Damian K. Dowling

Emerging evidence suggests mtDNA haplotypes contribute to fitness variation and local adaptation, with directional thermal selection and negative frequency-dependent selection shaping haplotype diversity. However, their interplay remains unexplored. We conducted experimental evolution using Drosophila melanogaster populations from opposite ends of an Australian latitudinal cline (Melbourne and Townsville), exposing them to contrasting temperatures (17°C versus 27°C) and varying starting frequencies of two mtDNA haplotypes (A1 and B1) that occur at appreciable frequencies in these populations. We paired this with population genetic simulations to estimate selection and its influence on haplotype trajectories. Haplotype frequencies were influenced by interactions involving temperature, starting frequency, and nuclear genomic background (Melbourne, Townsville, or admixed). Although prior work predicted A1 should be favoured at the warmer temperature and B1 at the cooler temperature, A1 was generally favoured across both temperatures. Simulations supported directional selection in populations evolving at 17°C in the Melbourne background; otherwise dynamics were best explained by balancing selection shaped by negative frequency-dependent fitness effects. Patterns also varied across nuclear backgrounds, suggestive of mito-nuclear epistasis. These findings challenge a simple thermal adaptation model of mtDNA dynamics, suggesting that mtDNA evolution is shaped by interacting effects of temperature, frequency-dependence, nuclear background and experimental environment.

Mitochondrial decline is a hallmark of ageing, yet the role of intergenomic compatibility in shaping ageing trajectories remains poorly understood, particularly in an ecologically relevant framework. Hormetic interventions have been proposed as strategies to modulate metabolism and lifespan, but it is unknown how this operates in the context of mitonuclear discordance. Here, we demonstrate that mitonuclear mismatch accelerates age-related mitochondrial decline, elevates reactive oxygen species production, and shortens lifespan. Strikingly, early-life mitochondrial stress induced by dietary modulation counteracts these effects, promoting mitochondrial homeostasis and longevity. Our findings reveal mitonuclear interactions shaping ageing trajectories in natural populations and provide unique evidence that targeted interventions can act as a buffer against the detrimental impact of genetic discordance.

Mitochondrial DNA (mtDNA) variation is increasingly recognized for its role in shaping evolutionary changes at the species and population levels. Yet, its evolutionary relevance within individuals remains less explored. Eukaryotic cells typically carry multiple copies of mtDNA. When these copies differ in sequence, heteroplasmy arises—a form of intra-organismal genetic diversity with potentially profound biological implications. To elucidate the evolutionary significance of heteroplasmy in animals, we first review how natural selection shapes adaptive mtDNA dynamics at broader biological levels, via cases of mito-nuclear coadaptation, environmental-mediated and sex-specific selection and balancing selection. We then explore whether analogous selective pressures may operate at the intra-individual level. Heteroplasmy introduces the potential for multi-level selection—from the genome to the organism—potentially yielding synergistic or antagonistic evolutionary outcomes. This framework encompasses both the selfish transmission of certain mtDNA variants and emerging evidence for adaptive shifts in heteroplasmy levels under environmental stress. These findings are supported by theoretical models suggesting that paternal mtDNA transmission—historically viewed as a stochastic anomaly—may confer adaptive benefits under specific ecological and evolutionary contexts by introducing intra-individual mtDNA diversity. Collectively, these insights suggest that heteroplasmy may act as an underappreciated reservoir of adaptive potential, enhancing the evolutionary capacity of organisms in a changing world. This article is part of the theme issue ‘Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya’.

Sex and mitochondria are inextricably linked in the eukaryotic tree of life, a confounding situation given the uniparental inheritance of mitochondria and the biparental inheritance that sexual reproduction entails. Unisexual vertebrate lineages, which arise via hybridization and asexually pass on their genetic material to clonal descendants, provide a unique opportunity to study mitochondrial evolution without potentially confounding effects of sex. Hybridity and clonality set unisexual vertebrates apart from other vertebrates and establish a distinct genetic environment that shapes their evolution, especially dynamics between mitochondrial and nuclear genomes. Here, we provide a perspective on the mitonuclear genomic interactions experienced by unisexual vertebrates and the implications of these interactions on mitochondrial function and integration into organismal performance and fitness. Building upon the hypothesis that sexual reproduction arose to maintain coadaptation between co-functioning nuclear and mitochondrial genes, we propose that unisexual vertebrates may be confined to predominantly ‘young’ lineages because mitonuclear incompatibilities—arising from either hybridity or clonality—increase the probability of extinction over time (the Mitonuclear Erosion Hypothesis). We provide a multidisciplinary collection of strategies to disentangle the effects of clonality and hybridity and quantify the relative degree to which these characteristics contribute to differences in mitochondrial function, organismal performance and fitness. This article is part of the theme issue ‘Evolutionary genetics of mitochondria: on diverse and common evolutionary constraints across eukarya’.

Sequence variation in mitochondrial DNA (mtDNA) was once considered neutral, but growing evidence indicates it can influence metabolic, physiological, and life-history traits. Two hypotheses offer explanations for this non-neutral mtDNA variation: the mitochondrial climatic adaptation hypothesis, which posits that natural selection shapes mtDNA variation to match local environments, and the mother’s curse hypothesis, which predicts the accumulation of male-harming variants due to maternal inheritance. We explored these hypotheses using genetic strains of Drosophila melanogaster bearing eight mtDNA haplotypes—nested within two distinct haplogroups (A1 and B1) that segregate along an Australian latitudinal cline. We measured the longevity of flies under cool (18°C) and warm (28°C) conditions, predicting that the A1 haplogroup—which has been reported to predominate at subtropical latitudes—would confer higher longevity in warm but reduced longevity in cool temperatures relative to the B1 counterpart. We also tested whether effects of mtDNA haplotype on longevity were larger in males, as predicted under the mother’s curse hypothesis. We found mtDNA haplogroup and haplotype is associated with longevity, with the magnitude of effects varying with temperature, but not in a pattern consistent with either hypothesis. Haplogroup-by-environment interactions did not align with reported spatial distributions of the haplogroups, and haplotype effects on longevity were similar across sexes. Our findings add to the growing evidence that mtDNA variation contributes to thermal plasticity in longevity, but do not provide clear insight into whether this variation is adaptive or maladaptive.

Mitochondrial function relies on close coordination between the mitochondrial and nuclear genomes. Disruption to this coordination—via mitonuclear mismatch—can impair metabolic efficiency, particularly under energetically demanding conditions such as during development. The nutritional environment further modulates mitochondrial demands, suggesting that mitonuclear genotype and diet may interact to shape life-history traits and behaviour. Here, we investigate how early-life diet and mitonuclear genotype jointly influence development time, adult body size, and nutritional preference in Drosophila melanogaster. Using a full-factorial panel of putatively matched and mismatched combinations (cybrids) of mitonuclear genotype derived from natural Australian populations, we reared flies on diets varying in their ratio of macronutrients and assessed how this influenced larval development and subsequent adult diet preference. Developmental rate was significantly influenced by mitonuclear coevolution and diet, with cybrids showing delayed development under all conditions, with dietary extremes exacerbating this effect. Despite this, egg-to-adult viability remained unaffected. Adult nutritional behaviour exhibited clear genotype- and diet-dependent effects. Flies reared on high-protein diets increased carbohydrate intake as adults, while those reared on high-carbohydrate diets increased protein intake, suggesting compensatory feeding responses. Mitonuclear mismatch further modulated nutrient consumption, particularly in females, whose carbohydrate intake was influenced by intergenomic compatibility and early-life dietary conditions. Males’ protein consumption was also impacted by mitonuclear coevolution across all developmental diets. Finally, body size was also shaped by interactions between mitonuclear genotype and diet. Together, our findings demonstrate that mitonuclear compatibility and the composition of the early nutritional environment interact to shape developmental and behavioural phenotypes. These results support a role for mitonuclear coadaptation in mediating metabolic plasticity, highlighting the evolutionary and physiological significance of genotype-specific mitonuclear coordination.

The discovery that mitochondrial genomes can harbor functional mutations despite the evolutionarily conserved role of mitochondria has spurred interest in better understanding the ecological and evolutionary consequences of such mitochondrial genetic variation. Because mitochondrial DNA (mtDNA) encodes products that must function in concert with products of the nuclear genome, and because mitochondria are largely maternally inherited, outstanding questions remain as to how, when, and why variation in mtDNA may affect phenotype. In this study, we developed a set of intraspecific “mitonuclear strains” of Drosophila melanogaster fruit flies that vary across 13 mtDNA haplotypes and 3 nuclear genetic backgrounds. We created a new apparatus called the Drop Tower to test the performance of these strains in negative geotaxis, a locomotory trait we predicted to be sensitive to variation at the level of mitochondria, across both sexes and two age classes. We found that both mitochondrial and nuclear genetic variation significantly altered how negative geotaxis performance changed with age and across the sexes, though interactions between mitochondrial and nuclear strains did not affect performance. Across most strains, male flies performed more poorly and suffered a steeper decline with age than did females, and young males appeared to vary more in performance across mitochondrial strains. In addition, we discovered a strong effect of small differences of parental age on negative geotaxis— and this effect also varied by mitochondrial strain. Collectively, the results of our study reveal that intraspecific variation in both mitochondrial and nuclear DNA can affect age- and sex-related differences in fruit fly locomotory performance. Further exploring the mechanisms linking these subtle genetic differences to locomotory phenotype and creating differences in response between the sexes will be important to understanding the evolutionary forces shaping the patterns we detected.

Emerging evidence suggests mtDNA haplotypes contribute to fitness variation and local adaptation, with studies highlighting the potential for directional selection, imposed by distinct thermal environments, and negative frequency-dependent selection to shape spatial patterns of mtDNA haplotype diversity. However, the interplay between these different forms of selection remains unexplored. To address this, we conducted experimental evolution using Drosophila melanogaster populations derived from opposite ends of a latitudinal cline in Australia (Melbourne and Townsville), exposing them to contrasting thermal environments and varying starting frequencies of two mtDNA haplotypes (A1 and B1) that each segregate at high frequencies in natural populations. We paired this approach with population genetic simulations to estimate selection and its influence on haplotype evolutionary trajectories. We found that mtDNA haplotype frequencies were influenced by complex interactions among temperature, starting frequency, and nuclear genomic background (Melbourne, Townsville, or admixed). Simulations supported directional selection as a driver of haplotype frequencies in populations evolving at 17°C in the Melbourne background, and otherwise selection was predominantly balancing and shaped by negative frequency-dependent fitness effects of the haplotypes. Finally, our results suggest that the thermal environment is not the sole environmental variable shaping mitochondrial evolutionary dynamics and point to a possible role for mito-nuclear epistasis.

There is considerable evidence for mitochondrial-nuclear co-adaptation as a key evolutionary driver. Hypotheses regarding the roles of sex-linkage have emphasized Z-linked nuclear genes with mitochondrial function (N-mt genes), whereas it remains contentious whether the perfect co-inheritance of W genes with mitogenomes could hinder or facilitate co-adaptation. Young (neo-) sex chromosomes that possess relatively many N-mt genes compared to older chromosomes provide unprecedented hypothesis-testing opportunities. Eastern Yellow Robin (EYR) lineages in coastal and inland habitats with different climates are diverged in mitogenomes, and in a ~ 15.4 Mb nuclear region enriched with N-mt genes, in contrast with otherwise-similar nuclear genomes. This nuclear region maps to passerine chromosome 1A, previously found to be neo-sex in the inland EYR genome. To compare sex-linked Chr1A-derived genes between lineages, we assembled and annotated the coastal EYR genome. We found that: (i) the coastal lineage shares a similar neo-sex system with the inland lineage, (ii) neo-W and neo-Z N-mt genes are not more diverged between lineages than are comparable non-N-mt genes, and showed little evidence for broad positive selection, (iii) however, W-linked N-mt genes are more diverged between lineages than are their Z-linked gametologs. The latter effect was ~7 times stronger for N-mt than non-N-mt genes, suggesting that W-linked N-mt genes might have diverged between lineages under environmental selection through co-evolution with mitogenomes. Finally, we identify a candidate gene driver for divergent selection, NDUFA12. Our data represent a rare example suggesting a possible role for W-associated mitochondrial-nuclear interactions in climate-associated adaptation and lineage differentiation.

Mitochondrial function depends on the effective interactions between proteins and RNA encoded by the mitochondrial and nuclear genomes. Evidence suggests that both genomes respond to thermal selection and promote adaptation. However, the contribution of their epistatic interactions to life history phenotypes in the wild remains elusive. We investigated the evolutionary implications of mitonuclear interactions in a real-world scenario that sees populations adapted to different environments, altering their geographical distribution while experiencing flow and admixture. We created a Drosophila melanogaster panel with replicate native populations from the ends of the Australian east-coast cline, into which we substituted the mtDNA haplotypes that were either predominant or rare at each cline-end, thus creating putatively mitonuclear matched and mismatched populations. Our results suggest that mismatching may impact phenotype, with populations harboring the rarer mtDNA haplotype suffering a trade-off between aerobic capacity and key fitness aspects such as reproduction, growth, and survival. We discuss the significance of mitonuclear interactions as modulators of life history phenotypes in the context of future adaptation and population persistence. Mitochondrial function depends on the harmonious coadaptation of mitochondrial and nuclear genomes. Even trivial incompatibilities can have catastrophic consequences on energy production and individual fitness. As separate populations adapt to their local environments and differ in their sets of mitonuclear genes, remixing mitonuclear variants through admixture events might lead to unpredictable fitness outcomes. This has the potential to alter the course of populations, from driving adaptation to even causing extinction if new mitonuclear combinations are not compatible. Understanding how intergenomic interactions may limit the adaptive capacity of natural populations is an important and timely question to address. Notably, in the light of extreme climate change, which is displacing species from their natural habitats, and for insects, which are experiencing a worldwide decline in abundance. Here, we explore how mitonuclear interactions shape mitochondrial and organismal performance in natural fly populations from the Australian east coast, using mitonuclear-matched populations that are locally adapted to different environments, plus two populations where the mitochondrial and nuclear genomes were reciprocally mismatched. Our results indicate that mitonuclear disruption constrains metabolic plasticity and fitness in mismatched populations, suggesting an important role played by intergenomic interactions in adaptation and population persistence.