Daily rhythms of behavioral and hormonal patterns in male dromedary camels housed in boxes
Background Daily rhythmicity has been observed for a number of hormonal and behavioral variables in mammals. It can be entrained by several external factors, such as light-dark cycle and scheduled feeding. In dromedary camels, daily rhythmicity has been documented only for melatonin secretion and body temperature. In this study, the daily rhythmicity of behavioral repertoire, cortisol and testosterone levels was investigated in captive male camels. Methods Six clinically healthy male dromedary camels (Camelus dromedarius) were used. The animals were housed in single boxes for 24 h daily and fed twice a day. Over a period of 48 h, behavioral observations were made and blood samples taken every two hours. The data were analyzed using diurnality index, conisor analysis and PROC mixed procedure. Results The diurnality index for rumination and lying down was close to 0 (respectively, 0.09 and 0.19), while the indices for stereotypy, standing, feeding and walking were close to 1 (respectively, 0.74, 0.84, 0.92 and 0.85). Cosinor analysis revealed daily rhythmicity for all behaviors and for cortisol levels (acrophase at 12:57) but not for testosterone. Rumination and lying down (inactive behaviors) reached a peak during the scotophase, whereas feeding, walking and stereotypy (active behaviors) reached a peak during the photophase around midday. Cortisol level and expression of stereotypies peaked before and after food distribution and were negatively correlated (r = − 0.287, P = 0.005). Testosterone levels and expression of sexual behaviors were stimulated by the visual and olfactory contacts with the females and were positively correlated (r = 0.164, P = 0.040). Testosterone was also negatively correlated with cortisol (r = − 0.297; P = 0.003). Discussion These preliminary results provided new knowledge about the daily rhythm of behaviors in camels housed in boxes, suggesting that camels exhibit diurnal behavior pattern in the maintenance conditions outlined in the study. Daily rhythmicity seemed to be entrained not only by the light-dark cycle but also by scheduled feeding. The rise in stereotypy after food distribution could be due to the persistence of feeding motivation and frustration after the ingestion of food. Therefore, feeding practices should be improved to satisfy the foraging and feeding motivation of these camels. Behavioral and hormonal daily patterns in camels should be taken in consideration to adapt the management system, giving the animals more freedom during the light period and a diet richer in fiber, so as to improve reproductive performance, health and welfare.
Aubè et al. (2017) Daily rhythms of behavioral and hormonal patterns in male dromedary camels housed in boxes. PeerJ 5:e3074 https://doi.org/10.7717/peerj.3074
The adaptive value of habitat preferences from a multi-scale spatial perspective: insights from marsh-nesting avian species
Background Habitat selection and its adaptive outcomes are crucial features for animal life-history strategies. Nevertheless, congruence between habitat preferences and breeding success has been rarely demonstrated, which may result from the single-scale evaluation of animal choices. As habitat selection is a complex multi-scale process in many groups of animal species, investigating adaptiveness of habitat selection in a multi-scale framework is crucial. In this study, we explore whether habitat preferences acting at different spatial scales enhance the fitness of bird species, and check the appropriateness of single vs. multi-scale models. We expected that variables found to be more important for habitat selection at individual scale(s), would coherently play a major role in affecting nest survival at the same scale(s). Methods We considered habitat preferences of two Rallidae species, little crake (Zapornia parva) and water rail (Rallus aquaticus), at three spatial scales (landscape, territory, and nest-site) and related them to nest survival. Single-scale versus multi-scale models (GLS and glmmPQL) were compared to check which model better described adaptiveness of habitat preferences. Consistency between the effect of variables on habitat selection and on nest survival was checked to investigate their adaptive value. Results In both species, multi-scale models for nest survival were more supported than single-scale ones. In little crake, the multi-scale model indicated vegetation density and water depth at the territory scale, as well as vegetation height at nest-site scale, as the most important variables. The first two variables were among the most important for nest survival and habitat selection, and the coherent effects suggested the adaptive value of habitat preferences. In water rail, the multi-scale model of nest survival showed vegetation density at territory scale and extent of emergent vegetation within landscape scale as the most important ones, although we found a consistent effect with the habitat selection model (and hence evidence for adaptiveness) only for the former. Discussion Our work suggests caution when interpreting adaptiveness of habitat preferences at a single spatial scale because such an approach may under- or over-estimate the importance of habitat factors. As an example, we found evidence only for a weak effect of water depth at territory scale on little crake nest survival; however, according to the multi-scale analysis, such effect turned out to be important and appeared highly adaptive. Therefore, multi-scale approaches to the study of adaptive explanations for habitat selection mechanisms should be promoted.
Jedlikowski et al. (2017) The adaptive value of habitat preferences from a multi-scale spatial perspective: insights from marsh-nesting avian species. PeerJ 5:e3164 https://doi.org/10.7717/peerj.3164
The Sensed Presence Questionnaire (SenPQ): initial psychometric validation of a measure of the “Sensed Presence” experience
Background The experience of ‘sensed presence’—a feeling or sense that another entity, individual or being is present despite no clear sensory or perceptual evidence—is known to occur in the general population, appears more frequently in religious or spiritual contexts, and seems to be prominent in certain psychiatric or neurological conditions and may reflect specific functions of social cognition or body-image representation systems in the brain. Previous research has relied on ad-hoc measures of the experience and no specific psychometric scale to measure the experience exists to date. Methods Based on phenomenological description in the literature, we created the 16-item Sensed Presence Questionnaire (SenPQ). We recruited participants from (i) a general population sample, and; (ii) a sample including specific selection for religious affiliation, to complete the SenPQ and additional measures of well-being, schizotypy, social anxiety, social imagery, and spiritual experience. We completed an analysis to test internal reliability, the ability of the SenPQ to distinguish between religious and non-religious participants, and whether the SenPQ was specifically related to positive schizotypical experiences and social imagery. A factor analysis was also conducted to examine underlying latent variables. Results The SenPQ was found to be reliable and valid, with religious participants significantly endorsing more items than non-religious participants, and the scale showing a selective relationship with construct relevant measures. Principal components analysis indicates two potential underlying factors interpreted as reflecting ‘benign’ and ‘malign’ sensed presence experiences. Discussion The SenPQ appears to be a reliable and valid measure of sensed presence experience although further validation in neurological and psychiatric conditions is warranted.
Barnby et al. (2017) The Sensed Presence Questionnaire (SenPQ): initial psychometric validation of a measure of the “Sensed Presence” experience. PeerJ 5:e3149 https://doi.org/10.7717/peerj.3149
SLIMM: species level identification of microorganisms from metagenomes
Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree. The former method is limited to making use of the reads which can be mapped to the curated regions, while the latter suffer from the lack of uniquely mapped reads at lower (more specific) taxonomic ranks. Moreover, even if the tools exhibited good performance in calling the organisms present in a sample, there is still room for improvement in determining the correct relative abundance of the organisms. We present a new method Species Level Identification of Microorganisms from Metagenomes (SLIMM) which addresses the above issues by using coverage information of reference genomes to remove unlikely genomes from the analysis and subsequently gain more uniquely mapped reads to assign at lower ranks of a taxonomic tree. SLIMM is based on a few, seemingly easy steps which when combined create a tool that outperforms state-of-the-art tools in run-time and memory usage while being on par or better in computing quantitative and qualitative information at species-level.
Dadi et al. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138 https://doi.org/10.7717/peerj.3138
Status of marine turtle rehabilitation in Queensland
Rehabilitation of marine turtles in Queensland has multifaceted objectives. It treats individual animals, serves to educate the public, and contributes to conservation. We examined the outcome from rehabilitation, time in rehabilitation, and subsequent recapture and restranding rates of stranded marine turtles between 1996 and 2013 to determine if the benefits associated with this practice are cost-effective as a conservation tool. Of 13,854 marine turtles reported as stranded during this 18-year period, 5,022 of these turtles were stranded alive with the remainder verified as dead or of unknown condition. A total of 2,970 (59%) of these live strandings were transported to a rehabilitation facility. Overall, 1,173/2,970 (39%) turtles were released over 18 years, 101 of which were recaptured: 77 reported as restrandings (20 dead, 13 alive subsequently died, 11 alive subsequently euthanized, 33 alive) and 24 recaptured during normal marine turtle population monitoring or fishing activities. Of the turtles admitted to rehabilitation exhibiting signs of disease, 88% of them died, either unassisted or by euthanasia and 66% of turtles admitted for unknown causes of stranding died either unassisted or by euthanasia. All turtles recorded as having a buoyancy disorder with no other presenting problem or disorder recorded, were released alive. In Queensland, rehabilitation costs approximately $1,000 per animal per year admitted to a center, $2,583 per animal per year released, and $123,750 per animal per year for marine turtles which are presumably successfully returned to the functional population. This practice may not be economically viable in its present configuration, but may be more cost effective as a mobile response unit. Further there is certainly benefit giving individual turtles a chance at survival and educating the public in the perils facing marine turtles. As well, rehabilitation can provide insight into the diseases and environmental stressors causing stranding, arming researchers with information to mitigate negative impacts.
Flint et al. (2017) Status of marine turtle rehabilitation in Queensland. PeerJ 5:e3132 https://doi.org/10.7717/peerj.3132
Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey
Predators use olfactory cues moved within water and air to locate prey. Because prey aggregations may produce more cue and be easier to detect, predation could limit aggregation size. However, disturbance in the flow may diminish the reliability of odour as a prey cue, impeding predator foraging success and efficiency. We explore how different cue concentrations (as a proxy for prey group size) affect risk to prey by fish predators in disturbed (more turbulent or mixed) and non-disturbed (less mixed) flowing water. We find that increasing odour cue concentration increases predation risk and disturbing the flow reduces predation risk. At high cue concentration fish were able to locate the cue source in both disturbed and non-disturbed flow, but at medium concentrations, predators only located the cue source more often than expected by chance in non-disturbed flow. This suggests that objects disturbing flow provide a sensory refuge allowing prey to form larger groups, but that group sizes may be limited by level of disturbance to the flow.
Johannesen et al. (2017) Disturbed flow in an aquatic environment may create a sensory refuge for aggregated prey. PeerJ 5:e3121 https://doi.org/10.7717/peerj.3121
Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe
Background Species identification is essential for controlling disease, understanding epidemiology, and to guide the implementation of phytosanitary measures against fungi from the genus Diaporthe. Accurate Diaporthe species separation requires using multi-loci phylogenies. However, defining the optimal set of loci that can be used for species identification is still an open problem. Methods Here we addressed that problem by identifying five loci that have been sequenced in 142 Diaporthe isolates representing 96 species: TEF1, TUB, CAL, HIS and ITS. We then used every possible combination of those loci to build, analyse, and compare phylogenetic trees. Results As expected, species separation is better when all five loci are simultaneously used to build the phylogeny of the isolates. However, removing the ITS locus has little effect on reconstructed phylogenies, identifying the TEF1-TUB-CAL-HIS 4-loci tree as almost equivalent to the 5-loci tree. We further identify the best 3-loci, 2-loci, and 1-locus trees that should be used for species separation in the genus. Discussion Our results question the current use of the ITS locus for DNA barcoding in the genus Diaporthe and suggest that TEF1 might be a better choice if one locus barcoding needs to be done.
Santos et al. (2017) Evaluating multi-locus phylogenies for species boundaries determination in the genus Diaporthe. PeerJ 5:e3120 https://doi.org/10.7717/peerj.3120
Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient
In the Western honey bee, Apis mellifera, queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the effect of RJ and the components affecting longevity of worker honey bees, we first determined the optimal dose for prolonging longevity of workers as 4% RJ in 50% sucrose solution, and developed a method of obtaining long lived workers. We then compared the effects of longevity extension by RJ 4% with bee-collected pollen from rapeseed (Brassica napus). Lastly, we determined that a water soluble RJ protein obtained by precipitation with 60% ammonium sulfate (RJP60) contained the main component for longevity extension after comparing the effects of RJ crude protein extract (RJCP), RJP30 (obtained by precipitation with 30% ammonium sulfate), and RJ ethanol extract (RJEE). Understanding what regulates worker longevity has potential to help increase colony productivity and improve crop pollination efficiency.
Yang et al. (2017) Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient. PeerJ 5:e3118 https://doi.org/10.7717/peerj.3118
Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay
Background The introduction of exotic species can have serious consequences for marine ecosystems. On the shores of the Cantabrian Sea (North of Spain) there are no routine examinations of seaweeds that combine molecular and morphological methods for early detection of exotic species making it difficult to assess in the early stages their establishment and expansion processes as a result of anthropogenic activities (e.g., shipping and/or aquaculture). Methods In this work we used both morphological identification and molecular barcoding (COI-5P and rbcL genes) of red algae collected in Asturias, Bay of Biscay (Gijón and Candás harbours) and from the University of Oviedo’s herbarium samples. Results The results confirmed the presence of exotic Asian seaweeds Pachymeniopsis gargiuli and Grateloupia turuturu Yamada on Cantabrian Sea shores. Several individuals of these species were fertile and developing cystocarps when collected, underlining the risk of possible expansion or continued establishment. This study constitutes the first report of the Asian P. gargiuli in this area of the Bay of Biscay. Conclusions Here the presence of the exotic species of the Halymeniales P. gargiuli is confirmed. We hypothesize that this species may have been established some time ago as a cryptic introduction with G. turuturu in Galician shores. The detection of these species on the shores of the Cantabrian Sea is relevant since introductions of Pachymeniopsis species could have been overlooked on other European coasts, probably mixed with G. turuturu and P. lanceolata. Our results confirm one new alien seaweed species that has been detected using molecular methods (COI-5P region and rbcL genes barcoding) on North Atlantic shores: the Asian native P. gargiuli. This demonstrates that routine screening for early detection of exotic algae in the Cantabrian Sea can be used for risk assessment. Genetic barcoding should be done using both rbcL gene and COI-5P regions since, although COI-databases are still poorer in sequences and this inhibits successful outcomes in Grateloupia-related species identifications, it is nonetheless a useful marker for species-level identifications in seaweeds.
Montes et al. (2017) Molecular barcoding confirms the presence of exotic Asian seaweeds (Pachymeniopsis gargiuli and Grateloupia turuturu) in the Cantabrian Sea, Bay of Biscay. PeerJ 5:e3116 https://doi.org/10.7717/peerj.3116
Some like it hot: a differential response to changing temperatures by the malaria vectors Anopheles funestus and An. gambiae s.l.
Background With the possible implications of global warming, the effect of temperature on the dynamics of malaria vectors in Africa has become a subject of increasing interest. Information from the field is, however, relatively sparse. We describe the effect of ambient temperature over a five-year period on the dynamics of An. funestus and An. gambiae s.l., collected from a single village in southern Mozambique where temperatures varied from a night-time minimum of 6 °C in the cool season to a daytime maximum of 35 °C in the hot season. Results Mean daily air temperatures varied from 34 °C to 20 °C and soil temperatures varied from 26 °C to 12 °C. Diurnal variation was greatest in the cooler months of the year and were greater in air temperatures than soil temperatures. During the study 301, 705 female An. funestus were collected in 6,043 light-trap collections, 161, 466 in 7,397 exit collections and 16, 995 in 1,315 resting collections. The equivalent numbers for An. gambiae s.l. are 72,475 in light-traps, 33, 868 in exit collections and 5,333 from indoor resting collections. Numbers of mosquito were greatest in the warmer months. Numbers of An. gambiae s.l. went through a one hundredfold change (from a mean of 0.14 mosquitoes a night to 14) whereas numbers of An. funestus merely doubled (from a mean of 20 to 40 a night). The highest environmental correlations and mosquito numbers were between mean air temperature (r2 = 0.52 for An. funestus and 0.77 for An. gambiae s.l.). Numbers of mosquito collected were not related to rainfall with lags of up to four weeks. Numbers of both gravid and unfed An. gambiae complex females in exit collections continued to increase at all temperatures recorded but gravid females of An. funestus decreased at temperatures above 28 °C. Overall the numbers of gravid and unfed An. funestus collected in exit collections were not correlated (p = 0.07). For an unknown reason the number of An. gambiae s.l. fell below monitoring thresholds during the study. Conclusions Mean air temperature was the most important environmental parameter affecting both vectors in this part of Mozambique. Numbers of An. gambiae s.l. increased at all temperatures recorded whilst An. funestus appeared to be adversely affected by temperatures of 28 °C and above. These differences may influence the distribution of the vectors as the planet warms.
Charlwood (2017) Some like it hot: a differential response to changing temperatures by the malaria vectors Anopheles funestus and An. gambiae s.l.. PeerJ 5:e3099 https://doi.org/10.7717/peerj.3099