TY - JOUR
T1 - Extreme Sensitivity of Fitness to Environmental Conditions
T2 - Lessons from #1BigBatch
AU - Kinsler, Grant
AU - Schmidlin, Kara
AU - Newell, Daphne
AU - Eder, Rachel
AU - Apodaca, Sam
AU - Lam, Grace
AU - Petrov, Dmitri
AU - Geiler-Samerotte, Kerry
N1 - Funding Information:
We are grateful to Sasha Levy, Marc Salit and the members of the Geiler-Samerotte and Petrov labs for helpful discussions. This work was supported by a National Institutes of Health grant R35GM133674 (to KGS), an Alfred P Sloan Research Fellowship in Computational and Molecular Evolutionary Biology grant FG-2021-15705 (to KGS), a National Science Foundation Biological Integration Institution grant 2119963 (to KGS), a National Institutes of Health grant R35GM118165 (to DP), a Chan Zuckerberg Investigator Award (to DP), and a Stanford Center for Computational, Evolutionary, and Human Genomics predoctoral fellowship (to GK).
Publisher Copyright:
© 2023, The Author(s).
PY - 2023/6
Y1 - 2023/6
N2 - The phrase “survival of the fittest” has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
AB - The phrase “survival of the fittest” has become an iconic descriptor of how natural selection works. And yet, precisely measuring fitness, even for single-celled microbial populations growing in controlled laboratory conditions, remains a challenge. While numerous methods exist to perform these measurements, including recently developed methods utilizing DNA barcodes, all methods are limited in their precision to differentiate strains with small fitness differences. In this study, we rule out some major sources of imprecision, but still find that fitness measurements vary substantially from replicate to replicate. Our data suggest that very subtle and difficult to avoid environmental differences between replicates create systematic variation across fitness measurements. We conclude by discussing how fitness measurements should be interpreted given their extreme environment dependence. This work was inspired by the scientific community who followed us and gave us tips as we live tweeted a high-replicate fitness measurement experiment at #1BigBatch.
KW - Barcodes
KW - Batch effects
KW - Experimental evolution
KW - Fitness
KW - Index misassignment
KW - Reproducibility
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U2 - 10.1007/s00239-023-10114-3
DO - 10.1007/s00239-023-10114-3
M3 - Article
C2 - 37237236
AN - SCOPUS:85160299686
SN - 0022-2844
VL - 91
SP - 293
EP - 310
JO - Journal of Molecular Evolution
JF - Journal of Molecular Evolution
IS - 3
ER -