Genotypic variability enhances the reproducibility of an ecological study

Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M.; Blouin, Manuel; Scheu, Stefan; Girin, Thomas; Frechet, Gregoire; Rose, Laura; Scherer‐Lorenzen, Michael; Lata, Jean‐Christophe; Cesarz, Simone; Eisenhauer, Nico; Gigon, Agnès; Weigelt, Alexandra; Hansart, Amandine; Greiner, A.; Pando, Anne; Geßler, Arthur; Grignani, Carlo; Assandri, Davide; Gleixner, Gerd; Galliard, Jean‐François Le; Urban‐Mead, Katherine R.; Zavattaro, Laura; Müller, Marina; Lange, Markus; Lukáč, Martin; Bonkowski, Michael; Mannerheim, Neringa; Buchnann, Nina; Butenschoen, Olaf; Rotter, Paula; Seyhun, Rahme; Devidal, Sébastien; Kayler, Zachary; Roy, Jacques

doi:10.1101/080119

Cited by 17 publications

(21 citation statements)

References 30 publications

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“…Medicago truncatula (L000738, L000530 and L000174) were first sterilized by soaking 100 397 seeds in 100 mL of a sodium hypochlorite solution with 2.6% active chlorine, and stirred for 15 398 min using a magnet. Thereafter, the seeds were rinsed 3 times in 250 mL of sterile water for 10-399 Milcu et al 2017 18/32 20 seconds under shaking. Sterilized seeds were germinated in trays (10 cm deep) filled with 400 vermiculite.…”

Section: Germination 395mentioning

confidence: 99%

“…Therefore, to test for the SETUP effect, we used an additional 487 complementary model including CSV and SETUP as fix effects and laboratory as a random 488 factor (R syntax: "model= lme (response variable ~ LEG*CSV*SETUP, random=~1|LAB/block, 489 weights=varIdent (form = ~1|LAB*LEG)") ( Supplementary Table 3). To test whether the results 490 were affected by the collinearity among the response variables, the two models also were run on 491 Milcu et al 2017 22/32 the first (PC1) and second (PC2) principal components the 12 response variables (Fig. 4ab).…”

Section: /32mentioning

confidence: 99%

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Genotypic variability enhances the reproducibility of an ecological study

Milcu

Puga-Freitas

Ellison

et al. 2016

Preprint

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Many scientific disciplines currently are experiencing a "reproducibility crisis" because 57 numerous scientific findings cannot be repeated consistently. A novel but controversial 58 hypothesis postulates that stringent levels of environmental and biotic standardization in 59 experimental studies reduces reproducibility by amplifying impacts of lab-specific 60 environmental factors not accounted for in study designs. A corollary to this hypothesis is 61 that the deliberate introduction of controlled systematic variability (CSV) in experimental 62 designs can increase reproducibility. We tested this hypothesis using a multi-laboratory 63 microcosm study in which the same ecological experiment was repeated in 14 laboratories 64 across Europe. Each laboratory introduced environmental and genotypic CSV within and 65

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Section: Germination 395mentioning

confidence: 99%

Section: /32mentioning

confidence: 99%

Genotypic variability enhances the reproducibility of an ecological study

Milcu

Puga-Freitas

Ellison

et al. 2016

Preprint

Self Cite

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“…The issue of reproducibility has been noted only recently in ecology 9,10 , but is likely prominent 11,12 . Because ecological studies often encompass uncontrollable or unaccountable factors 13 , it is especially important to report in detail the circumstances and methods that apply. Furthermore, ecological studies often depend on statistical models, such that reporting specific modelling methods and decisions and how they are intended to reflect biological knowledge or assumptions holds particular importance for reproducibility in ecology 14,15 .…”

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confidence: 99%

A checklist for maximizing reproducibility of ecological niche models

et al. 2019

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Reporting specific modelling methods and metadata is essential to the reproducibility of ecological studies, yet guidelines rarely exist regarding what information should be noted. Here, we address this issue for ecological niche modelling or species distribution modelling, a rapidly developing toolset in ecology used across many aspects of biodiversity science. Our quantitative review of the recent literature reveals a general lack of sufficient information to fully reproduce the work. Over two-thirds of the examined studies neglected to report the version or access date of the underlying data, and only half reported model parameters. To address this problem, we propose adopting a checklist to guide studies in reporting at least the minimum information necessary for ecological niche modelling reproducibility, offering a straightforward way to balance efficiency and accuracy. We encourage the ecological niche modelling community, as well as journal reviewers and editors, to utilize and further develop this framework to facilitate and improve the reproducibility of future work. The proposed checklist framework is generalizable to other areas of ecology, especially those utilizing biodiversity data, environmental data and statistical modelling, and could also be adopted by a broader array of disciplines.

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“…In animal experiments, batch-to-batch variation was described even under highly standardised conditions in the same lab [61]. Experiment heterogenisation and multi-laboratory design was suggested to produce more reliable data [61][62][63][64][65]. In the area of drug discovery, clear requirements for the generation of Researcher careers are driven by publications in as highly prestigious research journals as possible to gain visibility and attract research funding [19,71].…”

Section: Methodsmentioning

confidence: 99%

Researcher Conduct Determines Data Reliability

Wass¹,

Ray²,

Michaelis³

2018

Preprint

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A lack of data reproducibility (“reproducibility crisis”) is debated across many scientific and medical disciplines. A systematic analysis of the available evidence on the reliability of scientific data revealed that, although the existence of a reproducibility crisis is widely perceived, conclusive data on the scale of the problem are lacking. Most importantly we found that, although the debate is largely focused on methodological issues, researcher conduct defines research standards and in turn data reliability. The availability of reliable methods itself does not guarantee good practice. Moreover, research is typically characterised by a lack of established methods due to its immanent novelty. Despite the crucial importance of researcher conduct, research and conclusive data on the determinants of researcher behaviour are missing. In conclusion, meta-research is urgently needed that establishes an understanding of the factors that determine researcher behaviour. This knowledge can then be used to implement and iteratively improve measures, which incentivise researchers to apply the highest standards resulting in high quality data.

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Genotypic variability enhances the reproducibility of an ecological study

Cited by 17 publications

References 30 publications

Genotypic variability enhances the reproducibility of an ecological study

Genotypic variability enhances the reproducibility of an ecological study

A checklist for maximizing reproducibility of ecological niche models

Researcher Conduct Determines Data Reliability

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