title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1355
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Fish nursery value of algae habitats in temperate coastal reefs
link: https://peerj.com/articles/6797
last-modified: 2019-05-15
description: The nursery function of coastal habitats is one of the most frequently mentioned and recognized ecosystem services in the valuation of coastal ecosystems. Despite its importance our understanding of the precise habitat parameters and mechanisms that make a habitat important as a nursery area is still limited for many species. The study aimed to establish the importance of different algae morphotypes in providing shelter and food for juvenile coastal fish during the main settlement peaks, in early spring and late summer, in littoral rocky reef systems in the Northwestern Mediterranean. The results of our study showed strong seasonal differences in algae cover, composition and height between the two sampling periods. Overall, during spring the algae were well developed, while in late summer, both density and height, of most algae decreased considerably. Equally, prey biomass, in form of suitable sized invertebrate fauna associated to the algae, decreased. Accordingly, the shelter and food for the fish settling in this habitat during late summer were less abundant, indicating a mismatch between the observed presence of juvenile fish and optimal habitat conditions. Differences in prey densities were detected between algae morphotypes, with structurally more complex algae, such as Cystoseira spp. and Halopteris spp. consistently containing more prey, independent of season, compared to simpler structured morphotypes such as Dictoytales. The study furthermore related juvenile fish density to habitats dominated by different algae morphotypes. Out of the three-study species (Diplodus vulgaris, Symphodus ocellatus, Coris julis) only S. ocellatus showed a significant association with an algae habitat. S. ocellatus related positively to habitats dominated by Dictoytales which provided the highest cover during late summer but had the lowest prey densities. A strong association of this species with Cystoseira, as reported by other studies, could not be confirmed. Cystoseira was abundant within the study area but in a state of dieback, showing loss and reduced height of foliage, typical for the time of year within the study area. It is therefore likely that algae-fish associations are context-dependent and that several algae species may fulfil similar functions. We also discovered that prey biomass did not appear to have an important effect on juvenile abundances. Nevertheless, the availability of prey may influence juvenile fish condition, growth performance and ultimately long-term survival. We therefore suggest that future studies on habitat quality should also include, besides abundance, indicators related to the condition and growth of juveniles.
creator: Hilmar Hinz
creator: Olga Reñones
creator: Adam Gouraguine
creator: Andrew F. Johnson
creator: Joan Moranta
uri: https://doi.org/10.7717/peerj.6797
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Hinz et al.

title: Cosmetic colouring by Bearded Vultures Gypaetus barbatus: still no evidence for an antibacterial function
link: https://peerj.com/articles/6783
last-modified: 2019-05-15
description: Bearded Vultures regularly visit ferruginous springs for cosmetic purposes to obtain their reddish plumage colouration. Different hypotheses have been proposed to explain this deliberate application of adventitious colouration: (1) to signal individual dominance status; (2) to exploit an anti-bacterial effect of iron oxides or ochre to reduce feather degradation by bacteria and, in parallel (3) to enable incubating birds to transfer this protection to their developing embryos to increase hatching success. Here, we re-evaluate the antibacterial hypothesis using three experimental approaches: (a) by applying feather-degrading bacteria to stained and unstained bearded vulture feathers; (b) by assessing the antibacterial activity of ochre; and (c) by comparing the breeding success of orange individuals with pale ones. Our findings suggest that the in vitro addition of feather degrading Bacillus licheniformis to naturally stained Bearded Vulture feathers did not retard feather degradation compared to controls. Iron particles from red soil (ochre) or iron salts had no antibacterial effect on the growth of three species of bacteria (Escherichia coli, Kocuria rhizophila and Bacillus licheniformis), incubated either in the dark or under visible light. Finally, breeding success did not differ between territories occupied by pale individuals versus orange ones. These results run counter to the hypothesis that iron oxides have an antibacterial role in Bearded Vultures. The use of red soils by Bearded Vultures may function as a territorial status signal, but may also be involved in other processes, such as pair formation and the long-term maintenance of the pair bond, as suggested for the closely related Egyptian vulture Neophron percnopterus.
creator: Antoni Margalida
creator: Markus S. Braun
creator: Juan José Negro
creator: Karl Schulze-Hagen
creator: Michael Wink
uri: https://doi.org/10.7717/peerj.6783
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Margalida et al.

title: Foot pressure distribution in White Rhinoceroses (Ceratotherium simum) during walking
link: https://peerj.com/articles/6881
last-modified: 2019-05-15
description: White rhinoceroses (Ceratotherium simum) are odd-toed ungulates that belong to the group Perissodactyla. Being second only to elephants in terms of large body mass amongst extant tetrapods, rhinoceroses make fascinating subjects for the study of how large land animals support and move themselves. Rhinoceroses often are kept in captivity for protection from ivory poachers and for educational/touristic purposes, yet a detrimental side effect of captivity can be foot disease (i.e., enthesopathies and osteoarthritis around the phalanges). Foot diseases in large mammals are multifactorial, but locomotor biomechanics (e.g., pressures routinely experienced by the feet) surely can be a contributing factor. However, due to a lack of in vivo experimental data on rhinoceros foot pressures, our knowledge of locomotor performance and its links to foot disease is limited. The overall aim of this study was to characterize peak pressures and center of pressure trajectories in white rhinoceroses during walking. We asked two major questions. First, are peak locomotor pressures the lowest around the fat pad and its lobes (as in the case of elephants)? Second, are peak locomotor pressures concentrated around the areas with the highest reported incidence of pathologies? Our results show a reduction of pressures around the fat pad and its lobes, which is potentially due to the material properties of the fat pad or a tendency to avoid or limit “heel” contact at impact. We also found an even and gradual concentration of foot pressures across all digits, which may be a by-product of the more horizontal foot roll-off during the stance phase. While our exploratory, descriptive sample precluded hypothesis testing, our study provides important new data on rhinoceros locomotion for future studies to build on, and thus impetus for improved implementation in the care of captive/managed rhinoceroses.
creator: Olga Panagiotopoulou
creator: Todd C. Pataky
creator: John R. Hutchinson
uri: https://doi.org/10.7717/peerj.6881
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Panagiotopoulou et al.

title: Cells released from S. epidermidis biofilms present increased antibiotic tolerance to multiple antibiotics
link: https://peerj.com/articles/6884
last-modified: 2019-05-15
description: Biofilm released cells (Brc) are thought to present an intermediary phenotype between biofilm and planktonic cells and this has the potential of affecting their antimicrobial tolerance.AimCompare the antimicrobial tolerance profiles of Brc, planktonic or biofilm cultures of S. epidermidis.MethodologyPlanktonic, biofilm cultures or Brc from 11 isolates were exposed to peak serum concentrations (PSC) of antibiotics. The antimicrobial killing effect in the three populations was determined by CFU.ResultsIncreased Brc tolerance to vancomycin, teicoplanin, rifampicin, erythromycin, and tetracycline was confirmed in model strain 9142. Furthermore, significant differences in the susceptibility of Brc to vancomycin were further found in 10 other clinical isolates.ConclusionsBrc from distinct clinical isolates presented a decreased susceptibility to most antibiotics tested and maintained that enhanced tolerance despite growing planktonically for up to 6 h. Our data suggest that Brc maintain the typical enhanced antibiotic tolerance of biofilm populations, further suggesting that addressing antimicrobial susceptibility in planktonic cultures might not reflect the full potential of biofilm-associated bacteria to survive therapy.
creator: Vânia Gaio
creator: Nuno Cerca
uri: https://doi.org/10.7717/peerj.6884
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Gaio and Cerca

title: Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions
link: https://peerj.com/articles/6888
last-modified: 2019-05-15
description: BackgroundPoa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region.MethodsIn the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations.ResultsiPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula.DiscussionThe lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu’s FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic variation was surprisingly high, despite the observed significant traces of bottleneck/founder effect following demographic expansion, and was similar to that observed in populations from Poland and the Balkans. For the Antarctic population, the multiple introduction events from different sources are considered to be responsible for such an observation. Moreover, the results of STRUCTURE and PCoA showed that the P. annua from Antarctica has the highest genetic similarity to populations from Europe.ConclusionsThe observed polymorphism should be considered as a consequence of the joint influence of external abiotic stress and the selection process. Environmental changes, due to their ability to induce transposon activation, lead to the acceleration of evolutionary processes through the production of genetic variability.
creator: Piotr Androsiuk
creator: Justyna Koc
creator: Katarzyna Joanna Chwedorzewska
creator: Ryszard Górecki
creator: Irena Giełwanowska
uri: https://doi.org/10.7717/peerj.6888
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Androsiuk et al.

title: Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae
link: https://peerj.com/articles/6899
last-modified: 2019-05-15
description: BackgroundChlorophyceae is one of three most species-rich green algal classes and also the only class in core Chlorophyta whose monophyly remains uncontested as gene and taxon sampling improves. However, some key relationships within Chlorophyceae are less clear-cut and warrant further investigation. The present study combined genome-scale chloroplast data and rich sampling in an attempt to resolve the ordinal classification in Chlorophyceae. The traditional division into Sphaeropleales and Volvocales (SV), and a clade containing Oedogoniales, Chaetopeltidales, and Chaetophorales (OCC) was of particular interest with the addition of deeply branching members of these groups, as well as the placement of several incertae sedis taxa.MethodsWe sequenced 18 chloroplast genomes across Chlorophyceae to compile a data set of 58 protein-coding genes of a total of 68 chlorophycean taxa. We analyzed the concatenated nucleotide and amino acid datasets in the Bayesian and Maximum Likelihood frameworks, supplemented by analyses to examine potential discordant signal among genes. We also examined gene presence and absence data across Chlorophyceae.ResultsConcatenated analyses yielded at least two well-supported phylogenies: nucleotide data supported the traditional classification with the inclusion of the enigmatic Treubarinia into Sphaeropleales sensu lato. However, amino acid data yielded equally strong support for Sphaeropleaceae as sister to Volvocales, with the rest of the taxa traditionally classified in Sphaeropleales in a separate clade, and Treubarinia as sister to all of the above. Single-gene and other supplementary analyses indicated that the data have low phylogenetic signal at these critical nodes. Major clades were supported by genomic structural features such as gene losses and trans-spliced intron insertions in the plastome.DiscussionWhile the sequence and gene order data support the deep split between the SV and OCC lineages, multiple phylogenetic hypotheses are possible for Sphaeropleales s.l. Given this uncertainty as well as the higher-taxonomic disorder seen in other algal groups, dwelling on well-defined, strongly supported Linnaean orders is not currently practical in Chlorophyceae and a less formal clade system may be more useful in the foreseeable future. For example, we identify two strongly and unequivocally supported clades: Treubarinia and Scenedesminia, as well as other smaller groups that could serve a practical purpose as named clades. This system does not preclude future establishment of new orders, or emendment of the current ordinal classification if new data support such conclusions.
creator: Karolina Fučíková
creator: Paul O. Lewis
creator: Suman Neupane
creator: Kenneth G. Karol
creator: Louise A. Lewis
uri: https://doi.org/10.7717/peerj.6899
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Fučíková et al.

title: Development and feasibility study of an app (Ladle) for weight loss and behaviour change
link: https://peerj.com/articles/6907
last-modified: 2019-05-15
description: BackgroundWeight management interventions involving behaviour change often utilise face to face interventions which include evidence based behaviour change strategies yet are costly and time intensive. In contrast, digital interventions cost less and have a wider reach yet tend to lack an evidence base and are less effective.AimsThe present study therefore aimed to develop an evidence based behaviour change low cost app for weight management and to provide a preliminary analysis of its effectiveness.MethodsThe Ladle app was developed through evidence review and feedback from health care professionals and patients and consists of a 12 week course focusing on six habits and weight loss facilitated through 36 audio psychological lessons and 12 lessons specifically on the six habits. Each lesson was between 2–5 min (approx. 168 min of lessons). It was evaluated in terms of completion rate, weight loss, adoption of the six habits and participant feedback.ResultsThe results showed a completion rate of 44%, that 52% of Completers showed weight loss of at least 5%, 79% showed weight loss of at least 3%, the median % weight lost was −5% and the median weight loss was −3.8 kg. Further, by the end of 12 weeks the majority (>80%) of participants had adopted four of the six habits for at least 5 days a week and nearly half (45%) had adopted the remaining two habits for at least 4 days out of 7. Feedback comments were mainly positive (n = 80) focusing mostly on the content of the lessons. Some comments were neutral (n = 56) and involved a statement of commitment or a description of a challenge and a minority were negative (n = 23) describing some technical issues which were addressed as the evaluation progressed.ConclusionThe new Ladle app offers an evidenced based alternative to more intensive face to face interventions. On preliminary analysis it would seem to have lower completion rates than some more intensive interventions but comparable effectiveness for weight loss. It can also improve habits and is less time-intensive and costly to deliver. Participant feedback was generally positive.
creator: Jane Ogden
creator: Hazel Maxwell
creator: Adrian Wong
uri: https://doi.org/10.7717/peerj.6907
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Ogden et al.

title: The Equidae from Cooper’s D, an early Pleistocene fossil locality in Gauteng, South Africa
link: https://peerj.com/articles/6909
last-modified: 2019-05-15
description: Cooper’s D is a fossil locality in the Bloubank Valley close to other important sites such as Sterkfontein and Kromdraai in Gauteng, South Africa. The fossil deposits of Cooper’s D date to 1.38 ± 0.11 Ma. Hominins like Paranthropus robustus and early Homo have been recovered from Cooper’s Cave. We report here on the Equidae remains. Our sample contains specimens from the extinct Equus capensis, and a specimen which represents an extinct hipparion Eurygnathohippus cf. cornelianus. This particular specimen was previously identified as plains zebra (Equus quagga). The contribution of Equidae to the total fossil assemblage of Cooper’s D is relatively low, and these remains were likely accumulated by various predators such as spotted and brown hyenas and leopards. The Equidae, as well as the other fauna from Cooper’s D supports the existence of grassland, wooded and water components in the vicinity of the site.
creator: Shaw Badenhorst
creator: Christine M. Steininger
uri: https://doi.org/10.7717/peerj.6909
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2019 Badenhorst and Steininger

title: The effect of differential spatiotopic information on the acquisition and generalization of fear of movement-related pain
link: https://peerj.com/articles/6913
last-modified: 2019-05-15
description: Fear of movement-related pain significantly contributes to musculoskeletal chronic pain disability. Previous research has shown that fear of movement-related pain can be classically conditioned. That is, in a differential fear conditioning paradigm, after (repeatedly) pairing a neutral joystick movement (conditioned stimulus; CS+) with a painful stimulus (unconditioned stimulus; pain-US), that movement in itself starts to elicit self-reported fear and elevated psychophysiological arousal compared to a control joystick movement (CS−) that was never paired with pain. Further, it has been demonstrated that novel movements that are more similar to the original CS+ elicit more fear than novel movements that are more similar to the CS−, an adaptive process referred to as stimulus generalization. By default, movement/action takes place in reference to the three-dimensional space: a movement thus not only involves proprioceptive information, but it also contains spatiotopic information. Therefore, the aim of this study was to investigate to what extent spatiotopic information (i.e., endpoint location of movement) contributes to the acquisition and generalization of such fear of movement-related pain besides proprioception (i.e., movement direction). In a between-subjects design, the location group performed joystick movements from the middle position to left and right; the movement group moved the joystick from left and right to the middle. One movement (CS+) was paired with pain, another not (CS−). Feature overlap between CSs typically reduces differential learning. The endpoint of both CSs in the movement group is an overlapping feature whereas in the location group the endpoint of both CSs is distinct; therefore we hypothesized that there would be less differential fear learning in the movement group compared to the location group. We also tested generalization to movements with similar proprioceptive features but different endpoint location. Following the principle of stimulus generalization, we expected that novel movements in the same direction as the CS+ but with a different endpoint would elicit more fear than novel movement in the same direction of the CS− but with a different endpoint. Main outcome variables were self-reported fear and pain-US expectancy and eyeblink startle responses (electromyographic). Corroborating the feature overlap hypothesis, the location group showed greater differential fear acquisition. Fear generalization emerged for both groups in the verbal ratings, suggesting that fear indeed accrued to proprioceptive CS features; these effects, however, were not replicated in the startle measures.
creator: Ann Meulders
creator: Johan W. Vlaeyen
uri: https://doi.org/10.7717/peerj.6913
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Meulders and Vlaeyen

title: Effects of water level fluctuation on thermal stratification in a typical tributary bay of Three Gorges Reservoir, China
link: https://peerj.com/articles/6925
last-modified: 2019-05-15
description: Xiangxi River is a typical tributary of Three Gorges Reservoir (TGR) in China. Based on field observations in 2010, thermal stratification was significant in most months of the year. Through field data analysis and numerical simulations, the seasonal and spatial variation of thermal stratification as related to the impact of the operation of TGR were investigated. Thermal stratification was most pronounced from April to September in the Xiangxi River tributary. Air temperature (AT) and water level (WL) were the two dominant variables impacting thermal stratification. AT affected the surface water temperature promoting the formation of thermal stratification, and high WLs in TGR deepened the thermocline depth and thermocline bottom depth. These results provide a preliminary description of the seasonal variation and spatial distribution of thermal stratification, which is important for better understanding how thermal stratification affects algae blooms in Xiangxi River.
creator: Juxiang Jin
creator: Scott A. Wells
creator: Defu Liu
creator: Guolu Yang
creator: Senlin Zhu
creator: Jun Ma
creator: Zhengjian Yang
uri: https://doi.org/10.7717/peerj.6925
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2019 Jin et al.