Previous oil exposure alters Gulf Killifish Fundulus grandis oil avoidance behavior
Oil spills threaten the structure and function of ecological communities. The Deepwater Horizon spill was predicted to have catastrophic consequences for nearshore fishes, but field studies indicate resilience in populations and communities. Previous research indicates many marsh fishes exhibit avoidance of oil contaminated areas, representing one potential mechanism for this resilience. Here, we test whether prior oil exposure of Gulf killifish Fundulus grandis alters this avoidance response. Using choice tests between unoiled and oiled sediments at one of three randomized concentrations (low: 0.1 L oil m−2, medium: 0.5 L oil m−2, or high: 3.0 L oil m−2), we found that, even at low prior exposure levels, killifish lose recognition of oiled sediments compared to control, unexposed fish. Preference for unoiled sediments was absent across all oil concentrations after oil exposure, and some evidence for preference of oiled sediments at high exposure was demonstrated. These results highlight the lack of response to toxic environments in exposed individuals, indicating altered behavior despite organism survival. Future research should document additional sublethal consequences that affect ecosystem and food web functioning.
Environmental Contamination and Remediation
Martin et al. (2020) Previous oil exposure alters Gulf Killifish Fundulus grandis oil avoidance behavior. PeerJ 8:e10587 https://doi.org/10.7717/peerj.10587
Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study
Background Previous research has shown diverse vertical space use by various taxa, highlighting the importance of forest vertical structure. Yet, we know little about vertical space use of tropical forests, and we often fail to explore how this three-dimensional space use changes over time. Methods Here we use canopy tower systems in French Guiana and passive acoustic monitoring to measure Neotropical bat activity above and below the forest canopy throughout nine nights. We use a Bayesian generalized linear mixed effect model and kernel density estimates to demonstrate patterns in space-use over time. Results We found that different bats use both canopy and understory space differently and that these patterns change throughout the night. Overall, bats were more active above the canopy (including Cormura brevirostris, Molossus molossus, Peropteryx kappleri and Peropteryx macrotis), but multiple species or acoustic complexes (when species identification was impossible) were more active in the understory (such as Centronycteris maximiliani, Myotis riparius, Pteronotus alitonus and Pteronotus rubiginosus). We also found that most bats showed temporally-changing preferences in hourly activity. Some species were less active (e.g., P. kappleri and P. macrotis), whereas others were more active (Pteronotus gymnonotus, C. brevirostris, and M. molossus) on nights with higher moon illuminance. Discussion Here we show that Neotropical bats use habitat above the forest canopy and within the forest understory differently throughout the night. While bats generally were more active above the forest canopy, we show that individual groups of bats use space differently over the course of a night, and some prefer the understory. This work highlights the need to consider diel cycles in studies of space use, as animals use different habitats during different periods of the day.
Gomes et al. (2020) Time of night and moonlight structure vertical space use by insectivorous bats in a Neotropical rainforest: an acoustic monitoring study. PeerJ 8:e10591 https://doi.org/10.7717/peerj.10591
Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence
An integrative definition of sesamoid bones has been recently proposed, highlighting their relationship with tendons and ligaments, their genetic origin, the influence of epigenetic stimuli on their development, and their variable tissue composition. Sesamoid bones occur mainly associated with a large number of mobile joints in vertebrates, most commonly in the postcranium. Here, we present a survey of the distribution pattern of sesamoids in 256 taxa of Caudata and Gymnophiona and 24 taxa of temnospondyls and lepospondyls, based on dissections, high-resolution X-ray computed tomography from digital databases and literature data. These groups have a pivotal role in the interpretation of the evolution of sesamoids in Lissamphibia and tetrapods in general. Our main goals were: (1) to contribute to the knowledge of the comparative anatomy of sesamoids in Lissamphibia; (2) to assess the evolutionary history of selected sesamoids. We formally studied the evolution of the observed sesamoids by optimizing them in the most accepted phylogeny of the group. We identified only three bony or cartilaginous sesamoids in Caudata: the mandibular sesamoid, which is adjacent to the jaw articulation; one located on the mandibular symphysis; and one located in the posterior end of the maxilla. We did not observe any cartilaginous or osseous sesamoid in Gymnophiona. Mapping analyses of the sesamoid dataset of urodeles onto the phylogeny revealed that the very conspicuous sesamoid in the mandibular symphysis of Necturus beyeri and Amphiuma tridactylum is an independent acquisition of these taxa. On the contrary, the sesamoid located between the maxilla and the lower jaw is a new synapomorphy that supports the node of Hydromantes platycephalus and Karsenia coreana. The absence of a mandibular sesamoid is plesiomorphic to Caudata, whereas it is convergent in seven different families. The absence of postcranial sesamoids in salamanders might reveal a paedomorphic pattern that would be visible in their limb joints.
Ponssa et al. (2020) Sesamoids in Caudata and Gymnophiona (Lissamphibia): absences and evidence. PeerJ 8:e10595 https://doi.org/10.7717/peerj.10595
Utilizing sponge spicules in taxonomic, ecological and environmental reconstructions: a review
Most sponges produce skeletons formed by spicules, structural elements that develop in a wide variety of sizes and tridimensional shapes. The morphologies of spicules are often unique to clade- or even species-level taxa which makes them particularly useful in taxonomic assignments. When dead sponge bodies disintegrate, spicules become incorporated into sediments and sometimes accumulate into enormous agglomerations called spicule mats or beds, or fossilize to form special type of rocks called the spiculites. The record of fossil and subfossil sponge spicules is extraordinarily rich and often serves as a basis for far-reaching reconstructions of sponge communities, though spicules are also bearers of significant ecological and environmental information. Specific requirements and preferences of sponges can be used to interpret the environment in which they lived, and reconstruct oscillations in water depths, pH, temperatures, and other parameters, providing snapshots of past climate conditions. In turn, the silicon isotope compositions in spicules (δ30Si) are being increasingly often used to estimate the level of silicic acid in the marine settings throughout the geological history, which enables to reconstruct the past silica cycle and ocean circulation. This contribution provides a review of the use of sponge spicules in reconstructions of sponge communities, their ecology, and environments, and aims to detect the pertinent gaps in their utilization. Even though spicules are well known for their significance as bearers of taxonomic, ecological, and environmental data, their potential remains to be fully exploited.
Łukowiak (2020) Utilizing sponge spicules in taxonomic, ecological and environmental reconstructions: a review. PeerJ 8:e10601 https://doi.org/10.7717/peerj.10601
Mutational spectra of SARS-CoV-2 isolated from animals
Coronaviruses are ubiquitous and infect a wide spectrum of animals and humans. The newly emerged severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a worldwide pandemic. To address the role that animals may play in the evolution of SARS-CoV-2, the full genome sequences of SARS-CoV-2 isolated from animals were compared with SARS-CoV-2 human isolates from the same clade and geographic region. Phylogenetic analysis of SARS-CoV-2 isolated from the cat, dog, mink, mouse, and tiger revealed a close relationship with SARS-CoV-2 human isolates from the same clade and geographic region with sequence identities of 99.94–99.99%. The deduced amino acid sequence of spike (S) protein revealed the presence of a furin cleavage site (682RRAR▾685), which did not differ among all SARS-CoV-2 isolates from animals and humans. SARS-CoV-2 isolates from minks exhibited two amino acid substitutions (G261D, A262S) in the N-terminal domain of S protein and four (L452M, Y453F, F486L, N501T) in the receptor-binding motif (RBM). In the mouse, the S protein had two amino acid substitutions, one in the RBM (Q498H) and the other (N969S) in the heptad repeat 1. SARS-CoV-2 isolated from minks furtherly exhibited three unique amino acid substitutions in the nucleocapsid (N)protein. In the cat, two unique amino acid substitutions were discovered in the N (T247I) and matrix (T175M) proteins. Additionally, SARS-CoV-2 isolated from minks possessed sixteen, four, and two unique amino acid substitutions in the open reading frame 1ab (ORF1ab), ORF3a, and ORF6, respectively. Dog and cat SARS-CoV-2 isolates showed one and seven unique amino acid substitutions in ORF1ab, respectively. Further studies may be necessary to determine the pathogenic significance of these amino acid substitutions to understand the molecular epidemiology and evolution of SARS-CoV-2.
Elaswad et al. (2020) Mutational spectra of SARS-CoV-2 isolated from animals. PeerJ 8:e10609 https://doi.org/10.7717/peerj.10609
Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians
Background In 2020, to limit the spread of Coronavirus (COVID-19), many countries, including Italy, have issued a lengthy quarantine period for the entire population. For this reason lifestyle has changed, bringing inevitable repercussions to the Quality of Life (QoL). The present study aims to identify which psychosocial variables predict behaviors capable of affecting the QoL during the lockdown period, potentially highlighting factors that might promote well-being and health in the Italian population during the epidemic. Methods Between 27 April 2020 and 11 May 2020, we administered a web-survey to a sample of young Italian people (age M = 21.2; SD = 3.5; female = 57.7% of the sample). Employing variance-based structural equation modeling, we attempted to identify whether social connectedness, social support, and loneliness were variables predictive of the QoL of young Italians. We also sought to identify specific psychological factors, such as symbolic threat, realistic threat, and the threat from potentially contaminated objects, was correlated to COVID-19 fear and whether engaging in particular behaviors was likely to improve the QoL. Results Our results suggest that social connectedness and loneliness are significant predictors of QoL, while social support did not have a significant effect on QoL. Furthermore, we observed that symbolic and realistic threats and the threat from potentially contaminated objects are significant and positive predictors of COVID-19 fear. Moreover, COVID-19 fear had significant and positive relationships with the carrying out of specific behaviors, such as creative activities during the isolation period and that this related to affirming individuals’ country-specific identity. Finally, COVID-19 fear is a significant predictor of behavioral factors related to the adherence to public health advice in line with national guidance regarding the containment of COVID-19; this factor, however, did not correlate with QoL. Conclusion Our results suggest the importance of social context and psychological factors to help devise intervention strategies to improve the QoL during lockdown from epidemic events and, in particular, support the importance of promoting social communication and accurate information about the transmission of the virus.
Lardone et al. (2020) Psychosocial variables and quality of life during the COVID-19 lockdown: a correlational study on a convenience sample of young Italians. PeerJ 8:e10611 https://doi.org/10.7717/peerj.10611
Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island
In 2005, a chikungunya virus outbreak devastated the tropical island of Reunion, infecting a third of the total population. Motivated by the Reunion Island case study, we investigate the theoretic potential for two intervention measures under both voluntary and mandatory protocols to control a vector-borne disease when there is risk of the disease becoming endemic. The first measure uses insect repellent to prevent mosquito bites, while the second involves emigrating to the neighboring Mauritius Island to avoid infection. There is a threshold on the cost of using repellent above which both voluntary and mandatory regimes find it optimal to forgo usage. Below that threshold, mandatory usage protocols will eradicate the disease; however, voluntary adoption leaves the disease at a small endemic level. Emigrating from the island to avoid infection results in a tragedy-of-the-commons effect: while being potentially beneficial to specific susceptible individuals, the remaining islanders paradoxically face a higher risk of infection. Mandated relocation of susceptible individuals away from the epidemic is viable only if the cost of this relocation is several magnitudes lower than the cost of infection. Since this assumption is unlikely to hold for chikungunya, it is optimal to discourage such emigration for the benefit of the entire population. An underlying assumption about the conservation of human-vector encounter rates in mosquito biting behavior informs our conclusions and may warrant additional experimental verification.
Klein et al. (2020) Optimal voluntary and mandatory insect repellent usage and emigration strategies to control the chikungunya outbreak on Reunion Island. PeerJ 8:e10151 https://doi.org/10.7717/peerj.10151
A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment
Background The importance of the inland fisheries sector in food security as a provider of much-needed protein and income supplier has been highlighted. This is especially the case in poor rural communities in developing countries. Inland capture fisheries in Thailand are in place nationwide in rivers, lakes, swamps and reservoirs. The clown featherback (Chitala ornata) is popularly consumed and is an economically important fish in Thailand which is often used in food products such as fish balls and fish cakes. Along with other fish species, the clown featherback is one of fish of inland fisheries at Phayao Lake. Recent fish surveys from 2016-2018 at Phayao Lake using netting and electrofishing found that the number of clown featherback have been reducing since 2016 and could not be detected at all by 2018. This is despite the fact that there are still reports of their presence in the lake from locals. Methods We developed an eDNA-based method for detection of the clown featherback in Phayao Lake as an alternative tool. Water samples were collected in three different sampling months (February, June and September) at six sites located in the lake. Species-specific primers and the probe were designed to amplify a 183 bp fragment of the cytB region of the clown featherback. Results eDNA of the clown featherback can be detected in all different sampling months and sites. Concentration of the clown featherback found in Prayao Lake showed no difference over sampling month but between collecting sites. This proves that eDNA based survey is a sensitive and useful tool for monitoring and surveying the clown featherback at any time of the year.
Osathanunkul et al. (2020) A molecular survey based on eDNA to assess the presence of a clown featherback (Chitala ornata) in a confined environment. PeerJ 8:e10338 https://doi.org/10.7717/peerj.10338
The effect of decay and lexical uncertainty on processing long-distance dependencies in reading
To make sense of a sentence, a reader must keep track of dependent relationships between words, such as between a verb and its particle (e.g. turn the music down). In languages such as German, verb-particle dependencies often span long distances, with the particle only appearing at the end of the clause. This means that it may be necessary to process a large amount of intervening sentence material before the full verb of the sentence is known. To facilitate processing, previous studies have shown that readers can preactivate the lexical information of neighbouring upcoming words, but less is known about whether such preactivation can be sustained over longer distances. We asked the question, do readers preactivate lexical information about long-distance verb particles? In one self-paced reading and one eye tracking experiment, we delayed the appearance of an obligatory verb particle that varied only in the predictability of its lexical identity. We additionally manipulated the length of the delay in order to test two contrasting accounts of dependency processing: that increased distance between dependent elements may sharpen expectation of the distant word and facilitate its processing (an antilocality effect), or that it may slow processing via temporal activation decay (a locality effect). We isolated decay by delaying the particle with a neutral noun modifier containing no information about the identity of the upcoming particle, and no known sources of interference or working memory load. Under the assumption that readers would preactivate the lexical representations of plausible verb particles, we hypothesised that a smaller number of plausible particles would lead to stronger preactivation of each particle, and thus higher predictability of the target. This in turn should have made predictable target particles more resistant to the effects of decay than less predictable target particles. The eye tracking experiment provided evidence that higher predictability did facilitate reading times, but found evidence against any effect of decay or its interaction with predictability. The self-paced reading study provided evidence against any effect of predictability or temporal decay, or their interaction. In sum, we provide evidence from eye movements that readers preactivate long-distance lexical content and that adding neutral sentence information does not induce detectable decay of this activation. The findings are consistent with accounts suggesting that delaying dependency resolution may only affect processing if the intervening information either confirms expectations or adds to working memory load, and that temporal activation decay alone may not be a major predictor of processing time.
Stone et al. (2020) The effect of decay and lexical uncertainty on processing long-distance dependencies in reading. PeerJ 8:e10438 https://doi.org/10.7717/peerj.10438
Digitizing abdominal palpation with a pressure measurement and positioning device
An abdominal physical examination is one of the most important tools in evaluating patients with acute abdominal pain. We focused on palpation, in which assessment is made according to the patient’s response and force feedback. Since palpation is performed manually by the examiner, the uniformity of force and location is difficult to achieve during examinations. We propose an integrated system to quantify palpation pressure and location. A force sensor continuously collects pressure data, while a camera locates the precise position of contact. The system recorded, displayed average and maximum pressure by creating a pressure/time curve for computer-aided diagnosis. Compared with previous work on pressure sensors of quantifying abdominal palpation, our proposed system is the integrated approach to measure palpation force and track the corresponding position at the same time, for further diagnosis. In addition, we only make use of a sensing device and a general web camera, rather than commercial algometry and infrared cameras used in the previous work. Based on our clinical trials, the statistics of palpation pressure values and the corresponding findings are also reported. We performed abdominal palpation with our system for twenty-three healthy participants, including fourteen males and nine females. We applied two grades of force on the abdomen (light and deep) by four-quadrant and nine-region schemes, record the value of pressure and location. In the four-quadrant scheme, the average pressures of abdominal palpation with light and deep force levels were 0.506(N) and 0.552(N), respectively. In the nine-region scheme, the average pressures were 0.496(N) and 0.577(N), respectively. Two episodes of contact dermal reaction were identified. According to our experiment statistics, there is no significant difference in the force level between the four-quadrant and nine-region scheme. Our results have the potential to be used as a reference guide while designing digital abdominal palpation devices.
Hsu et al. (2020) Digitizing abdominal palpation with a pressure measurement and positioning device. PeerJ 8:e10511 https://doi.org/10.7717/peerj.10511