A model of extranuclear genomes and the substitution rate under within-generation selection

Evolution and maintenance of mtDNA gene content across eukaryotes

Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.

Sex-specific effects of sympatric mitonuclear variation on fitness in Drosophila subobscura

Background

A number of recent studies have shown that the pattern of mitochondrial DNA variation and evolution is at odds with a neutral equilibrium model. Theory has suggested that selection on mitonuclear genotypes can act to maintain stable mitonuclear polymorphism within populations. However, this effect largely relies upon selection being either sex-specific or frequency dependent. Here, we use mitonuclear introgression lines to assess differences in a series of key life-history traits (egg-to-adult developmental time, viability, offspring sex-ratio, adult longevity and resistance to desiccation) in Drosophila subobscura fruit flies carrying one of three different sympatric mtDNA haplotypes.

Results

We found functional differences between these sympatric mtDNA haplotypes, but these effects were contingent upon the nuclear genome with which they were co-expressed. Further, we demonstrate a significant mitonuclear genetic effect on adult sex ratio, as well as a sex × mtDNA × nuDNA interaction for adult longevity.

Conclusions

The observed effects suggest that sex specific mitonuclear selection contributes to the maintenance of mtDNA polymorphism and to mitonuclear linkage disequilibrium in this model system.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0421-2) contains supplementary material, which is available to authorized users.

Intergenomic epistasis for fitness: within-population interactions between cytoplasmic and nuclear genes in Drosophila melanogaster

The symbiotic relationship between the mitochondrial and nuclear genomes coordinates metabolic energy production and is fundamental to life among eukaryotes. Consequently, there is potential for strong selection to shape interactions between these two genomes. Substantial research attention has focused on the possibility that within-population sequence polymorphism in mitochondrial DNA (mtDNA) is maintained by mitonuclear fitness interactions. Early theory predicted that selection will often eliminate mitochondrial polymorphisms. However, recent models demonstrate that intergenomic interactions can promote the maintenance of polymorphism, especially if the nuclear genes involved are linked to the X chromosome. Most empirical studies to date that have assessed cytonuclear fitness interactions have studied variation across populations and it is still unclear how general and strong such interactions are within populations. We experimentally tested for cytonuclear interactions within a laboratory population of Drosophila melanogaster using 25 randomly sampled cytoplasmic genomes, expressed in three different haploid nuclear genetic backgrounds, while eliminating confounding effects of intracellular bacteria (e.g., Wolbachia). We found sizable cytonuclear fitness interactions within this population and present limited evidence suggesting that these effects were sex specific. Moreover, the relative fitness of cytonuclear genotypes was environment specific. Sequencing of mtDNA (2752 bp) revealed polymorphism within the population, suggesting that the observed cytoplasmic genetic effects may be mitochondrial in origin.

Germline bottlenecks, biparental inheritance and selection on mitochondrial variants: a two-level selection model

Selection on mitochondrial mutations potentially occurs at different levels: at the mitochondria, cell, and organism levels. Several factors affect the strength of selection at these different levels; in particular, mitochondrial bottlenecks during germline development and reduced paternal transmission decrease the genetic variance within cells, while they increase the variance between cells and between organisms, thus decreasing the strength of selection within cells and increasing the strength of selection between cells and organisms. However, bottlenecks and paternal transmission also affect the effective mitochondrial population size, thus affecting genetic drift. In this article, we use a simple model of a unicellular life cycle to investigate the effects of bottlenecks and paternal transmission on the probability of fixation of mitochondrial mutants and their frequency at mutation-selection equilibrium. We find that bottlenecks and reduced paternal transmission decrease the mean frequency of alleles with sm>sc (approximately), where sm and sc are the strengths of selection for an allele within and between cells, respectively, and increase the frequency of alleles with sm<sc. Effects on fixation probabilities are different; for example, bottlenecks reduce the fixation probability of mutants with sm>0 (unless sm is very small relative to sc) and increase the fixation probability of mutants with sm<0.

Temperature-dependent selection in the transmission of mitochondrial DNA in Drosophila

We previously reported a selective mode of mitochondrial DNA (mtDNA) transmission in mtDNA heteroplasmy that was induced artificially in Drosophila melanogaster; the transmission bias appeared to depend on the particular temperature at which heteroplasmic lines were maintained. Here we report investigations of the temperature-dependent mode of mtDNA transmission in heteroplasmic lines for intra- and interspecific combinations maintained separately at 22.5 degrees C, 25 degrees C and 29 degrees C for 20 generations. We have examined a selection model for mitochondrial transmission, similar to genetic selection in haploid organisms. Changes in the relative proportions of two types of mtDNA fit the expectations from the model well. The intensity of selection estimated as a selection coefficient depends on temperature. Temperature-sensitive processes thus appear to be involved in the transmission and maintenance of mitochondria.

Population genetic aspects of deleterious cytoplasmic genomes and their effect on the evolution of sexual reproduction

A conflict of interest may arise between intra-cellular genomes and their host cell. The example explicitly investigated is that of a 'selfish' mitochondrion which increases its own rate of replication at the cost of reduced metabolic activity which is deleterious to the host cell. The results apply to deleterious cytoplasmic agents in general, such as intracellular parasites. Numerical simulation suggests that selfish mitochondria are able to invade an isogamous sexual population and are capable of reducing its fitness to below 5% of that prior to their invasion. Their spread is enhanced by decreasing the number of mitotic divisions between meioses, and this may constitute a significant constraint on the evolution of lifecycles. The presence of such deleterious cytoplasmic agents favours a nuclear mutation whose expression prevents cytoplasm from the other gamete entering the zygote at fertilization, resulting in uniparental inheritance of cytoplasm. Such a mutation appears physiologically plausible and can increase in frequency despite its deleterious effect in halving the amount of cytoplasm in the zygote. It is suggested that these were the conditions under which anisogamy evolved. These results have implications for the evolution of sexual reproduction. Standard theory suggests there is no immediate cost of sex, a twofold cost being incurred later as anisogamy evolves. The analysis described here predicts a large, rapid reduction in fitness associated with isogamous sexual reproduction, due to the spread of deleterious cytoplasmic agents with fitness only subsequently rising to a maximum twofold cost as uniparental inheritance of cytoplasm and anisogamy evolve.

Mitochondrial DNA insertion polymorphism and germ line heteroplasmy in the Triturus cristatus complex

Restriction enzyme analysis of mitochondrial (mt) DNA isolated from oocytes of 185 individuals of the T. cristatus complex collected from 10 European countries has demonstrated that large length variation (greater than 40 bp) is a common feature of the group. Insertion polymorphism was found both within and among populations, and in all cases maps to the control region of the molecule. In addition, 2 individuals from Pisa, (Italy) were each found to be heteroplasmic for 2 large insertions comprising tandem repeats of 1100 bp of the control region. Large-scale length variation has been described in a few other lower vertebrates, but some of the insertion variants within populations described here are of unprecedented size (up to 8500 bp). This is in dramatic contrast to mammalian mtDNA in which size variation is largely restricted to small (less than 15 bp) insertions and deletions.

Introgression of extranuclear genomes in finite populations: nucleo-cytoplasmic incompatibility

A ‘two locus two allele’ model is developed with special reference to the introgression of extranuclear genomes between two species of finite size. The model assumes that one locus, coded by a nuclear genome, causes the reproductive barrier while the other locus, coded by an extranuclear genome, causes nucleo-cytoplasmic incompatibility in particular genotypes. To fully study this model, simulations are conducted, and a diffusion equation is derived when introgression or extranuclear gene flow occurs in one direction. It is shown that although selection against the nuclear genome can reduce the levels of extranuclear gene flow and retard the introgression process, the dynamics are very similar to those without such selection. In contrast, the nucleo-cytoplasmic incompatibility directly affects the dynamics of introgressing extranuclear genomes: in large populations the ability of incompatibility to overcome extranuclear gene flow is conspicuous, but in small populations it is overshadowed by random sampling drift. Paternal leakage of extranuclear genomes, if present, is of evolutionary importance only when the male's migration rate is much larger than the female's. When the sizes of two populations are unequal, the introgression is most likely to occur from the larger population to the smaller one in the absence of mating preferences of backcross progeny. Recent observations on interspecific mitochondrial transfer in various species do not support the ubiquitousness of nucleo-cytoplasmic incompatibility as an efficient reproductive barrier.