title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1738 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi link: https://peerj.com/articles/3017 last-modified: 2017-03-08 description: American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes. This analysis allowed us to delineate specific transcriptomic profiling for each stage, and also to identify those biological processes of major relevance in each state. Stage specific expression profiling evidenced the plasticity of T. cruzi to adapt quickly to different conditions, with particular focus on membrane remodeling and metabolic shifts along the life cycle. Epimastigotes, which replicate in the gut of insect vectors, showed higher expression of genes related to energy metabolism, mainly Krebs cycle, respiratory chain and oxidative phosphorylation related genes, and anabolism related genes associated to nucleotide and steroid biosynthesis; also, a general down-regulation of surface glycoprotein coding genes was seen at this stage. Trypomastigotes, living extracellularly in the bloodstream of mammals, express a plethora of surface proteins and signaling genes involved in invasion and evasion of immune response. Amastigotes mostly express membrane transporters and genes involved in regulation of cell cycle, and also express a specific subset of surface glycoprotein coding genes. In addition, these results allowed us to improve the annotation of the Dm28c genome, identifying new ORFs and set the stage for construction of networks of co-expression, which can give clues about coded proteins of unknown functions. creator: Luisa Berná creator: Maria Laura Chiribao creator: Gonzalo Greif creator: Matias Rodriguez creator: Fernando Alvarez-Valin creator: Carlos Robello uri: https://doi.org/10.7717/peerj.3017 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Berná et al. title: True’s beaked whale (Mesoplodon mirus) in Macaronesia link: https://peerj.com/articles/3059 last-modified: 2017-03-07 description: The True’s beaked whale (Mesoplodon mirus, True 1913) is a poorly known member of the Ziphiidae family. Its distribution in the northern hemisphere is thought to be restricted to the temperate or warm temperate waters of the North Atlantic, while a few stranding records from the southern hemisphere suggest a wider and antitropical distribution, extending to waters from the Atlantic coast of Brazil to South Africa, Mozambique, Australia and the Tasman Sea coast of New Zealand. This paper (i) reports the first molecular confirmation of the occurrence of the True’s beaked whale at the southern limit of its distribution recorded in the northeast Atlantic: the Azores and Canary Islands (macaronesian ecoregion); (ii) describes a new colouration for this species using evidence from a whale with molecular species confirmation; and (iii) contributes to the sparse worldwide database of live sightings, including the first underwater video recording of this species and close images of a calf. Species identification was confirmed in two cases using mitochondrial DNA control region and cytochrome b gene markers: a subadult male True’s beaked whale that stranded in El Hierro, Canary Islands, in November 2012, and a subadult male found floating dead near Faial, the Azores, in July 2004. The whale that stranded in the Canary Islands had a clearly delimited white area on its head, extending posteriorly from the tip of the beak to cover the blowhole dorsally and the gular grooves ventrally. This colouration contrasts with previous descriptions for the species and it may be rare, but it exemplifies the variability of the colouration of True’s beaked whales in the North Atlantic, further confirmed here by live sightings data. The recording of several observations of this species in deep but relatively coastal waters off the Azores and the Canary Islands suggests that these archipelagos may be unique locations to study the behaviour of the enigmatic True’s beaked whale. creator: Natacha Aguilar de Soto creator: Vidal Martín creator: Monica Silva creator: Roland Edler creator: Cristel Reyes creator: Manuel Carrillo creator: Agustina Schiavi creator: Talia Morales creator: Belen García-Ovide creator: Anna Sanchez-Mora creator: Nerea Garcia-Tavero creator: Lisa Steiner creator: Michael Scheer creator: Roland Gockel creator: Dylan Walker creator: Enrico Villa creator: Petra Szlama creator: Ida K. Eriksson creator: Marisa Tejedor creator: Monica Perez-Gil creator: João Quaresma creator: Wojtek Bachara creator: Emma Carroll uri: https://doi.org/10.7717/peerj.3059 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Aguilar de Soto et al. title: Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens link: https://peerj.com/articles/3071 last-modified: 2017-03-07 description: This study compared the effects of wheat- and sorghum-based diets on broiler chickens. The growth performance and caecal microbial community of chickens were measured and correlations between productivity and specific gut microbes were observed. Cobb broilers 15 days of age were individually caged and two dietary treatments were used, one with a wheat-based diet (n = 48) and another one with a sorghum-based diet (n = 48). Growth performance measurements were taken over a 10 day period and samples for microbiota analysis were taken at the end of that period. Caecal microbiota was characterised by sequencing of 16S bacterial rRNA gene amplicons. Overall, the results indicated that a sorghum-based diet produced higher apparent metabolisable energy (AME) and body-weight gain (BWG) values in chickens, compared to a wheat-based diet. Nevertheless, sorghum-fed birds had higher feed conversion ratio (FCR) values than wheat-fed birds, possibly because of some anti-nutritional factors in sorghum. Further analyses showed that caecal microbial community was significantly associated with AME values, but microbiota composition differed between dietary treatments. A number of bacteria were individually correlated with growth performance measurements. Numerous OTUs assigned to strains of Lactobacillus crispatus and Lachnospiraceae, which were prevalent in sorghum-fed chickens, were correlated with high AME and BWG values, respectively. Additionally, a number of OTUs assigned to Clostridiales that were prevalent in wheat-fed chickens were correlated with low FCR values. Overall, these results suggest that between-diet variations in growth performance were partly associated with changes in the caecal microbiota. creator: Eduardo Crisol-Martínez creator: Dragana Stanley creator: Mark S. Geier creator: Robert J. Hughes creator: Robert J. Moore uri: https://doi.org/10.7717/peerj.3071 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Crisol-Martínez et al. title: Most ornamental plants on sale in garden centres are unattractive to flower-visiting insects link: https://peerj.com/articles/3066 last-modified: 2017-03-07 description: BackgroundGardeners and park managers seeking to support biodiversity in urban areas often plant ornamentals attractive to flower-visiting insects. There is a huge diversity of garden plant varieties, and some recommendations are available as to which are attractive to insects. However, these are largely not based on rigorous empirical data. An important factor in consumer choice is the range of varieties available for purchase. In the UK, garden centres are a key link in the supply chain between growers and private gardens. This study is the first to determine the proportions of flowering ornamentals being sold that are attractive to flower-visiting insects.MethodsWe surveyed six garden centres in Sussex, UK, each over two days in 2015, by making 12 counts of insects visiting patches of each ornamental plant on display for sale that was in bloom. To provide a consistent baseline among different locations, we brought with us and surveyed marjoram (Origanum vulgare) plants in pots, which are known to be attractive to a wide range of flower-visiting insects. The attractiveness of plant varieties to insects was then expressed in two ways: the absolute number and relative to that on marjoram (‘marjoram score’), both per unit area of plant cover. In addition, we noted whether each variety was recommended as pollinator-friendly either via a symbol on the label, or by being included in the Royal Horticultural Society’s ‘Perfect for Pollinators’ list. Furthermore, we compared the attractiveness of plants that are typically grown for more than one year versus only one year.ResultsWe surveyed 59–74 plant varieties in bloom across the six garden centres. In each garden centre, the distributions of variety attractiveness were highly skewed to the right, with most varieties being relatively unattractive, and few varieties highly attractive to flower-visiting insects. The median attractiveness of varieties with a recommendation was 4.2× higher than that of varieties without. But, due to the large variation there was a substantial number of both poor varieties that had a recommendation and good varieties that did not. Median attractiveness of multi-year plants was 1.6× that of single-year plants, with a similar overlap in distributions.DiscussionOur study demonstrates the practicality of carrying out plant surveys in garden centres. Garden centres display large numbers of varieties for sale, most of which are in bloom. Furthermore, data gathered in garden centres appear to correlate well with data gathered in two previous studies in Sussex for plants established in gardens. Although it is unclear whether the varieties being sold in garden centres are a fair representation of varieties that are actually grown by gardeners, our results suggest that there might be considerable scope for making parks and gardens considerably more insect-friendly through judicious variety choices. creator: Mihail Garbuzov creator: Karin Alton creator: Francis L.W. Ratnieks uri: https://doi.org/10.7717/peerj.3066 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Garbuzov et al. title: Evolution of sexual dimorphism and Rensch’s rule in the beetle genus Limnebius (Hydraenidae): is sexual selection opportunistic? link: https://peerj.com/articles/3060 last-modified: 2017-03-07 description: Sexual size dimorphism (SSD) is widespread among animals, with larger females usually attributed to an optimization of resources in reproduction and larger males to sexual selection. A general pattern in the evolution of SSD is Rensch’s rule, which states that SSD increases with body size in species with larger males but decreases when females are larger. We studied the evolution of SSD in the genus Limnebius (Coleoptera, Hydraenidae), measuring SSD and male genital size and complexity of ca. 80% of its 150 species and reconstructing its evolution in a molecular phylogeny with 71 species. We found strong support for a higher evolutionary lability of male body size, which had an overall positive allometry with respect to females and higher evolutionary rates measured over the individual branches of the phylogeny. Increases in SSD were associated to increases in body size, but there were some exceptions with an increase associated to changes in only one sex. Secondary sexual characters (SSC) in the external morphology of males appeared several times independently, generally on species that had already increased their size. There was an overall significant correlation between SSD, male body size and male genital size and complexity, although some lineages with complex genitalia had low SSD, and some small species with complex genitalia had no SSD. Our results suggest that the origin of the higher evolutionary variance of male body size may be due to lack of constraints rather than to sexual selection, that may start to act in species with already larger males due to random variation. creator: Andrey Rudoy creator: Ignacio Ribera uri: https://doi.org/10.7717/peerj.3060 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Rudoy and Ribera title: When moult overlaps migration: moult-related changes in plasma biochemistry of migrating common snipe link: https://peerj.com/articles/3057 last-modified: 2017-03-07 description: Moult of feathers entails considerable physiological and energetic costs to an avian organism. Even under favourable feeding conditions, endogenous body stores and energy reserves of moulting birds are usually severely depleted. Thus, most species of birds separate moult from other energy-demanding activities, such as migration or reproduction. Common snipe Gallinago gallinago is an exception, as during the first autumn migration many young snipe initiate the post-juvenile moult, which includes replacement of body feathers, lesser and median wing coverts, tertials, and rectrices. Here, we evaluated moult-related changes in blood plasma biochemistry of the common snipe during a period of serious trade-off in energy allocation between moult and migration. For this purpose, concentrations of basic metabolites in plasma were evaluated in more than 500 young snipe migrating through Central Europe. We found significant changes in the plasma concentrations of total protein, triglyceride and glucose over the course of moult, while the concentrations of uric acid and albumin did not change. Total protein concentration increased significantly in the initial stage of moult, probably as a result of increased production of keratin, but it decreased to the pre-moult level at the advanced stage of moult. Plasma triglyceride concentration decreased during the period of tertial and rectrice moult, which reflected depletion of endogenous fat reserves. By contrast, glucose concentration increased steadily during the course of moult, which could be caused by increased catabolism of triglycerides (via gluconeogenesis) or, alternatively, due to increased glucocorticoids as a stress response. Our results suggest that physiological changes associated with moult may be considered important determinants of the low pace of migration typical of the common snipe. creator: Patrycja Podlaszczuk creator: Radosław Włodarczyk creator: Tomasz Janiszewski creator: Krzysztof Kaczmarek creator: Piotr Minias uri: https://doi.org/10.7717/peerj.3057 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Podlaszczuk et al. 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: