title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1734
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus
link: https://peerj.com/articles/3056
last-modified: 2017-03-07
description: Mourasuchus (Alligatoroidea, Caimaninae) is one of the most peculiar crocodyliforms due to the skull morphology consisting of a long, wide, dorsoventrally flat rostrum with long, slender mandibular rami. Despite these peculiarities, the systematics, phylogeny and feeding habits of this taxon have not been properly studied. In this paper, we describe a new species of the genus, Mourasuchus pattersoni sp. nov., from the late Miocene of the Urumaco Formation of Venezuela. The new species differs from the other Mourasuchus species in having a lateromedially wide, dorsoventrally high jugal bone and a circular incisive foramen, which both represent autapomorphies of the new taxon. Phylogenetically, M. pattersoni sp. nov. is more closely related to M. amazonensis and the specimen UFAC-1424 (formely attributed to M. nativus) than to M. arendsi or M. atopus, whilst Mourasuchus is recovered once more as a monophyletic group. Furthermore, the cladistic analysis performed in this contribution offers a new phylogenetic assessment of Caimaninae, including many taxa described recently for the group. In this study, we also discuss the crocodylian diversity of the Urumaco Formation as well as how paleoenvironment may have contributed toward its evolution. In addition, we provide a discussion of the potential feeding habits of Mourasuchus. In this contribution, Mourasuchus is regarded as a taxon that likely preferred to prey on small animals. The unusual skull morphology of this group may have evolved to cover a large area with the rostrum, allowing for a more efficient prey capture, while the prey may have consisted predominantly of large amounts of small animals.
creator: Giovanne M. Cidade
creator: Andrés Solórzano
creator: Ascanio Daniel Rincón
creator: Douglas Riff
creator: Annie Schmaltz Hsiou
uri: https://doi.org/10.7717/peerj.3056
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Cidade et al.

title: Taxonomic and functional trait diversity of wild bees in different urban settings
link: https://peerj.com/articles/3051
last-modified: 2017-03-07
description: Urbanization is one of the major anthropogenic processes contributing to local habitat loss and extirpation of numerous species, including wild bees, the most widespread pollinators. Little is known about the mechanisms through which urbanization impacts wild bee communities, or the types of urban green spaces that best promote their conservation in cities. The main objective of this study was to describe and compare wild bee community diversity, structure, and dynamics in two Canadian cities, Montreal and Quebec City. A second objective was to compare functional trait diversity among three habitat types (cemeteries, community gardens and urban parks) within each city. Bees were collected using pan traps and netting on the same 46 sites, multiple times, over the active season in 2012 and 2013. A total of 32,237 specimens were identified, representing 200 species and 6 families, including two new continental records, Hylaeus communis Nylander (1852) and Anthidium florentinum (Fabricius, 1775). Despite high community evenness, we found significant abundance of diverse species, including exotic ones. Spatio-temporal analysis showed higher stability in the most urbanized city (Montreal) but low nestedness of species assemblages among the three urban habitats in both cities. Our study demonstrates that cities are home to diverse communities of wild bees, but in turn affect bee community structure and dynamics. We also found that community gardens harbour high levels of functional trait diversity. Urban agriculture therefore contributes substantially to the provision of functionally diverse bee communities and possibly to urban pollination services.
creator: Étienne Normandin
creator: Nicolas J. Vereecken
creator: Christopher M. Buddle
creator: Valérie Fournier
uri: https://doi.org/10.7717/peerj.3051
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Normandin et al.

title: Molecular phylogenies confirm the presence of two cryptic Hemimycale species in the Mediterranean and reveal the polyphyly of the genera Crella and Hemimycale (Demospongiae: Poecilosclerida)
link: https://peerj.com/articles/2958
last-modified: 2017-03-07
description: BackgroundSponges are particularly prone to hiding cryptic species as their paradigmatic plasticity often favors species phenotypic convergence as a result of adaptation to similar habitat conditions. Hemimycale is a sponge genus (Family Hymedesmiidae, Order Poecilosclerida) with four formally described species, from which only Hemimycale columella has been recorded in the Atlanto-Mediterranean basin, on shallow to 80 m deep bottoms. Contrasting biological features between shallow and deep individuals of Hemimycale columella suggested larger genetic differences than those expected between sponge populations. To assess whether shallow and deep populations indeed belong to different species, we performed a phylogenetic study of Hemimycale columella across the Mediterranean. We also included other Hemimycale and Crella species from the Red Sea, with the additional aim of clarifying the relationships of the genus Hemimycale.MethodsHemimycale columella was sampled across the Mediterranean, and Adriatic Seas. Hemimycale arabica and Crella cyathophora were collected from the Red Sea and Pacific. From two to three specimens per species and locality were extracted, amplified for Cytochrome C Oxidase I (COI) (M1–M6 partition), 18S rRNA, and 28S (D3–D5 partition) and sequenced. Sequences were aligned using Clustal W v.1.81. Phylogenetic trees were constructed under neighbor joining (NJ), Bayesian inference (BI), and maximum likelihood (ML) criteria as implemented in Geneious software 9.01. Moreover, spicules of the target species were observed through a Scanning Electron microscope.ResultsThe several phylogenetic reconstructions retrieved both Crella and Hemimycale polyphyletic. Strong differences in COI sequences indicated that C. cyathophora from the Red Sea might belong in a different genus, closer to Hemimycale arabica than to the Atlanto-Mediterranean Crella spp. Molecular and external morphological differences between Hemimycale arabica and the Atlanto-Mediterranean Hemimycale also suggest that Hemimycale arabica fit in a separate genus. On the other hand, the Atlanto-Mediterranean Crellidae appeared in 18S and 28S phylogenies as a sister group of the Atlanto-Mediterranean Hemimycale. Moreover, what was known up to now as Hemimycale columella, is formed by two cryptic species with contrasting bathymetric distributions. Some small but consistent morphological differences allow species distinction.ConclusionsA new family (Hemimycalidae) including the genus Hemimycale and the two purported new genera receiving C. cyathophora and Hemimycale arabica might be proposed according to our phylogenetic results. However, the inclusion of additional Operational Taxonomic Unit (OTUs) appears convenient before taking definite taxonomical decisions. A new cryptic species (Hemimycale mediterranea sp. nov.) is described. Morphologically undifferentiated species with contrasting biological traits, as those here reported, confirm that unidentified cryptic species may confound ecological studies.
creator: Maria J. Uriz
creator: Leire Garate
creator: Gemma Agell
uri: https://doi.org/10.7717/peerj.2958
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Uriz et al.

title: Reanalyzing Head et al. (2015): investigating the robustness of widespread p-hacking
link: https://peerj.com/articles/3068
last-modified: 2017-03-02
description: Head et al. (2015) provided a large collection of p-values that, from their perspective, indicates widespread statistical significance seeking (i.e., p-hacking). This paper inspects this result for robustness. Theoretically, the p-value distribution should be a smooth, decreasing function, but the distribution of reported p-values shows systematically more reported p-values for .01, .02, .03, .04, and .05 than p-values reported to three decimal places, due to apparent tendencies to round p-values to two decimal places. Head et al. (2015) correctly argue that an aggregate p-value distribution could show a bump below .05 when left-skew p-hacking occurs frequently. Moreover, the elimination of p = .045 and p = .05, as done in the original paper, is debatable. Given that eliminating p = .045 is a result of the need for symmetric bins and systematically more p-values are reported to two decimal places than to three decimal places, I did not exclude p = .045 and p = .05. I conducted Fisher’s method .04 < p < .05 and reanalyzed the data by adjusting the bin selection to .03875 < p ≤ .04 versus .04875 < p ≤ .05. Results of the reanalysis indicate that no evidence for left-skew p-hacking remains when we look at the entire range between .04 < p < .05 or when we inspect the second-decimal. Taking into account reporting tendencies when selecting the bins to compare is especially important because this dataset does not allow for the recalculation of the p-values. Moreover, inspecting the bins that include two-decimal reported p-values potentially increases sensitivity if strategic rounding down of p-values as a form of p-hacking is widespread. Given the far-reaching implications of supposed widespread p-hacking throughout the sciences Head et al. (2015), it is important that these findings are robust to data analysis choices if the conclusion is to be considered unequivocal. Although no evidence of widespread left-skew p-hacking is found in this reanalysis, this does not mean that there is no p-hacking at all. These results nuance the conclusion by Head et al. (2015), indicating that the results are not robust and that the evidence for widespread left-skew p-hacking is ambiguous at best.
creator: Chris H.J. Hartgerink
uri: https://doi.org/10.7717/peerj.3068
license: http://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: Survey of owner motivations and veterinary input of owners feeding diets containing raw animal products
link: https://peerj.com/articles/3031
last-modified: 2017-03-02
description: BackgroundThe practice of feeding of diets containing raw animal products (RAP) to pets (dogs and cats) is discouraged by veterinary organizations and governmental public health organizations. Nevertheless, the practice of feeding RAP to pets is increasing in popularity. Pet owner motivations for feeding RAP diets to pets have not been explored and the benefits of RAP diets remain largely anecdotal. We hypothesized that pet owners feeding RAP diets would not rely on veterinary advice in choosing their pet’s diet. We also hypothesized that these owners would have lower levels of trust in veterinary advice with respect to nutrition relative to pet owners not feeding RAP.MethodsAn anonymous web-based survey was developed to identify pet owner motivations for feeding RAP diets, and to characterize the veterinarian-client relationships of individuals feeding RAP diets.ResultsThere were 2,337 respondents and 2,171 completed surveys. Of survey respondents, 804 reported feeding RAP at the time of the survey. While 20% of pet owners feeding RAP relied on online resources to determine what or how much RAP to feed, only 9% reported consulting with a veterinarian in making decisions about feeding RAP. Pet owners feeding RAP reported lower levels of trust in veterinary advice both ‘in general’ and ‘with respect to nutrition’ than pet owners not feeding RAP. Most pet owners reported that a discussion regarding their pet’s nutrition does not occur at every veterinary appointment.DiscussionPet owners feeding a RAP diet have lower trust in veterinary advice than pet owners not feeding a RAP diet. Owners feeding RAP are more reliant on online resources than their own veterinarian in deciding what and how much RAP to feed. Pet owners perceive that nutrition is not discussed at most veterinary appointments. Therefore, there is room for improvement in the veterinarian-client communication with regards to nutrition.
creator: Stewart K. Morgan
creator: Susan Willis
creator: Megan L. Shepherd
uri: https://doi.org/10.7717/peerj.3031
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Morgan et al.

title: New in vitro system to predict chemotherapeutic efficacy of drug combinations in fresh tumor samples
link: https://peerj.com/articles/3030
last-modified: 2017-03-02
description: BackgroundTo find the best individual chemotherapy for cancer patients, the efficacy of different chemotherapeutic drugs can be predicted by pretesting tumor samples in vitro via the chemotherapy-resistance (CTR)-Test®. Although drug combinations are widely used among cancer therapy, so far only single drugs are tested by this and other tests. However, several first line chemotherapies are combining two or more chemotherapeutics, leading to the necessity of drug combination testing methods.MethodsWe established a system to measure and predict the efficacy of chemotherapeutic drug combinations with the help of the Loewe additivity concept in combination with the CTR-test. A combination is measured by using half of the monotherapy’s concentration of both drugs simultaneously. With this method, the efficacy of a combination can also be calculated based on single drug measurements.ResultsThe established system was tested on a data set of ovarian carcinoma samples using the combination carboplatin and paclitaxel and confirmed by using other tumor species and chemotherapeutics. Comparing the measured and the calculated values of the combination testings revealed a high correlation. Additionally, in 70% of the cases the measured and the calculated values lead to the same chemotherapeutic resistance category of the tumor.ConclusionOur data suggest that the best drug combination consists of the most efficient single drugs and the worst drug combination of the least efficient single drugs. Our results showed that single measurements are sufficient to predict combinations in specific cases but there are exceptions in which it is necessary to measure combinations, which is possible with the presented system.
creator: Frank Christian Kischkel
creator: Julia Eich
creator: Carina I. Meyer
creator: Paula Weidemüller
creator: Jens Krapfl
creator: Rauaa Yassin-Kelepir
creator: Laura Job
creator: Marius Fraefel
creator: Ioana Braicu
creator: Annette Kopp-Schneider
creator: Jalid Sehouli
creator: Rudy Leon De Wilde
uri: https://doi.org/10.7717/peerj.3030
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Kischkel et al.

title: The effects of elevated pain inhibition on endurance exercise performance
link: https://peerj.com/articles/3028
last-modified: 2017-03-02
description: BackgroundThe ergogenic effects of analgesic substances suggest that pain perception is an important regulator of work-rate during fatiguing exercise. Recent research has shown that endogenous inhibitory responses, which act to attenuate nociceptive input and reduce perceived pain, can be increased following transcranial direct current stimulation of the hand motor cortex. Using high-definition transcranial direct current stimulation (HD-tDCS; 2 mA, 20 min), the current study aimed to examine the effects of elevated pain inhibitory capacity on endurance exercise performance. It was hypothesised that HD-tDCS would enhance the efficiency of the endogenous pain inhibitory response and improve endurance exercise performance.MethodsTwelve healthy males between 18 and 40 years of age (M = 24.42 ± 3.85) were recruited for participation. Endogenous pain inhibitory capacity and exercise performance were assessed before and after both active and sham (placebo) stimulation. The conditioned pain modulation protocol was used for the measurement of pain inhibition. Exercise performance assessment consisted of both maximal voluntary contraction (MVC) and submaximal muscular endurance performance trials using isometric contractions of the non-dominant leg extensors.ResultsActive HD-tDCS (pre-tDCS, −.32 ± 1.33 kg; post-tDCS, −1.23 ± 1.21 kg) significantly increased pain inhibitory responses relative to the effects of sham HD-tDCS (pre-tDCS, −.91 ± .92 kg; post-tDCS, −.26 ± .92 kg; p = .046). Irrespective of condition, peak MVC force and muscular endurance was reduced from pre- to post-stimulation. HD-tDCS did not significantly influence this reduction in maximal force (active: pre-tDCS, 264.89 ± 66.87 Nm; post-tDCS, 236.33 ± 66.51 Nm; sham: pre-tDCS, 249.25 ± 88.56 Nm; post-tDCS, 239.63 ± 67.53 Nm) or muscular endurance (active: pre-tDCS, 104.65 ± 42.36 s; post-tDCS, 93.07 ± 33.73 s; sham: pre-tDCS, 123.42 ± 72.48 s; post-tDCS, 100.27 ± 44.25 s).DiscussionDespite increasing pain inhibitory capacity relative to sham stimulation, active HD-tDCS did not significantly elevate maximal force production or muscular endurance. These findings question the role of endogenous pain inhibitory networks in the regulation of exercise performance.
creator: Andrew Flood
creator: Gordon Waddington
creator: Richard J. Keegan
creator: Kevin G. Thompson
creator: Stuart Cathcart
uri: https://doi.org/10.7717/peerj.3028
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Flood et al.

title: Key bacterial families (Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae) are related to the digestion of protein and energy in dogs
link: https://peerj.com/articles/3019
last-modified: 2017-03-02
description: BackgroundMuch of the recent research in companion animal nutrition has focussed on understanding the role of diet on faecal microbiota composition. To date, diet-induced changes in faecal microbiota observed in humans and rodents have been extrapolated to pets in spite of their very different dietary and metabolic requirements. This lack of direct evidence means that the mechanisms by which microbiota influences health in dogs are poorly understood. We hypothesised that changes in faecal microbiota correlate with physiological parameters including apparent macronutrient digestibility.MethodsFifteen adult dogs were assigned to two diet groups, exclusively fed either a premium kibbled diet (kibble; K; n = 8) or a raw red meat diet (meat; M; n = 7) for nine weeks. Apparent digestibility of macronutrients (protein, fat, gross energy and dry matter), faecal weight, faecal health scores, faecal VFA concentrations and faecal microbial composition were determined. Datasets were integrated using mixOmics in R.ResultsFaecal weight and VFA levels were lower and the apparent digestibility of protein and energy were higher in dogs on the meat diet. Diet significantly affected 27 microbial families and 53 genera in the faeces. In particular, the abundances of Bacteriodes, Prevotella, Peptostreptococcus and Faecalibacterium were lower in dogs fed the meat diet, whereas Fusobacterium, Lactobacillus and Clostridium were all more abundant.DiscussionOur results show clear associations of specific microbial taxa with diet composition. For example, Clostridiaceae, Erysipelotrichaceae and Bacteroidaceae were highly correlated to parameters such as protein and fat digestibility in the dog. By understanding the relationship between faecal microbiota and physiological parameters we will gain better insights into the effects of diet on the nutrition of our pets.
creator: Emma N. Bermingham
creator: Paul Maclean
creator: David G. Thomas
creator: Nicholas J. Cave
creator: Wayne Young
uri: https://doi.org/10.7717/peerj.3019
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Bermingham et al.

title: Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae)
link: https://peerj.com/articles/3018
last-modified: 2017-03-02
description: The iconic gastropod genus Cyphoma is commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genus Cyphoma has a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisability Cyphoma gibbosum has been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S) for three Cyphoma species (C. gibbosum, C. mcgintyi, C. signatum) and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a result C. mcgintyi and C. signatum are synonymised with C. gibbosum, which is a key result for future work using C. gibbosum as a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism), or incipient speciation.
creator: Bastian T. Reijnen
creator: Sancia E.T. van der Meij
uri: https://doi.org/10.7717/peerj.3018
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Reijnen and Van der Meij

title: Asymmetry of mandibular dentition is associated with dietary specialization in snail-eating snakes
link: https://peerj.com/articles/3011
last-modified: 2017-03-02
description: BackgroundIn vertebrates, the left-and-right pairs of homologous organs are generally present in equal numbers. A remarkable exception is known in the snail-eating snakes of the family Pareidae: almost all the pareid snakes have much more teeth on the right mandible than on the left for functional specialization in feeding on the dextral majority of land snails. Because the only exceptional species with symmetric dentition has been regarded as a slug-eater, the extent of dietary specialization on slugs could shape the degree of the lateral asymmetry of mandibular dentition (dentition asymmetry) even among snail eaters.MethodsTo test this, I compared the morphology and behavior of two sympatric species of Taiwanese snail-eating snakes, Pareas atayal and P. formosensis.ResultsSpecimens collected in the same locality showed that the dentition asymmetry of P. formosensis was significantly smaller than that of P. atayal. Congruent to its weak asymmetry, P. formosensis showed a strong preference of slugs to snails in the feeding experiment.DiscussionThe dietary specialization of P. formosensis on slugs would contribute to niche partitioning from the sympatric congener P. atayal. This study suggests that the diverse variation in the dentition asymmetry of pareid snakes is the result of their dietary specialization and divergence.
creator: Masaki Hoso
uri: https://doi.org/10.7717/peerj.3011
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Hoso