title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1821 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Stable isotopes in bivalves as indicators of nutrient source in coastal waters in the Bocas del Toro Archipelago, Panama link: https://peerj.com/articles/2278 last-modified: 2016-08-02 description: To examine N-isotope ratios (15N/14N) in tissues and shell organic matrix of bivalves as a proxy for natural and anthropogenic nutrient fluxes in coastal environments, Pinctada imbricata, Isognomon alatus, and Brachidontes exustusbivalves were live-collected and analyzed from eight sites in Bocas del Toro, Panama. Sites represent a variety of coastal environments, including more urbanized, uninhabited, riverine, and oceanic sites. Growth under differing environmental conditions is confirmed by δ18O values, with open ocean Escudo de Veraguas shells yielding the highest average δ18O (−1.0‰) value and freshwater endmember Rio Guarumo the lowest (−1.7‰). At all sites there is no single dominant source of organic matter contributing to bivalve δ15N and δ13C values. Bivalve δ15N and δ13C values likely represent a mixture of mangrove and seagrass N and C, although terrestrial sources cannot be ruled out. Despite hydrographic differences between end-members, we see minimal δ15N and δ13C difference between bivalves from the river-influenced Rio Guarumo site and those from the oceanic Escudo de Veraguas site, with no evidence for N from open-ocean phytoplankton in the latter. Populated sites yield relative 15N enrichments suggestive of anthropogenic nutrient input, but low δ15N values overall make this interpretation equivocal. Lastly, δ15N values of tissue and shell organic matrix correlate significantly for pterioideans P. imbricata and I. alatus. Thus for these species, N isotope studies of historical and fossil shells should provide records of ecology of past environments. creator: Lauren E. Graniero creator: Ethan L. Grossman creator: Aaron O’Dea uri: https://doi.org/10.7717/peerj.2278 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Graniero et al. title: Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model link: https://peerj.com/articles/2256 last-modified: 2016-08-02 description: One of the simplest models of adaptation to a new environment is Fisher’s Geometric Model (FGM), in which populations move on a multidimensional landscape defined by the traits under selection. The predictions of this model have been found to be consistent with current observations of patterns of fitness increase in experimentally evolved populations. Recent studies investigated the dynamics of allele frequency change along adaptation of microbes to simple laboratory conditions and unveiled a dramatic pattern of competition between cohorts of mutations, i.e., multiple mutations simultaneously segregating and ultimately reaching fixation. Here, using simulations, we study the dynamics of phenotypic and genetic change as asexual populations under clonal interference climb a Fisherian landscape, and ask about the conditions under which FGM can display the simultaneous increase and fixation of multiple mutations—mutation cohorts—along the adaptive walk. We find that FGM under clonal interference, and with varying levels of pleiotropy, can reproduce the experimentally observed competition between different cohorts of mutations, some of which have a high probability of fixation along the adaptive walk. Overall, our results show that the surprising dynamics of mutation cohorts recently observed during experimental adaptation of microbial populations can be expected under one of the oldest and simplest theoretical models of adaptation—FGM. creator: Jorge A. Moura de Sousa creator: João Alpedrinha creator: Paulo R.A. Campos creator: Isabel Gordo uri: https://doi.org/10.7717/peerj.2256 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Moura de Sousa et al. title: Decoupling the response of an estuarine shrimp to architectural components of habitat structure link: https://peerj.com/articles/2244 last-modified: 2016-08-02 description: In order to explore biotic attraction to structure, we examined how the amount and arrangement of artificial biotic stalks affected responses of a shrimp, Palaemon macrodactylus, absent other proximate factors such as predation or interspecific competition. In aquaria, we tested the effect of differing densities of both un-branched and branched stalks, where the amount of material in the branched stalk equaled four-times that of the un-branched. The results clearly showed that it was the amount of material, not how it was arranged, that elicited responses from shrimp. Also, although stalks were not purposefully designed to mimic structural elements found in nature, they did resemble biogenic structure such as hydroids, algae, or plants. In order to test shrimp attraction to a different, perhaps more unfamiliar habitat type, we examined responses to plastic “army men.” These structural elements elicited similar attraction of shrimp, and, in general, shrimp response correlated well with the fractal dimension of both stalks and army men. Overall, these results indicate that attraction to physical structure, regardless of its nature, may be an important driver of high abundances often associated with complex habitats. creator: Jeffrey A. Crooks creator: Andrew L. Chang creator: Gregory M. Ruiz uri: https://doi.org/10.7717/peerj.2244 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Crooks et al. title: Effects of salinity change on two superoxide dismutases (SODs) in juvenile marbled eel Anguilla marmorata link: https://peerj.com/articles/2149 last-modified: 2016-08-02 description: Salinity is one of the most important factors that affect the fish growth and survival. Superoxide dismutases (SODs), as the primary antioxidant enzymes, play a first role in the process of preventing oxidative stress caused by excessive superoxide anion (O${}_{2}^{-}$2−) in living organisms. In the present study, we investigated the effects of salinity on the gene expressions as well as enzymatic activities of MnSOD and Cu/ZnSOD in gill, intestine, kidney, liver and muscle tissues of the marbled eel Anguilla marmorata. We found that the liver might possess stronger redox capacity compared with other tissues. Furthermore, the gene expressions and enzymatic activities of SODs in juvenile marbled eels could be effectively enhanced by low salinity but inhibited when the salinity was higher than the body tolerance. Our findings indicated that MnSOD and Cu/ZnSOD played vital roles in the adaptation of marbled eels to salinity variation, which contributed to the elucidation of physiological adaptation and regulatory mechanism of SODs in eels. creator: Li Wang creator: Xiaolu Wang creator: Shaowu Yin uri: https://doi.org/10.7717/peerj.2149 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Wang et al. title: The masquerade game: marine mimicry adaptation between egg-cowries and octocorals link: https://peerj.com/articles/2051 last-modified: 2016-08-02 description: Background. Background matching, as a camouflage strategy, is one of the most outstanding examples of adaptation, where little error or mismatch means high vulnerability to predation. It is assumed that the interplay of natural selection and adaptation are the main evolutionary forces shaping the great diversity of phenotypes observed in mimicry; however, there may be other significant processes that intervene in the development of mimicry such as phenotypic plasticity. Based on observations of background mismatching during reproduction events of egg-cowries, sea snails of the family Ovulidae that mimic the octocoral where they inhabit, we wondered if they match the host species diversity. Using observations in the field and molecular systematics, we set out to establish whether the different egg-cowrie color/shape polymorphisms correspond to distinct lineages restricted to specific octocoral species.Methods. Collection and observations of egg-cowries and their octocoral hosts were done using SCUBA diving between 2009 and 2012 at two localities in the Tropical Eastern Pacific (TEP), Malpelo Island and Cabo Corrientes (Colombia). Detailed host preference observations were done bi-annually at Malpelo Island. We analyzed the DNA sequence of the mitochondrial genes COIand 16S rDNA, extensively used in phylogenetic and DNA barcoding studies, to assess the evolutionary relationship among different egg-cowrie colorations and morphologies.Results. No genetic divergence among egg-cowries associated to different species of the same octocoral genus was observed based on the two mitochondrial genes analyzed. For instance, all egg-cowrie individuals from the two sampled localities observed on 8 different Pacifigorgia-Eugorgia species showed negligible mitochondrial divergence yet large morphologic divergence, which suggests that morphologies belonging to at least two sea snail species, Simnia avena(=S. aequalis) and Simnialena rufa, can cross-fertilize.Discussion. Our study system comprised background-matching mimicry, of the masquerade type, between egg-cowries (Simnia/Simnialena) and octocorals (Pacifigorgia/Eugorgia/Leptogorgia). We observed mimicry mismatches related to fitness trade-offs, such as reproductive aggregations vs. vulnerability against predators. Despite the general assumption that coevolution of mimicry involves speciation, egg-cowries with different hosts and colorations comprise the same lineages. Consequently, we infer that there would be significant tradeoffs between mimicry and the pursuit of reproductive aggregations in egg-cowries. The findings of this study not only contribute to the understanding of the evolution of mimicry in egg-cowries, a poorly studied group of marine gastropods, but also to the development of a new biologically meaningful board game that could be implemented as a learning tool. creator: Juan A. Sánchez creator: Angela P. Fuentes-Pardo creator: Íde Ní Almhain creator: Néstor E. Ardila-Espitia creator: Jaime Cantera-Kintz creator: Manu Forero-Shelton uri: https://doi.org/10.7717/peerj.2051 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sánchez et al. title: Will 1,2-dihydro-1,2-azaborine-based drugs resist metabolism by cytochrome P450 compound I? link: https://peerj.com/articles/2299 last-modified: 2016-07-28 description: 1,2-dihydro-1,2-azaborine is a structural and electronic analogue of benzene which is able to occupy benzene-binding pockets in T4 lysozyme and has been proposed as suitable arene-mimicking group for biological and pharmaceutical applications. Its applicability in a biological context requires it to be able to resist modification by xenobiotic-degrading enzymes like the P450 cytochromes. Quantum chemical computations described in this work show that 1,2-dihydro-1,2-azaborine is much more prone to modification by these enzymes than benzene, unless steric crowding of the ring prevents it from reaching the active site, or otherwise only allows reaction at the less reactive C4-position. This novel heterocyclic compound is therefore expected to be of limited usefulness as an aryl bioisostere. creator: Pedro J. Silva uri: https://doi.org/10.7717/peerj.2299 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Silva title: Vocal correlates of individual sooty mangabey travel speed and direction link: https://peerj.com/articles/2298 last-modified: 2016-07-28 description: Many group-living animals coordinate movements with acoustic signals, but so far most studies have focused on how group movements are initiated. In this study, we investigated movement patterns of wild sooty mangabeys (Cercocebus atys), a mostly terrestrial, forest-dwelling primate. We provide quantitative results showing that vocalization rates of mangabey subgroups, but not of focal individuals, correlated with focal individuals’ current movement patterns. More interestingly, vocal behaviour predicted whether individuals changed future speed, and possibly future travel direction. The role of vocalizations as a potential mechanism for the regulation of group movement was further highlighted by interaction effects that include subgroup size and the quality of poly-specific associations. Collectively, our results suggest that primate vocal behaviour can function beyond travel initiation in coordination and regulation of group movements. creator: Christof Neumann creator: Klaus Zuberbühler uri: https://doi.org/10.7717/peerj.2298 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Neumann & Zuberbühler title: Larval settlement and metamorphosis in a marine gastropod in response to multiple conspecific cues link: https://peerj.com/articles/2295 last-modified: 2016-07-28 description: Larvae of the marine gastropod Crepidula fornicata must complete a transition from the plankton, where they are highly dispersed, to an aggregated group of benthic adults. Previous research has shown that selective settlement of larvae on conspecific adults is mediated by a water-borne chemical cue. However, variable experimental conditions have been used to study this cue, and standardization is needed in order to investigate factors that may have weak effects on settlement. In this study, we developed a time-course bioassay based on a full-factorial design with temporal blocking and statistical analysis of larval settlement rates in the lab. We tested this bioassay by examining settlement in the presence of an abiotic cue (KCl), and biotic cues (water conditioned with adult conspecifics and conspecific pedal mucus). Results confirmed settlement in the presence of both KCl and adult-conditioned water, and discovered the induction of settlement by pedal mucus. This optimized, standardized bioassay will be used in future experiments to characterize the complex process of larval settlement in C. fornicata, particularly to measure components of potentially small effect. creator: Abigail E. Cahill creator: Spencer A. Koury uri: https://doi.org/10.7717/peerj.2295 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cahill and Koury title: Engineering a light-controlled F1 ATPase using structure-based protein design link: https://peerj.com/articles/2286 last-modified: 2016-07-28 description: The F1 sub-complex of ATP synthase is a biological nanomotor that converts the free energy of ATP hydrolysis into mechanical work with an astonishing efficiency of up to 100% (Kinosita et al., 2000). To probe the principal mechanics of the machine, I re-engineered the active site of E.coli F1 ATPase with a structure-based protein design approach: by incorporation of a site-specific, photoswitchable crosslinker, whose end-to-end distance can be modulated by illumination with light of two different wavelengths, a dynamic constraint was imposed on the inter-atomic distances of the α and β subunits. Crosslinking reduced the ATP hydrolysis activity of four designs tested in vitro and in one case created a synthetic ATPase whose activity can be reversibly modulated by subsequent illumination with near UV and blue light. The work is a first step into the direction of the long-term goal to design nanoscaled machines based on biological parts that can be precisely controlled by light. creator: Daniel Hoersch uri: https://doi.org/10.7717/peerj.2286 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2016 Hoersch title: Site fidelity, size, and morphology may differ by tidal position for an intertidal fish, Bathygobius cocosensis (Perciformes-Gobiidae), in Eastern Australia link: https://peerj.com/articles/2263 last-modified: 2016-07-28 description: The intertidal zone is a transitional environment that undergoes daily environmental fluctuations as tides rise and fall. Relatively few fish species are adapted to endure the physiological pressures of this environment. This study focused on Bathygobius cocosensis (Gobiidae), a common intertidal fish in New South Wales, Australia. We investigated whether shore height impacted site fidelity, survival probability, fish size, and morphological traits with respect to tidal height. Mark-recapture methods were used over a five month period to determine if individuals in high shore pools had greater site fidelity; fish in high tide pools were more than twice as likely to be recaptured in their original pool than fish from low tide pools. High pool individuals were, on average, smaller with larger eyes and longer snouts relative to their size as compared to low pool individuals. We discuss several mechanisms that could cause the observed pattern in morphological variation. Ultimately, this study suggests that within species behaviour and morphology differ by tidal position for an intertidal fish. creator: Lucie A. Malard creator: Katrina McGuigan creator: Cynthia Riginos uri: https://doi.org/10.7717/peerj.2263 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Malard et al.