A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses.

RNA-Sequencing is widely used to investigate changes in gene expression at the transcription level in plants. Most plant RNA-Seq analysis pipelines base the normalization approaches on the assumption that total transcript levels do not vary between samples. However, this assumption has not been demonstrated. In fact, many common experimental treatments and genetic alterations affect transcription efficiency or RNA stability, resulting in unequal transcript abundance. The addition of synthetic RNA controls is a simple correction that controls for variation in total mRNA levels. However, adding spike-ins appropriately is challenging with complex plant tissue, and carefully considering how they are added is essential to their successful use. We demonstrate that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants. We illustrate the use of RNA spike-ins with 3' RNA-Seq and present a normalization pipeline that accounts for differences in total transcriptional levels. We evaluate the effect of normalization methods on identifying differentially expressed genes in the context of identifying the effect of the time of day on gene expression and response to chilling stress in sorghum.

Impact of translational regulation on diel expression revealed by time-series ribosome profiling in Arabidopsis.

Plants have developed the ability to adjust to the day/night cycle through the expression of diel genes, which allow them to effectively respond to environmental changes and optimise their growth and development. Diel oscillations also have substantial implications in many physiological processes, including photosynthesis, floral development, and environmental stress responses. The expression of diel genes is regulated by a combination of the circadian clock and responses to environmental cues, such as light and temperature. A great deal of information is available on the transcriptional regulation of diel gene expression. However, the extent to which translational regulation is involved in controlling diel changes in expression is not yet clear. To investigate the impact of translational regulation on diel expression, we conducted Ribo-seq and RNA-seq analyses on a time-series sample of Arabidopsis shoots cultivated under a 12 h light/dark cycle. Our results showed that translational regulation is involved in about 71% of the genes exhibiting diel changes in mRNA abundance or translational activity, including clock genes, many of which are subject to both translational and transcriptional control. They also revealed that the diel expression of glycosylation and ion-transporter-related genes is mainly established through translational regulation. The expression of several diel genes likely subject to translational regulation through upstream open-reading frames was also determined.

Removal of Exogenous Stimuli Reveals a Canalization of Circadian Physiology in a Vertically Migrating Copepod.

Diel rhythms are observed across taxa and are important for maintaining synchrony between the environment and organismal physiology. A striking example of this is the diel vertical migration undertaken by zooplankton, some of which, such as the 5 mm-long copepod Pleuromamma xiphias (P. xiphias), migrate hundreds of meters daily between the surface ocean and deeper waters. Some of the molecular pathways that underlie the expressed phenotype at different stages of this migration are entrained by environmental variables (e.g., day length and food availability), while others are regulated by internal clocks. We identified a series of proteomic biomarkers that vary across ocean DVM and applied them to copepods incubated in 24 h of darkness to assess circadian control. The dark-incubated copepods shared some proteomic similarities to the ocean-caught copepods (i.e., increased abundance of carbohydrate metabolism proteins at night). Shipboard-incubated copepods demonstrated a clearer distinction between night and day proteomic profiles, and more proteins were differentially abundant than in the in situ copepods, even in the absence of the photoperiod and other environmental cues. This pattern suggests that there is a canalization of rhythmic diel physiology in P. xiphias that reflects likely circadian clock control over diverse molecular pathways.

Diurnal gene oscillations modulated by RNA metabolism in tomato.

Diurnal rhythms are known to regulate the expression of a large number of genes, coordinating plant growth and development with diel changes in light and temperature. However, the impact of RNA metabolism on rhythmic gene oscillations in plant is not yet fully understood. To address this question, we performed transcriptome and degradome profiling on tomato leaves at 6 time points during one 24 h cycle, using RNA-seq and genome-wide mapping of uncapped and cleavage transcripts (GMUCT). Time-series profiling of RNA-seq revealed 9342 diurnal-oscillated genes, which were enriched in various metabolic processes. To quantify the general level of RNA degradation for each gene, we utilized the Proportion Uncapped (PU) metric, which represents the GMUCT/RNA-seq ratio. Oscillated PU analysis revealed that 3885 genes were regulated by rhythmic RNA degradation. The RNA decay of these diurnal genes was highly coordinated with mRNA downregulation during oscillation, highlighting the critical role of internal transcription-degradation balance in rhythmic gene oscillation. Furthermore, we identified 2190 genes undergoing co-translational RNA decay (CTRD) with 5' phosphate read ends enriched at the boundary of ribosomes stalling at translational termination sites. Interestingly, diurnal-changed mRNAs with large amplitudes tended to be co-translationally decay, suggesting that CTRD contributed to the rapid turnover of diurnal mRNAs. Finally, we also identified several genes, whose miRNA cleavage efficiency oscillated in a diurnal manner. Taken together, these findings uncovered the vital functions of RNA metabolism, including rhythmic RNA degradation, CTRD, and miRNA cleavage, in modulating the diurnal mRNA oscillations during diel change at post-transcriptional level in tomato.

Circadian clock period length is not consistently linked to chronotype in a wild songbird.

Circadian clock properties vary between individuals and relate to variation in entrained timing in captivity. How this variation translates into behavioural differences in natural settings, however, is poorly understood. Here, we tested in great tits whether variation in the free-running period length (tau) under constant dim light (LL) was linked to the phase angle of the entrained rhythm ("chronotype") in captivity and in the wild, as recently indicated in our study species. We also assessed links between tau and the timing of first activity onset and offset under LL relative to the last experienced light-dark (LD) cycle. We kept 66 great tits, caught in two winters, in LL for 14 days and subsequently released them with a radio transmitter back to the wild, where their activity and body temperature rhythms were tracked for 1 to 22 days. For a subset of birds, chronotype was also recorded in the lab before release. Neither wild nor lab chronotypes were related to tau. We also found no correlation between lab and wild chronotypes. However, the first onset in LL had a positive relationship with tau, but only in males. Our results demonstrate that links between tau and phase of entrainment, postulated on theoretical grounds, may not consistently hold under natural conditions, possibly due to strong masking. This calls for more holistic research on how the many components of the circadian system interact with the environment to shape timing in the wild. Wild birds showed chronotypes in the field that were unlinked to their circadian period length tau measured in captivity. In males only, the first onset of activity after exposure to constant dim light did correlate with tau. Our study emphasises the need to investigate clocks in the real world, including a need to better understand masking.

Rhythmic lipid and gene expression responses to chilling in panicoid grasses.

Chilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one 24 hour cycle in chilling-tolerant foxtail millet (Setaria italica), and chilling-sensitive sorghum (Sorghum bicolor), and Urochloa (browntop signal grass, Urochloa fusca, lipids only), leveraging their evolutionary relatedness and differing levels of chilling-stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis (Arabidopsis thaliana), suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for time of day. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet.

Pre-natal exposure to glucocorticoids causes changes in developmental circadian clock gene expression and post-natal behaviour in the Japanese quail.

The embryonic environment is critical in shaping developmental trajectories and consequently post-natal phenotypes. Exposure to elevated stress hormones during this developmental stage is known to alter a variety of post-natal phenotypic traits, and it has been suggested that pre-natal stress can have long term effects on the circadian rhythm of glucocorticoid hormone production. Despite the importance of the circadian system, the potential impact of developmental glucocorticoid exposure on circadian clock genes, has not yet been fully explored. Here, we showed that pre-natal exposure to corticosterone (CORT, a key glucocorticoid) resulted in a significant upregulation of two key hypothalamic circadian clock genes during the embryonic period in the Japanese quail (Coturnix japonica). Altered expression was still present 10 days into post-natal life for both genes, but then disappeared by post-natal day 28. At post-natal day 28, however, diel rhythms of eating and resting were influenced by exposure to pre-natal CORT. Males exposed to pre-natal CORT featured an earlier acrophase, alongside spending a higher proportion of time feeding. Females exposed to pre-natal CORT featured a less pronounced shift in acrophase and spent less time eating. Both males and females exposed to pre-natal CORT spent less time inactive during the day. Pre-natal CORT males appeared to feature a delay in peak activity levels. Our novel data suggest that these circadian clock genes and aspects of diurnal behaviours are highly susceptible to glucocorticoid disruption during embryonic development, and these effects are persistent across developmental stages, at least into early post-natal life.

Warming, stochastic diel thermal fluctuations affect physiological performance and gill plasticity in an amphibious mangrove fish.

Natural temperature variation in many marine ecosystems is stochastic and unpredictable, and climate change models indicate that this thermal irregularity is likely to increase. Temperature acclimation may be more challenging when conditions are highly variable and stochastic, and there is a need for empirical physiological data in these thermal environments. Using the hermaphroditic, amphibious mangrove rivulus (Kryptolebias marmoratus), we hypothesized that compared with regular, warming diel thermal fluctuations, stochastic warm fluctuations would negatively affect physiological performance. To test this, we acclimated fish to: (1) non-stochastic and (2) stochastic thermal fluctuations with a similar thermal load (27-35°C), and (3) a stable/consistent control temperature at the low end of the cycle (27°C). We determined that fecundity was reduced in both cycles, with reproduction ceasing in stochastic thermal environments. Fish acclimated to non-stochastic thermal cycles had growth rates lower than those of control fish. Exposure to warm, fluctuating cycles did not affect emersion temperature, and only regular diel cycles modestly increased critical thermal tolerance. We predicted that warm diel cycling temperatures would increase gill surface area. Notably, fish acclimated to either thermal cycle had a reduced gill surface area and increased intralamellar cell mass when compared with control fish. This decreased gill surface area with warming contrasts with what is observed for exclusively aquatic fish and suggests a preparatory gill response for emersion in these amphibious fish. Collectively, our data reveal the importance of considering stochastic thermal variability when studying the effects of temperature on fishes.

A model-based hypothesis framework to define and estimate the diel niche via the 'Diel.Niche' R package.

How animals use the diel period (24-h light-dark cycle) is of fundamental importance to understand their niche. While ecological and evolutionary literature abound with discussion of diel phenotypes (e.g. diurnal, nocturnal, crepuscular, cathemeral), they lack clear and explicit quantitative definitions. As such, inference can be confounded when evaluating hypotheses of animal diel niche switching or plasticity across studies because researchers may be operating under different definitions of diel phenotypes. We propose quantitative definitions of diel phenotypes using four alternative hypothesis sets (maximizing, traditional, general and selection) aimed at achieving different objectives. Each hypothesis set is composed of mutually exclusive hypotheses defined based on the activity probabilities in the three fundamental periods of light availability (twilight, daytime and night-time). We develop a Bayesian modelling framework that compares diel phenotype hypotheses using Bayes factors and estimates model parameters using a multinomial model with linear inequality constraints. Model comparison, parameter estimation and visualizing results can be done in the Diel.Niche R package. A simplified R Shiny web application is also available. We provide extensive simulation results to guide researchers on the power to discriminate among hypotheses for a range of sample sizes (10-1280). We also work through several examples of using data to make inferences on diel activity, and include online vignettes on how to use the Diel.Niche package. We demonstrate how our modelling framework complements other analyses, such as circular kernel density estimators and animal movement modelling. Our aim is to encourage standardization of the language of diel activity and bridge conceptual frameworks and hypotheses in diel research with data and models. Lastly, we hope more research focuses on the ecological and conservation importance of understanding how animals use diel time.

The spatiotemporal context of individual specialization in resource use and environmental associations.

1. Individual niche specialization is widespread in natural populations and has key implications for higher levels of biological organization. This phenomenon, however, has been primarily quantified in resource niche axes, overlooking individual variation in environmental associations (i.e. abiotic conditions organisms experience). 2. Here, we explore what we can learn from a multidimensional perspective of individual niche specialization that integrates resource use and environmental associations into a common framework. 3. By combining predictions from theory and simple simulations, we illustrate how (i) multidimensional intraspecific niche variation and (ii) the spatiotemporal context of interactions between conspecifics scale up to shape emergent patterns of the population niche. 4. Contemplating individual specialization as a multidimensional, unifying concept across biotic and abiotic niche axes is a fundamental step towards bringing this concept closer to the n-dimensional niche envisioned by Hutchinson.

1. A especialização individual de nicho é prevalente em populações naturais e tem implicações importantes para níveis de organização biológica superiores. Esse fenômeno, entretanto, tem sido principalmente quantificado em eixos do nicho que representam o uso de recursos, negligenciando a variação individual em associações ambientais (i.e. as condições abióticas que organismos experimentam). 2. Aqui, exploramos o que podemos aprender a partir de uma perspectiva multidimensional da especialização individual que integra o uso de recursos e associações ambientais em uma abordagem única. 3. Ao combinar predições da teoria e simulações simples, ilustramos como (i) a variação intraespecífica multidimensional de nicho e (ii) o contexto espaço­temporal de interações entre conspecíficos podem moldar padrões emergentes do nicho de populações. 4. Encarar a especialização individual como um conceito multidimensional e unificador em eixos do nicho bióticos e abióticos é um passo fundamental na direção de aproximar esse conceito do nicho n­dimensional idealizado por Hutchinson.

Compound-specific stable isotope analyses of fatty acids indicate feeding zones of zooplankton across the water column of a subalpine lake.

Spatial and temporal zooplankton feeding dynamics across the water column of lakes are key for understanding site-specific acquisition of diet sources. During this 6-week lake study, we examined stable carbon (δ13C) and nitrogen (δ15N) isotopes and conducted compound-specific fatty acid (FA) stable isotope analysis (CSIA) of edible seston in the epi-, meta-, and hypolimnion, and zooplankton of Lake Lunz, Austria. We predicted that CSIA of essential FA can discern the foraging grounds of zooplankton more accurately than the commonly used bulk stable isotopes. The δ13C and δ15N values of seston from different lake strata were similar, whereas a dual CSIA approach using stable carbon and hydrogen isotopes of FA (δ13CFA and δ2HFA) provided sufficient isotopic difference in essential FA to discern different lake strata-specific diet sources throughout the study period. We present a CSIA model that suggests strata-specific foraging grounds for different zooplankton groups, indicating higher preference of cladocerans for feeding on epilimnetic diet sources, while calanoid copepods retained more hypolimnetic resources. The CSIA approach thus yields strata-specific information on foraging strategies of different zooplankton taxa and provides more details on the spatial and temporal trophodynamics of planktonic food webs than commonly used bulk stable isotopes.

Seasonal and diurnal variations in soil respiration rates at a treeline ecotone and a lower distribution limit of subalpine forests.

This study examined the seasonal and diurnal variations in soil respiration rates (RS) during a growing season at the treeline ecotone (2,800 m) and the lower distribution limit (1,600 m) of subalpine forests on a volcanic mountain in Japan. The aboveground biomass, the total RS during the growing season, and the RS per day during the growing season were lower at 2,800 m than those at 1,600 m. Seasonal RS variations positively correlated with those of soil and air temperatures at both elevations, and this tendency was more apparent at 1,600 m than 2,800 m. The mean volumetric soil water content (WS) during the growing season was much lower at 2,800 m than 1,600 m because of the scoria substrate at 2,800 m. The monthly mean diel cycle of RS was positively correlated with the soil temperature at each elevation every month, whereas that at 1,600 m was negatively correlated with that of the WS. The RS at 2,800 m decreased during the daytime especially in August, despite no changes in the WS. The decrease in RS after precipitation at 1,600 m was higher than that at 2,800 m. Seasonal and diurnal RS variations could be reproduced from soil and air temperatures, and WS. Estimating soil respiration rate from these variables will help understand the future carbon budget of forests due to global warming.

Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities.

The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.

Warm nights disrupt transcriptome rhythms in field-grown rice panicles.

In rice, a small increase in nighttime temperature reduces grain yield and quality. How warm nighttime temperatures (WNT) produce these detrimental effects is not well understood, especially in field conditions where the typical day-to-night temperature fluctuation exceeds the mild increase in nighttime temperature. We observed genome-wide disruption of gene expression timing during the reproductive phase in field-grown rice panicles acclimated to 2 to 3 °C WNT. Transcripts previously identified as rhythmically expressed with a 24-h period and circadian-regulated transcripts were more sensitive to WNT than were nonrhythmic transcripts. The system-wide perturbations in transcript levels suggest that WNT disrupt the tight temporal coordination between internal molecular events and the environment, resulting in reduced productivity. We identified transcriptional regulators whose predicted targets are enriched for sensitivity to WNT. The affected transcripts and candidate regulators identified through our network analysis explain molecular mechanisms driving sensitivity to WNT and identify candidates that can be targeted to enhance tolerance to WNT.

Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications.

Circadian rhythms, characterized by approximately 24 h cycles, play a pivotal role in enabling various organisms to synchronize their biological activities with daily variations. While ubiquitous in Eukaryotes, circadian clocks remain exclusively characterized in Cyanobacteria among Prokaryotes. These rhythms are regulated by a core oscillator, which is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Interestingly, recent studies revealed rhythmic activities, potentially tied to a circadian clock, in other Prokaryotes, including purple bacteria such as Rhodospirillum rubrum, known for its applications in fuel and plastic bioproduction. However, the pivotal question of how light and dark cycles influence protein dynamics and the expression of putative circadian clock genes remains unexplored in purple non-sulfur bacteria. Unraveling the regulation of these molecular clocks holds the key to unlocking optimal conditions for harnessing the biotechnological potential of R. rubrum. Understanding how its proteome responds to different light regimes-whether under continuous light or alternating light and dark cycles-could pave the way for precisely fine-tuning bioproduction processes. Here, we report for the first time the expressed proteome of R. rubrum grown under continuous light versus light and dark cycle conditions using a shotgun proteomic analysis. In addition, we measured the impact of light regimes on the expression of four putative circadian clock genes (kaiB1, kaiB2, kaiC1, kaiC2) at the transcriptional and translational levels using RT-qPCR and targeted proteomic (MRM-MS), respectively. The data revealed significant effects of light conditions on the overall differential regulation of the proteome, particularly during the early growth stages. Notably, several proteins were found to be differentially regulated during the light or dark period, thus impacting crucial biological processes such as energy conversion pathways and the general stress response. Furthermore, our study unveiled distinct regulation of the four kai genes at both the mRNA and protein levels in response to varying light conditions. Deciphering the impact of the diel cycle on purple bacteria not only enhances our understanding of their ecology but also holds promise for optimizing their applications in biotechnology, providing valuable insights into the origin and evolution of prokaryotic clock mechanisms.

Diel variation of plankton in the highly impacted freshwater zone of Hooghly estuary in relation to ecological alteration.

Plankton are promising ecological monitoring tool that responds quickly to any sort of aquatic ecological alteration, of which many of them are much susceptible to ecological variations. Therefore, monitoring shifts in plankton composition can indicate changes in water quality and aid to identify potential pollution sources. In the present study, the variation in plankton dynamics in relation to ecological variables were monitored in the freshwater zone of the Hooghly estuary from May 2020 to April 2021. The study was conducted in the interval of every six hours. i.e., at 6 A.M., 12 P.M., 6 P.M., and 12 A.M. The present finding revealed the occurrence of 54 phytoplankton and 20 zooplankton taxa/species. Diel variation revealed that among different time intervals, the highest abundance of phytoplankton was recorded 28,307 cells l-1 at 12 P.M, while the lowest was recorded 10,632 cells l-1 at 6 A.M. However, the highest zooplankton abundance was observed 804 ind l-1 at 6 A.M., and the lowest was recorded 156 ind l-1 at 6 P.M. The ANOVA (p < 0.05) analysis indicated significant diel variation for many planktonic genera. The CCA exhibited that most of the phytoplankton were influenced by multiple water quality variables such as temperature, turbidity, calcium, pH, salinity, DO, and nutrients. However, the majority of the zooplankton were affected by turbidity, total phosphorus, sulphate, calcium and available nitrogen. Significant seasonal variation in plankton composition has also been observed. The present study will help to determine the varying diel pattern of planktons in retort to alterations in the water quality parameters and varying ecological niches.

Spontaneous recurrence of a summer-like diel rhythm in the body temperature of the Syrian hamster after hibernation.

Mammalian hibernation is a survival strategy characterized by metabolic suppression and drastically lowering body temperature (Tb), used during harsh seasons with food shortages and cold. The Syrian hamster commences hibernation in response to a short photoperiod and cold but spontaneously concludes hibernation after several months without environmental cues. Little is known about the changes in diel rhythms during hibernation. Using long-term and high-resolution Tb data, we analysed the diel Tb rhythm time-course changes in Syrian hamsters raised under summer-like conditions (long photoperiod (LP) and warm; LP-warm) and transferred to winter-like conditions (short photoperiod (SP) and cold; SP-cold). The diel Tb rhythm was undetectable during the hibernation period (HIBP), reappearing after the HIBP. The phase of this returning rhythm reverted to the LP entrainment phase characteristics despite the ambient SP and then re-entrained to the ambient SP as if the hamsters were transferred from the LP-warm to SP-cold conditions. The diel Tb rhythm reverted from the SP- to LP-type in a hibernation-dependent manner. Under constant dark and cold conditions, the circadian Tb rhythm recovered without photic stimuli following the HIBP. These findings suggest that hibernation involves a program that anticipates the ambient photoperiod when animals emerge from hibernation.

Convergent evolutionary shifts in rhodopsin retinal release explain shared opsin repertoires in monotremes and crocodilians.

The visual ecology of early mammals remains poorly resolved. Studies of ancestral photopigments suggest an ancient transition from nocturnal to more crepuscular conditions. By contrast, the phenotypic shifts following the split of monotremes and therians-which lost their SWS1 and SWS2 opsins, respectively-are less clear. To address this, we obtained new phenotypic data on the photopigments of extant and ancestral monotremes. We then generated functional data for another vertebrate group that shares the same photopigment repertoire as monotremes: the crocodilians. By characterizing resurrected ancient pigments, we show that the ancestral monotreme underwent a dramatic acceleration in its rhodopsin retinal release rate. Moreover, this change was likely mediated by three residue replacements, two of which also arose on the ancestral branch of crocodilians, which exhibit similarly accelerated retinal release. Despite this parallelism in retinal release, we detected minimal to moderate changes in the spectral tuning of cone visual pigments in these groups. Our results imply that ancestral forms of monotremes and crocodilians independently underwent niche expansion to encompass quickly changing light conditions. This scenario-which accords with reported crepuscular activity in extant monotremes-may help account for their loss of the ultraviolet-sensitive SWS1 pigment but retention of the blue-sensitive SWS2.

When death comes: linking predator-prey activity patterns to timing of mortality to understand predation risk.

The assumption that activity and foraging are risky for prey underlies many predator-prey theories and has led to the use of predator-prey activity overlap as a proxy of predation risk. However, the simultaneous measures of prey and predator activity along with timing of predation required to test this assumption have not been available. Here, we used accelerometry data on snowshoe hares (Lepus americanus) and Canada lynx (Lynx canadensis) to determine activity patterns of prey and predators and match these to precise timing of predation. Surprisingly we found that lynx kills of hares were as likely to occur during the day when hares were inactive as at night when hares were active. We also found that activity rates of hares were not related to the chance of predation at daily and weekly scales, whereas lynx activity rates positively affected the diel pattern of lynx predation on hares and their weekly kill rates of hares. Our findings suggest that predator-prey diel activity overlap may not always be a good proxy of predation risk, and highlight a need for examining the link between predation and spatio-temporal behaviour of predator and prey to improve our understanding of how predator-prey behavioural interactions drive predation risk.

Microbial circadian clocks: host-microbe interplay in diel cycles.

BACKGROUND: Circadian rhythms, observed across all domains of life, enable organisms to anticipate and prepare for diel changes in environmental conditions. In bacteria, a circadian clock mechanism has only been characterized in cyanobacteria to date. These clocks regulate cyclical patterns of gene expression and metabolism which contribute to the success of cyanobacteria in their natural environments. The potential impact of self-generated circadian rhythms in other bacterial and microbial populations has motivated extensive research to identify novel circadian clocks. MAIN TEXT: Daily oscillations in microbial community composition and function have been observed in ocean ecosystems and in symbioses. These oscillations are influenced by abiotic factors such as light and the availability of nutrients. In the ocean ecosystems and in some marine symbioses, oscillations are largely controlled by light-dark cycles. In gut systems, the influx of nutrients after host feeding drastically alters the composition and function of the gut microbiota. Conversely, the gut microbiota can influence the host circadian rhythm by a variety of mechanisms including through interacting with the host immune system. The intricate and complex relationship between the microbiota and their host makes it challenging to disentangle host behaviors from bacterial circadian rhythms and clock mechanisms that might govern the daily oscillations observed in these microbial populations. CONCLUSIONS: While the ability to anticipate the cyclical behaviors of their host would likely be enhanced by a self-sustained circadian rhythm, more evidence and further studies are needed to confirm whether host-associated heterotrophic bacteria possess such systems. In addition, the mechanisms by which heterotrophic bacteria might respond to diel cycles in environmental conditions has yet to be uncovered.