| 1. |
- Menkveld, Albert J., et al.
(författare)
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Nonstandard Errors
- 2024
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Ingår i: JOURNAL OF FINANCE. - : Wiley-Blackwell. - 0022-1082 .- 1540-6261. ; 79:3, s. 2339-2390
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Tidskriftsartikel (refereegranskat)abstract
- In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence-generating process (EGP). We claim that EGP variation across researchers adds uncertainty-nonstandard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for more reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants.
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| 2. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Farrell, Edward D. D., et al.
(författare)
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A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c
- 2022
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Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 9:9
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Tidskriftsartikel (refereegranskat)abstract
- Atlantic herring in International Council for Exploration of the Sea (ICES) Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographical delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 single-nucleotide polymorphisms, derived from whole-genome sequencing, were used to genotype 3480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy greater than 90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1514 individuals) from Divisions 6.a, 7.b-c indicated previously unrecognized levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.
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| 4. |
- Andersson, Leif, et al.
(författare)
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How Fish Population Genomics Can Promote Sustainable Fisheries : A Road Map
- 2024
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Ingår i: Annual Review of Animal Biosciences. - : ANNUAL REVIEWS. - 2165-8102 .- 2165-8110. ; 12, s. 1-20
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Forskningsöversikt (refereegranskat)abstract
- Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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| 5. |
- Bekkevold, Dorte, et al.
(författare)
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Mixed-stock analysis of Atlantic herring (Clupea harengus) : a tool for identifying management units and complex migration dynamics
- 2023
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Ingår i: ICES Journal of Marine Science. - : Oxford University Press. - 1054-3139 .- 1095-9289. ; 80:1, s. 173-184
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Tidskriftsartikel (refereegranskat)abstract
- We developed and validated a mixed-stock analysis (MSA) method with 59 single-nucleotide polymorphisms selected from genome-wide data to assign individuals to populations in mixed-stock samples of Atlantic herring from the North and Baltic seas. We analysed 3734 herring from spawning locations and scientific catches of mixed feeding stocks to demonstrate a "one-fits-all" tool with unprecedented accuracy for monitoring spatio-temporal dynamics throughout a large geographical range with complex stock mixing. We re-analysed time-series data (2002-2021) and compared inferences about stock composition with estimates from morphological data. We show that contributions from the western Baltic spring-spawning stock complex, which is under management concern, have likely been overestimated. We also show that a genetically distinctive population of western Baltic autumn spawners, ascribed low fisheries importance, contributes non-negligible and potentially temporally increasing proportions to mixed-stock aggregations, calling for a re-evaluation of stock definitions. MSA data can be implemented in stock assessment and in a variety of applications, including marine ecosystem description, impact assessment of specific fleets, and stock-rebuilding plans.
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| 6. |
- Chan, Kai M. A., et al.
(författare)
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Levers and leverage points for pathways to sustainability
- 2020
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Ingår i: People and Nature. - : Wiley. - 2575-8314. ; 2:3, s. 693-717
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Tidskriftsartikel (refereegranskat)abstract
- 1. Humanity is on a deeply unsustainable trajectory. We are exceeding planetary boundaries and unlikely to meet many international sustainable development goals and global environmental targets. Until recently, there was no broadly accepted framework of interventions that could ignite the transformations needed to achieve these desired targets and goals.2. As a component of the IPBES Global Assessment, we conducted an iterative expert deliberation process with an extensive review of scenarios and pathways to sustainability, including the broader literature on indirect drivers, social change and sustainability transformation. We asked, what are the most important elements of pathways to sustainability?3. Applying a social-ecological systems lens, we identified eight priority points for intervention (leverage points) and five overarching strategic actions and priority interventions (levers), which appear to be key to societal transformation. The eight leverage points are: (1) Visions of a good life, (2) Total consumption and waste, (3) Latent values of responsibility, (4) Inequalities, (5) Justice and inclusion in conservation, (6) Externalities from trade and other telecouplings, (7) Responsible technology, innovation and investment, and (8) Education and knowledge generation and sharing. The five intertwined levers can be applied across the eight leverage points and more broadly. These include: (A) Incentives and capacity building, (B) Coordination across sectors and jurisdictions, (C) Pre-emptive action, (D) Adaptive decision-making and (E) Environmental law and implementation. The levers and leverage points are all non-substitutable, and each enables others, likely leading to synergistic benefits.4. Transformative change towards sustainable pathways requires more than a simple scaling-up of sustainability initiatives-it entails addressing these levers and leverage points to change the fabric of legal, political, economic and other social systems. These levers and leverage points build upon those approved within the Global Assessment's Summary for Policymakers, with the aim of enabling leaders in government, business, civil society and academia to spark transformative changes towards a more just and sustainable world.
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| 7. |
- Fuentes-Pardo, Angela P., et al.
(författare)
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The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)
- 2023
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Ingår i: Evolutionary Applications. - : John Wiley & Sons. - 1752-4571. ; 16:6, s. 1201-1219
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how populations adapt to their environment is increasingly important to prevent biodiversity loss due to overexploitation and climate change. Here we studied the population structure and genetic basis of local adaptation of Atlantic horse mackerel, a commercially and ecologically important marine fish that has one of the widest distributions in the eastern Atlantic. We analyzed whole-genome sequencing and environmental data of samples collected from the North Sea to North Africa and the western Mediterranean Sea. Our genomic approach indicated low population structure with a major split between the Mediterranean Sea and the Atlantic Ocean and between locations north and south of mid-Portugal. Populations from the North Sea are the most genetically distinct in the Atlantic. We discovered that most population structure patterns are driven by a few highly differentiated putatively adaptive loci. Seven loci discriminate the North Sea, two the Mediterranean Sea, and a large putative inversion (9.9 Mb) on chromosome 21 underlines the north-south divide and distinguishes North Africa. A genome-environment association analysis indicates that mean seawater temperature and temperature range, or factors correlated to them, are likely the main environmental drivers of local adaptation. Our genomic data broadly support the current stock divisions, but highlight areas of potential mixing, which require further investigation. Moreover, we demonstrate that as few as 17 highly informative SNPs can genetically discriminate the North Sea and North African samples from neighboring populations. Our study highlights the importance of both, life history and climate-related selective pressures in shaping population structure patterns in marine fish. It also supports that chromosomal rearrangements play a key role in local adaptation with gene flow. This study provides the basis for more accurate delineation of the horse mackerel stocks and paves the way for improving stock assessments.
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| 8. |
- Han, Fan, et al.
(författare)
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Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci
- 2020
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Ingår i: eLIFE. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.
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