Geology topics

Mariah Meek

Publications and source records attributed to Mariah Meek.

6 recordsLinked to original sources

USGS2023

Imperfect detection and misidentification affect inferences from data informing water operation decisions

Objective Managers can modify river flow regimes using fish monitoring data to minimize impacts from water management infrastructure. For example, operation of the gate-controlled Delta Cross Channel (DCC) in California can negatively affect the endangered Sacramento River winter-run Chinook Salmon Oncorhynchus tshawytscha . Although guidelines have been developed for DCC operations by using real-time juvenile fish sampling count data, there is uncertainty about how environmental conditions influence fish occupancy and the extent to which those relationships are affected by sampling and identification error. Methods We evaluated the effect of environmental conditions, imperfect detection, and misidentification error on salmon occupancy by analyzing data using hierarchical multistate occupancy models. A total of 14,147 trawl tows and beach seine hauls were conducted on 1058 sampling days between October and December from 1996 to 2019. During these surveys, 2803 juvenile winter-run Chinook Salmon were identified, and approximately 29% of the sampling days had at least one winter-run juvenile detected. Result The probability of misidentifying an individual juvenile winter-run Chinook Salmon in the field was estimated to be 0.056 based on fish identification examinations and genetic sampling. Occupancy varied considerably and was related to flow characteristics, water clarity, weather, time of year, and whether occupancy was detected during the previous sampling day. However, these relationships and their significance changed considerably when accounting for imperfect detection and the probability of misidentifying individual juvenile salmon. Detection was <0.3 under average sampling conditions during a single sample and was influenced by flow, water clarity, site, and volume sampled. Conclusion Our modeling results indicate that DCC gate closure decisions could occur on fewer days when imperfect detection and misidentification error are not accounted for. These findings demonstrate the need to account for identification and detection error while using monitoring data to assess factors influencing fish occupancy and inform future management decisions.

North American Journal of Fisheries Management↗

USGS2022

Conservation genetics and wild trout: Evolving opportunities to support management

It is increasingly apparent that our planet is undergoing rapid, unprecedented environmental change. These changes are already impacting wild trout populations, leading to declines in occupancy and abundance across increasingly fragmented landscapes. Many changes are projected to intensify in the coming decades, which are likely to be crucial to the future of many wild populations. While there is some uncertainty in exactly how changes will manifest, we can be confident that many populations will need to rapidly adapt to change if they are to persist. The foundation of such rapid change is genetic diversity, and conservation strategies are most likely to be successful when they consider the role of genetics in the outlook for wild trout populations. While not a panacea, rapid advances in the field of conservation genetics allow longstanding questions to be addressed with greater rigor and present new opportunities to support management against a backdrop of accelerating change. Here, we review major advances in conservation genetics as they relate to wild trout and highlight potential opportunities to support conservation in the Anthropocene and key areas of continuing uncertainty.

Conference Paper↗

USGS2021

Understanding genetics for successful conservation and restoration of resilient Chesapeake Bay brook trout populations

Traditionally, fisheries management has focused on the abundance, distribution, and size structure of populations. Although these factors remain key aspects of management, a large and growing body of evidence highlights the importance of genetics in conserving wild populations, especially when populations are small and isolated (Frankham et al. 2017). Local adaptations are very common among fishes and help populations cope with specific conditions in their local environment (Fraser et al. 2011). The field of conservation genetics and genomics is highly technical and has advanced rapidly in recent years, offering a wealth of information to support brook trout conservation and restoration. A major impediment to successfully incorporating these advances into conservation outcomes is that most fisheries managers have only a basic understanding of fish genetics and its relevance to their management decisions.

Maryland, Virginia↗

USGS2021

Global commitments to conserving and monitoring genetic diversity are now necessary and feasible

Global conservation policy and action have largely neglected protecting and monitoring genetic diversity—one of the three main pillars of biodiversity. Genetic diversity (diversity within species) underlies species’ adaptation and survival, ecosystem resilience, and societal innovation. The low priority given to genetic diversity has largely been due to knowledge gaps in key areas, including the importance of genetic diversity and the trends in genetic diversity change; the perceived high expense and low availability and the scattered nature of genetic data; and complicated concepts and information that are inaccessible to policymakers. However, numerous recent advances in knowledge, technology, databases, practice, and capacity have now set the stage for better integration of genetic diversity in policy instruments and conservation efforts. We review these developments and explore how they can support improved consideration of genetic diversity in global conservation policy commitments and enable countries to monitor, report on, and take action to maintain or restore genetic diversity.

BioScience↗

USGS2020

Attack of the PCR clones: Rates of clonality have little effect on RAD-seq genotype calls

Interpretation of high-throughput sequence data requires an understanding of how decisions made during bioinformatic data processing can influence results. One source of bias that is often cited is PCR clones (or PCR duplicates). PCR clones are common in restriction site-associated sequencing (RAD-seq) data sets, which are increasingly being used for molecular ecology. To determine the influence PCR clones and the bioinformatic handling of clones have on genotyping, we evaluate four RAD-seq data sets. Data sets were compared before and after clones were removed to estimate the number of clones present in RAD-seq data, quantify how often the presence of clones in a data set causes genotype calls to change compared to when clones were removed, investigate the mechanisms that lead to genotype call changes and test whether clones bias heterozygosity estimates. Our RAD-seq data sets contained 30%–60% PCR clones, but 95% of RAD-tags had five or fewer clones. Relatively few genotypes changed once clones were removed (5%–10%), and the vast majority of these changes (98%) were associated with genotypes switching from a called to no-call state or vice versa. PCR clones had a larger influence on genotype calls in individuals with low read depth but appeared to influence genotype calls at all loci similarly. Removal of PCR clones reduced the number of called genotypes by 2% but had almost no influence on estimates of heterozygosity. As such, while steps should be taken to limit PCR clones during library preparation, PCR clones are likely not a substantial source of bias for most RAD-seq studies.

Molecular Ecology Resources↗

USGS2019

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high-throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced-representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long-term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.

Molecular Ecology Resources↗