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Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

Eddie K. H. Ho, E.S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, View ORCID ProfileS. Schaack
doi: https://doi.org/10.1101/2020.09.21.307181
Eddie K. H. Ho
1Department of Biology, Reed College, Portland, OR 97202
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E.S. Bellis
1Department of Biology, Reed College, Portland, OR 97202
2Arkansas Biosciences Institute and Department of Computer Science, Arkansas State University, State University, AR 72467
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Jaclyn Calkins
1Department of Biology, Reed College, Portland, OR 97202
3Stein Institute for Research on Aging - Center for Healthy Aging, University of California San Diego, La Jolla, CA 92093
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Jeffrey R. Adrion
4Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403
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Leigh C. Latta IV
1Department of Biology, Reed College, Portland, OR 97202
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S. Schaack
1Department of Biology, Reed College, Portland, OR 97202
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  • ORCID record for S. Schaack
  • For correspondence: schaack@reed.edu
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Abstract

Transposable elements (TEs) represent a large and dynamic portion of most eukaryotic genomes, yet little is known about their mutation rates or the correspondence between rates and long-term patterns of accrual. We compare TE activity over long and short time periods by quantifying TE profiles and mutation rates (with and without minimizing selection) among 9 genotypes from three populations of Daphnia magna sampled along a latitudinal gradient. The patterns of genome-wide variation observed in nature mirror direct estimates of rates and spectra observed in a multi-year laboratory mutation accumulation experiment, where net rates range from -11.98 to 12.79 x 10-5 per copy per generation across genotypes. Overall, gains outnumber losses and both types of events are highly deleterious based on comparing lines with and without selection minimized. The rate and spectrum of TE mutations vary widely among genotypes and across TE families/types, even within the same population. We compare TE mutation rates to previously published rates of base substitution, microsatellite mutation, and gene conversion for the same genotypes, and show a correlation only with the latter. Our study provides strong evidence for the notion that TEs represent a highly mutagenic force in the genome. Furthermore, the variation we observe underscores the need to expand the repertoire of mutations studied to include a wider array of mutation types with different underlying mechanisms in order to better understand the evolution of the mutation rate and the ways in which genetic variation is generated genome wide.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 21, 2020.
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Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna
Eddie K. H. Ho, E.S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, S. Schaack
bioRxiv 2020.09.21.307181; doi: https://doi.org/10.1101/2020.09.21.307181
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Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna
Eddie K. H. Ho, E.S. Bellis, Jaclyn Calkins, Jeffrey R. Adrion, Leigh C. Latta IV, S. Schaack
bioRxiv 2020.09.21.307181; doi: https://doi.org/10.1101/2020.09.21.307181

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