title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1496 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: ­Characterization of pyruvate kinase from the anoxia tolerant turtle, Trachemys scripta elegans: a potential role for enzyme methylation during metabolic rate depression link: https://peerj.com/articles/4918 last-modified: 2018-06-08 description: BackgroundPyruvate kinase (PK) is responsible for the final reaction in glycolysis. As PK is a glycolytic control point, the analysis of PK posttranslational modifications (PTM) and kinetic changes reveals a key piece of the reorganization of energy metabolism in an anoxia tolerant vertebrate.MethodsTo explore PK regulation, the enzyme was isolated from red skeletal muscle and liver of aerobic and 20-hr anoxia-exposed red eared-slider turtles (Trachemys scripta elegans). Kinetic analysis and immunoblotting were used to assess enzyme function and the corresponding covalent modifications to the enzymes structure during anoxia.ResultsBoth muscle and liver isoforms showed decreased affinity for phosphoenolpyruvate substrate during anoxia, and muscle PK also had a lower affinity for ADP. I50 values for the inhibitors ATP and lactate were lower for PK from both tissues after anoxic exposure while I50 L-alanine was only reduced in the liver. Both isozymes showed significant increases in threonine phosphorylation (by 42% in muscle and 60% in liver) and lysine methylation (by 43% in muscle and 70% in liver) during anoxia which have been linked to suppression of PK activity in other organisms. Liver PK also showed a 26% decrease in tyrosine phosphorylation under anoxia.DiscussionAnoxia responsive changes in turtle muscle and liver PK coordinate with an overall reduced activity state. This reduced affinity for the forward glycolytic reaction is likely a key component of the overall metabolic rate depression that supports long term survival in anoxia tolerant turtles. The coinciding methyl- and phospho- PTM alterations present the mechanism for tissue specific enzyme modification during anoxia. creator: Amanda M.S. Mattice creator: Isabelle A. MacLean creator: Christine L. Childers creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.4918 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Mattice et al. title: Does bathymetry drive coastal whale shark (Rhincodon typus) aggregations? link: https://peerj.com/articles/4904 last-modified: 2018-06-08 description: BackgroundThe whale shark (Rhincodon typus) is known to aggregate in a number of coastal locations globally, however what causes these aggregations to form where they do is largely unknown. This study examines whether bathymetry is an important driver of coastal aggregation locations for R. typus through bathymetry’s effect on primary productivity and prey availability. This is a global study taking into account all coastal areas within R. typus’ range.MethodsR. typus aggregation locations were identified through an extensive literature review. Global bathymetric data were compared at R. typus aggregation locations and a large random selection of non-aggregation areas. Generalised linear models were used to assess which bathymetric characteristic had the biggest influence on aggregation presence.ResultsAggregation sites were significantly shallower than non-aggregation sites and in closer proximity to deep water (the mesopelagic zone) by two orders of magnitude. Slope at aggregation sites was significantly steeper than non-aggregation sites. These three bathymetric variables were shown to have the biggest association with aggregation sites, with up to 88% of deviation explained by the GLMs.DiscussionThe three key bathymetric characteristics similar at the aggregation sites are known to induce upwelling events, increase primary productivity and consequently attract numerous other filter feeding species. The location of aggregation sites in these key areas can be attributed to this increased prey availability, thought to be the main reason R. typus aggregations occur, extensively outlined in the literature. The proximity of aggregations to shallow areas such as reefs could also be an important factor why whale sharks thermoregulate after deep dives to feed. These findings increase our understanding of whale shark behaviour and may help guide the identification and conservation of further aggregation sites. creator: Joshua P. Copping creator: Bryce D. Stewart creator: Colin J. McClean creator: James Hancock creator: Richard Rees uri: https://doi.org/10.7717/peerj.4904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2018 Copping et al.