Effects of preservation methods of muscle tissue from upper-trophic level reef fishes on stable isotope values (δ13C and δ15N)

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PeerJ 3 (2015): e874, doi:10.7717/peerj.874.Research that uses stable isotope analysis often involves a delay between sample collection in the field and laboratory processing, therefore requiring preservation to prevent or reduce tissue degradation and associated isotopic compositions. Although there is a growing literature describing the effects of various preservation techniques, the results are often contextual, unpredictable and vary among taxa, suggesting the need to treat each species individually. We conducted a controlled experiment to test the effects of four preservation methods of muscle tissue from four species of upper trophic-level reef fish collected from the eastern Gulf of Mexico (Red Grouper Epinephelus morio, Gag Mycteroperca microlepis, Scamp Mycteroperca phenax, and Red Snapper Lutjanus campechanus). We used a paired design to measure the effects on isotopic values for carbon and nitrogen after storage using ice, 95% ethanol, and sodium chloride (table salt), against that in a liquid nitrogen control. Mean offsets for both δ13C and δ15N values from controls were lowest for samples preserved on ice, intermediate for those preserved with salt, and highest with ethanol. Within species, both salt and ethanol significantly enriched the δ15N values in nearly all comparisons. Ethanol also had strong effects on the δ13C values in all three groupers. Conversely, for samples preserved on ice, we did not detect a significant offset in either isotopic ratio for any of the focal species. Previous studies have addressed preservation-induced offsets in isotope values using a mass balance correction that accounts for changes in the isotope value to that in the C/N ratio. We tested the application of standard mass balance corrections for isotope values that were significantly affected by the preservation methods and found generally poor agreement between corrected and control values. The poor performance by the correction may have been due to preferential loss of lighter isotopes and corresponding low levels of mass loss with a substantial change in the isotope value of the sample. Regardless of mechanism, it was evident that accounting for offsets caused by different preservation methods was not possible using the standard correction. Caution is warranted when interpreting the results from specimens stored in either ethanol or salt, especially when using those from multiple preservation techniques. We suggest the use of ice as the preferred preservation technique for muscle tissue when conducting stable isotope analysis as it is widely available, inexpensive, easy to transport and did not impart a significant offset in measured isotopic values. Our results provide additional evidence that preservation effects on stable isotope analysis can be highly contextual, thus requiring their effects to be measured and understood for each species and isotopic ratio of interest before addressing research questions.Funding was provided by a grant to CD Stallings and TS Switzer from the National Oceanic and Atmospheric Administration, Cooperative Research Program (NA12NMF4540081)

Local and regional stressors interact to drive a salinization-induced outbreak of predators on oyster reefs

Predator outbreaks are predicted to increasingly decimate economically and ecologically important prey populations because global climate change and food-web modifications frequently facilitate predators and stress prey. Natural systems are organized hierarchically, with processes operating at multiple scales giving rise to patterns of biodiversity, so predicting and managing outbreaks requires a framework that accounts for the effects of both local and regional stressors. Here, we used the comparative experimental approach to investigate whether the collapse of a nationally important oyster fishery in the Gulf of Mexico (Apalachicola Bay, Florida) could have been (1) caused proximally by a predator outbreak and (2) whether this outbreak was mediated by local-and/or regional-scale forces. During the fishery collapse, we paired experiments with monitoring in Apalachicola Bay and found elevated water salinity, high abundance of predatory snails, and intense oyster mortality due to predation. By repeating these experiments over 4 yr, we found that periods of reduced water salinity inhibited predation on oysters. To partition the influence of local-versus-regional factors on this predator outbreak, we simultaneously replicated the paired experiments and monitoring in a nearby bay (Ochlockonee Bay) that shares the same regional-scale rainfall conditions. Increasing freshwater withdrawals from the watershed that drains into Apalachicola Bay have increased salinities in that bay, but there have not been similar withdrawals in the Ochlockonee Bay watershed. Therefore, Apalachicola Bay experienced a localized anthropogenic stress, while both bays experienced regional stress from drought. In Ochlockonee Bay, our experiments demonstrated that the river maintained sufficiently low salinity to provide similar to 50% of oyster reefs with a refuge from predation. In contrast, salinity-dependent predation in Apalachicola Bay extended up to the river mouth. Given the stark differences in upstream water withdrawals between these watersheds, it is reasonable to surmise that these withdrawals exacerbated the stress of regional drought, created the difference in predation between the two bays, and thus may have precipitated the oyster fishery collapse. Our study provides empirical support for recent theory about the hierarchical organization of ecosystems, which predicts that stressors will interact across scales to cause localized predator outbreaks

Density dependence and population regulation in marine fish: a large-scale, long-term field manipulation

dependence and regulation of relatively large local populations? If so, what are the causative mechanisms and their implications? We conducted an eight-year multigeneration study of population dynamics of bicolor damselfish (Stegastes partitus) inhabiting four large coral reefs in the Bahamas. After a four-year baseline period, it was clear that two populations naturally received very few settlement-stage larvae, so recruitment of recently settled fish was artificially enhanced at one low-settlement reef and reduced at one high-settlement reef to ensure a broad range of population sizes over which to test for regulation. Over all eight years, populations on the two naturally high-settlement reefs experienced temporal density dependence in multiple per capita demographic rates: mortality, survival to adulthood, and fecundity. These local populations also displayed components of regulation: persistence, boundedness, and return tendency. Reefs supporting regulated populations were structurally complex, providing sufficient prey refuges that ensured high survival at low densities. In contrast, populations at low-settlement reefs experienced either density-independent or slightly inversely density-dependent demographic rates, even though recruitment was artificially augmented to high levels at one reef. There was no evidence of regulation at these reefs, and indeed, one local population suffered temporary extirpation. Here, habitat complexity was relatively low, increasing the risk of predation, especially at low population densities when fish would have to travel longer distances when finding mates or home sites inhabited by conspecifics. Among all demographic parameters, density dependence in individual growth (an indicator of within-species competition for food) was least correlated with the presence or absence of local population regulation. We conclude that, for systems like these, the environmental context of a local population, especially predation risk and the distribution and abundance of spatial refuges, is more important than the magnitude of larval supply alone in determining the existence of regulating density dependence. At the broader metapopulation scale, density dependence in both survival and fecundity exogenously caused by predation may provide regulation for the entire stock, even when endogenous within-species competition (assumed to be important in most fisheries models) is weak.Keywords: Predation, Fecundity, Recruitment, Mortality, Scaling, Population dynamics, Growth, Coral-reef fish, Marine metapopulation, Fisheries, Competitio

Fishery-Independent Data Reveal Negative Effect of Human Population Density on Caribbean Predatory Fish Communities

BACKGROUND: Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations. METHODOLOGY/PRINCIPAL FINDINGS: Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species. CONCLUSIONS/SIGNIFICANCE: Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable

Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects

Shared genetic risk between eating disorder- and substance-use-related phenotypes:Evidence from genome-wide association studies

First published: 16 February 202

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

RRM adjacent TARDBP mutations disrupt RNA binding and enhance TDP-43 proteinopathy

Amyotrophic lateral sclerosis (ALS) presents with focal muscle weakness due to motor neuron degeneration that becomes generalized,leading to death from respiratory failure within 3–5 years from symptom onset. Despite the heterogeneity of aetiology, TDP- 43 proteinopathy is a common pathological feature that is observed in 495% of ALS and tau-negative frontotemporal dementia(FTD) cases. TDP-43 is a DNA/RNA-binding protein that in ALS and FTD translocates from being predominantly nuclear to formdetergent-resistant, hyperphosphorylated aggregates in the cytoplasm of affected neurons and glia. Mutations in TARDBP accountfor 1–4% of all ALS cases and almost all arise in the low complexity C-terminal domain that does not affect RNA binding andprocessing. Here we report an ALS/FTD kindred with a novel K181E TDP-43 mutation that is located in close proximity to the RRM1 domain. To offer predictive gene testing to at-risk family members, we undertook a series of functional studies to characterizethe properties of the mutation. Spectroscopy studies of the K181E protein revealed no evidence of significant misfolding.Although it is unable to bind to or splice RNA, it forms abundant aggregates in transfected cells. We extended our study to includeother ALS-linked mutations adjacent to the RRM domains that also disrupt RNA binding and greatly enhance TDP-43 aggregation,forming detergent-resistant and hyperphosphorylated inclusions. Lastly, we demonstrate that K181E binds to, and sequesters, wild-type TDP-43 within nuclear and cytoplasmic inclusions. Thus, we demonstrate that TDP-43 mutations that disrupt RNAbinding greatly enhance aggregation and are likely to be pathogenic as they promote wild-type TDP-43 to mislocalize andaggregate acting in a dominant-negative manner. This study highlights the importance of RNA binding to maintain TDP-43solubility and the role of TDP-43 aggregation in disease pathogenesis

Experimental Test of Preference by a Predatory Fish for Prey at Different Densities

Preference for a particular prey implies that a behavioral choice is made by the predator, requiring an experimental approach to separate process from observed patterns in nature. For example, pink shrimp (Farfantepenaeus duorarum) and pinfish (Lagodon rhomboides) are dominant prey observed in the diet of juvenile gag (Mycteroperca microlepis) collected from natural habitats, but it is unclear whether their approximate equal representation is due to a lack of preference between the two. Furthermore, both prey are captured in high quantities as targeted (shrimp) and non-targeted (pinfish) components of a trawl fishery operating in the same seagrass habitats where juvenile gag are found, thus requiring examination as to whether reductions in prey densities affect consumption rates and preference. In the current study, I used laboratory feeding experiments and applied new analytical techniques derived in a series of recent papers published in this journal to examine preference by juvenile gag on these two morphologically and behaviorally different prey. Consumption rates were higher for shrimp than pinfish and were not related to the initial density of prey presented to gag. However, gag did not exhibit a feeding preference for either prey across 10 controlled comparisons. Experimental results in the laboratory therefore reflected patterns observed in the field for the diet of this predatory fish. Moreover, by examining the effects of reduced prey densities on food web processes, the approach used in this study may be applied to inform ecosystem-based management on indirect effects of fishing

Indirect Effects of an Exploited Predator on Recruitment of Coral-Reef Fishes

The more ecologists examine the role of trait-mediated indirect interactions (TMIIs), especially in regulating predator–prey interactions, the more we recognize their fundamental role in structuring food webs. However, most empirical evidence for TMIIs comes from studies that are either conducted in laboratory or mesocosm venues or are restricted to simple food webs involving lower trophic-level animals. Here, I quantified the direct and indirect effects of interactions between high-level vertebrate predators on their vertebrate prey using a field experiment. Specifically, I tested how varying densities of a large-bodied, top predator (Nassau grouper; Epinephelus striatus) affected persistence, growth, and behavior of two smaller-bodied, intermediate predators (coney and graysby groupers; Cephalopholis fulva and C. cruentata) on 20 isolated patch reefs in the Bahamas. Large-bodied groupers are capable of consuming their smaller-bodied counterparts, and previous observational studies have indicated that local abundances of these groupers are negatively correlated. I measured the effects of interactions among groupers on lower trophic-level prey by quantifying recruitment of coral-reef fishes to the reefs. The field experiment demonstrated a strong trophic cascade that was entirely mediated by modified behavior of the intermediate predators. These results indicate that indirect, nonlethal interactions in natural systems can have strong cascading effects even at high trophic levels and in high-diversity food webs. Incorporating the complexity of such indirect effects into fisheries management may improve the sustainability of fished populations and strengthen marine conservation efforts; however these results also indicate that the effects of fishing are complex and difficult to predict