title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1790 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Variation in habitat soundscape characteristics influences settlement of a reef-building coral link: https://peerj.com/articles/2557 last-modified: 2016-10-13 description: Coral populations, and the productive reef ecosystems they support, rely on successful recruitment of reef-building species, beginning with settlement of dispersing larvae into habitat favourable to survival. Many substrate cues have been identified as contributors to coral larval habitat selection; however, the potential for ambient acoustic cues to influence coral settlement responses is unknown. Using in situ settlement chambers that excluded other habitat cues, larval settlement of a dominant Caribbean reef-building coral, Orbicella faveolata, was compared in response to three local soundscapes, with differing acoustic and habitat properties. Differences between reef sites in the number of larvae settled in chambers isolating acoustic cues corresponded to differences in sound levels and reef characteristics, with sounds at the loudest reef generating significantly higher settlement during trials compared to the quietest site (a 29.5 % increase). These results suggest that soundscapes could be an important influence on coral settlement patterns and that acoustic cues associated with reef habitat may be related to larval settlement. This study reports an effect of soundscape variation on larval settlement for a key coral species, and adds to the growing evidence that soundscapes affect marine ecosystems by influencing early life history processes of foundational species. creator: Ashlee Lillis creator: DelWayne Bohnenstiehl creator: Jason W. Peters creator: David Eggleston uri: https://doi.org/10.7717/peerj.2557 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Lillis et al. title: Evaluation of reference genes for gene expression in red-tailed phascogale (Phascogale calura) liver, lung, small intestine and spleen link: https://peerj.com/articles/2552 last-modified: 2016-10-13 description: BackgroundReference genes serve an important role as an endogenous control/standard for data normalisation in gene expression studies. Although reference genes have recently been suggested for marsupials, independent analysis of reference genes on different immune tissues is yet to be tested. Therefore, an assessment of reference genes is needed for the selection of stable, expressed genes across different marsupial tissues.MethodsThe study was conducted on red-tailed phascogales (Phascogale calura) using five juvenile and five adult males. The stability of five reference genes (glyceraldehyde-3-phosphate dehydrogenase, GAPDH; β-actin, ACTB; 18S rRNA, 18S; 28S rRNA, 28S; and ribosomal protein L13A, RPL13A) was investigated using SYBR Green and analysed with the geNorm application available in qBasePLUS software.ResultsGene stability for juvenile and adult tissue samples combined show that GAPDH was most stable in liver and lung tissue, and 18S in small intestine and spleen. While all reference genes were suitable for small intestine and spleen tissues, all reference genes except 28S were stable for lung and only 18S and 28S were stable for liver tissue. Separating the two age groups, we found that two different reference genes were considered stable in juveniles (ACTB and GAPDH) and adults (18S and 28S), and RPL13A was not stable for juvenile small intestine tissue. Except for 28S, all reference genes were stable in juvenile and adult lungs, and all five reference genes were stable in spleen tissue.DiscussionBased on expression stability, ACTB and GAPDH are suitable for all tissues when studying the expression of marsupials in two age groups, except for adult liver tissues. The expression stability between juvenile and adult liver tissue was most unstable, as the stable reference genes for juveniles and adults were different. Juvenile and adult lung, small intestine and spleen share similar stable reference genes, except for small intestine tissues where all reference genes were stable in adults but RPL13A was not suitable in juveniles. creator: Oselyne T.W. Ong creator: Lauren J. Young creator: Julie M. Old uri: https://doi.org/10.7717/peerj.2552 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ong et al. title: Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes link: https://peerj.com/articles/2551 last-modified: 2016-10-13 description: BackgroundAssembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes.MethodsWe employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms.ResultsThe unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition.DiscussionVariation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space. creator: Laura M. Cisneros creator: Matthew E. Fagan creator: Michael R. Willig uri: https://doi.org/10.7717/peerj.2551 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Cisneros et al. title: Aboveground and belowground arthropods experience different relative influences of stochastic versus deterministic community assembly processes following disturbance link: https://peerj.com/articles/2545 last-modified: 2016-10-13 description: BackgroundUnderstanding patterns of biodiversity is a longstanding challenge in ecology. Similar to other biotic groups, arthropod community structure can be shaped by deterministic and stochastic processes, with limited understanding of what moderates the relative influence of these processes. Disturbances have been noted to alter the relative influence of deterministic and stochastic processes on community assembly in various study systems, implicating ecological disturbances as a potential moderator of these forces.MethodsUsing a disturbance gradient along a 5-year chronosequence of insect-induced tree mortality in a subalpine forest of the southern Rocky Mountains, Colorado, USA, we examined changes in community structure and relative influences of deterministic and stochastic processes in the assembly of aboveground (surface and litter-active species) and belowground (species active in organic and mineral soil layers) arthropod communities. Arthropods were sampled for all years of the chronosequence via pitfall traps (aboveground community) and modified Winkler funnels (belowground community) and sorted to morphospecies. Community structure of both communities were assessed via comparisons of morphospecies abundance, diversity, and composition. Assembly processes were inferred from a mixture of linear models and matrix correlations testing for community associations with environmental properties, and from null-deviation models comparing observed vs. expected levels of species turnover (Beta diversity) among samples.ResultsTree mortality altered community structure in both aboveground and belowground arthropod communities, but null models suggested that aboveground communities experienced greater relative influences of deterministic processes, while the relative influence of stochastic processes increased for belowground communities. Additionally, Mantel tests and linear regression models revealed significant associations between the aboveground arthropod communities and vegetation and soil properties, but no significant association among belowground arthropod communities and environmental factors.DiscussionOur results suggest context-dependent influences of stochastic and deterministic community assembly processes across different fractions of a spatially co-occurring ground-dwelling arthropod community following disturbance. This variation in assembly may be linked to contrasting ecological strategies and dispersal rates within above- and below-ground communities. Our findings add to a growing body of evidence indicating concurrent influences of stochastic and deterministic processes in community assembly, and highlight the need to consider potential variation across different fractions of biotic communities when testing community ecology theory and considering conservation strategies. creator: Scott Ferrenberg creator: Alexander S. Martinez creator: Akasha M. Faist uri: https://doi.org/10.7717/peerj.2545 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ferrenberg et al. title: Highly divergent mussel lineages in isolated Indonesian marine lakes link: https://peerj.com/articles/2496 last-modified: 2016-10-13 description: Marine lakes, with populations in landlocked seawater and clearly delineated contours, have the potential to provide a unique model to study early stages of evolution in coastal marine taxa. Here we ask whether populations of the mussel Brachidontes from marine lakes in Berau, East Kalimantan (Indonesia) are isolated from each other and from the coastal mangrove systems. We analyzed sequence data of one mitochondrial marker (Cytochrome Oxidase I (COI)), and two nuclear markers (18S and 28S). In addition, we examined shell shape using a geometric morphometric approach. The Indonesian populations of Brachidontes spp. harbored four deeply diverged lineages (14–75% COI corrected net sequence divergence), two of which correspond to previously recorded lineages from marine lakes in Palau, 1,900 km away. These four lineages also showed significant differences in shell shape and constitute a species complex of at least four undescribed species. Each lake harbored a different lineage despite the fact that the lakes are separated from each other by only 2–6 km, while the two mangrove populations, at 20 km distance from each other, harbored the same lineage and shared haplotypes. Marine lakes thus represent isolated habitats. As each lake contained unique within lineage diversity (0.1–0.2%), we suggest that this may have resulted from in situdivergence due to isolation of founder populations after the formation of the lakes (6,000–12,000 years before present). Combined effects of stochastic processes, local adaptation and increased evolutionary rates could produce high levels of differentiation in small populations such as in marine lake environments. Such short-term isolation at small spatial scales may be an important contributing factor to the high marine biodiversity that is found in the Indo-Australian Archipelago. creator: Leontine E. Becking creator: Christiaan A. de Leeuw creator: Bram Knegt creator: Diede L. Maas creator: Nicole J. de Voogd creator: Abdunnur creator: Iwan Suyatna creator: Katja T.C.A. Peijnenburg uri: https://doi.org/10.7717/peerj.2496 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Becking et al. title: Ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae link: https://peerj.com/articles/2536 last-modified: 2016-10-12 description: Parrotfish are fundamental species in controlling algal phase-shifts and ensuring the resilience of coral reefs. Nevertheless, little is known on their ecological role in the south-western Atlantic Ocean. The present study analysed the ontogenetic foraging activity and feeding selectivity of the Brazilian endemic parrotfish Scarus zelindae using behavioural observation and benthic composition analyses. We found a significant negative relationship between fish size and feeding rates for S. zelindae individuals. Thus, terminal phase individuals forage with lower feeding rates compared to juveniles and initial phase individuals. The highest relative foraging frequency of S. zelindae was on epilithic algae matrix (EAM) with similar values for juveniles (86.6%), initial phase (88.1%) and terminal phase (88.6%) individuals. The second preferred benthos for juveniles was sponge (11.6%) compared with initial (4.5%) and terminal life phases (1.3%). Different life phases of S. zelindae foraged on different benthos according to their availability. Based on Ivlev’s electivity index, juveniles selected EAM and sponge, while initial phase and terminal phase individuals only selected EAM. Our findings demonstrate that the foraging frequency of the endemic parrotfish S. zelindae is reduced according to body size and that there is a slight ontogenetic change in feeding selectivity. Therefore, ecological knowledge of ontogenetic variations on resource use is critical for the remaining parrotfish populations which have been dramatically reduced in the Southwestern Atlantic Ocean. creator: Pedro H.C. Pereira creator: Marcus Santos creator: Daniel L. Lippi creator: Pedro Silva uri: https://doi.org/10.7717/peerj.2536 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Pereira et al. title: LIMK1/2 inhibitor LIMKi 3 suppresses porcine oocyte maturation link: https://peerj.com/articles/2553 last-modified: 2016-10-12 description: LIMKi 3 is a specific selective LIMK inhibitor against LIMK1 and LIMK2, while LIMK1 and LIMK2 are the main regulators of actin cytoskeleton to participate in many cell activities. However, the effect of LIMKi 3 in porcine oocyte meiosis is still unclear. The present study was designed to investigate the effects of LIMKi 3 and potential regulatory role of LIMK1/2 on porcine oocyte meiotic maturation. Immunofluorescent staining of p-LIMK1/2 antibody showed that LIMK1/2 was localized mainly to the cortex of porcine oocyte, which co-localized with actin. After LIMKi 3 treatment, the diffusion of COCs became weak and the rate of polar body extrusion was decreased. This could be rescued by moving oocytes to fresh medium. After prolonging the culture time of oocytes, the maturation rate of porcine oocyte increased in LIMKi 3 groups, indicating that LIMKi 3 may suppress the cell cycle during porcine oocyte maturation. We also found that after LIMKi 3 treatment actin distribution was significantly disturbed at porcine oocyte membranes and cytoplasm, indicating the conserved roles of LIMK1/2 on actin dynamics. Next we examined the meiotic spindle positioning in porcine oocyte, and the results showed that a majority of spindles were not attached to the cortex of porcine oocyte, indicating that LIMKi 3 may affect actin-mediated spindle positioning. Taken together, these results showed that LIMK1/2 inhibitor LIMKi 3 had a repressive role on porcine oocyte meiotic maturation. creator: Ru-Xia Jia creator: Xing Duan creator: Si-Jing Song creator: Shao-Chen Sun uri: https://doi.org/10.7717/peerj.2553 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Jia et al. title: Common metabolic constraints on dive duration in endothermic and ectothermic vertebrates link: https://peerj.com/articles/2569 last-modified: 2016-10-12 description: Dive duration in air-breathing vertebrates is thought to be constrained by the volume of oxygen stored in the body and the rate at which it is consumed (i.e., “oxygen store/usage hypothesis”). The body mass-dependence of dive duration among endothermic vertebrates is largely supportive of this model, but previous analyses of ectothermic vertebrates show no such body mass-dependence. Here we show that dive duration in both endotherms and ectotherms largely support the oxygen store/usage hypothesis after accounting for the well-established effects of temperature on oxygen consumption rates. Analyses of the body mass and temperature dependence of dive duration in 181 species of endothermic vertebrates and 29 species of ectothermic vertebrates show that dive duration increases as a power law with body mass, and decreases exponentially with increasing temperature. Thus, in the case of ectothermic vertebrates, changes in environmental temperature will likely impact the foraging ecology of divers. creator: April Hayward creator: Mariela Pajuelo creator: Catherine G. Haase creator: David M. Anderson creator: James F. Gillooly uri: https://doi.org/10.7717/peerj.2569 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Hayward et al. title: Invasion of the tropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Oligochaeta) in temperate grasslands link: https://peerj.com/articles/2572 last-modified: 2016-10-12 description: The tropical earthworm Pontoscolex corethrurus (Rhinodrilidae, Oligochaeta) presents a broad distribution (e.g., 56 countries from four continents). It is generally assumed that temperature appears to limit the success of tropical exotic species in temperate climates. However, the distribution range of this species could advance towards higher elevations (with lower temperatures) where no tropical species currently occur. The aim of this study was to evaluate the soil and climatic variables that could be closely associated with the distribution of P. corethrurus in four sites along an altitudinal gradient in central Veracruz, Mexico. We predicted that the distribution of P. corethrurus would be more related to climate variables than edaphic parameters. Five sampling points (in the grassland) were established at each of four sites along an altitudinal gradient: Laguna Verde (LV), La Concepción (LC), Naolinco (NA) and Acatlán (AC) at 11–55, 992–1,025, 1,550–1,619 y 1,772–1,800 masl, respectively. The climate ranged from tropical to temperate along the altitudinal gradient. Ten earthworm species (5 Neotropical, 4 Palearctic and 1 Nearctic) were found along the gradient, belonging to three families (Rhinodrilidae, Megascolecide and Lumbricidae). Soil properties showed a significant association (positive for Ngrass, pH, permanent wilting point, organic matter and P; and negative for Total N, K and water-holding capacity) with the abundance of the earthworm community. Also there seems to be a relationship between climate and earthworm distribution along the altitudinal gradient. P. corethrurus was recorded at tropical (LV and LC) and temperate sites (NA) along the altitudinal gradient. Our results reveal that soil fertility determines the abundance of earthworms and site (climate) can act as a barrier to their migration. Further research is needed to determine the genetic structure and lineages of P. corethrurus along altitudinal gradients. creator: Diana Ortiz-Gamino creator: Paulino Pérez-Rodríguez creator: Angel I. Ortiz-Ceballos uri: https://doi.org/10.7717/peerj.2572 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ortiz-Gamino et al. title: Diversity of planktonic fish larvae along a latitudinal gradient in the Eastern Atlantic Ocean estimated through DNA barcodes link: https://peerj.com/articles/2438 last-modified: 2016-10-12 description: Mid-trophic pelagic fish are essential components of marine ecosystems because they represent the link between plankton and higher predators. Moreover, they are the basis of the most important fisheries resources; for example, in African waters. In this study, we have sampled pelagic fish larvae in the Eastern Atlantic Ocean along a latitudinal gradient between 37°N and 2°S. We have employed Bongo nets for plankton sampling and sorted visually fish and fish larvae. Using the cytochrome oxidase I gene (COI) as a DNA barcode, we have identified 44 OTUs down to species level that correspond to 14 families, with Myctophidae being the most abundant. A few species were cosmopolitan and others latitude-specific, as was expected. The latitudinal pattern of diversity did not exhibit a temperate-tropical cline; instead, it was likely correlated with environmental conditions with a decline in low-oxygen zones. Importantly, gaps and inconsistencies in reference DNA databases impeded accurate identification to the species level of 49% of the individuals. Fish sampled from tropical latitudes and some orders, such as Perciformes, Myctophiformes and Stomiiformes, were largely unidentified due to incomplete references. Some larvae were identified based on morphology and COI analysis for comparing time and costs employed from each methodology. These results suggest the need of reinforcing DNA barcoding reference datasets of Atlantic bathypelagic tropical fish that, as main prey of top predators, are crucial for ecosystem-based management of fisheries resources. creator: Alba Ardura creator: Elvira Morote creator: Marc Kochzius creator: Eva Garcia-Vazquez uri: https://doi.org/10.7717/peerj.2438 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Ardura et al.