Dataset Information

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon.

ABSTRACT: Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) that allow fast and accurate identification of the imperiled Chinook salmon in the Great Central Valley of California. We show that 80 well-chosen loci, drawn from a pool of over 11,500 SNPs developed from restriction site-associated DNA sequencing, can accurately identify Chinook salmon runs and select populations within run. No other SNP panel for Central Valley Chinook salmon has been able to achieve the high accuracy of assignment we show here. This panel will greatly improve our ability to study and manage this ecologically, economically, and socially important species and demonstrates the great utility of using genomics to study migratory species.

SUBMITTER: Meek MH

PROVIDER: S-EPMC6093154 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon.

Meek Mariah H MH Baerwald Melinda R MR Stephens Molly R MR Goodbla Alisha A Miller Michael R MR Tomalty Katharine M H KMH May Bernie B

Ecology and evolution 20161005 21

Effective conservation and management of migratory species requires accurate identification of unique populations, even as they mix along their migratory corridors. While telemetry has historically been used to study migratory animal movement and habitat use patterns, genomic tools are emerging as a superior alternative in many ways, allowing large-scale application at reduced costs. Here, we demonstrate the usefulness of genomic resources for identifying single-nucleotide polymorphisms (SNPs) t ...[more]

PMID: 30128122

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Project description:ObjectivesCalifornia Senate Bill 41 (SB41), effective January 2012, is a human immunodeficiency virus/hepatitis C virus prevention measure designed to expand syringe access among injection drug users (IDUs) by allowing pharmacies to sell syringes without a prescription. This study assesses self-reported implementation of SB41 and characterizes barriers amenable to intervention.DesignInterviewer-administered survey.Setting and participantsFresno and Kern Counties, CA. Pharmacists and other pharmacy staff (n = 404) at 212 pharmacies.Outcome measureSelf-reported nonprescription pharmacy sales to known or suspected IDUs.ResultsOverall, 29.3% of participants said their pharmacy would sell nonprescription syringes to a known or suspected IDU, whereas a far higher proportion (79.3%) would sell nonprescription syringes to a person with diabetes. More than one-half said that their pharmacy requires nonprescription syringe purchasers to enter their signature and name and address in a log book although that is not required under SB41. Fewer than 2 out of 3 participants (61.1%) knew that it is legal to sell nonprescription syringes to IDUs. That knowledge, as well as having syringe sales practices based on both store policy and discretion, were positively associated with IDU syringe sales after controlling for other factors. Working at an independent pharmacy, agreeing that only people with "medical conditions" such as diabetes should be able to buy syringes, and viewing syringe sales to IDUs as "not good business" were independently but negatively associated with IDU syringe sales.ConclusionThis study complements an earlier syringe purchase trial documenting low participation in voluntary nonprescription syringe sales under SB41 in Fresno and Kern Counties. In the absence of legislation requiring mandatory syringe sales, interventions should be developed to increase knowledge of the law and frame addiction as a medical condition, with a special focus on independent pharmacies. Informational interventions should stress the need to eliminate log book documentation requirements, which may serve as a barrier to IDU purchase.

Project description:Upriver movements were determined for Chinook salmon Oncorhynchus tshawytscha returning to the Yukon River, a large, virtually pristine river basin. These returns have declined dramatically since the late 1990s, and information is needed to better manage the run and facilitate conservation efforts. A total of 2,860 fish were radio tagged during 2002-2004. Most (97.5%) of the fish tracked upriver to spawning areas displayed continual upriver movements and strong fidelity to the terminal tributaries entered. Movement rates were substantially slower for fish spawning in lower river tributaries (28-40 km d-1) compared to upper basin stocks (52-62 km d-1). Three distinct migratory patterns were observed, including a gradual decline, pronounced decline, and substantial increase in movement rate as the fish moved upriver. Stocks destined for the same region exhibited similar migratory patterns. Individual fish within a stock showed substantial variation, but tended to reflect the regional pattern. Differences between consistently faster and slower fish explained 74% of the within-stock variation, whereas relative shifts in sequential movement rates between "hares" (faster fish becoming slower) and "tortoises" (slow but steady fish) explained 22% of the variation. Pulses of fish moving upriver were not cohesive. Fish tagged over a 4-day period took 16 days to pass a site 872 km upriver. Movement rates were substantially faster and the percentage of atypical movements considerably less than reported in more southerly drainages, but may reflect the pristine conditions within the Yukon River, wild origins of the fish, and discrete run timing of the returns. Movement data can provide numerous insights into the status and management of salmon returns, particularly in large river drainages with widely scattered fisheries where management actions in the lower river potentially impact harvests and escapement farther upstream. However, the substantial variation exhibited among individual fish within a stock can complicate these efforts.

Project description:BackgroundPyrethroid pesticide use is increasing worldwide, although the full extent of associated health effects is unknown. An epigenome-wide association study (EWAS) with exploratory pathway analysis may help identify potential pyrethroid-related health effects.MethodsWe performed an exploratory EWAS of chronic ambient pyrethroid exposure using control participants' blood in the Parkinson's Environment and Genes Study in the Central Valley of California (N = 237). We estimated associations of living and working near agricultural pyrethroid pesticide applications in the past 5 years (binary) with site-specific differential methylation, and used a false discovery rate (FDR) cut off of 0.05 for significance. We controlled for age, sex, education, cell count, and an ancestral marker for Hispanic ethnicity. We normalized methylation values for Type I/II probe bias using Beta-Mixture Quantile (BMIQ) normalization, filtered out cross-reactive probes, and evaluated for remaining bias with Surrogate Variable Analysis (SVA). We also evaluated the effects of controlling for cell count and normalizing for Type I/II probe bias by comparing changes in effect estimates and p-values for the top hits across BMIQ and GenomeStudio normalization methods, and controlling for cell count. To facilitate broader interpretation, we annotated genes to the CpG sites and performed gene set overrepresentation analysis, using genes annotated to CpG sites that were associated with pyrethroids at a raw p < 0.05, and controlling for background representation of CpG sites on the chip. We did this for both a biological process context (Gene Ontology terms) using missMethyl, and a disease set context using WebGestalt. For these gene set overrepresentation analyses we also used an FDR cut off of 0.05 for significance of gene sets.ResultsAfter controlling for cell count and applying BMIQ normalization, 4 CpG sites were differentially methylated in relation to pyrethroid exposures. When using GenomeStudio's Illumina normalization, 415 CpG sites were differentially methylated, including all four identified with the BMIQ method. In the gene set overrepresentation analyses, we identified 6 GO terms using BMIQ normalization, and 76 using Illumina normalization, including the 6 identified by BMIQ. For disease sets, we identified signals for Alzheimer's disease, leukemia and several other cancers, diabetes, birth defects, and other diseases, for both normalization methods. We identified minimal changes in effect estimates after controlling for cell count, and controlling for cell count generally weakened p-values. BMIQ normalization, however, resulted in different beta coefficients and weakened p-values.ConclusionsChronic ambient pyrethroid exposure is associated with differential methylation at CpG sites that annotate to a wide variety of disease states and biological mechanisms that align with prior research. However, this EWAS also implicates several novel diseases for future investigation, and highlights the relative importance of different background normalization methods in identifying associations.

Project description:BackgroundBetween 2013 and 2015, a large part of the western United States, including the Central Valley of California, sustained an extreme drought. The Central Valley is recognized as a region of hemispheric importance for waterbirds, which use flooded agriculture and wetlands as habitat. Thus, the impact of drought on the distribution of surface water needed to be assessed to understand the effects on waterbird habitat availability.MethodsWe used remote sensing data to quantify the impact of the recent extreme drought on the timing and extent of waterbird habitat during the non-breeding season (July-May) by examining open water in agriculture (rice, corn, and other crops) and managed wetlands across the Central Valley. We assessed the influence of habitat incentive programs, particularly The Nature Conservancy's BirdReturns and The Natural Resources Conservation Service's Waterbird Habitat Enhancement Program (WHEP), at offsetting habitat loss related to drought.ResultsOverall, we found statistically significant declines in open water in post-harvest agriculture (45-80% declines) and in managed wetlands (39-60% declines) during the 2013-2015 drought compared to non-drought years during the period of 2000-2011. Crops associated with the San Joaquin Basin, specifically corn, as well as wetlands in that part of the Central Valley exhibited larger reductions in open water than rice and wetlands in the Sacramento Valley. Semi-permanent wetlands on protected lands had significantly lower (39-49%) open water in the drought years than those on non-protected lands while seasonal wetlands on protected lands had higher amounts of open water. A large fraction of the daily open water in rice during certain times of the year, particularly in the fall for BirdReturns (61%) and the winter for WHEP (100%), may have been provided through incentive programs which underscores the contribution of these programs. However, further assessment is needed to know how much the incentive programs directly offset the impact of drought in post-harvest rice by influencing water management or simply supplemented funding for activities that might have been done regardless.DiscussionOur landscape analysis documents the significant impacts of the recent extreme drought on freshwater wetland habitats in the Central Valley, the benefits of incentive programs, and the value of using satellite data to track surface water and waterbird habitats. More research is needed to understand subsequent impacts on the freshwater dependent species that rely on these systems and how incentive programs can most strategically support vulnerable species during future extreme drought.

Dataset Information

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon.

Publications

Sequencing improves our ability to study threatened migratory species: Genetic population assignment in California's Central Valley Chinook salmon.

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