Applied Conservation Genetics and the Need for Quality Control and Reporting of Genetic Data Used in Fisheries and Wildlife Management (original) (raw)
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Marine and Freshwater Research, 2015
The lack of independently verifiable estimates of catches and fisheries independent estimates of abundance and fishing mortality are major sources of uncertainty in the management of many fisheries. DNA profiling provides the potential to substantially improve the quality of data for assessments and act as an additional deterrent to illegal, unreported, and unregulated (IUU) fishing. Barriers to the implementation of this technology include cost of sample collection and processing, forensic grade quality control, and the ability to apply undetectable tags. We present the results of a comparison of two current and one new (gene tag tool, GTT) sampling techniques, using the highly valued southern bluefin tuna as an example. We demonstrate that fish sampled with two techniques are highly unlikely to be recognised as ‘tagged’, whereas one technique was easily recognisable after 73 days. The GTT reduced handling before DNA extraction, whereas both other techniques require additional labo...
Linking genomics and fish conservation decision making: a review
Reviews in Fish Biology and Fisheries, 2020
Despite the promising applications of genome-wide information to conservation, the field of conservation genomics remains hindered by a research-practice gap. Identifying the benefits from genomics in relation to fish conservation planning and decision-making could contribute to bridging this gap. The goals of our study were twofold. First, we reviewed the fish conservation genomic literature to determine how genomic information has been used to inform conservation decision making; and second, we examined how genomic information can be linked to an existing conservation decision framework. Our review showed that, as fish conservation genomics studies accumulate over time, collaborations between researchers and conservation practitioners are becoming increasingly frequent. While the field is dominated by studies of economically important families (e.g. salmonids, acipenserids) in first-world countries (North America, Europe), it has a broad taxonomic coverage where species of both local and global conservation concern are well represented. We also show that genomic information can readily be harnessed to guide decisions within existing conservation decision frameworks, from the conceptualization (identification of conservation targets and threats) to the implementation and the monitoring of conservation actions. In addition, our review identifies some limitations related to genomic inferences for conservation and proposes solutions to address these uncertainties and improve communication between conservation genomic scientists and practitioners. For genomic researchers, we outline how conservation decisions are made; for practitioners, we illustrate how genomic information can inform decision-making.
Genetica, 2011
Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size (‘size shifts’), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.
Assigning individual fish to populations using microsatellite DNA markers
Fish and Fisheries, 2001
New statistical developments combined with the use of highly polymorphic microsatellite DNA markers enable the determination of the population of origin of single fish, resulting in numerous new research possibilities and applications in practical management of fish populations. We first describe three main categories of methods available, i.e. (i) assignment tests and related methods, (ii) discriminant function analysis and (iii) artificial neural networks. In all these, individuals can be assigned to the population from which their multilocus genotypes are most likely to be derived. Assignment tests are based on calculations of the likelihood of multilocus genotypes in populations, based on allele frequencies. Discriminant function analysis is based on multivariate statistics, whereas artificial neural networks formulate predictions through exposure to correct solutions. Assignment tests are the methods of choice when considering genetic data alone, whereas discriminant function analysis and artificial neural networks may be useful when genetic data are combined with, for instance, morphological and ecological data. Assignment tests can be used to assess the genetic distinctness of populations, for discriminating among closely related species and to directly identify immigrants or individuals of immigrant ancestry, and thereby study patterns of dispersal among populations, including sex-biased dispersal. In a conservation context, assignment tests can be used to assess the genetic impact of domesticated fish on wild populations and for determining if extant fish populations are in fact indigenous or descendants from stocked fish or strayers, and they can be applied in forensics, for instance to reveal poaching. Assignment tests are at present most useful for studies of freshwater and anadromous fishes owing to stronger genetic differentiation among populations than in marine fishes. However, some genetically divergent populations of marine fishes have been discovered, which could be used as natural laboratories for studying dispersal and gene flow. It is foreseen that ongoing developments in statistical methods, combined with improved techniques for screening large numbers of loci, will permit assignment methods to become standard tools in studies on the biology of fishes.
Biological Conservation, 2019
Fish and wildlife managers are faced with the daunting task of making informed and sensible decisions in the face of conflicting objectives and rapid environmental change. Conservation genomicsthe use of new genomic techniques and genome-wide information to solve biological conservation problemsis an emerging scientific field that holds much promise in delivering practical knowledge to inform decisions, policies, and practices for conservation and management. However, the impact of genomics on conservation and management has been rather limited to date, described as the "conservation genomics gap". We set out to identify perceived benefits and existing barriers supporting or limiting the use of conservation genomics in conservation practice by analyzing how potential knowledge users (conservation practitioners) perceive and evaluate genomics using the case of managed Rainbow Trout (Oncorhynchus mykiss) fisheries in the Canadian province of British Columbia. We interviewed 33 government employees and 32 representatives from nongovernmental stakeholder groups involved in fisheries management. We found that very few knowledge users were familiar with genomics or understood the difference between genetics and genomics. Despite low genomics familiarity, respondents generally view conservation genomics favorably, as a reliable and promising tool that could provide them with novel knowledge that would help them improve management or make better decisions. However, the exact benefits or outcomes genomics could provide in applied contexts are potentially limited by politics, communication, expertise, interpretation, cost, competing conservation practices, and time. Our research suggests that genomics has considerable potential in applied conservation and management if clearer communication between researchers and practitioners is achieved. We recommend genomic researchers and funding agencies identify wide-ranging practitioners and instate knowledge and sharing interfaces at project outset focused on practitioner objectives and improving practitioner knowledge and familiarity.
Detection of Genetic Patterns in Endangered Marine Species Is Affected by Small Sample Sizes
Animals
Knowledge of Genetic diversity and its spatial distribution is crucial to improve conservation plans for endangered species. Genetic tools help ensure species’ long-term persistence by unraveling connectivity patterns and evolutionary trajectories of populations. Here, microsatellite genotypes of individuals from populations of Patella ferruginea are used to assess the effect of sample size on metrics of within-and between-population genetic diversity by combining empirical and simulated data. Within-population metrics are slightly to moderately affected by small sample size, albeit the magnitude of the bias is proportional to the effective population size and gene flow. The power of detecting genetic differentiation among populations increases with sample size, albeit the gain of increasing the number of sampled individuals tends to be negligible between 30 and 50. Our results line up with those of previous studies and highlight that small sample sizes are not always a hindrance to...
Microsatellite genotyping is a common DNAcharacterization technique in population, ecological andevolutionary genetics research. Since different alleles aresized relative to internal size-standards, different laboratoriesmust calibrate and standardize allelic designationswhen exchanging data. This interchange of microsatellitedata can often prove problematic. Here, 16 microsatelliteloci were calibrated and standardized for the Atlantic salmon,Salmo salar, across 12 laboratories. Althoughinconsistencies were observed, particularly due to differencesbetween migration of DNA fragments and actualallelic size ('size shifts'), inter-laboratory calibration wassuccessful. Standardization also allowed an assessment ofthe degree and partitioning of genotyping error. Notably,the global allelic error rate was reduced from 0.05 ± 0.01prior to calibration to 0.01 ± 0.002 post-calibration. Mosterrors were found to occur during analysis (i.e. when sizecallingalleles; the mean proportion of all errors that wereanalytical errors across loci was 0.58 after calibration). Noevidence was found of an association between the degreeof error and allelic size range of a locus, number of alleles,nor repeat type, nor was there evidence that genotypingerrors were more prevalent when a laboratory analyzedsamples outside of the usual geographic area theyencounter. The microsatellite calibration between laboratoriespresented here will be especially important forgenetic assignment of marine-caught Atlantic salmon,