The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L
Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism. Results for codon usage and relative synonymous codon usage show a strong bias towards NNA and NNT codons in the two cp genomes. Analysis of a plot of the effective number of codons (ENc) for five Morus spp. cp genomes showed that most genes follow the standard curve, but several genes have ENc values below the expected curve. The results indicate that both natural selection and mutational bias have contributed to the codon bias. Ten highly variable regions were identified among the five Morus spp. cp genomes, and 154 single-nucleotide polymorphism mutation events were accurately located in the gene coding region.
Kong et al. (2017) The complete chloroplast genome sequence of Morus cathayana and Morus multicaulis, and comparative analysis within genus Morus L. PeerJ 5:e3037 https://doi.org/10.7717/peerj.3037
BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation
Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
Graham et al. (2017) BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation. PeerJ 5:e3035 https://doi.org/10.7717/peerj.3035
Attachment anxiety is associated with a fear of becoming fat, which is mediated by binge eating
Background Previous work demonstrated that individuals with higher levels of attachment anxiety are prone to increased binge eating (Alexander & Siegel, 2013). Given that our society rejects obese individuals and individuals with higher levels of attachment anxiety tend to be highly sensitive to rejection (Downey & Feldman, 1996), it follows that those with increased attachment anxiety may be especially fearful of becoming fat. Methods Undergraduate psychology students (n = 148) completed surveys measuring attachment, binge eating, and fear of becoming fat. Results The data demonstrate that attachment anxiety is positively associated with a fear of becoming fat (β = .30, p < .001) and binge eating mediates this relationship. In other words, binge eating underlies the fear of becoming fat. Discussion These findings contribute to a more refined understanding of binge eating which may create pathways for professionals to develop targeted interventions.
Alexander (2017) Attachment anxiety is associated with a fear of becoming fat, which is mediated by binge eating. PeerJ 5:e3034 https://doi.org/10.7717/peerj.3034
Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi
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.
Berná et al. (2017) Transcriptomic analysis reveals metabolic switches and surface remodeling as key processes for stage transition in Trypanosoma cruzi. PeerJ 5:e3017 https://doi.org/10.7717/peerj.3017
True’s beaked whale (Mesoplodon mirus) in Macaronesia
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.
Aguilar de Soto et al. (2017) True’s beaked whale (Mesoplodon mirus) in Macaronesia. PeerJ 5:e3059 https://doi.org/10.7717/peerj.3059
Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens
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.
Crisol-Martínez et al. (2017) Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens. PeerJ 5:e3071 https://doi.org/10.7717/peerj.3071
Most ornamental plants on sale in garden centres are unattractive to flower-visiting insects
Background Gardeners 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. Methods We 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. Results We 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. Discussion Our 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.
Garbuzov et al. (2017) Most ornamental plants on sale in garden centres are unattractive to flower-visiting insects. PeerJ 5:e3066 https://doi.org/10.7717/peerj.3066
Evolution of sexual dimorphism and Rensch’s rule in the beetle genus Limnebius (Hydraenidae): is sexual selection opportunistic?
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.
Rudoy et al. (2017) Evolution of sexual dimorphism and Rensch’s rule in the beetle genus Limnebius (Hydraenidae): is sexual selection opportunistic?. PeerJ 5:e3060 https://doi.org/10.7717/peerj.3060
When moult overlaps migration: moult-related changes in plasma biochemistry of migrating common snipe
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.
Podlaszczuk et al. (2017) When moult overlaps migration: moult-related changes in plasma biochemistry of migrating common snipe. PeerJ 5:e3057 https://doi.org/10.7717/peerj.3057
A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus
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.
Cidade et al. (2017) A new Mourasuchus (Alligatoroidea, Caimaninae) from the late Miocene of Venezuela, the phylogeny of Caimaninae and considerations on the feeding habits of Mourasuchus. PeerJ 5:e3056 https://doi.org/10.7717/peerj.3056