Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841)
Temperature is a crucial factor determining biology and ecology of poikilothermic animals. It often constitutes an important barrier for invasive species originating from different climate zones but, on the other hand, may facilitate the invasion process of animals with wide thermal preferences and high resistance to extreme temperatures. In our experimental study, we investigated the thermal behaviour of two Ponto-Caspian amphipod crustaceans—Dikerogammarus villosus and Dikerogammarus haemobaphes. Both species are known to live under a wide range of thermal conditions which may promote their invasion. Moreover, both these amphipods are hosts for microsporidian parasites which co-evolved with them within the Ponto-Caspian region and spread in European waters. As the presence of a parasite may influence the thermal preferences of its host, we expected to observe behavioural changes in infected individuals of the studied amphipods leading to (1) behavioural fever (selecting a warmer habitat) or (2) anapyrexia (selecting a colder habitat). The experiment (N = 20) was carried out for 30 min in a 100 cm. 20 cm from boths sides were not avaliable for amphipods long thermal gradient (0–40 °C), using 30 randomly selected adult amphipod individuals of one species. At the end of each trial, we checked the position of amphipods along the gradient and determined their sex and infection status (uninfected or infected by one of microsporidium species). D. villosus was infected with Cucumispora dikerogammari whereas D. haemobaphes was a host for C. dikerogammari, Dictyocoela muelleri or D. berillonum. Thermal preferences of amphipods depended on their species and sex. Females of D. villosus preferred warmer microhabitats (often much above 30 °C) than conspecific males and females of D. haemobaphes, whereas no significant differences were found among males of both species and both sexes of D. haemobaphes. Moreover, infected males of D. villosus stayed in warmer water more often than uninfected males of this species, selecting temperatures higher than 30 °C, which may be explained either as a behavioural fever constituting a defence mechanism of a host against the infection, or as a parasite manipulation of the host behaviour increasing the parasite fitness. On the other hand, none of the parasite species affected the thermal preferences of D. haemobaphes, including also C. dikerogammari, changing the behaviour of D. villosus. Our research presents the complexity of the thermal behaviour of studied amphipods and the evidence that microsporidia may trigger a change in temperature preferendum of their host species and those observations may be the result of different host-parasite coevolution time which may vary for the two host species (Poulin, 2010).
Rachalewski et al. (2018) Some like it hot: factors impacting thermal preferences of two Ponto-Caspian amphipods Dikerogammarus villosus (Sovinsky, 1894) and Dikerogammarus haemobaphes (Eichwald, 1841). PeerJ 6:e4871 https://doi.org/10.7717/peerj.4871
Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations
Background Anuran vocalizations, such as advertisement and release calls, are informative for taxonomy because species recognition can be based on those signals. Thus, a proper acoustic description of the calls may support taxonomic decisions and may contribute to knowledge about amphibian phylogeny. Methods Here we present a perspective on advertisement call descriptions of the frog subfamily Lophyohylinae, through a literature review and a spatial analysis presenting bioacoustic coldspots (sites with high diversity of species lacking advertisement call descriptions) for this taxonomic group. Additionally, we describe the advertisement and release calls of the still poorly known treefrog, Itapotihyla langsdorffii. We analyzed recordings of six males using the software Raven Pro 1.4 and calculated the coefficient of variation for classifying static and dynamic acoustic properties. Results and Discussion We found that more than half of the species within the subfamily do not have their vocalizations described yet. Most of these species are distributed in the western and northern Amazon, where recording sampling effort should be strengthened in order to fill these gaps. The advertisement call of I. langsdorffii is composed of 3–18 short unpulsed notes (mean of 13 ms long), presents harmonic structure, and has a peak dominant frequency of about 1.4 kHz. This call usually presents amplitude modulation, with decreasing intensity along the sequence of notes. The release call is a simple unpulsed note with an average duration of 9 ms, and peak dominant frequency around 1.8 kHz. Temporal properties presented higher variations than spectral properties at both intra- and inter-individual levels. However, only peak dominant frequency was static at intra-individual level. High variability in temporal properties and lower variations related to spectral ones is usual for anurans; The first set of variables is determined by social environment or temperature, while the second is usually related to species-recognition process. Here we review and expand the acoustic knowledge of the subfamily Lophyohylinae, highlighting areas and species for future research.
Forti et al. (2018) Current knowledge on bioacoustics of the subfamily Lophyohylinae (Hylidae, Anura) and description of Ocellated treefrog Itapotihyla langsdorffii vocalizations. PeerJ 6:e4813 https://doi.org/10.7717/peerj.4813
The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco
We describe a nearly complete pedal ungual phalanx, discovered in the Kem Kem Beds (Cenomanian) of Tafilalt region, south-eastern Morocco. The bone is symmetric, pointed, low, elongate, and almost flat ventrally in lateral aspect. This peculiar morphology allows to refer the specimen to the smallest known individual of the genus Spinosaurus. The bone belongs to an early juvenile individual and it is proportionally identical to the ungual of the third digit of a large partial skeleton recently found, suggesting an isometric growth for this part of the pes and the retention of peculiar locomotor adaptations—such as traversing soft substrates or paddling—during the entire lifespan.
Maganuco et al. (2018) The smallest biggest theropod dinosaur: a tiny pedal ungual of a juvenile Spinosaurus from the Cretaceous of Morocco. PeerJ 6:e4785 https://doi.org/10.7717/peerj.4785
Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays
Urban estuarine sediments are sinks to a range of contaminants of anthropogenic origin, and a key challenge is to characterize the risk of these compounds to receiving environments. In this study, the toxicity of urban estuarine sediments was tested using acute and chronic bioassays in the benthic harpacticoid Quinquelaophonte sp., and in the planktonic calanoid Gladioferens pectinatus, two New Zealand copepod species. The sediment samples from the estuary tributary sites significantly impacted reproduction in Quinquelaophonte sp. However, results from one of the estuary sites were not significantly different to those from the tributaries sites, suggesting that chemicals other than trace metals, polycyclic aromatic hydrocarbons and ammonia may be the causative stressors. Sediment elutriate samples had significant effects on reproductive endpoints in G. pectinatus, and on the induction of DNA damage in cells, as shown by the comet assay. The results indicate that sediment contamination at the Ahuriri Estuary has the potential to impact biological processes of benthic and pelagic organisms. The approach used provides a standardized methodology to assess the toxicity of estuarine sediments.
Charry et al. (2018) Assessment of the ecotoxicity of urban estuarine sediment using benthic and pelagic copepod bioassays. PeerJ 6:e4936 https://doi.org/10.7717/peerj.4936
Urbanization alters small rodent community composition but not abundance
Desert ecosystems are one of the fastest urbanizing areas on the planet. This rapid shift has the potential to alter the abundances and species richness of herbivore and plant communities. Herbivores, for example, are expected to be more abundant within urban desert remnant parks located within cities due to anthropogenic activities that concentrate food resources and reduce native predator populations. Despite this assumption, previous research conducted around Phoenix, AZ, USA has shown that top-down herbivory led to equally reduced plant biomass in both urban and outlying locations. It is unclear if this insignificant difference in herbivory at urban and outlying sites is due to unaltered desert herbivore populations or altered activity levels that counteract abundance differences. Small rodent herbivore/granivore populations were surveyed at four sites inside and four sites outside of the core of Phoenix during fall 2014 and spring 2015 in order to determine whether abundances and richness differ significantly between urban and rural sites. In order to survey species composition and abundance at these sites, 100 Sherman traps and eight larger wire traps that are designed to attract and capture small vertebrates such as mice, rats, and squirrels were set at each site for two consecutive trap nights. Results suggest that the commonly assumed effect of urbanization on herbivore abundances does not apply to small rodent populations in a desert city, as overall small rodent abundances were statistically similar regardless of location. Though a significant difference was not found for species richness, a significant difference between small rodent genus richness at these sites was observed, with altered community composition. The compositional differences likely reflect the altered vegetative community and may impact ecological interactions at these sites.
Alvarez Guevara et al. (2018) Urbanization alters small rodent community composition but not abundance. PeerJ 6:e4885 https://doi.org/10.7717/peerj.4885
A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil
Based on concordant differences in male advertisement call, tadpole morphology, and absence of haplotype sharing in the barcoding 16S mitochondrial DNA, we describe here a new species of spotted leaf frog of the genus Phasmahyla from Atlantic Forest, State of Rio de Janeiro, Southeast Brazil. The new species is most similar to P. cochranae (type locality) and P. spectabilis (type locality). It differs from these species by the size of the calcar, moderate-sized body (snout-vent length 30.4–34.4 mm in adult eight males), and in the advertisement call. The tadpoles of Phasmahyla lisbella sp. nov. differ from P. exilis, P. spectabilis, P. timbo, P. guttata and P. jandaia because they do not have row of teeth in the anterior part; differ from P. cruzi by the shape of the anterior end of the oral disc. Through genetic data (phylogenetic distance and haplotype genealogy) we diagnosed the new species where the genetic divergences among its congeners is about 3–6% in a fragment of the 16S rRNA gene, which is above the threshold typically characterizing distinct species of anurans. However, the new species can be distinguished from other congeneric species based on an integrative approach (molecular, bioacoustics, larval, and adult morphology).
Pereira et al. (2018) A new species of spotted leaf frog, genus Phasmahyla (Amphibia, Phyllomedusidae) from Southeast Brazil. PeerJ 6:e4900 https://doi.org/10.7717/peerj.4900
Top-down and bottom-up controls on southern New England salt marsh crab populations
Southern New England salt marsh vegetation and habitats are changing rapidly in response to sea-level rise. At the same time, fiddler crab (Uca spp.) distributions have expanded and purple marsh crab (Sesarma reticulatum) grazing on creekbank vegetation has increased. Sea-level rise and reduced predation pressure drive these changing crab populations but most studies focus on one species; there is a need for community-level assessments of impacts from multiple crab species. There is also a need to identify additional factors that can affect crab populations. We sampled crabs and environmental parameters in four Rhode Island salt marshes in 2014 and compiled existing data to quantify trends in crab abundance and multiple factors that potentially affect crabs. Crab communities were dominated by fiddler and green crabs (Carcinus maenas); S. reticulatum was much less abundant. Burrow sizes suggest that Uca is responsible for most burrows. On the marsh platform, burrows and Carcinus abundance were negatively correlated with elevation, soil moisture, and soil percent organic matter and positively correlated with soil bulk density. Uca abundance was negatively correlated with Spartina patens cover and height and positively correlated with Spartina alterniflora cover and soil shear strength. Creekbank burrow density increased dramatically between 1998 and 2016. During the same time, fishing effort and the abundance of birds that prey on crabs decreased, and water levels increased. Unlike in other southern New England marshes where recreational overfishing is hypothesized to drive increasing marsh crab abundance, we propose that changes in crab abundance were likely unrelated to recreational finfish over-harvest; instead, they better track sea-level rise and changing abundances of alternate predators, such as birds. We predict that marsh crab abundance will continue to expand with ongoing sea-level rise, at least until inundation thresholds for crab survival are exceeded.
Raposa et al. (2018) Top-down and bottom-up controls on southern New England salt marsh crab populations. PeerJ 6:e4876 https://doi.org/10.7717/peerj.4876
Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management
Background Precision Livestock Farming (PLF) is a promising approach to minimize the conflicts between socio-economic activities and landscape conservation. However, its application on extensive systems of livestock production can be challenging. The main difficulties arise because animals graze on large natural pastures where they are exposed to competition with wild herbivores for heterogeneous and scarce resources, predation risk, adverse weather, and complex topography. Considering that the 91% of the world’s surface devoted to livestock production is composed of extensive systems (i.e., rangelands), our general aim was to develop a PLF methodology that quantifies: (i) detailed behavioural patterns, (ii) feeding rate, and (iii) costs associated with different behaviours and landscape traits. Methods For this, we used Merino sheep in Patagonian rangelands as a case study. We combined data from an animal-attached multi-sensor tag (tri-axial acceleration, tri-axial magnetometry, temperature sensor and Global Positioning System) with landscape layers from a Geographical Information System to acquire data. Then, we used high accuracy decision trees, dead reckoning methods and spatial data processing techniques to show how this combination of tools could be used to assess energy balance, predation risk and competition experienced by livestock through time and space. Results The combination of methods proposed here are a useful tool to assess livestock behaviour and the different factors that influence extensive livestock production, such as topography, environmental temperature, predation risk and competition for heterogeneous resources. We were able to quantify feeding rate continuously through time and space with high accuracy and show how it could be used to estimate animal production and the intensity of grazing on the landscape. We also assessed the effects of resource heterogeneity (inferred through search times), and the potential costs associated with predation risk, competition, thermoregulation and movement on complex topography. Discussion The quantification of feeding rate and behavioural costs provided by our approach could be used to estimate energy balance and to predict individual growth, survival and reproduction. Finally, we discussed how the information provided by this combination of methods can be used to develop wildlife-friendly strategies that also maximize animal welfare, quality and environmental sustainability.
di Virgilio et al. (2018) Multi-dimensional Precision Livestock Farming: a potential toolbox for sustainable rangeland management. PeerJ 6:e4867 https://doi.org/10.7717/peerj.4867
Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach
Tumor samples obtained from a single cancer patient spatially or temporally often consist of varying cell populations, each harboring distinct mutations that uniquely characterize its genome. Thus, in any given samples of a tumor having more than two haplotypes, defined as a scaffold of single nucleotide variants (SNVs) on the same homologous genome, is evidence of heterogeneity because humans are diploid and we would therefore only observe up to two haplotypes if all cells in a tumor sample were genetically homogeneous. We characterize tumor heterogeneity by latent haplotypes and present state-space formulation of the feature allocation model for estimating the haplotypes and their proportions in the tumor samples. We develop an efficient sequential Monte Carlo (SMC) algorithm that estimates the states and the parameters of our proposed state-space model, which are equivalently the haplotypes and their proportions in the tumor samples. The sequential algorithm produces more accurate estimates of the model parameters when compared with existing methods. Also, because our algorithm processes the variant allele frequency (VAF) of a locus as the observation at a single time-step, VAF from newly sequenced candidate SNVs from next-generation sequencing (NGS) can be analyzed to improve existing estimates without re-analyzing the previous datasets, a feature that existing solutions do not possess.
Ogundijo et al. (2018) Characterization of tumor heterogeneity by latent haplotypes: a sequential Monte Carlo approach. PeerJ 6:e4838 https://doi.org/10.7717/peerj.4838
Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves
Passiflora suberosa L. belonging to the family Passifloraceae is an important medicinal plant used in traditional medicinal system in Sri Lanka to treat diabetes, hypertension and skin diseases. We extracted P. suberosa leaves under reflux conditions using different solvents (hexane, chloroform, methanol and water), then subjected to phytochemical screening. Alkaloids, flavonoids and saponins and saponins and anthraquinones were present in hexane and chloroform extracts. Alkaloids, unsaturated sterols, triterpenes, saponins, flavonoids and tannins were observed in both methanol and aqueous extracts. Proanthocyanidins were observed only in the aqueous extract. Hence, aqueous and methanol extracts with most classes of phytochemicals present were subjected to antimicrobial, antioxidant, antihaemolytic activities and Brine shrimp lethality studies. Antibacterial activity and minimum inhibition concentrations were evaluated using three Gram-positive (Bacillus subtilis, Staphylococcus aureus and Enterococcus faecium) and three Gram-negative bacteria (Pseudumonas aeruginosa, Salmonella typhimuriam and Escherichia coli). The results indicated that only the methanol extract of P. suberosa exhibited antibacterial activities against all the strains of Gram-negative and Gram-positive bacterial with stronger activity against Gram-negative bacteria. DPHH (2,2-diphenyl-1-picrylhydrazy) scavenging assay was adopted to evaluate antioxidant properties while antihaemolytic and toxic activities were studied respectively using cow blood and Brine shrimp lethality assay. The IC50 values of the aqueous extract in both antioxidant and antihaemolytic assays were significantly lower than the standard ascorbic acid. Similar results were observed in the Brine shrimp lethality assay. In conclusion both aqueous and methanol extracts of P. suberosa leaves showed the presence of majority of phytochemicals including proanthocyanidins. Antibacterial activity was obtained only for methanol extract with better activity against Gram-negative bacteria. The aqueous extract showed better antioxidant, antihaemolytic and toxic activities than the methanol extract and their respective standards. Further investigations on the chemical composition and possible isolation of active ingredients is warranted.
Bandara et al. (2018) Potent antibacterial, antioxidant and toxic activities of extracts from Passiflora suberosa L. leaves. PeerJ 6:e4804 https://doi.org/10.7717/peerj.4804