Larval dispersal in marine fishes: novel methods reveal patterns of self-recruitment and population connectivity

Many marine fish populations are severely declining due to over-fishing, loss of both juvenile and adult habitats, and accelerating environmental degradation. Fisheries management and the implementation of marine protected areas (MPAs) and other conservation tools are currently hindered by large gaps in knowledge about larval dispersal and its subsequent effects on population dynamics and regulation. This lack of knowledge is due to the inherent difficulty associated with tracking miniscule marine fish larvae. Population genetics approaches are particularly promising, but current methods have been of limited use for inferring ecologically relevant rates of population connectivity because of the large population sizes and high amounts of gene flow present in most marine species. To address these issues, I developed novel genetic methods of identifying parent-offspring pairs to directly track the origin and settlement of larvae in natural populations. These parentage methods fully account for large numbers of pair-wise comparisons and do not require any demographic assumptions or observational data. Furthermore, these methods can be used when only a small proportion of candidate parents can be sampled, which is often the case in large marine populations. I also employed Bayes’ theorem to take into account the frequencies of shared alleles in putative parent-offspring pairs, which can maximize statistical power when faced with fixed numbers of loci. I accounted for genotyping errors by introducing a quantitative method to determine the number of loci to allow to mismatch based upon study-specific error rates. These novel parentage methods were applied to yellow tang (Zebrasoma flavescens, Acanthuridae) sampled around the Island of Hawai'i (measuring 140 km by 129 km) during the summer of 2006. We identified four parent-offspring pairs, which documented dispersal distances ranging from 15 to 184 kilometers. Two of the parents were located within MPAs and their offspring dispersed to unprotected areas. This observation provided direct evidence that MPAs can successfully seed unprotected sites with larvae that survive to become established juveniles. All four offspring were found to the north of their parents and a detailed oceanographic analysis from relevant time periods demonstrated that passive transport initially explained the documented dispersal patterns. However, passive dispersal could not explain how larvae eventually settled on the same island from which they were spawned, indicating a role for larval behavior interacting with fine-scale oceanographic features. Two findings together suggested that sampled reefs did not contribute equally to successful recruitment: (1) low levels of genetic differentiation among all recruit samples, and (2) the fact that the 4 documented parents occurred at only 2 sites. These findings empirically demonstrated the effectiveness of MPAs as useful conservation and management tools and highlighted the value of identifying both the sources and successful settlement sites of marine larvae. I next examined patterns of larval dispersal in bicolor damselfish (Stegastes partitus, Pomacentridae) collected during the summers of 2004 and 2005 from reefs lining the Exuma Sound, Bahamas (measuring 205 km by 85 km). Parentage analysis directly documented two parent-offspring pairs located within the two northern-most sites, which indicated self-recruitment at these sites. Multivariate analyses of pair-wise relatedness values confirmed that self-recruitment was common at all sampled populations. I also found evidence of “sweepstakes events”, whereby only a small proportion of mature adults contributed to subsequent generations. Independent sweepstakes events were indentified in both space and time, bolstering the direct observations of self-recruitment and suggesting a role for sweepstakes analyses to identify the scale of larval dispersal events. This dissertation provides insights into the patterns of larval dispersal in coral-reef fishes. The coupling of direct (e.g., parentage) and indirect (e.g., assignment methods, sweepstakes analyses) methods in conjunction with continued technological and methodological advances will soon provide large-scale, ecologically relevant, rates of larval exchange. By uncovering the dynamics of these enigmatic processes, the implementation of conservation and management strategies for marine fishes in general will undoubtedly experience greater success

A Continuous, Fluorescence-based Assay of µ-Opioid Receptor Activation in AtT-20 Cells

Opioids are widely prescribed analgesics, but their use is limited due to development of tolerance and addiction, as well as high variability in individual response. The development of improved opioid analgesics requires high-throughput functional assays to assess large numbers of potential opioid ligands. In this study, we assessed the ability of a proprietary "no-wash" fluorescent membrane potential dye to act as a reporter of µ-opioid receptor (MOR) activation and desensitization via activation of G-protein-coupled inwardly rectifying potassium channels. AtT-20 cells stably expressing mouse MOR were assayed in 96-well plates using the Molecular Devices FLIPR membrane potential dye. Dye emission intensity decreased upon membrane hyperpolarization. Fluorescence decreased in a concentration-dependent manner upon application of a range of opioid ligands to the cells, with high-efficacy agonists producing a decrease of 35% to 40% in total fluorescence. The maximum effect of morphine faded in the continued presence of agonist, reflecting receptor desensitization. The effects of opioids were prevented by prior treatment with pertussis toxin and blocked by naloxone. We have demonstrated this assay to be an effective method for assessing ligand signaling at MOR, which may potentially be scaled up as an additional high-throughput screening technique for characterizing novel opioid ligands.NHMRC Grant Numbers: 1011979 & 104596

New insights into seasonal foraging ranges and migrations of minke whales from the Salish Sea and coastal British Columbia.

In the Salish Sea and coastal waters of British Columbia, minke whales are known to establish small home ranges during the feeding season. Beyond the feeding season little is known of their movements or distribution. To determine movement patterns of minke whales in these waters we used photo-identification data that were collected opportunistically from 2005-2012. These data were from four non-overlapping areas between 48ºN and 53ºN. Despite year-round search effort, minke whales were only encountered between April and October. Most of the 44 unique minke whales identified in 405 encounters displayed fidelity to areas both within and among feeding seasons. Five of these individuals also made relatively large-scale intra-annual movements between areas on six occasions. They were documented to move up to at least 424km in a northerly direction early in the season and up to at least 398km in a southerly direction late in the season. We believe that the seasonal patterns of these movements provide new insight into the foraging ranges and migrations of individuals. Ecological markers provide further evidence that the minke whales we photographed undertake annual long distance migrations. Scars believed to be from cookiecutter shark bites were observed on 43 individuals and the majority of minke whales documented with good quality images each year had acquired new scars since the previous feeding season. Furthermore, the commensal barnacle Xenobalanus globicipitis was observed on three individuals. Since these sharks and barnacles are from warm waters, it can be inferred that they interacted with the minke whales at lower latitudes. These findings may have important implications for our understanding of minke whale populations in the Salish Sea and the management of this species in the North Pacific

Microvascular resistance predicts myocardial salvage and infarct characteristics in ST-elevation myocardial infarction

<b>Background:</b> The pathophysiology of myocardial injury and repair in patients with ST‐elevation myocardial infarction is incompletely understood. We investigated the relationships among culprit artery microvascular resistance, myocardial salvage, and ventricular function.<p></p> <b>Methods and Results:</b> The index of microvascular resistance (IMR) was measured by means of a pressure‐ and temperature‐sensitive coronary guidewire in 108 patients with ST‐elevation myocardial infarction (83% male) at the end of primary percutaneous coronary intervention. Paired cardiac MRI (cardiac magnetic resonance) scans were performed early (2 days; n=108) and late (3 months; n=96) after myocardial infarction. T2‐weighted‐ and late gadolinium–enhanced cardiac magnetic resonance delineated the ischemic area at risk and infarct size, respectively. Myocardial salvage was calculated by subtracting infarct size from area at risk. Univariable and multivariable models were constructed to determine the impact of IMR on cardiac magnetic resonance–derived surrogate outcomes. The median (interquartile range) IMR was 28 (17–42) mm Hg/s. The median (interquartile range) area at risk was 32% (24%–41%) of left ventricular mass, and the myocardial salvage index was 21% (11%–43%). IMR was a significant multivariable predictor of early myocardial salvage, with a multiplicative effect of 0.87 (95% confidence interval 0.82 to 0.92) per 20% increase in IMR; P<0.001. In patients with anterior myocardial infarction, IMR was a multivariable predictor of early and late myocardial salvage, with multiplicative effects of 0.82 (95% confidence interval 0.75 to 0.90; P<0.001) and 0.92 (95% confidence interval 0.88 to 0.96; P<0.001), respectively. IMR also predicted the presence and extent of microvascular obstruction and myocardial hemorrhage.<p></p> <b>Conclusion:</b> Microvascular resistance measured during primary percutaneous coronary intervention significantly predicts myocardial salvage, infarct characteristics, and left ventricular ejection fraction in patients with ST‐elevation myocardial infarction.<p></p&gt

Bayesian parentage analysis with systematic accountability of genotyping error, missing data, and false matching

Motivation: The goal of any parentage analysis is to identify as many parent-offspring relationships as possible, while minimizing incorrect assignments. Existing methods can achieve these ends, but require additional information in the form of demographic data, thousands of markers, and/or estimates of genotyping error rates. For many non-model systems, it is simply not practical, cost-effective, or logistically feasible to obtain this information. Here, we develop a Bayesian parentage method that only requires the sampled genotypes in order to account for genotyping error, missing data, and false matches. Results: Extensive testing with microsatellite and SNP data sets reveals that our Bayesian parentage method reliably controls for the number of false assignments, irrespective of the genotyping error rate. When the number of loci is limiting, our approach maximizes the number of correct assignments by accounting for the frequencies of shared alleles. Comparisons with exclusion and likelihood-based methods on an empirical salmon data set revealed that our Bayesian method had the highest ratio of correct to incorrect assignments. Availability: Our program SOLOMON is available as an R package from the CRAN website. SOLOMON comes with a fully functional graphical user interface, requiring no user knowledge about the R programming environment. In addition to performing Bayesian parentage analysis, SOLOMON includes Mendelian exclusion and a priori power analysis modules. Further information and user support can be found at https://sites.google.com/site/parentagemethods/.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by Oxford University Press and can be found at: http://bioinformatics.oxfordjournals.org/

Inflammation and Immune-Related Candidate Gene Associations with Acute Lung Injury Susceptibility and Severity: A Validation Study

Introduction: Common variants in genes related to inflammation, innate immunity, epithelial cell function, and angiogenesis have been reported to be associated with risks for Acute Lung Injury (ALI) and related outcomes. We tested whether previously-reported associations can be validated in an independent cohort at risk for ALI. Methods: We identified 37 genetic variants in 27 genes previously associated with ALI and related outcomes. We prepared allelic discrimination assays for 12 SNPs from 11 genes with MAF>0.05 and genotyped these SNPs in Caucasian subjects from a cohort of critically ill patients meeting criteria for the systemic inflammatory response syndrome (SIRS) followed for development of ALI, duration of mechanical ventilation, and in-hospital death. We tested for associations using additive and recessive genetic models. Results: Among Caucasian subjects with SIRS (n = 750), we identified a nominal association between rs2069832 in IL6 and ALI susceptibility (OR$_{adj}$ 1.61; 95% confidence interval [CI], 1.04–2.48, P = 0.03). In a sensitivity analysis limiting ALI cases to those who qualified for the Acute Respiratory Distress Syndrome (ARDS), rs61330082 in NAMPT was nominally associated with risk for ARDS. In terms of ALI outcomes, SNPs in MBL2 (rs1800450) and IL8 (rs4073) were nominally associated with fewer ventilator-free days (VFDs), and SNPs in NFE2L2 (rs6721961) and NAMPT (rs61330082) were nominally associated with 28-day mortality. The directions of effect for these nominal associations were in the same direction as previously reported but none of the associations survived correction for multiple hypothesis testing. Conclusion: Although our primary analyses failed to statistically validate prior associations, our results provide some support for associations between SNPs in IL6 and NAMPT and risk for development of lung injury and for SNPs in IL8, MBL2, NFE2L2 and NAMPT with severity in ALI outcomes. These associations provide further evidence that genetic factors in genes related to immunity and inflammation contribute to ALI pathogenesis

Editorial workflow of a community-led, all-volunteer scientific journal: lessons from the launch of Seismica

Seismica is a community-led, volunteer-run, diamond open-access journal for seismology and earthquake science, and Seismica's mission and core values align with the principles of Open Science. This article describes the editorial workflow that Seismica uses to go from a submitted manuscript to a published article. In keeping with Open Science principles, the main goals of sharing this workflow description are to increase transparency around academic publishing, and to enable others to use elements of Seismica's workflow for journals of a similar size and ethos. We highlight aspects of Seismica's workflow that differ from practices at journals with paid staff members, and also discuss some of the challenges encountered, solutions developed, and lessons learned while this workflow was developed and deployed over Seismica's first year of operations

Larval Connectivity in an Effective Network of Marine Protected Areas

Acceptance of marine protected areas (MPAs) as fishery and conservation tools has been hampered by lack of direct evidence that MPAs successfully seed unprotected areas with larvae of targeted species. For the first time, we present direct evidence of large-scale population connectivity within an existing and effective network of MPAs. A new parentage analysis identified four parent-offspring pairs from a large, exploited population of the coral-reef fish Zebrasoma flavescens in Hawai'i, revealing larval dispersal distances ranging from 15 to 184 km. In two cases, successful dispersal was from an MPA to unprotected sites. Given high adult abundances, the documentation of any parent-offspring pairs demonstrates that ecologically-relevant larval connectivity between reefs is substantial. All offspring settled at sites to the north of where they were spawned. Satellite altimetry and oceanographic models from relevant time periods indicated a cyclonic eddy that created prevailing northward currents between sites where parents and offspring were found. These findings empirically demonstrate the effectiveness of MPAs as useful conservation and management tools and further highlight the importance of coupling oceanographic, genetic, and ecological data to predict, validate and quantify larval connectivity among marine populations