DOI: 10.5061/dryad.1vhhmgr2z
title: Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans data

description: Mitochondrial genomes exist in a nested hierarchy of populations where
 mitochondrial variants are subject to genetic drift and selection
 at each level of organization, sometimes engendering conflict
 between different levels of selection, and between the nuclear and
 mitochondrial genomes. Deletion mutants in the Caenorhabditis
 elegans mitochondrial genome can reach high intracellular
 frequencies despite strongly detrimental effects on fitness. During a
 mutation accumulation (MA) experiment in C. elegans, a 499 bp
 deletion in ctb-1 rose to 90% frequency within cells while
 significantly reducing fitness. During the experiment, the
 deletion-bearing mtDNA acquired three additional mutations in
 nd5, namely two single insertion frameshift mutations in a
 homopolymeric run, and a base substitution. Despite an additional fitness
 cost of these secondary mutations, all deletion-bearing molecules
 contained the nd5 mutations at the termination of the MA
 experiment. The presence of mutant mtDNA was associated
 with increased mtDNA copy-number. Variation in mtDNA copy-number
 was greater in the MA lines than in a wildtype nuclear
 background, including a severe reduction in copy-number at
 one generational timepoint. Evolutionary replay experiments using
 different generations of the MA experiment as starting points
 suggests that two of the secondary mutations contribute to
 the proliferation of the original ctb-1 deletion by unknown
 mechanisms. 
description: # Dissecting the Sequential Evolution of a Selfish Mitochondrial Genome in
 Caenorhabditis elegans Data
 [https://doi.org/10.5061/dryad.1vhhmgr2z](https://doi.org/10.5061/dryad.1vhhmgr2z) This data set contains four csv files Fitness_data.xlsx contains raw measurements for four fitness traits measured in five populations of *C. elegans.* Heteroplasmic_frequencies_Fig3.csv contains four tables of heteroplasmic frequencies of mitochondrial mutations from a mutation accumulation (MA) replay experiment mtDNA_copynumber_backcrossed_lines_Fig4.csv contains a table of mitochondrial DNA copy numbers per nuclear genome in backcrossed lines normalized to the average of the wild-type N2 copy number mtDNA_copynumber_MA_lines_Fig4.csv contains a table of mitochondrial DNA copy numbers per nuclear genome in MA lines normalized to the average of the wild-type N2 copy number ## Description of the data and file structure * Fitness_data.xlsx * ``` These lines were created by backcrossing the mitochondrial background of mutation accumulation (MA) lines into a wild-type nuclear background. ``` * ``` The 5 lines were derived from line MA line 1G, at generations 0 (preMA), 71, 96, 221, and 350 ``` * ``` The four fitness traits measured were productivity, measured as the number of progeny produced by a single nematode; survivorship to adulthood, measured as the % of full sibling nematodes that survived to adulthood; longevity, measured as the number of days until the nematode died/was no longer respiring or responsive; and developmental time, measured as the number of hours an individual nematode took to reach adulthood. ``` * ``` Each sheet contains all the raw measurements for a given fitness trait in columns grouped by line. Mean, standard deviation, and n also provided. ``` * Heteroplasmic_frequencies_Fig3.csv * ``` Each table contains the heteroplasmic frequencies of a mitochondrial mutation of interest at generations 0, 5, and 10 of MA replay. ``` * ``` G71 contains the heteroplasmic frequencies of a ctb-1 deletion as determined by ddPCR (Bio-Rad) ``` * ``` G96 contains the heteroplasmic frequencies of an nd5 frameshift mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI ``` * ``` G136 contains the heteroplasmic frequencies of an nd5 missense mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI ``` * ``` G300 contains the heteroplasmic frequencies of a subsequent nd5 frameshift mutation determined by analyzing peak heights in sanger sequencing chromatograms via FIJI ``` cells with a value "n/a" are present in the data. These cells and represent samples lost due to single worm DNA extractions yielding too little or too degraded DNA for sequencing and ddPCR * mtDNA_copynumber_backcrossed_lines_Fig4.csv * ``` Mitochondrial copy number was determined via ddPCR (Bio-Rad) ``` * ``` Relative mtDNA copy-number was calculated by dividing the copy number of each replicate by the mean copy number of wild-type N2 (WT in table) ``` * ``` Average was calculated by taking the average of each replicate for each line ``` * mtDNA_copynumber_MA_lines_Fig4.csv * ``` Mitochondrial copy number was determined via ddPCR (Bio-Rad) ``` * ``` Relative mtDNA copy-number was calculated by dividing the copy number of each replicate by the mean copy number of wild-type N2 (WT in table) ``` * ``` Average was calculated by taking the average of each replicate for each line ```