbial community compositions and soil respiration (Rs) along an elevation gradient of 853-4420 m a.s.l. in the southeastern Tibetan Plateau, which is renowned as one of the world's biodiversity hotspots. There were significant distance-decay relationships for both bacterial and fungal communities. Stochastic processes played a dominant role in shaping bacterial and fungal community compositions, while soil temperature was the most important environmental factor that affected microbial communities. We evaluated BEF relationships based on α-diversity measured by species richness and β-diversity measured by community dispersions, revealing significantly positive correlations between microbial β-diversities and Rs. These correlations became stronger with increasing sample size, differing from those between microbial α-diversities and Rs. Using Structural Equation Modeling (SEM), we found that soil temperature, soil moisture, and total nitrogen were the most important edaphic properties in explaining Rs. Meanwhile, stochastic processes (e.g., homogenous dispersal and dispersal limitation) significantly mediated effects between microbial β-diversities and Rs. Microbial α-diversity poorly explained Rs, directly or indirectly. In a nutshell, we identified a previously unknown BEF relationship between microbial β-diversity and Rs. By complementing common practices to examine BEF with α-diversity, we demonstrate that a focus on β-diversity could be leveraged to explain Rs.

Exposure to Persistent Organic Pollutants in Australian Waterbirds

There is growing worldwide recognition of the threat posed by persistent organic pollutants (POPs) to wildlife populations. We aimed to measure exposure levels to POPs in a Southern Hemisphere aquatic waterbird species, the nomadic gray teal (Anas gracilis), which is found across Australia. We collected wings from 39 ducks harvested by recreational hunters at two sites (one coastal, one inland) in Victoria, southeastern Australia, in 2021. We examined three groups of POPs: nine congeners of polychlorinated biphenyls (PCBs), 13 organochlorine pesticides (OCPs), and 12 polycyclic aromatic hydrocarbons (PAHs). The PCBs, OCPs, and PAHs were detected at quantifiable levels in 13%, 72%, and 100% of birds, respectively. Of the congeners we tested for in PCBs, OCPs, and PAHs, 33%, 38%, and 100% were detected at quantifiable levels, respectively. The highest levels of exposure to POPs that we found were to the PAH benzo[b]fluoranthene, occurring at a concentration range of 1.78 to 161.05 ng/g wet weight. There were some trends detected relating to differences between geographical sites, with higher levels of several PAHs at the coastal versus inland site. There were several strong, positive associations among PAHs found. We discuss potential sources for the POPs detected, including industrial and agricultural sources, and the likely role of large-scale forest fires in PAH levels. Our results confirm that while Australian waterbirds are exposed to a variety of POPs, exposure levels are currently relatively low. Additional future investigations are required to further characterize POPs within Australian waterbird species. Environ Toxicol Chem 2024;43:736-747. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Application of lidar to assess the habitat selection of an endangered small mammal in an estuarine wetland environment

Light detection and ranging (lidar) has emerged as a valuable tool for examining the fine-scale characteristics of vegetation. However, lidar is rarely used to examine coastal wetland vegetation or the habitat selection of small mammals. Extensive anthropogenic modification has threatened the endemic species in the estuarine wetlands of the California coast, such as the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). A better understanding of SMHM habitat selection could help managers better protect this species. We assessed the ability of airborne topographic lidar imagery in measuring the vegetation structure of SMHM habitats in a coastal wetland with a narrow range of vegetation heights. We also aimed to better understand the role of vegetation structure in habitat selection at different spatial scales. Habitat selection was modeled from data compiled from 15 small mammal trapping grids collected in the highly urbanized San Francisco Estuary in California, USA. Analyses were conducted at three spatial scales: microhabitat (25 m2), mesohabitat (2025 m2), and macrohabitat (~10,000 m2). A suite of structural covariates was derived from raw lidar data to examine vegetation complexity. We found that adding structural covariates to conventional habitat selection variables significantly improved our models. At the microhabitat scale in managed wetlands, SMHM preferred areas with denser and shorter vegetation and selected for proximity to levees and taller vegetation in tidal wetlands. At the mesohabitat scale, SMHM were associated with a lower percentage of bare ground and with pickleweed (Salicornia pacifica) presence. All covariates were insignificant at the macrohabitat scale. Our results suggest that SMHM preferentially selected microhabitats with access to tidal refugia and mesohabitats with consistent food sources. Our findings showed that lidar can contribute to improving our understanding of habitat selection of wildlife in coastal wetlands and help to guide future conservation of an endangered species.

Diverse functional interaction driven by control-default network hubs supports creative thinking

Complex cognitive processes, like creative thinking, rely on interactions among multiple neurocognitive processes to generate effective and innovative behaviors on demand, for which the brain's connector hubs play a crucial role. However, the unique contribution of specific hub sets to creative thinking is unknown. Employing three functional magnetic resonance imaging datasets (total N = 1,911), we demonstrate that connector hub sets are organized in a hierarchical manner based on diversity, with "control-default hubs"-which combine regions from the frontoparietal control and default mode networks-positioned at the apex. Specifically, control-default hubs exhibit the most diverse resting-state connectivity profiles and play the most substantial role in facilitating interactions between regions with dissimilar neurocognitive functions, a phenomenon we refer to as "diverse functional interaction". Critically, we found that the involvement of control-default hubs in facilitating diverse functional interaction robustly relates to creativity, explaining both task-induced functional connectivity changes and individual creative performance. Our findings suggest that control-default hubs drive diverse functional interaction in the brain, enabling complex cognition, including creative thinking. We thus uncover a biologically plausible explanation that further elucidates the widely reported contributions of certain frontoparietal control and default mode network regions in creativity studies.

Wolves alter the trajectory of forests by shaping the central place foraging behaviour of an ecosystem engineer

Predators can directly and indirectly alter the foraging behaviour of prey through direct predation and the risk of predation, and in doing so, initiate indirect effects that influence myriad species and ecological processes. We describe how wolves indirectly alter the trajectory of forests by constraining the distance that beavers, a central place forager and prolific ecosystem engineer, forage from water. Specifically, we demonstrate that wolves wait in ambush and kill beavers on longer feeding trails than would be expected based on the spatio-temporal availability of beavers. This pattern is driven by temporal dynamics of beaver foraging: beavers make more foraging trips and spend more time on land per trip on longer feeding trails that extend farther from water. As a result, beavers are more vulnerable on longer feeding trails than shorter ones. Wolf predation appears to be a selective evolutionary pressure propelled by consumptive and non-consumptive mechanisms that constrain the distance from water beavers forage, which in turn limits the area of forest around wetlands, lakes and rivers beavers alter through foraging. Thus, wolves appear intricately linked to boreal forest dynamics by shaping beaver foraging behaviour, a form of natural disturbance that alters the successional and ecological states of forests.

Co-localization of clusters of TCR-regulated genes with TAD rearrangements

BACKGROUND

Gene expression has long been known to be influenced by the relative proximity of DNA regulatory elements. Topologically associating domains (TADs) are self-interacting genomic regions involved in regulating gene expression by controlling the proximity of these elements. Prior studies of TADs and their biological roles have revealed correlations between TAD changes and cellular differentiation. Here, we used Hi-C and RNA-seq data to correlate TCR-induced changes in TAD structure and gene expression in human CD4+ T cells.

RESULTS

We developed a pipeline, Differentially Expressed Gene Enrichment Finder (DEGEF), that identifies regions of differentially expressed gene enrichment. Using DEGEF, we found that TCR-regulated genes cluster non-uniformly across the genome and that these clusters preferentially localized in regions of TAD rearrangement. Interestingly, clusters of upregulated genes preferentially formed new Hi-C contacts compared to downregulated clusters, suggesting that TCR-activated CD4+ T cells may regulate genes by changing stimulatory contacts rather than inhibitory contacts.

CONCLUSIONS

Our observations support a significant relationship between TAD rearrangements and changes in local gene expression. These findings indicate potentially important roles for TAD rearrangements in shaping their local regulatory environments and thus driving differential expression of nearby genes during CD4+ T cell activation. Moreover, they provide new insights into global mechanisms that regulate gene expression.

In a hub-and-spoke network, spoke-administered thrombolysis reduces mechanical thrombectomy procedure time and number of passes

BACKGROUND

The utility of intravenous thrombolysis (IVT) prior to mechanical thrombectomy (MT) in large vessel occlusion stroke (LVO) is controversial. Some data suggest IVT increases MT technical difficulty. Within our hub-and-spoke telestroke network, we examined how spoke-administered IVT affected hub MT procedure time and pass number.

METHODS

Patients presenting to 25 spoke hospitals who were transferred to the hub and underwent MT from 2018 to 2020 were identified from a prospectively maintained database. MT procedure time, fluoroscopy time, and pass number were obtained from operative reports.

RESULTS

Of 107 patients, 48 received IVT at spokes. Baseline characteristics and NIHSS were similar. The last known well (LKW)-to-puncture time was shorter among IVT patients (4.3 ± 1.9 h vs. 10.5 ± 6.5 h, p < 0.0001). In patients that received IVT, mean MT procedure time was decreased by 18.8 min (50.5 ± 29.4 vs. 69.3 ± 46.7 min, p = 0.02) and mean fluoroscopy time was decreased by 11.3 min (21.7 ± 15.8 vs. 33.0 ± 30.9 min, p = 0.03). Furthermore, IVT-treated patients required fewer MT passes (median 1 pass [IQR 1.0, 1.80] vs. 2 passes [1.0, 2.3], p = 0.0002) and were more likely to achieve reperfusion in ≤2 passes (81.3% vs. 59.3%, p = 0.01). An increased proportion of IVT-treated patients achieved TICI 2b-3 reperfusion after MT (93.9% vs. 83.8%, p = 0.045). There were no associations between MT procedural characteristics and LKW-to-puncture time.

CONCLUSION

Within our network, hub MT following spoke-administered IVT was faster, required fewer passes, and achieved improved reperfusion. This suggests spoke-administered IVT does not impair MT, but instead may enhance it.

Linking glucocorticoid variations to monthly and daily behavior in a wild endangered neotropical primate

Identifying the factors swaying physiological stress levels in wild animals can help depict how they cope with environmental and social stressors, shedding light on their feeding ecology, behavioral plasticity, and adaptability. Here, we used noninvasive methods to explore the link between glucocorticoid levels and behavior in an endangered neotropical primate facing habitat fragmentation pressure, the black lion tamarin (Leontopithecus chrysopygus). We investigated monthly and day-to-day glucocorticoid variations independently to attempt to disentangle the complex nature of the adrenocortical activity. Between May 2019 to March 2020, we followed two groups of black lion tamarins in two different areas, a continuous forest and a small fragment, and gathered behavioral data (over 95 days in total; 8.6 ± 3.9 days/month) and fecal samples (N_samples  = 468; 4.93 ± 3.5 samples/day) simultaneously. Preliminary analyses enabled us to identify circadian variations linked to the biological rhythm, which were taken into account in subsequent models. Monthly analyses revealed that black lion tamarin fecal glucocorticoid metabolite levels vary according to changes in activity budget associated with the fruit consumption, movement, and resting time of the groups. At a day-to-day level, while intergroup encounters led to increases in fecal glucocorticoid metabolite concentrations, we found that changes in food intake or activity level did not trigger physiological stress responses. These findings suggest that diet and ranging patterns, driven by food availability and distribution, influence physiological stress at a seasonal scale, while acute stressors such as interspecific competition trigger short-term stress responses. Exploring fecal glucocorticoid metabolite variations over different timescales can help uncover the predictive and reactive facets of physiological stress in wild species. Moreover, having a comprehensive understanding of the physiological state of species is a valuable conservation tool for evaluating how they cope in changing environments.

Abundance modulates the ecosystem functional contributions of two sympatric Caribbean sea cucumbers

In highly diverse systems such as coral reefs, many species appear to fulfil similar ecological roles, suggesting that they might be ecologically equivalent. However, even if species provide similar functions, the magnitude of those roles could modulate their impact within ecosystems. Here, we compare the functional contributions of two common, co-occurring Caribbean sea cucumber species, Holothuria mexicana and Actynopyga agassizii, in terms of ammonium provisioning and sediment processing on Bahamian patch reefs. We quantified these functions through empirical measures of ammonium excretion, and in situ observations of sediment processing coupled with fecal pellet collections. On a per-individual level, H. mexicana excreted approximately 23% more ammonium and processed approximately 53% more sediment per hour than A. agassizii. However, when we combined these species-specific functional rates to species abundances to produce reef-wide estimates, we found that A. agassizii contributed more than H. mexicana to sediment processing at 57% of reefs (1.9 times more per unit area across all surveyed reefs), and more to ammonium excretion at 83% of reefs (5.6 times more ammonium per unit area across all surveyed reefs), owing to its higher abundance. We conclude that sea cucumber species can differ in the rates at which they deliver per capita ecosystem functions but their ecological impacts at the population level depend on their abundance at a given location.

Spoke-administered thrombolysis improves large vessel occlusion early recanalization: the real-world experience of a large academic hub-and-spoke telestroke network

Introduction

Intravenous thrombolysis (IVT) prior to mechanical thrombectomy (MT) for large vessel occlusion (LVO) stroke is increasingly controversial. Recent trials support MT without IVT for patients presenting directly to MT-capable "hub" centers. However, bypassing IVT has not been evaluated for patients presenting to IVT-capable "spoke" hospitals that require hub transfer for MT. A perceived lack of efficacy of IVT to result in LVO early recanalization (ER) is often cited to support bypassing IVT, but ER data for IVT in patients that require interhospital transfer is limited. Here we examined LVO ER rates after spoke-administered IVT in our hub-and-spoke stroke network.

Methods

Patients presenting to 25 spokes before hub transfer for MT consideration from 2018-2020 were retrospectively identified from a prospectively maintained database. Inclusion criteria were pre-transfer CTA-defined LVO, ASPECTS ≥6, and post-transfer repeat vessel imaging.

Results

Of 167 patients, median age was 69 and 51% were female. 76 received spoke IVT (+spokeIVT) and 91 did not (-spokeIVT). Alteplase was the only IVT used in this study. Comorbidities and NIHSS were similar between groups. ER frequency was increased 7.2-fold in +spokeIVT patients [12/76 (15.8%) vs. 2/91 (2.2%), P<0.001]. Spoke-administered IVT was independently associated with ER (aOR=11.5, 95% CI=2.2,99.6, p<0.05) after adjusting for timing of last known well, interhospital transfer, and repeat vessel imaging. Interval NIHSS was improved in patients with ER (median -2 (IQR -6.3, -0.8) vs. 0 (-2.5, 1), p<0.05).

Conclusion

Within our network, +spokeIVT patients had a 7.2-fold increased ER relative likelihood. This real-world analysis supports IVT use in eligible patients with LVO at spoke hospitals before hub transfer for MT.

Egg corticosterone can stimulate telomerase activity and promote longer telomeres during embryo development

It is often assumed that the transfer of maternal glucocorticoids (GCs; e.g., corticosterone or cortisol) to offspring is an inevitable cost associated with adverse or stressful conditions experienced by mothers. However, recent evidence indicates that maternal GCs may adaptively programme particular physiological and molecular pathways during development to enhance offspring fitness. In this context, an important mechanism through which maternal GCs may lastingly affect offspring phenotypic quality and survival is via effects on embryo telomerase activity and so on offspring postnatal telomere length. Here, using a field experimental design for which we manipulated the corticosterone content in yellow-legged gull (Larus michahellis) eggs, we show that embryos from corticosterone-injected eggs not only had a higher telomerase activity but also longer telomeres just after hatching. A complementary analysis further revealed that gull hatchlings with longer telomeres had a higher survival probability during the period when most of the chick mortality occurs. Given the important role that telomere length and its restoring mechanisms have on ageing trajectories and disease risk, our findings provide a new mechanistic link by which mothers may presumably shape offspring life-history trajectories and phenotype.

Contrast-Enhanced Ultrasonography with Arrival Time Parametric Imaging as a Non-Invasive Diagnostic Tool for Liver Cirrhosis

Liver biopsy is the gold standard method for staging liver fibrosis, but it is an invasive procedure that is associated with some complications. There are also non-invasive techniques for assessing liver fibrosis, such as elastography and biological tests, but these techniques can fail in detection or generate false measurements depending on the subject’s condition. This study aimed to determine whether liver fibrosis can be evaluated using contrast-enhanced ultrasonography with arrival time parametric imaging using the ultrasound machine’s parametric image software, the method being called (CEUS-PAT). CEUS-PAT was performed on each subject using SonoVue as a contrast agent, and images showing liver parenchyma and the right kidney on a single screen were used for analysis in parametric imaging, which was performed using the proprietary software of the ultrasound system. The ratio between the kidney and liver arrival times was calculated. The study included 64 predominantly male (56.3%) subjects, 37 cirrhotic patients, and 27 healthy volunteers, with a mean age of 58.98 ± 8.90 years. Significant differences were found between the liver cirrhosis and healthy groups regarding CEUS-PAT, 0.83 ± 0.09 vs. 0.49 ± 0.11, p < 0.0001. The correlation between CEUS-PAT and VCTE was r = 0.81. The optimal cut-off value for detecting liver cirrhosis was >0.7, with an AUC of 0.98, p < 0.001, Se = 89.19%, Sp = 100%, PPV = 100%, and NPV = 87.1%. We demonstrate that CEUS-PAT achieves excellent performance in diagnosing liver cirrhosis and is a fast method for diagnosing liver cirrhosis that can even be applied in situations where the use of other methods is excluded.

Computationally efficient mechanism discovery for cell invasion with uncertainty quantification

Parameter estimation for mathematical models of biological processes is often difficult and depends significantly on the quality and quantity of available data. We introduce an efficient framework using Gaussian processes to discover mechanisms underlying delay, migration, and proliferation in a cell invasion experiment. Gaussian processes are leveraged with bootstrapping to provide uncertainty quantification for the mechanisms that drive the invasion process. Our framework is efficient, parallelisable, and can be applied to other biological problems. We illustrate our methods using a canonical scratch assay experiment, demonstrating how simply we can explore different functional forms and develop and test hypotheses about underlying mechanisms, such as whether delay is present. All code and data to reproduce this work are available at https://github.com/DanielVandH/EquationLearning.jl.

Dietary Long-Chain n-3 Polyunsaturated Fatty Acid Supplementation Alters Electrophysiological Properties in the Nucleus Accumbens and Emotional Behavior in Naïve and Chronically Stressed Mice

Long-chain (LC) n-3 polyunsaturated fatty acids (PUFAs) have drawn attention in the field of neuropsychiatric disorders, in particular depression. However, whether dietary supplementation with LC n-3 PUFA protects from the development of mood disorders is still a matter of debate. In the present study, we studied the effect of a two-month exposure to isocaloric diets containing n-3 PUFAs in the form of relatively short-chain (SC) (6% of rapeseed oil, enriched in α-linolenic acid (ALA)) or LC (6% of tuna oil, enriched in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) PUFAs on behavior and synaptic plasticity of mice submitted or not to a chronic social defeat stress (CSDS), previously reported to alter emotional and social behavior, as well as synaptic plasticity in the nucleus accumbens (NAc). First, fatty acid content and lipid metabolism gene expression were measured in the NAc of mice fed a SC (control) or LC n-3 (supplemented) PUFA diet. Our results indicate that LC n-3 supplementation significantly increased some n-3 PUFAs, while decreasing some n-6 PUFAs. Then, in another cohort, control and n-3 PUFA-supplemented mice were subjected to CSDS, and social and emotional behaviors were assessed, together with long-term depression plasticity in accumbal medium spiny neurons. Overall, mice fed with n-3 PUFA supplementation displayed an emotional behavior profile and electrophysiological properties of medium spiny neurons which was distinct from the ones displayed by mice fed with the control diet, and this, independently of CSDS. Using the social interaction index to discriminate resilient and susceptible mice in the CSDS groups, n-3 supplementation promoted resiliency. Altogether, our results pinpoint that exposure to a diet rich in LC n-3 PUFA, as compared to a diet rich in SC n-3 PUFA, influences the NAc fatty acid profile. In addition, electrophysiological properties and emotional behavior were altered in LC n-3 PUFA mice, independently of CSDS. Our results bring new insights about the effect of LC n-3 PUFA on emotional behavior and synaptic plasticity.

Lack of Statistical Rigor in DNA Barcoding Likely Invalidates the Presence of a True Species' Barcode Gap

DNA barcoding has been largely successful in satisfactorily exposing levels of standing genetic diversity for a wide range of taxonomic groups through the employment of only one or a few universal gene markers. However, sufficient coverage of geographically-broad intra-specific haplotype variation within genomic databases like the Barcode of Life Data Systems (BOLD) and GenBank remains relatively sparse. As reference sequence libraries continue to grow exponentially in size, there is now the need to identify novel ways of meaningfully analyzing vast amounts of available DNA barcode data. This is an important issue to address promptly for the routine tasks of specimen identification and species discovery, which have seen broad adoption in areas as diverse as regulatory forensics and resource conservation. Here, it is demonstrated that the interpretation of DNA barcoding data is lacking in statistical rigor. To highlight this, focus is set specifically on one key concept that has become a household name in the field: the DNA barcode gap. Arguments outlined herein specifically center on DNA barcoding in animal taxa and stem from three angles: (1) the improper allocation of specimen sampling effort necessary to capture adequate levels of within-species genetic variation, (2) failing to properly visualize intra-specific and interspecific genetic distances, and (3) the inconsistent, inappropriate use, or absence of statistical inferential procedures in DNA barcoding gap analyses. Furthermore, simple statistical solutions are outlined which can greatly propel the use of DNA barcoding as a tool to irrefutably match unknowns to knowns on the basis of the barcoding gap with a high degree of confidence. Proposed methods examined herein are illustrated through application to DNA barcode sequence data from Canadian Pacific fish species as a case study.

Geomorphically controlled coral distribution in degraded shallow reefs of the Western Caribbean

The development of coral reefs results from the interaction between ecological and geological processes in space and time. Their difference in scale, however, makes it difficult to detect the impact of ecological changes on geological reef development. The decline of coral cover over the last 50 years, for example, has dramatically impaired the function of ecological processes on reefs. Yet given the limited-resolution of their Holocene record, it is uncertain how this will impact accretion and structural integrity over longer timescales. In addition, reports of this ecological decline have focused on intrinsic parameters such as coral cover and colony size at the expense of extrinsic ones such as geomorphic and environmental variables. Despite these problems, several attempts have been made to predict the long-term accretion status of reefs based entirely on the contemporary health status of benthic communities. Here we explore how this ecological decline is represented within the reef geomorphic structure, which represents the long-term expression of reef development. Using a detailed geomorphic zonation scheme, we analyze the distribution and biodiversity of reef-building corals in fringing-reef systems of the Mesoamerican Reef tract. We find a depth-related pattern in community structure which shows that the relative species distribution between geomorphic zones is statistically different. Despite these differences, contemporary coral assemblages in all zones are dominated by the same group of pioneer generalist species. These findings imply that first, coral species distribution is still controlled by extrinsic processes that generate the geomorphic zonation; second, that coral biodiversity still reflects species zonation patterns reported by early studies; and third that dominance of pioneer species implies that modern coral assemblages are in a prolonged post-disturbance adjustment stage. In conclusion, any accurate assessment of the future viability of reefs requires a consideration of the geomorphic context or risks miscalculating the impact of ecological changes on long-term reef development.

Assessing the Global and Local Uncertainty of Scientific Evidence in the Presence of Model Misspecification

Scientists need to compare the support for models based on observed phenomena. The main goal of the evidential paradigm is to quantify the strength of evidence in the data for a reference model relative to an alternative model. This is done via an evidence function, such as ΔSIC, an estimator of the sample size scaled difference of divergences between the generating mechanism and the competing models. To use evidence, either for decision making or as a guide to the accumulation of knowledge, an understanding of the uncertainty in the evidence is needed. This uncertainty is well characterized by the standard statistical theory of estimation. Unfortunately, the standard theory breaks down if the models are misspecified, as is commonly the case in scientific studies. We develop non-parametric bootstrap methodologies for estimating the sampling distribution of the evidence estimator under model misspecification. This sampling distribution allows us to determine how secure we are in our evidential statement. We characterize this uncertainty in the strength of evidence with two different types of confidence intervals, which we term “global” and “local.” We discuss how evidence uncertainty can be used to improve scientific inference and illustrate this with a reanalysis of the model identification problem in a prominent landscape ecology study using structural equations.

Co-option of immune effectors by the hormonal signalling system triggering metamorphosis in Drosophila melanogaster

Insect metamorphosis is triggered by the production, secretion and degradation of 20-hydroxyecdysone (ecdysone). In addition to its role in developmental regulation, increasing evidence suggests that ecdysone is involved in innate immunity processes, such as phagocytosis and the induction of antimicrobial peptide (AMP) production. AMP regulation includes systemic responses as well as local responses at surface epithelia that contact with the external environment. At pupariation, Drosophila melanogaster increases dramatically the expression of three AMP genes, drosomycin (drs), drosomycin-like 2 (drsl2) and drosomycin-like 5 (drsl5). We show that the systemic action of drs at pupariation is dependent on ecdysone signalling in the fat body and operates via the ecdysone downstream target, Broad. In parallel, ecdysone also regulates local responses, specifically through the activation of drsl2 expression in the gut. Finally, we confirm the relevance of this ecdysone dependent AMP expression for the control of bacterial load by showing that flies lacking drs expression in the fat body have higher bacterial persistence over metamorphosis. In contrast, local responses may be redundant with the systemic effect of drs since reduction of ecdysone signalling or of drsl2 expression has no measurable negative effect on bacterial load control in the pupa. Together, our data emphasize the importance of the association between ecdysone signalling and immunity using in vivo studies and establish a new role for ecdysone at pupariation, which impacts developmental success by regulating the immune system in a stage-dependent manner. We speculate that this co-option of immune effectors by the hormonal system may constitute an anticipatory mechanism to control bacterial numbers in the pupa, at the core of metamorphosis evolution.

Dynamic modelling of tetrazolium-based microbial toxicity assay-a parametric proxy of traditional dose-response relationship

Microbial toxicity of test substances in tetrazolium assay is often quantified while referring to their IC₅₀ values. However, the implication of such an estimate is very limited and can differ across studies depending on prevailing test conditions. In this work, a factorial design-based end-point microbial toxicity assay was performed, which suggests a significant interaction (P= 0.041) between inoculum and tetrazolium dose on formazan production. Subsequently, a dynamic model framework was utilized to capture the nonlinearities in biomass, substrate, formazan profiles and to project the toxicant inhibition parameter as a robust alternative to IC₅₀ value. Microbial growth, glucose uptake and formazan production in the presence or absence of toxicant (Cu²⁺) from designed batch experiments were used for sequential estimation of model parameters, and their confidence intervals. A logistic growth model with multiplicative inhibition terms for formazan content and toxicant concentration fits the experimental data reasonably well (R²>0.96). Dynamic relative sensitivity analysis revealed that both microbial growth and formazan production profiles were sensitive to toxicant inhibition parameter. The modelling framework not only provides a better insight into the underlying toxic effect but also offers a stable toxicity index for the test substances that can be extended to design a versatile, robust in vitro assay system.

Indels in SARS-CoV-2 occur at template-switching hotspots

The evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ignored the role of insertions and deletions (indels) as well as recombination in SARS-CoV-2 evolution. Using sequences from the GISAID database, we catalogue over 100 insertions and deletions in the SARS-CoV-2 consensus sequences. We hypothesize that these indels are artifacts of recombination events between SARS-CoV-2 replicates whereby RNA-dependent RNA polymerase (RdRp) re-associates with a homologous template at a different loci ("imperfect homologous recombination"). We provide several independent pieces of evidence that suggest this. (1) The indels from the GISAID consensus sequences are clustered at specific regions of the genome. (2) These regions are also enriched for 5' and 3' breakpoints in the transcription regulatory site (TRS) independent transcriptome, presumably sites of RNA-dependent RNA polymerase (RdRp) template-switching. (3) Within raw reads, these indel hotspots have cases of both high intra-host heterogeneity and intra-host homogeneity, suggesting that these indels are both consequences of de novo recombination events within a host and artifacts of previous recombination. We briefly analyze the indels in the context of RNA secondary structure, noting that indels preferentially occur in "arms" and loop structures of the predicted folded RNA, suggesting that secondary structure may be a mechanism for TRS-independent template-switching in SARS-CoV-2 or other coronaviruses. These insights into the relationship between structural variation and recombination in SARS-CoV-2 can improve our reconstructions of the SARS-CoV-2 evolutionary history as well as our understanding of the process of RdRp template-switching in RNA viruses.

A 'How to' guide for interpreting parameters in habitat-selection analyses

Habitat‐selection analyses allow researchers to link animals to their environment via habitat‐selection or step‐selection functions, and are commonly used to address questions related to wildlife management and conservation efforts. Habitat‐selection analyses that incorporate movement characteristics, referred to as integrated step‐selection analyses, are particularly appealing because they allow modelling of both movement and habitat‐selection processes.

Despite their popularity, many users struggle with interpreting parameters in habitat‐selection and step‐selection functions. Integrated step‐selection analyses also require several additional steps to translate model parameters into a full‐fledged movement model, and the mathematics supporting this approach can be challenging for many to understand.

Using simple examples, we demonstrate how weighted distribution theory and the inhomogeneous Poisson point process can facilitate parameter interpretation in habitat‐selection analyses. Furthermore, we provide a ‘how to’ guide illustrating the steps required to implement integrated step‐selection analyses using the amt package

By providing clear examples with open‐source code, we hope to make habitat‐selection analyses more understandable and accessible to end users.

Wolves choose ambushing locations to counter and capitalize on the sensory abilities of their prey

Comprehensive knowledge of ambush behavior requires an understanding of where a predator expects prey to be, which is generally unknowable because ambush predators often hunt mobile prey that exhibit complex, irregular, or inconspicuous movements. Wolves (Canis lupus) are primarily cursorial predators, but they use ambush strategies to hunt beavers (Castor canadensis). Terrestrial beaver activity is predictable because beavers use well-defined, conspicuous habitat features repeatedly. Thus, studying where wolves wait-in-ambush for beavers provides a unique opportunity to understand how predators choose ambush locations in relation to prey activity. We searched 11 817 clusters of GPS locations from wolves in the Greater Voyageurs Ecosystem, International Falls, MN, and documented 748 ambushing sites and 214 instances where wolves killed beavers. Wolves chose ambush locations: 1) with olfactory concealment to avoid detection from the highly developed olfactory senses of beavers and 2) close (generally &lt;5 m) to beaver habitat features to take advantage of beavers’ inability to visually detect motionless predators. Our work describes in detail the ambush strategies wolves use to hunt beavers and continues to overturn the traditional notion that wolves rely solely on cursorial hunting strategies. We also demonstrate that ambush predators can anticipate the movements and behavior of their prey due to a fundamental understanding of their prey’s sensory abilities. Wolves, therefore, and likely ambush predators in general, appear capable of simultaneously accounting for abiotic and biotic factors when choosing ambush locations, ultimately allowing them to counter and capitalize on the sensory abilities of their prey.

The role of geomorphic zonation in long-term changes in coral-community structure on a Caribbean fringing reef

Ecological processes on coral reefs commonly have limited spatial and temporal scales and may not be recorded in their long-term geological history. The widespread degradation of Caribbean coral reefs over the last 40 years therefore provides an opportunity to assess the impact of more significant ecological changes on the geological and geomorphic structure of reefs. Here, we document the changing ecology of communities in a coral reef seascape within the context of its geomorphic zonation. By comparing basic ecological indices between historical and modern data we show that in 35 years the reef-front zone was transformed from a complex coral assemblage with a three-dimensional structure, to a size-homogenized and flattened one that is quasi indistinguishable from the adjacent non-accretional coral-ground zone. Today coral assemblages at Punta Maroma are characterized by the dominance of opportunistic species which are either tolerant to adverse environmental conditions, including sedimentation, or are known to be the first scleractinian species to recruit on disturbed reefs, implying they reflect a post-hurricane stage of adjustment. Despite an increase in similarity in ecological indices, the reef-front and coral-ground geomorphic zones still retain significant differences in coral assemblages and benthic habitat and are not homogeneous. The partial convergence of coral assemblages certainly has important consequences for the ecology and geological viability of the reef and its role in coastal protection, but environmental physical drivers continue to exert a fundamental role in the character and zonation of benthic communities of this reef seascape.