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- Dabrowski, Michal, et al.
(author)
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Reliability assessment of null allele detection : inconsistencies between and within different methods
- 2014
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In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 14:2, s. 361-373
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Journal article (peer-reviewed)abstract
- Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.
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| 2. |
- Bus, Magdalena M., et al.
(author)
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High efficiency protocol of DNA extraction from Micromys minutus mandibles from owl pellets : a tool for molecular research of cryptic mammal species
- 2014
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In: Acta Theriologica. - : Springer Science and Business Media LLC. - 0001-7051 .- 2190-3743. ; 59:1, s. 99-109
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Journal article (peer-reviewed)abstract
- Owl pellets have high potential as a source of DNA. However, this noninvasive method of collecting DNA is rarely used, and its methodological aspects are poorly understood. We investigated the methodology for DNA extraction and amplification from owl pellets containing the smallest European rodent-the Harvest mouse Micromys minutus-as an example. We used mandibles identified in owl pellets for mitochondrial and nuclear DNA amplification. For DNA extraction, we tested two commercial protocols and utilized a protocol being a combination of two commercial kits which ensured high efficiency of DNA extraction. Additionally, we recorded that the amount of DNA was five times higher in extracts from teeth as compared to DNA extracts from jawbones derived from the same mandible. The quantity of DNA was significantly positively correlated with biological sample weight; however, the age of the pellet remains had an impact on the level of inhibition. We recorded inhibition in 40 % of mtDNA extracts derived from pellets older than 150 months, whereas in DNA extracts from pellets younger than 80 months, we did not observe a negative impact of inhibition on PCR efficiency. The amplification success rate was 89.9 % for the mitochondrial fragment and 39.4 % in the case of the nuclear fragment. We observed partial degradation of DNA evidenced by the fact that the longest fragments that we were able to amplify in the case of mtDNA were 450 and 200 bp for nuDNA. The study shows that pellets can be considered as a source of DNA and have high potential for molecular research in the case of threatened species and species that are difficult to study using standard field techniques.
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| 3. |
- Josefsson, Jonas, et al.
(author)
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Improving scientific rigour in conservation evaluations and a plea deal for transparency on potential biases
- 2020
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In: Conservation Letters. - : Wiley. - 1755-263X. ; 13:5
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Research review (peer-reviewed)abstract
- The delivery of rigorous and unbiased evidence on the effects of interventions lay at the heart of the scientific method. Here we examine scientific papers evaluating agri-environment schemes, the principal instrument to mitigate farmland biodiversity declines worldwide. Despite previous warnings about rudimentary study designs in this field, we found that the majority of studies published between 2008 and 2017 still lack robust study designs to strictly evaluate intervention effects. Potential sources of bias that arise from the correlative nature are rarely mentioned, and results are still promoted by using a causal language. This lack of robust study designs likely results from poor integration of research and policy, while the erroneous use of causal language and an unwillingness to discuss bias may stem from publication pressures. We conclude that scientific reporting and discussion of study limitations in intervention research must improve and propose some practices toward this goal.
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