Diet adaptation in dog reflects spread of prehistoric agriculture.

Adaptations allowing dogs to thrive on a diet rich in starch, including a significant AMY2B copy number gain, constituted a crucial step in the evolution of the dog from the wolf. It is however not clear whether this change was associated with the initial domestication, or represents a secondary shift related to the subsequent development of agriculture. Previous efforts to study this process were based on geographically limited data sets and low-resolution methods, and it is therefore not known to what extent the diet adaptations are universal among dogs and whether there are regional differences associated with alternative human subsistence strategies. Here we use droplet PCR to investigate worldwide AMY2B copy number diversity among indigenous as well as breed dogs and wolves to elucidate how a change in dog diet was associated with the domestication process and subsequent shifts in human subsistence. We find that AMY2B copy numbers are bimodally distributed with high copy numbers (median 2nAMY2B=11) in a majority of dogs but no, or few, duplications (median 2nAMY2B=3) in a small group of dogs originating mostly in Australia and the Arctic. We show that this pattern correlates geographically to the spread of prehistoric agriculture and conclude that the diet change may not have been associated with initial domestication but rather the subsequent development and spread of agriculture to most, but not all regions of the globe.

Paternal transmission of mitochondrial DNA as an integral part of mitochondrial inheritance in metapopulations of Drosophila simulans.

Maternal inheritance is one of the hallmarks of animal mitochondrial DNA (mtDNA) and central to its success as a molecular marker. This mode of inheritance and subsequent lack of heterologous recombination allows us to retrace evolutionary relationships unambiguously down the matriline and without the confounding effects of recombinant genetic information. Accumulating evidence of biparental inheritance of mtDNA (paternal leakage), however, challenges our current understanding of how this molecule is inherited. Here, using Drosophila simulans collected from an East African metapopulation exhibiting recurring mitochondrial heteroplasmy, we conducted single fly matings and screened F1 offspring for the presence of paternal mtDNA using allele-specific PCR assays (AS-PCR). In all, 27 out of 4092 offspring were identified as harboring paternal mtDNA, suggesting a frequency of 0.66% paternal leakage in this species. Our findings strongly suggest that recurring mtDNA heteroplasmy as observed in natural populations of Drosophila simulans is most likely caused by repeated paternal leakage. Our findings further suggest that this phenomenon to potentially be an integral part of mtDNA inheritance in these populations and consequently of significance for mtDNA as a molecular marker.

Mitochondrial DNA variants influence mitochondrial bioenergetics in Drosophila melanogaster.

The influence of mitochondrial DNA (mtDNA) mutations on human disease has been extensively studied, but the impact of mutations within the adaptive range is debated. We studied males from lines of Drosophila melanogaster that have a highly standardized nuclear genome but different mtDNA, at two ages. We measured mitochondrial respiration on permeabilized muscle fibers, hydrogen peroxide production of isolated mitochondria and mtDNA copy number of whole individuals. The results show that a small set of naturally occurring mtDNA mutations can have a significant influence on mitochondrial bioenergetics that may change as the organism ages.

Mitochondrial DNA variants in Drosophila melanogaster are expressed at the level of the organismal phenotype.

A plethora of experimental studies use mtDNA as a marker of demographic processes without questioning the possibility that selection may bias their interpretations. We studied four lines of Drosophila melanogaster that have a standardized nuclear DNA but variable mtDNA. We completed the sequencing of the mitochondrial genomes (excluding the A+T rich region) and compiled the differences. We then assayed male influence on oviposition, starvation resistance, lipid proportion and physical activity. We discuss these results in terms of the known differences between the lines and conclude that naturally occurring mtDNA variants in D. melanogaster are expressed at the level of the organismal phenotype.

Linking the mitochondrial genotype to the organismal phenotype.

One of the grand challenges of the postgenomics era is to mechanistically link the genotype with the phenotype. Here, we consider the link between the mitochondrial genotype and the organismal phenotype that is provided by bioenergetic studies of the electron transport chain. That linkage is pertinent for the fields of molecular ecology and phylogeography as it tests if, and potentially how, natural selection can influence the evolutionary and demographic past of both populations and species. We introduce the mitochondrial genotype in terms of mitochondrial-encoded genes, nuclear-encoded genes that produce structural proteins imported into the mitochondria, and mitochondrial DNA-nuclear interactions. We then review the potential for quaternary structure modelling to predict the functional consequence of specific naturally occurring mutations. We discuss how the energy-producing reactions of oxidative phosphorylation can be used to provide a mechanistic biochemical link between genotype and phenotype. Experimental manipulations can then be used to test the functional consequences of specific mutations in multiple genetic backgrounds. Finally, we examine how mitochondria can influence the organismal mitochondrial phenotype using the examples of lifespan, fertility and starvation resistance and discuss how mitochondria may be involved in establishing both the upper and lower thermal limits of organisms. We conclude that mitochondrial DNA mutations can be important in determining aspects of organism life history. The question that remains to be resolved is how common are these adaptive mutations?

Tetracycline treatment influences mitochondrial metabolism and mtDNA density two generations after treatment in Drosophila.

Tetracycline is commonly used to clear Wolbachia from infected insects. Studies then compare specific biochemical and/or life-history traits between infected and uninfected individuals with the same genetic background. We investigated the potential for tetracycline to influence mitochondrial efficiency and mitochondrial (mt)DNA density two generations after treatment in Drosophila simulans. We observed that antibiotic treatment resulted in a decline in inorganic phosphate incorporated into ATP per mole of oxygen consumed (ADP:O ratio). Further, tetracycline treatment caused a significant increase in mtDNA density in naturally Wolbachia-uninfected but not in naturally Wolbachia-infected lines suggesting a dosage effect. These data suggest that the current practice of comparing Wolbachia-infected and Wolbachia-uninfected insects two generations after tetracycline treatment needs to be re-evaluated.

What maintains noncytoplasmic incompatibility inducing Wolbachia in their hosts: a case study from a natural Drosophila yakuba population.

Cytoplasmic incompatibility (CI) allows Wolbachia to invade hosts populations by specifically inducing sterility in crosses between infected males and uninfected females. In some species, non-CI inducing Wolbachia, that are thought to derive from CI-inducing ancestors, are common. In theory, the maintenance of such infections is not possible unless the bacterium is perfectly transmitted to offspring--and/or provides a fitness benefit to infected females. The present study aims to test this view by investigating a population of Drosophila yakuba from Gabon, West Africa. We did not find any evidence for CI using wild caught females. Infected females from the field transmitted the infection to 100% of their offspring. A positive effect on female fecundity was observed one generation after collecting, but this was not retrieved five generations later, using additional lines. Similarly, the presence of Wolbachia was found to affect mating behaviour, but the results of two experiments realized five generations apart were not consistent. Finally, Wolbachia was not found to affect sex ratio. Overall, our results would suggest that Wolbachia behaves like a neutral or nearly neutral trait in this species, and is maintained in the host by perfect maternal transmission.

Dynamics of double and single Wolbachia infections in Drosophila simulans from New Caledonia.

The bacterial symbiont Wolbachia can cause cytoplasmic incompatibility in Drosophila simulans flies: if an infected male mates with an uninfected female, or a female with a different strain of Wolbachia, there can be a dramatic reduction in the number of viable eggs produced. Here we explore the dynamics associated with double and single Wolbachia infections in New Caledonia. Doubly infected females were compatible with all males in the population, explaining the high proportion of doubly infected flies. In this study, males that carry only wHa or wNo infections showed reduced incompatibility when mated to uninfected females, compared with previous reports. These data suggest that either the DNA of these bacterial isolates have diverged from those previously collected, or the genetic background of the host has lead to a reduction in the phenotype of incompatibility. Mitochondrial sequence polymorphism at two sites within the host genome was assayed to investigate population structure related to infection types. There was no correlation between sequence polymorphism and infection type suggesting that double infections are the stable type, with singly infected and uninfected flies arising from stochastic segregation of bacterial strains. Finally, we discuss the nomenclature of Wolbachia strain designation.