Selfish drive can trump function when animal mitochondrial genomes compete

Abstract

Mitochondrial genomes compete for transmission from mother to progeny. We explored this competition by introducing a second genome into Drosophila melanogaster to follow transmission. Competitions between closely related genomes favored those functional in electron transport, resulting in a host-beneficial purifying selection. In contrast, matchups between distantly related genomes often favored those with negligible, negative or lethal consequences, indicating selfish selection. Exhibiting powerful selfish selection, a genome carrying a detrimental mutation displaced a complementing genome, leading to population death after several generations. In a different pairing, opposing selfish and purifying selection counterbalanced to give stable transmission of two genomes. Sequencing of recombinant mitochondrial genomes showed that the noncoding region, containing origins of replication, governs selfish transmission. Uniparental inheritance prevents encounters between distantly related genomes. Nonetheless, in each maternal lineage, constant competition among sibling genomes selects for super-replicators. We suggest that this relentless competition drives positive selection, promoting change in the sequences influencing transmission.

Figure 1

Selection based on selfish drive in a heteroplasmic line containing the ATP6[1] genome and the temperature sensitive double-mutant: mt:ND2^del1 + mt:CoI^T300I. (a) Decline of the ATP6[1] genome when co-existing with mt:ND2^del1 + mt:CoI^T300I. A schematic (upper left) of D. melanogaster mitochondrial genome with protein coding genes (blue), rDNA loci (light cyan), tRNAs (pink) and the non-coding region (brown). Key features distinguishing the ATP6[1] and temperature sensitive genomes are indicated (upper right panel). A PCR primer set that selectively amplifies the intact ND2 locus of the ATP6[1] genome is indicated (BglII site, yellow highlight). The relative abundance of the ATP6[1] genome as assessed by qPCR for five lines maintained at 25 °C and 29 °C for multiple generations. After the ATP6[1] abundance fell to a low level (illustrated), the flies at 29 °C started to die (not shown), but in one line a few survivors expanded and showed an increasing abundance in a genome with the ATP6[1] ND2 region (red line, black arrow). (b) The map of the recombinant genome sequenced by PacBio SMRT technology. Red lines indicate the distribution of SNPs characteristic of mt:ND2^del1 + mt:CoI^T300I genome that are present in the recombinant. The ATP6[1] genome also lacks ~1.6 kb of the non-coding region. (c) The transmission of the recombinant genome was favored when paired with the temperature sensitive genome. The directional arrows indicate how the abundance of a particular genotype was increasing or decreasing at any given generation.

Figure 2

Stable transmission of the D. yakuba mtDNA in the D. melanogaster nuclear background. (a) A heteroplasmic line was established by transferring cytoplasm of D. yakuba embryos into embryos carrying the mt:ND2^del1 + mt:CoI^T300I genome. (b) The proportion of D. yakuba mtDNA was maintained at ~4% for over 30 generations in two independent heteroplasmic lines at 29 °C. (c) The abundance of the D. yakuba mtDNA oscillated during development: high in newly deposited eggs, declined during development and rose in oogenesis to reach a high level in eggs again at 29 °C. The first three entries come from analysis of different stages of the lifecycle across one generation. As expected for a stably propagated stock, an analysis of eggs collected at a different time (egg population 2) gave the same relative abundance for the S. yakuba genome. However, when mothers were shifted to 22 °C at the end of 3rd instar larval stage so that oogenesis occurred at the permissive temperature, the eggs laid had a reduced abundance of the D. yakuba genome (egg population 3). Results are means ± SD (n = 4 for each data point). Unpaired Student’s t-test was performed to compare the difference in the abundance of D. yakuba mtDNA between newly deposited eggs, 3^rd instar larvae and adult flies (** = p < 0.01, *** = p < 0.001).

Figure 3

Cross species analysis of functional conservation and competitive strength of mitochondrial genomes. (a) The D. melanogaster genome was eliminated from a heteroplasmic line by expressing PstI that is targeted to mitochondria. (b) D. mel (mito-yakuba) flies climb faster than D. melanogaster flies carrying various native mitochondrial genomes. Time (means ± SD, n = 3) required for 50% of flies (25 °C) of the indicated age (D = days) and sex to climb to a prescribed height after being gently knocked down was recorded. Significance of differences is based on unpaired Student’s t-test (* = p < 0.05, ** = p < 0.01, *** = p < 0.001). (c) Lifespan of congenic flies with different mitochondrial genotypes at 25 °C and 29 °C. Survivorship was recorded every two days (n > 80, see Supplementary Table 1a). The D. yakuba mitochondrial genome supports robust survival that exceeds that supported by several native genomes (see Supplementary Table 1b & c for statistical analysis). (d) The D. yakuba mitochondrial genome was quickly outcompeted by various D. melanogaster genomes at 25 °C. Native mitochondrial genomes were introduced into the D. mel (mito-yakuba) line, and the relative abundance of the D. yakuba genome was followed over generations by qPCR (see Online Methods). The differently colored lines represent independently produced heteroplasmic lines. The D. yakuba mtDNA was only maintained when partnered with the temperature sensitive genome at 29 °C.