title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1500 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cortical bone adaptation and mineral mobilization in the subterranean mammal Bathyergus suillus (Rodentia: Bathyergidae): effects of age and sex link: https://peerj.com/articles/4944 last-modified: 2018-06-11 description: The patterns of bone modeling and mineral mobilization (skeletal homeostasis) among mammals other than humans and laboratory rodents are still poorly known. In this study we assessed the pattern of bone formation and bone resorption in the femur of a wild population of Cape dune molerats, Bathyergus suillus (n = 41) (Bathyergidae), a solitary subterranean mammal with a marked extended longevity among rodents, and which also lives in a naturally deficient state of vitamin D. In order to determine ontogenetic and sex effects on histomorphometric parameters of transversal undecalcified bone sections, two-way ANOVA, linear mixed-effects model and regression statistical analyses were performed. During ontogeny, B. suillus increased their cross sectional area, cortical area and cortical thickness, and most importantly, they showed scarce endosteal bone resorption which resulted in a retained medullary cavity size during ontogeny. This resulted in a positively imbalanced bone modeling, where bone formation considerably surpasses bone loss by almost 100-fold in adulthood. This differs markedly from other terrestrial mammals with relatively thin cortical walls. Regarding bone loss and remodeling, three main processes involving intracortical resorption were observed: modeling-related bone loss in early postnatal growth; secondary osteon formation occurring in both sexes; and subendosteal secondary reconstruction observed only in females. The latter is accompanied by females having six-fold more relative bone loss than males, which is evidenced by the development of enlarged resorption cavities (RCs) distributed circumferentially around the medullary cavity. Males have smaller, more circular and randomly distributed RCs. In general, our data indicate no age-related decline in mineral content in B. suillus, and provides strong support for a pattern of sexual dimorphism in skeletal homeostasis, similar to that occurring in humans and other mammals, with females losing more bone throughout aging as compared to males due to reproductive factors. Interestingly as well, despite the high mechanical loads experienced during burrow construction, bone remodeling in B. suillus is kept at very low levels throughout their lifespan, and dense Haversian tissue never forms. This study represents the first comprehensive assessment of skeletal homeostasis in a subterranean mammal, and it enables a better understanding of the complex processes governing the acquisition and maintenance of bone properties in this species with extraordinary fossorial adaptations. creator: Germán Montoya-Sanhueza creator: Anusuya Chinsamy uri: https://doi.org/10.7717/peerj.4944 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Montoya-Sanhueza and Chinsamy title: Sex-based differences in anti-predator response of crickets to chemical cues of a mammalian predator link: https://peerj.com/articles/4923 last-modified: 2018-06-11 description: Anti-predator behaviors like vigilance or hiding come at the expense of other fitness increasing behaviors such as foraging. To compensate for this trade-off, prey assess predation risk and modify the frequency of anti-predator behaviors according to the likelihood of the threat. In this study, we tested the ability of house crickets (Acheta domesticus) to indirectly assess predation risk via odors from a mammalian predator, Elliot’s short-tailed shrew (Blarina hylophaga). As natural differences in encounter rates and predation risk differs between sexes, we tested if male and female crickets perceive similar rates of predation risk from the presence of shrew odor measured via anti-predator behavioral response. Crickets were placed in enclosed, cardboard-lined chambers either treated with shrew odor or control, along with a food source. Time until foraging was measured for each individual and compared across treatment and sex. We found that in the presence of shrew odor, female crickets delayed foraging while males showed no response. These results suggest adult crickets can use chemical cues to detect mammalian predators. Furthermore, we demonstrate that female crickets associate greater predation risk from shrew predators than do male crickets, which are more stationary yet acoustically conspicuous. As predation risk potentially differs drastically for each sex, changes to the operational sex ratios of wild cricket populations could be influenced by the identity of the predator community. creator: Brian P. Tanis creator: Bradley Bott creator: Brian J. Gaston uri: https://doi.org/10.7717/peerj.4923 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Tanis et al. title: Diversity and abundance of conspicuous macrocrustaceans on coral reefs differing in level of degradation link: https://peerj.com/articles/4922 last-modified: 2018-06-11 description: Coral reefs sustain abundant and diverse macrocrustaceans that perform multiple ecological roles, but coral reefs are undergoing massive degradation that may be driving changes in the species composition and abundance of reef-associated macrocrustaceans. To provide insight into this issue, we used non-destructive visual census techniques to compare the diversity and abundance of conspicuous macrocrustaceans (i.e., those >1 cm and visible without disturbance) between two shallow Caribbean coral reefs similar in size (∼1.5 km in length) and close to each other, but one (“Limones”) characterized by extensive stands of the branching coral Acropora palmata, and the other (“Bonanza”) dominated by macroalgae and relic coral skeletons and rubble (i.e., degraded). We also assessed the structural complexity of each reef and the percent cover of various benthic community components. Given the type of growth of A. palmata, we expected to find a greater structural complexity, a higher cover of live coral, and a lower cover of macroalgae on Limones, and hence a more diverse and abundant macrocrustacean community on this reef compared with Bonanza. Overall, we identified 63 macrocrustacean species (61 Decapoda and two Stomatopoda). Contrary to our expectations, structural complexity did not differ significantly between the back-reef zones of these reefs but varied more broadly on Limones, and the diversity and abundance of macrocrustaceans were higher on Bonanza than on Limones despite live coral cover being higher on Limones and macroalgal cover higher on Bonanza. However, the use of various types of microhabitats by macrocrustaceans differed substantially between reefs. On both reefs, the dominant species were the clinging crab Mithraculus coryphe and the hermit crab Calcinus tibicen, but the former was more abundant on Bonanza and the latter on Limones. M. coryphe occupied a diverse array of microhabitats but mostly coral rubble and relic skeletons, whereas C. tibicen was often, but not always, found associated with colonies of Millepora spp. A small commensal crab of A. palmata, Domecia acanthophora, was far more abundant on Limones, emerging as the main discriminant species between reefs. Our results suggest that local diversity and abundance of reef-associated macrocrustaceans are partially modulated by habitat degradation, the diversity of microhabitat types, and the establishment of different commensal associations rather than by structural complexity alone. creator: Roberto González-Gómez creator: Patricia Briones-Fourzán creator: Lorenzo Álvarez-Filip creator: Enrique Lozano-Álvarez uri: https://doi.org/10.7717/peerj.4922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 González-Gómez et al. title: BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees link: https://peerj.com/articles/4987 last-modified: 2018-06-08 description: Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recently, we introduced Bad Clade Deletion (BCD) supertrees which combines the graph-based computation of minimum cuts with optimizing a global objective function on the matrix representation of the input trees. The BCD supertree method has guaranteed polynomial running time and is very swift in practice. The quality of reconstructed supertrees was superior to matrix representation with parsimony (MRP) and usually on par with SuperFine for simulated data; but particularly for biological data, quality of BCD supertrees could not keep up with SuperFine supertrees. Here, we present a beam search extension for the BCD algorithm that keeps alive a constant number of partial solutions in each top-down iteration phase. The guaranteed worst-case running time of the new algorithm is still polynomial in the size of the input. We present an exact and a randomized subroutine to generate suboptimal partial solutions. Both beam search approaches consistently improve supertree quality on all evaluated datasets when keeping 25 suboptimal solutions alive. Supertree quality of the BCD Beam Search algorithm is on par with MRP and SuperFine even for biological data. This is the best performance of a polynomial-time supertree algorithm reported so far. creator: Markus Fleischauer creator: Sebastian Böcker uri: https://doi.org/10.7717/peerj.4987 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Fleischauer and Böcker title: Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam link: https://peerj.com/articles/4970 last-modified: 2018-06-08 description: Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate sponge-associated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to sponge-prokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region. creator: Ton That Huu Dat creator: Georg Steinert creator: Nguyen Thi Kim Cuc creator: Hauke Smidt creator: Detmer Sipkema uri: https://doi.org/10.7717/peerj.4970 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Dat et al. title: Gorgonopsian therapsids (Nochnitsa gen. nov. and Viatkogorgon) from the Permian Kotelnich locality of Russia link: https://peerj.com/articles/4954 last-modified: 2018-06-08 description: The early evolution of gorgonopsians is poorly understood. New material from the Kotelnich locality in Russia expands our knowledge of middle/earliest late Permian gorgonopsians from Laurasia. Two gorgonopsian taxa are recognized from Kotelnich: Viatkogorgon ivakhnenkoi Tatarinov, 1999 and Nochnitsa geminidens gen. et sp. nov. Nochnitsa can be distinguished from all known gorgonopsians by its unique upper postcanine tooth row, composed of pairs of teeth (a small anterior and larger posterior) separated by diastemata. Both Viatkogorgon and Nochnitsa are relatively small gorgonopsians, comparable in size to the South African middle Permian taxon Eriphostoma. Inclusion of Viatkogorgon and Nochnitsa in a phylogenetic analysis of gorgonopsians recovers them in basal positions, with Nochnitsa representing the earliest-diverging gorgonopsian genus. All other sampled gorgonopsians fall into two major subclades: one made up entirely of Russian taxa (Inostrancevia, Pravoslavlevia, Sauroctonus, and Suchogorgon) and the other containing only African gorgonopsians. The high degree of endemism indicated in this analysis for gorgonopsians is remarkable, especially given the extensive intercontinental dispersal inferred for coeval therapsid groups. creator: Christian F. Kammerer creator: Vladimir Masyutin uri: https://doi.org/10.7717/peerj.4954 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kammerer et al. title: Process-based allometry describes the influence of management on orchard tree aboveground architecture link: https://peerj.com/articles/4949 last-modified: 2018-06-08 description: We evaluated allometric relationships in length, diameter, and mass of branches for two variably managed orchard tree species (tart cherry, Prunus cerasus; apple, Malus spp.). The empirically estimated allometric exponents (a) of the orchard trees were described in the context of two processed-based allometry models that make predictions for a: the West, Brown and Enquist fractal branching model (WBE) and the recently introduced Flow Similarity model (FS). These allometric models make predictions about relationships in plant morphology (e.g., branch mass, diameter, length, volume, surface area) based on constraints imposed on plant growth by physical and physiological processes. We compared our empirical estimates of a to the model predictions to interpret the physiological implications of pruning and management in orchard systems. Our study found strong allometric relationships among the species and individuals studied with limited agreement with the expectations of either model. The 8/3-power law prediction of the mass ∼ diameter relationship by the WBE, indicative of biomechanical limitations, was marginally supported by this study. Length-including allometric relationships deviated from predictions of both models, but shift toward the expectation of flow similarity. In this way, managed orchard trees deviated from strict adherence to the idealized expectations of the models, but still fall within the range of model expectations in many cases despite intensive management. creator: Zachary T. Brym creator: S.K. Morgan Ernest uri: https://doi.org/10.7717/peerj.4949 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Brym and Ernest title: A new therocephalian (Gorynychus masyutinae gen. et sp. nov.) from the Permian Kotelnich locality, Kirov Region, Russia link: https://peerj.com/articles/4933 last-modified: 2018-06-08 description: A new therocephalian taxon (Gorynychus masyutinae gen. et sp. nov.) is described based on a nearly complete skull and partial postcranium from the Permian Kotelnich locality of Russia. Gorynychus displays an unusual mixture of primitive (“pristerosaurian”) and derived (eutherocephalian) characters. Primitive features of Gorynychus include extensive dentition on the palatal boss and transverse process of the pterygoid, paired vomers, and a prominent dentary angle; derived features include the absence of the postfrontal. Gorynychus can be distinguished from all other therocephalians by its autapomorphic dental morphology, with roughly denticulated incisors and postcanines. Phylogenetic analysis recovers Gorynychus as a non-lycosuchid, non-scylacosaurid therocephalian situated as sister-taxon to Eutherocephalia. The identification of Gorynychus as the largest predator from Kotelnich indicates that therocephalians acted as apex predators in middle–late Permian transition ecosystems in Russia, corroborating a pattern observed in South African faunas. However, other aspects of the Kotelnich fauna, and Permian Russian tetrapod faunas in general, differ markedly from those of South Africa and suggest that Karoo faunas are not necessarily representative of global patterns. creator: Christian F. Kammerer creator: Vladimir Masyutin uri: https://doi.org/10.7717/peerj.4933 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Kammerer and Masyutin title: Literature-based latitudinal distribution and possible range shifts of two US east coast dune grass species (Uniola paniculata and Ammophila breviligulata) link: https://peerj.com/articles/4932 last-modified: 2018-06-08 description: Previous work on the US Atlantic coast has generally shown that coastal foredunes are dominated by two dune grass species, Ammophila breviligulata (American beachgrass) and Uniola paniculata (sea oats). From Virginia northward, A. breviligulata dominates, while U. paniculata is the dominant grass south of Virginia. Previous work suggests that these grasses influence the shape of coastal foredunes in species-specific ways, and that they respond differently to environmental stressors; thus, it is important to know which species dominates a given dune system. The range boundaries of these two species remains unclear given the lack of comprehensive surveys. In an attempt to determine these boundaries, we conducted a literature survey of 98 studies that either stated the range limits and/or included field-based studies/observations of the two grass species. We then produced an interactive map that summarizes the locations of the surveyed papers and books. The literature review suggests that the current southern range limit for A. breviligulata is Cape Fear, NC, and the northern range limit for U. paniculata is Assateague Island, on the Maryland and Virginia border. Our data suggest a northward expansion of U. paniculata, possibly associated with warming trends observed near the northern range limit in Painter, VA. In contrast, the data regarding a range shift for A. breviligulata remain inconclusive. We also compare our literature-based map with geolocated records from the Global Biodiversity Information Facility and iNaturalist research grade crowd-sourced observations. We intend for our literature-based map to aid coastal researchers who are interested in the dynamics of these two species and the potential for their ranges to shift as a result of climate change. creator: Evan B. Goldstein creator: Elsemarie V. Mullins creator: Laura J. Moore creator: Reuben G. Biel creator: Joseph K. Brown creator: Sally D. Hacker creator: Katya R. Jay creator: Rebecca S. Mostow creator: Peter Ruggiero creator: Julie C. Zinnert uri: https://doi.org/10.7717/peerj.4932 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2018 Goldstein et al. title: MipLAAO, a new L-amino acid oxidase from the redtail coral snake Micrurus mipartitus link: https://peerj.com/articles/4924 last-modified: 2018-06-08 description: L-amino acid oxidases (LAAOs) are ubiquitous enzymes in nature. Bioactivities described for these enzymes include apoptosis induction, edema formation, induction or inhibition of platelet aggregation, as well as antiviral, antiparasite, and antibacterial actions. With over 80 species, Micrurus snakes are the representatives of the Elapidae family in the New World. Although LAAOs in Micrurus venoms have been predicted by venom gland transcriptomic studies and detected in proteomic studies, no enzymes of this kind have been previously purified from their venoms. Earlier proteomic studies revealed that the venom of M. mipartitus from Colombia contains ∼4% of LAAO. This enzyme, here named MipLAAO, was isolated and biochemically and functionally characterized. The enzyme is found in monomeric form, with an isotope-averaged molecular mass of 59,100.6 Da, as determined by MALDI-TOF. Its oxidase activity shows substrate preference for hydrophobic amino acids, being optimal at pH 8.0. By nucleotide sequencing of venom gland cDNA of mRNA transcripts obtained from a single snake, six isoforms of MipLAAO with minor variations among them were retrieved. The deduced sequences present a mature chain of 483 amino acids, with a predicted pI of 8.9, and theoretical masses between 55,010.9 and 55,121.0 Da. The difference with experimentally observed mass is likely due to glycosylation, in agreement with the finding of three putative N-glycosylation sites in its amino acid sequence. A phylogenetic analysis of MmipLAAO placed this new enzyme within the clade of homologous proteins from elapid snakes, characterized by the conserved Serine at position 223, in contrast to LAAOs from viperids. MmipLAAO showed a potent bactericidal effect on S. aureus (MIC: 2 µg/mL), but not on E. coli. The former activity could be of interest to future studies assessing its potential as antimicrobial agent. creator: Paola Rey-Suárez creator: Cristian Acosta creator: Uday Torres creator: Mónica Saldarriaga-Córdoba creator: Bruno Lomonte creator: Vitelbina Núñez uri: https://doi.org/10.7717/peerj.4924 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Rey-Suárez et al.