The conflict within: origin, proliferation and persistence of a spontaneously arising selfish mitochondrial genome

Abstract

Mitochondrial genomes can sustain mutations that are simultaneously detrimental to individual fitness and yet, can proliferate within individuals owing to a replicative advantage. We analysed the fitness effects and population dynamics of a mitochondrial genome containing a novel 499 bp deletion in the cytochrome b(1) (ctb-1) gene (Δctb-1) encoding the cytochrome b of complex III in Caenorhabditis elegans. Δctb-1 reached a high heteroplasmic frequency of 96% in one experimental line during a mutation accumulation experiment and was linked to additional spontaneous mutations in nd5 and tRNA-Asn. The Δctb-1 mutant mitotype imposed a significant fitness cost including a 65% and 52% reduction in productivity and competitive fitness, respectively, relative to individuals bearing wild-type (WT) mitochondria. Deletion-bearing worms were rapidly purged within a few generations when competed against WT mitochondrial DNA (mtDNA) bearing worms in experimental populations. By contrast, the Δctb-1 mitotype was able to persist in large populations comprising heteroplasmic individuals only, although the average intracellular frequency of Δctb-1 exhibited a slow decline owing to competition among individuals bearing different frequencies of the heteroplasmy. Within experimental lines subjected to severe population bottlenecks (n = 1), the relative intracellular frequency of Δctb-1 increased, which is a hallmark of selfish drive. A positive correlation between Δctb-1 and WT mtDNA copy-number suggests a mechanism that increases total mtDNA per se, and does not discern the Δctb-1 mitotype from the WT mtDNA. This study demonstrates the selfish nature of the Δctb-1 mitotype, given its transmission advantage and substantial fitness load for the host, and highlights the importance of population size for the population dynamics of selfish mtDNA. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.

Keywords: fitness; genomic conflict; heteroplasmy; mitochondrial deletion; selection; selfish genetic element.

Figure 1.

Identification and location of the ctb-1 deletion in MA line 1G. (a) A 499 bp frameshift mtDNA deletion in ctb-1 (Δctb-1) occurred spontaneously in a C. elegans spontaneous mutation accumulation line, 1G, and was detected via whole-genome sequencing [44]. The figure shows the read depth from Illumina whole genome sequencing mapped to the ctb-1 region of the C. elegans mitochondrial genome in line 1G. The read depth inside the deletion is only 4% of the read depth of the sequences immediately flanking the deletion, suggesting that the frequency of the Δctb-1 mitotype is 96% within this MA line. (b) A map of the C. elegans mitochondrial genome (adapted from [48]), illustrating the location, extent and the sequence context of Δctb-1. The protein-coding sequence of the ctb-1 gene spans 1110 bp (protein length 370 aa). (Online version in colour.)

Figure 2.

Frequency trajectories of four spontaneous mtDNA mutations that arose in MA line 1G during the course of the MA experiment. The vertical axis represents the intracellular frequency of individual mtDNA mutations as estimated by ddPCR (Δctb-1) or Sanger sequencing. The horizontal axis represents the number of generations since the start of the MA experiment. (Online version in colour.)

Figure 3.

Relative trait means of Δctb-1 bearing 1G replicate lines and the WT N2 control. Mean fitness values for each of the four traits were measured across six 1G lines (orange), each with 15 replicates where possible (n = 87 or 90) and three N2 control lines (grey), each with 15 replicates (n = 45). Phenotypic assays were conducted for four fitness-related traits, namely productivity, survivorship to adulthood, developmental rate and longevity. For simplicity, the mean relative fitness value for each of the four traits in the WT N2 control was scaled to a value of 1. All of the lines bearing the Δctb-1 mtDNA perform significantly worse than the WT N2 line. **p ≤ 0.01, ****p ≤ 0.0001. Error bars represent one standard error. (Online version in colour.)

Figure 4.

Evolutionary dynamics of Δctb-1 mtDNA under competitive conditions. (a) Population-level frequencies of the Δctb-1 mtDNA heteroplasmy in five 1G replicate lines under non-competed (grey lines) versus competitive conditions (coloured lines). In competitive assay populations established with equal ratios of Δctb-1 and WT mtDNA bearing worms (50 Δctb-1 bearing 1G hermaphrodites+50 WT mtDNA-bearing N2 hermaphrodites), the population dynamics of the Δctb-1 mitotype displays a steep decline in frequency with time. The Δctb-1 mtDNA heteroplasmy remains in high frequency (approx. 1.0) within each replicate line across generations under noncompetitive (control) conditions. In general, there is a significant reduction in the frequency of the Δctb-1 mitotype from 0.5 to less than 0.2 within two generations under competitive conditions, and eventual loss (undetectable via PCR) from the population between generations 3–8. The Δctb-1 mitotype remained undetected between generations 9–16. (b) A linear regression of the change in log[f(Δctb-1/WT mtDNA)] with time (generations). The single data point for each generation represents the average values of the Δctb-1 mutant mitotype and WT mtDNA across five independent replicates of line 1G (1G.C, 1G.L, 1G.N, 1G.T and 1G.U). The relative fitness, w, of the Δctb-1 mutant mitotype was calculated from the slope of the regression line and estimated to be 0.48, implicating a large deleterious fitness cost of the ctb-1 deletion bearing mtDNA and its gradual eradication in large competitive populations via purifying selection. (Online version in colour.)

Figure 5.

A box plot of the Δctb-1 frequency across time in non-competed large populations of lines 1G.C, 1G.N, 1G.T and 1G.U. The average frequency of Δctb-1 is 93.4%, 93.2% and 74.0% at generation 0, 30 and 75, respectively. (Online version in colour.)

Figure 6.

A box plot of the relative mtDNA copy-number across time in non-competed large populations of lines 1G.C, 1G.N, 1G.T and 1G.U as determined by ddPCR. The relative mtDNA copy-number for WT N2 mtDNA is displayed for reference. (Online version in colour.)

Figure 7.

Relationship between the copy-number of Δctb-1 and WT mtDNA. (a) A scatterplot of the relationship between relative copy-number of Δctb-1 and WT mtDNA at generation 0 in large populations. The plot combines ddPCR results for lines 1G.C, 1G.N, 1G.T and 1G.U. There is a significant correlation between Δctb-1 and WT mtDNA copy-number at generation 0 (r = 0.42, p = 0.001). (b) Individual correlation coefficients between Δctb-1 and WT mtDNA copy-number as a function of time (number of generations) for non-competed populations of 1G.C, 1G.N, 1G.T and 1G.U. The strength of the correlation between Δctb-1 and WT mtDNA copy number declines with time (r = −0.69, p = 0.013). (Online version in colour.)

Figure 8.

The distribution of the frequency of Δctb-1 mtDNA in 25 lines after six generations of bottlenecking via single progeny descent. All 25 lines were descended from an individual with a Δctb-1 frequency of 37%, indicated by the dashed vertical line. The frequency of Δctb-1 mtDNA exhibited a rapid and significant increase (average 54%) under this regime of minimal selection between individuals.