High mutational rates of large-scale duplication and deletion in Daphnia pulex
- Nathan Keith1,10,
- Abraham E. Tucker2,10,
- Craig E. Jackson1,
- Way Sung3,
- José Ignacio Lucas Lledó4,
- Daniel R. Schrider5,
- Sarah Schaack6,
- Jeffry L. Dudycha7,
- Matthew Ackerman3,
- Andrew J. Younge8,
- Joseph R. Shaw1,9,11 and
- Michael Lynch3,11
- 1School of Public and Environmental Affairs, Indiana University, Bloomington, Indiana 47405, USA;
- 2Biology Department, Southern Arkansas University, Magnolia, Arkansas 71753, USA;
- 3Department of Biology, Indiana University, Bloomington, Indiana 47405, USA;
- 4Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, 16775 Germany;
- 5Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA;
- 6Biology Department, Reed College, Portland, Oregon 97202, USA;
- 7Department of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA;
- 8School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA;
- 9School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
- Corresponding authors: rnkeith{at}umail.iu.edu, joeshaw{at}indiana.edu, milynch{at}indiana.edu
Abstract
Knowledge of the genome-wide rate and spectrum of mutations is necessary to understand the origin of disease and the genetic variation driving all evolutionary processes. Here, we provide a genome-wide analysis of the rate and spectrum of mutations obtained in two Daphnia pulex genotypes via separate mutation-accumulation (MA) experiments. Unlike most MA studies that utilize haploid, homozygous, or self-fertilizing lines, D. pulex can be propagated ameiotically while maintaining a naturally heterozygous, diploid genome, allowing the capture of the full spectrum of genomic changes that arise in a heterozygous state. While base-substitution mutation rates are similar to those in other multicellular eukaryotes (about 4 × 10−9 per site per generation), we find that the rates of large-scale (>100 kb) de novo copy-number variants (CNVs) are significantly elevated relative to those seen in previous MA studies. The heterozygosity maintained in this experiment allowed for estimates of gene-conversion processes. While most of the conversion tract lengths we report are similar to those generated by meiotic processes, we also find larger tract lengths that are indicative of mitotic processes. Comparison of MA lines to natural isolates reveals that a majority of large-scale CNVs in natural populations are removed by purifying selection. The mutations observed here share similarities with disease-causing, complex, large-scale CNVs, thereby demonstrating that MA studies in D. pulex serve as a system for studying the processes leading to such alterations.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.191338.115.
- Received February 20, 2015.
- Accepted October 13, 2015.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
