The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Background

One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.

Findings

We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog.

Conclusions

These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology

Background

One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed.

Findings

We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog.

Conclusions

These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.

Ancestral dietary change alters the development of Drosophila larvae through MAPK signalling

Studies in a broad range of animal species have revealed phenotypes that are caused by ancestral life experiences, including stress and diet. Ancestral dietary macronutrient composition and quantity (over- and under-nutrition) have been shown to alter descendent growth, metabolism and behaviour. Molecules have been identified in gametes that are changed by ancestral diet and are required for transgenerational effects. However, there is less understanding of the developmental pathways altered by inherited molecules during the period between fertilization and adulthood. To investigate this non-genetic inheritance, we exposed great grand-parental and grand-parental generations to defined protein to carbohydrate (P:C) dietary ratios. Descendent developmental timing was consistently faster in the period between the embryonic and pupal stages when ancestors had a higher P:C ratio diet. Transcriptional analysis revealed extensive and long-lasting changes to the MAPK signalling pathway, which controls growth rate through the regulation of ribosomal RNA transcription. Pharmacological inhibition of both MAPK and rRNA pathways recapitulated the ancestral diet-induced developmental changes. This work provides insight into non-genetic inheritance between fertilization and adulthood.

What physiological role(s) does the alternative oxidase perform in animals?

Although the alternative oxidase, AOX, was known to be widespread in the animal kingdom by 2004, its exact physiological role in animals remains poorly understood. Here we present what evidence has accumulated thus far, indicating that it may play a role in enabling animals to resist various kinds of stress, including toxins, abnormal oxygen or nutrient levels, protein unfolding, dessication and pathogen attack. Much of our knowledge comes from studies in model organisms, where any benefits from exogenously expressed AOX may be masked by its unregulated expression, which may itself be stressful. The further question arises as to why AOX has been lost from some major crown groups, namely vertebrates, insects and cephalopods, if it plays important roles favouring the survival of other animals. We conclude by presenting some speculative ideas addressing this question, and an outline of how it might be approached experimentally.

Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease

BACKGROUND

The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis.

METHODS

Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD.

RESULTS

Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism.

CONCLUSIONS

Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.

The Australian dingo is an early offshoot of modern breed dogs

Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.

Eye contact and sociability data suggests that Australian dingoes were never domesticated

Dogs were the first animal to become domesticated by humans, and they represent a classic model system for unraveling the processes of domestication. We compare Australian dingo eye contact and socialization with Basenji and German Shepherd dog (GSD) breeds. Australian dingoes arrived in Australia 5,000–8,000 BP, and there is debate whether they were domesticated before their arrival. The Basenji represents a primitive breed that diverged from the remaining breeds early in the domestication process, while GSDs are a breed dog selected from existing domestic dogs in the late 1800s. We conducted a 4-phase study with unfamiliar and familiar investigators either sitting passively or actively calling each canid. We found 75% of dingoes made eye contact in each phase. In contrast, 86% of Basenjis and 96% of GSDs made eye contact. Dingoes also exhibited shorter eye-gaze duration than breed dogs and did not respond to their name being called actively. Sociability, quantified as a canid coming within 1 m of the experimenter, was lowest for dingoes and highest for GSDs. For sociability duration, dingoes spent less time within 1 m of the experimenter than either breed dog. When compared with previous studies, these data show that the dingo is behaviorally intermediate between wild wolves and Basenji dogs and suggest that it was not domesticated before it arrived in Australia. However, it remains possible that the accumulation of mutations since colonization has obscured historical behaviors, and dingoes now exist in a feralized retamed cycle. Additional morphological and genetic data are required to resolve this conundrum.

Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome

BACKGROUND

Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness.

RESULTS

Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection.

CONCLUSIONS

The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

Towards understanding the evolutionary dynamics of mtDNA

Historically, mtDNA was considered a selectively neutral marker that was useful for estimating the population genetic history of the maternal lineage. Over time there has been an increasing appreciation of mtDNA and mitochondria in maintaining cellular and organismal health. Beyond energy production, mtDNA and mitochondria have critical cellular roles in signalling. Here we briefly review the structure of mtDNA and the role of the mitochondrion in energy production. We then discuss the predictions that can be obtained from quaternary structure modelling and focus on mitochondrial complex I. Complex I is the primary entry point for electrons into the electron transport system is the largest respiratory complex of the chain and produces about 40% of the proton flux used to synthesize ATP. A focus of the review is Drosophila's utility as a model organism to study the selective advantage of specific mutations. However, we note that the incorporation of insights from a multitude of systems is necessary to fully understand the range of roles that mtDNA has in organismal fitness. We speculate that dietary changes can illicit stress responses that influence the selective advantage of specific mtDNA mutations and cause spatial and temporal fluctuations in the frequencies of mutations. We conclude that developing our understanding of the roles mtDNA has in determining organismal fitness will enable increased evolutionary insight and propose we can no longer assume it is evolving as a strictly neutral marker without testing this hypothesis.

Canfam_GSD: De novo chromosome-length genome assembly of the German Shepherd Dog (Canis lupus familiaris) using a combination of long reads, optical mapping, and Hi-C

BACKGROUND

The German Shepherd Dog (GSD) is one of the most common breeds on earth and has been bred for its utility and intelligence. It is often first choice for police and military work, as well as protection, disability assistance, and search-and-rescue. Yet, GSDs are well known to be susceptible to a range of genetic diseases that can interfere with their training. Such diseases are of particular concern when they occur later in life, and fully trained animals are not able to continue their duties.

FINDINGS

Here, we provide the draft genome sequence of a healthy German Shepherd female as a reference for future disease and evolutionary studies. We generated this improved canid reference genome (CanFam_GSD) utilizing a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. The GSD assembly is ∼80 times as contiguous as the current canid reference genome (20.9 vs 0.267 Mb contig N50), containing far fewer gaps (306 vs 23,876) and fewer scaffolds (429 vs 3,310) than the current canid reference genome CanFamv3.1. Two chromosomes (4 and 35) are assembled into single scaffolds with no gaps. BUSCO analyses of the genome assembly results show that 93.0% of the conserved single-copy genes are complete in the GSD assembly compared with 92.2% for CanFam v3.1. Homology-based gene annotation increases this value to ∼99%. Detailed examination of the evolutionarily important pancreatic amylase region reveals that there are most likely 7 copies of the gene, indicative of a duplication of 4 ancestral copies and the disruption of 1 copy.

CONCLUSIONS

GSD genome assembly and annotation were produced with major improvement in completeness, continuity, and quality over the existing canid reference. This resource will enable further research related to canine diseases, the evolutionary relationships of canids, and other aspects of canid biology.

Yin and Yang of mitochondrial ROS in Drosophila

In this study, we test the hypothesis that Drosophila larvae producing mildly elevated levels of endogenous mitochondrial reactive oxygen species (ROS) benefit in stressful environmental conditions due to the priming of antioxidant responses. Reactive oxygen species (ROS) are produced as a by-product of oxidative phosphorylation and may be elevated when mutations decrease the efficiency of ATP production. In moderation, ROS are necessary for cell signaling and organismal health, but in excess can damage DNA, proteins, and lipids. We utilize two Drosophila melanogaster strains (Dahomey and Alstonville) that share the same nuclear genetic background but differ in their mitochondrial DNA haplotypes. Previously, we reported that Dahomey larvae harboring the V161L ND4 mtDNA mutation have reduced proton pumping and higher levels of mitochondrial ROS than Alstonville larvae when they are fed a 1:2 protein: carbohydrate (P:C) diet. Here, we explore the potential for mitochondrial ROS to provide resistance to dietary stressors by feeding larvae 1:2 P:C food supplemented with ethanol or hydrogen peroxide (H₂O₂). When fed a diet supplemented with ethanol or H₂O₂, Dahomey develop more quickly than Alstonville into larger pupae, while Alstonville developed faster on the control. Dahomey larvae displayed higher antioxidant capacity than Alstonville on all diets, with mitochondrial H₂O₂ levels unchanged after the addition of stressors. Addition of stressors to the diet did not affect the mitochondrial functions of Dahomey larvae as measured by mitochondrial membrane potential, respiratory control ratio, or larval survival after bacterial challenge. In contrast, Alstonville larvae developed slower, had lower pupal weight, higher cytosolic H₂O₂, and had reduced mitochondrial functions. Further, Alstonville larvae fed the ethanol treated diet had lower survival after bacterial infection than those fed the control diet. Surprisingly, they had greater survival when fed diet with H₂O₂ indicating a mitotype by stressor interaction that influences the immune response. Overall, these data suggest that elevated mitochondrial ROS in Dahomey can result in greater antioxidant capacity that prevents oxidative damage from exogenous stressors and may be a conserved response to high ethanol found in rotting fruit.

Dietary Macronutrient Management to Treat Mitochondrial Dysfunction in Parkinson's Disease

Mitochondrial dysfunction has been demonstrated to play an important role in the pathogenesis of Parkinson’s disease (PD). The products of several PD-associated genes, including alpha-synuclein, parkin, pink1, protein deglycase DJ-1, and leucine rich repeat kinase 2, have important roles in mitochondrial biology. Thus, modifying mitochondrial function could be a potential therapeutic strategy for PD. Dietary management can alter mitochondrial function as shifts in dietary macronutrients and their ratios in food can alter mitochondrial energy metabolism, morphology and dynamics. Our studies have established that a low protein to carbohydrate (P:C) ratio can increase lifespan, motor ability and mitochondrial function in a parkin mutant Drosophila model of PD. In this review, we describe mitochondrial dysfunction in PD patients and models, and dietary macronutrient management strategies to reverse it. We focus on the effects of protein, carbohydrate, fatty acids, and their dietary ratios. In addition, we propose potential mechanisms that can improve mitochondrial function and thus reverse or delay the onset of PD.

The Australian dingo: untamed or feral?

BACKGROUND

The Australian dingo continues to cause debate amongst Aboriginal people, pastoralists, scientists and the government in Australia. A lingering controversy is whether the dingo has been tamed and has now reverted to its ancestral wild state or whether its ancestors were domesticated and it now resides on the continent as a feral dog. The goal of this article is to place the discussion onto a theoretical framework, highlight what is currently known about dingo origins and taxonomy and then make a series of experimentally testable organismal, cellular and biochemical predictions that we propose can focus future research.

DISCUSSION

We consider a canid that has been unconsciously selected as a tamed animal and the endpoint of methodical or what we now call artificial selection as a domesticated animal. We consider wild animals that were formerly tamed as untamed and those wild animals that were formerly domesticated as feralized. Untamed canids are predicted to be marked by a signature of unconscious selection whereas feral animals are hypothesized to be marked by signatures of both unconscious and artificial selection. First, we review the movement of dingo ancestors into Australia. We then discuss how differences between taming and domestication may influence the organismal traits of skull morphometrics, brain and size, seasonal breeding, and sociability. Finally, we consider cellular and molecular level traits including hypotheses concerning the phylogenetic position of dingoes, metabolic genes that appear to be under positive selection and the potential for micronutrient compensation by the gut microbiome.

CONCLUSIONS

Western Australian Government policy is currently being revised to allow the widespread killing of the Australian dingo. These policies are based on an incomplete understanding of the evolutionary history of the canid and assume the dingo is feralized. However, accumulated evidence does not definitively show that the dingo was ever domesticated and additional focused research is required. We suggest that incorporating ancient DNA data into the debate concerning dingo origins will be pivotal to understanding the evolutionary history of the canid. Further, we advocate that future morphological, behavioural and genetic studies should focus on including genetically pure Alpine and Desert dingoes and not dingo-dog hybrids. Finally, we propose that future studies critically examine genes under selection in the dingo and employ the genome from a wild canid for comparison.

Mitotype Interacts With Diet to Influence Longevity, Fitness, and Mitochondrial Functions in Adult Female Drosophila

Mitochondrial DNA (mtDNA) and the dietary macronutrient ratio are known to influence a wide range of phenotypic traits including longevity, fitness and energy production. Commonly mtDNA mutations are posited to be selectively neutral or reduce fitness and, to date, no selectively advantageous mtDNA mutations have been experimentally demonstrated in adult female Drosophila. Here we propose that a ND V161L mutation interacted with diets differing in their macronutrient ratios to influence organismal physiology and mitochondrial traits, but further studies are required to definitively show no linked mtDNA mutations are functionally significant. We utilized two mtDNA types (mitotypes) fed either a 1:2 Protein: Carbohydrate (P:C) or 1:16 P:C diet. When fed the former diet, Dahomey females harboring the V161L mitotype lived longer than those with the Alstonville mitotype and had higher climbing, basal reactive oxygen species (ROS) and elevated glutathione S-transferase E1 expression. The short lived Alstonville females ate more, had higher walking speed and elevated mitochondrial functions as suggested by respiratory control ratio (RCR), mtDNA copy number and expression of mitochondrial transcription termination factor 3. In contrast, Dahomey females fed 1:16 P:C were shorter lived, had higher fecundity, walking speed and mitochondrial functions. They had reduced climbing. This result suggests that mtDNA cannot be assumed to be a strictly neutral evolutionary marker when the dietary macronutrient ratio of a species varies over time and space and supports the hypothesis that mtDNA diversity may reflect the amount of time since the last selective sweep rather than strictly demographic processes.

Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness

Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.

Dietary management and physical exercise can improve climbing defects and mitochondrial activity in Drosophila melanogaster parkin null mutants

Physical exercise can improve gait, balance, tremor, flexibility, grip strength and motor coordination in Parkinson's disease (PD) patients. Several lines of evidence have also shown the therapeutic potential of dietary management and supplementation in halting the progression of PD. However, there is a lack of research on the combined effects of physical activity and nutrition in the progression of PD. We test the effects exercise and dietary modification in a Drosophila model of PD. In this study, we fed Drosophila parkin mutants high protein and high carbohydrate diets without and with stearic acid (4 treatments in total). In parallel, we subjected mutants to a regimen of exercise using a purpose-built 'Power tower' exercise machine. We then measured climbing ability, aconitase activity, and basal mitochondrial ROS levels. We observed that exercising parkin mutants fed the high protein diet improved their climbing ability and increased aconitase activity. There was an additional improvement in climbing and aconitase activity in exercised parkin mutants fed the high protein diet supplemented with stearic acid. No benefits of exercise were seen in parkin mutants fed the high carbohydrate diet. Combined, these results suggest that dietary management along with physical activty has potential to improve mitochondrial biogenesis and delay the progression of PD in Drosophila parkin mutants.

Elucidating biogeographical patterns in Australian native canids using genome wide SNPs

Dingoes play a strong role in Australia's ecological framework as the apex predator but are under threat from hybridization and agricultural control programs. Government legislation lists the conservation of the dingo as an important aim, yet little is known about the biogeography of this enigmatic canine, making conservation difficult. Mitochondrial and Y chromosome DNA studies show evidence of population structure within the dingo. Here, we present the data from Illumina HD canine chip genotyping for 23 dingoes from five regional populations, and five New Guinea Singing Dogs to further explore patterns of biogeography using genome-wide data. Whole genome single nucleotide polymorphism (SNP) data supported the presence of three distinct dingo populations (or ESUs) subject to geographical subdivision: southeastern (SE), Fraser Island (FI) and northwestern (NW). These ESUs should be managed discretely. The FI dingoes are a known reservoir of pure, genetically distinct dingoes. Elevated inbreeding coefficients identified here suggest this population may be genetically compromised and in need of rescue; current lethal management strategies that do not consider genetic information should be suspended until further data can be gathered. D statistics identify evidence of historical admixture or ancestry sharing between southeastern dingoes and South East Asian village dogs. Conservation efforts on mainland Australia should focus on the SE dingo population that is under pressure from domestic dog hybridization and high levels of lethal control. Further data concerning the genetic health, demographics and prevalence of hybridization in the SE and FI dingo populations is urgently needed to develop evidence based conservation and management strategies.

Sex-specific influences of mtDNA mitotype and diet on mitochondrial functions and physiological traits in Drosophila melanogaster

Here we determine the sex-specific influence of mtDNA type (mitotype) and diet on mitochondrial functions and physiology in two Drosophila melanogaster lines. In many species, males and females differ in aspects of their energy production. These sex-specific influences may be caused by differences in evolutionary history and physiological functions. We predicted the influence of mtDNA mutations should be stronger in males than females as a result of the organelle's maternal mode of inheritance in the majority of metazoans. In contrast, we predicted the influence of diet would be greater in females due to higher metabolic flexibility. We included four diets that differed in their protein: carbohydrate (P:C) ratios as they are the two-major energy-yielding macronutrients in the fly diet. We assayed four mitochondrial function traits (Complex I oxidative phosphorylation, reactive oxygen species production, superoxide dismutase activity, and mtDNA copy number) and four physiological traits (fecundity, longevity, lipid content, and starvation resistance). Traits were assayed at 11 d and 25 d of age. Consistent with predictions we observe that the mitotype influenced males more than females supporting the hypothesis of a sex-specific selective sieve in the mitochondrial genome caused by the maternal inheritance of mitochondria. Also, consistent with predictions, we found that the diet influenced females more than males.

Conservation implications for dingoes from the maternal and paternal genome: Multiple populations, dog introgression, and demography

It is increasingly common for apex predators to face a multitude of complex conservation issues. In Australia, dingoes are the mainland apex predator and play an important role in ecological functioning. Currently, however, they are threatened by hybridization with modern domestic dogs in the wild. As a consequence, we explore how increasing our understanding of the evolutionary history of dingoes can inform management and conservation decisions. Previous research on whole mitochondrial genome and nuclear data from five geographical populations showed evidence of two distinct lineages of dingo. Here, we present data from a broader survey of dingoes around Australia using both mitochondrial and Y chromosome markers and investigate the timing of demographic expansions. Biogeographic data corroborate the presence of at least two geographically subdivided genetic populations, southeastern and northwestern. Demographic modeling suggests that dingoes have undergone population expansion in the last 5,000 years. It is not clear whether this stems from expansion into vacant niches after the extinction of thylacines on the mainland or indicates the arrival date of dingoes. Male dispersal is much more common than female, evidenced by more diffuse Y haplogroup distributions. There is also evidence of likely historical male biased introgression from domestic dogs into dingoes, predominately within southeastern Australia. These findings have critical practical implications for the management and conservation of dingoes in Australia; particularly a focus must be placed upon the threatened southeastern dingo population.

Drosophila mitotypes determine developmental time in a diet and temperature dependent manner

It is well known that specific mitochondrial (mt) DNA mutations can reduce organismal fitness and influence mitochondrial-nuclear interactions. However, determining specific mtDNA mutations that are beneficial has been elusive. In this study, we vary the diet and environmental temperature to study larval development time of two Drosophila melanogaster mitotypes (Alstonville and Dahomey), in two nuclear genetic backgrounds, and investigate developmental differences through weight, feeding rate, and movement. To manipulate the diet, we utilize the nutritional geometric framework to manipulate isocaloric diets of differing macronutrient ratios (1:2 and 1:16 protein: carbohydrate (P:C) ratios) and raise flies at three temperatures (19°C, 23°C and 27°C). Larvae with Dahomey mtDNA develop more slowly than Alstonville when fed the 1:2 P:C diet at all temperatures and developed more quickly when fed the 1:16 P:C diet at 23°C and 27°C. We determined that Dahomey larvae eat more, move less, and weigh more than Alstonville larvae when raised on the 1:16 P:C diet and that these physiological responses are modified by temperature. We suggest that 1 (or more) of 4 mtDNA changes is likely responsible for the observed effects and posit the mtDNA changes moderate a physiological trade-off between consumption and foraging.

Epigallocatechin-3-gallate induces oxidative phosphorylation by activating cytochrome c oxidase in human cultured neurons and astrocytes

Mitochondrial dysfunction and resulting energy impairment have been identified as features of many neurodegenerative diseases. Whether this energy impairment is the cause of the disease or the consequence of preceding impairment(s) is still under discussion, however a recovery of cellular bioenergetics would plausibly prevent or improve the pathology. In this study, we screened different natural molecules for their ability to increase intracellular adenine triphosphate purine (ATP). Among them, epigallocatechin-3-gallate (EGCG), a polyphenol from green tea, presented the most striking results. We found that it increases ATP production in both human cultured astrocytes and neurons with different kinetic parameters and without toxicity.

Specifically, we showed that oxidative phosphorylation in human cultured astrocytes and neurons increased at the level of the routine respiration on the cells pre-treated with the natural molecule. Furthermore, EGCG-induced ATP production was only blocked by sodium azide (NaN₃) and oligomycin, inhibitors of cytochrome c oxidase (CcO; complex IV) and ATP synthase (complex V) respectively. These findings suggest that the EGCG modulates CcO activity, as confirmed by its enzymatic activity. CcO is known to be regulated differently in neurons and astrocytes. Accordingly, EGCG treatment is acting differently on the kinetic parameters of the two cell types. To our knowledge, this is the first study showing that EGCG promotes CcO activity in human cultured neurons and astrocytes. Considering that CcO dysfunction has been reported in patients having neurodegenerative diseases such as Alzheimer's disease (AD), we therefore suggest that EGCG could restore mitochondrial function and prevent subsequent loss of synaptic function.

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 2n_AMY2B=11) in a majority of dogs but no, or few, duplications (median 2n_AMY2B=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.

Assessing bioenergetic functions from isolated mitochondria in Drosophila melanogaster

Mitochondria are involved in generating more than 90 percent of cellular energy and are responsible for many cellular processes such as metabolism, cell signalling, apoptosis and ageing. Currently, there are a number of different experimental approaches employed to measure mitochondrial health and function. Here, we demonstrate a novel approach that quantifies substrate induced mitochondrial respiration from Drosophila. This protocol is optimized for mitochondria isolated from third instar larvae, and can also be used for mitochondria isolated from adult thoraces. This procedure outlines how to perform high throughput and high resolution mitochondria specific measurements for state II, state III, state IV_O respiration and residual oxygen consumption.

The ratio of macronutrients, not caloric intake, dictates cardiometabolic health, aging, and longevity in ad libitum-fed mice

The fundamental questions of what represents a macronutritionally balanced diet and how this maintains health and longevity remain unanswered. Here, the Geometric Framework, a state-space nutritional modeling method, was used to measure interactive effects of dietary energy, protein, fat, and carbohydrate on food intake, cardiometabolic phenotype, and longevity in mice fed one of 25 diets ad libitum. Food intake was regulated primarily by protein and carbohydrate content. Longevity and health were optimized when protein was replaced with carbohydrate to limit compensatory feeding for protein and suppress protein intake. These consequences are associated with hepatic mammalian target of rapamycin (mTOR) activation and mitochondrial function and, in turn, related to circulating branched-chain amino acids and glucose. Calorie restriction achieved by high-protein diets or dietary dilution had no beneficial effects on lifespan. The results suggest that longevity can be extended in ad libitum-fed animals by manipulating the ratio of macronutrients to inhibit mTOR activation.

What can symbiont titres tell us about co-evolution of Wolbachia and their host?

There is a long-standing prediction that associations with vertically transmitted symbionts evolve towards maximisation of host reproductive success, eventually leading to mutualist symbiosis and coadaptation. Under this scenario, the regulation of symbiont titres in host tissues would be expected to be greater when partners have coevolved for a long time than when they have recently met. Wolbachia pipientis, a common vertically transmitted symbiont of invertebrates, often has the capacity to spread through the host population without being beneficial to the hosts, by means of reducing the hatch rate in crosses between uninfected females and infected males. This manipulation, namely cytoplasmic incompatibility (CI), may exert strong selection on the accuracy of infection transmission from mother to offspring, and therefore, on regulation of symbiont titres in the ova. Here, we examined the symbiont density dynamics in gonads of Drosophila simulans infected with the wMa strain of Wolbachia, known to cause mild CI and likely to be the oldest Wolbachia infection known to this fly species. Further, we compared these results with those obtained for the more recent association between D. simulans and the potent CI-inducer wHa (Correa and Ballard, 2012). We aimed to determine if the regulation of Wolbachia density in fly gonads is greater in the older association, as would be predicted solely by gradual coadaptation, or if the selection exerted by CI on reproductive fitness could also play a role, therefore showing tighter regulation on flies with the stronger CI-inducing strain. We observed that Wolbachia density in gonads of wMa infected flies changed with laboratory adaptation and were disturbed by environmental challenges, which contrasted with the stability of ovarian wHa density to the same treatments. Our observations are in line with the prediction that selection on reproductive fitness influences the evolution symbiont density regulation in Drosophila, and may provide insights into the evolutionary processes involved in the maintenance or loss of Wolbachia.

Assessment of temporal genetic variability of two epibenthic amphipod species in an eastern Australian estuarine environment and their suitability as biological monitors

Population studies often assume temporally stable and consistent patterns of genetic variability. Violations of this assumption can lead to misrepresentation of the amount and patterns of genetic variability in natural populations, which can be problematic in basic research and environmental monitoring studies that are designed to detect environmental perturbation. We collected two endemic species of amphipods, Melita plumulosa and Melita matilda, in a major eastern Australian waterway between November 2009 and October 2011, and assessed genetic variation at the mitochondrial cytochromec oxidase subunitI locus. Overall, M. plumulosa was found to be more genetically variable than M. matilda. No distinct temporal trends in levels and patterns of genetic variation were identified in either species. These findings, combined with the published results demonstrating that M. plumulosa has greater sensitivity to a range of sediment-bound metals and organic contaminants, suggests it to be an informative species for environmental monitoring purposes.

Liver aging and pseudocapillarization in a Werner syndrome mouse model

Werner syndrome is a progeric syndrome characterized by premature atherosclerosis, diabetes, cancer, and death in humans. The knockout mouse model created by deletion of the RecQ helicase domain of the mouse Wrn homologue gene (Wrn(∆hel/∆hel)) is of great interest because it develops atherosclerosis and hypertriglyceridemia, conditions associated with aging liver and sinusoidal changes. Here, we show that Wrn(∆hel/∆hel) mice exhibit increased extracellular matrix, defenestration, decreased fenestration diameter, and changes in markers of liver sinusoidal endothelial cell inflammation, consistent with age-related pseudocapilliarization. In addition, hepatocytes are larger, have increased lipofuscin deposition, more frequent nuclear morphological anomalies, decreased mitochondria number, and increased mitochondrial diameter compared to wild-type mice. The Wrn(∆hel/∆hel) mice also have altered mitochondrial function and altered nuclei. Microarray data revealed that the Wrn(∆hel/∆hel) genotype does not affect the expression of many genes within the isolated hepatocytes or liver sinusoidal endothelial cells. This study reveals that Wrn(∆hel/∆hel) mice have accelerated typical age-related liver changes including pseudocapillarization. This confirms that pseudocapillarization of the liver sinusoid is a consistent feature of various aging models. Moreover, it implies that DNA repair may be implicated in normal aging changes in the liver.

Differential survival and reproductive performance across three mitochondrial lineages in Melita plumulosa following naphthalene exposure

Populations subject to anthropogenic contaminants often display altered patterns of genetic variation, including decreased genetic variability. Selective pressures of contaminant exposure are also reflected in differential tolerance between genotypes. An industrial chemical spill in a major eastern Australian waterway in July 2006 resulted in altered patterns of genetic variability in a nearby population of the amphipod, Melita plumulosa for up to one year post-spill, despite the site being declared clean after 48 h. Here, we investigate the toxicant response of three mitochondrial lines naturally occurring at the impacted site by comparing survivorship and life-history trait variables following naphthalene exposure. Overall, M. plumulosa demonstrated differential survivorship between mitochondrial lines under exposure to high concentrations of naphthalene. In addition, we identified differential fecundity and frequencies of gravidity in female amphipods between the mitochondrial haplotypes examined. These findings suggest that the patterns of genetic variability previously identified may be linked with differential tolerance and/or reproductive performance between mitochondrial lineages.

The effects of temperature and diet on age grading and population age structure determination in Drosophila

The age structure of natural population is of interest in physiological, life history and ecological studies but it is often difficult to determine. One methodological problem is that samples may need to be invasively sampled preventing subsequent taxonomic curation. A second problem is that it can be very expensive to accurately determine the age structure of given population because large sample sizes are often necessary. In this study, we test the effects of temperature (17 °C, 23 °C and 26 °C) and diet (standard cornmeal and low calorie diet) on the accuracy of the non-invasive, inexpensive and high throughput near-infrared spectroscopy (NIRS) technique to determine the age of Drosophila flies. Composite and simplified calibration models were developed for each sex. Independent sets for each temperature and diet treatments with flies not involved in calibration model were then used to validate the accuracy of the calibration models. The composite NIRS calibration model was generated by including flies reared under all temperatures and diets. This approach permits rapid age measurement and age structure determination in large population of flies as less than or equal to 9 days, or more than 9 days old with 85-97% and 64-99% accuracy, respectively. The simplified calibration models were generated by including flies reared at 23 °C on standard diet. Low accuracy rates were observed when simplified calibration models were used to identify (a) Drosophila reared at 17 °C and 26 °C and (b) 23 °C with low calorie diet. These results strongly suggest that appropriate calibration models need to be developed in the laboratory before this technique can be reliably used in field. These calibration models should include the major environmental variables that change across space and time in the particular natural population to be studied.

Diet influences the intake target and mitochondrial functions of Drosophila melanogaster males

In this study, we examine the dietary protein to carbohydrate ratio (P:C) on the mitochondrial functions of two Drosophila melanogaster mtDNA haplotypes. We investigated multiple physiological parameters on flies fed with either 1:12 P:C or 1:3 P:C diets. Our results provide experimental evidence that a specific haplotype has a reduction of complex I activity when the flies are fed with the 1:12 P:C diet. This study is of particular importance to understand the influence of diet on mitochondrial evolution in invasive and broadly distributed species including humans.

Physiological adaptations to reproduction. II. Mitochondrial adjustments in livers of lactating mice

Reproduction imposes significant costs and is characterized by an increased energy demand. As a consequence, individuals adjust their cellular structure and function in response to this physiological constraint. Because mitochondria are central to energy production, changes in their functional properties are likely to occur during reproduction. Such changes could cause adjustments in reactive oxygen species (ROS) production and consequently in oxidative stress levels. In this study, we investigated several mechanisms involved in energy production, including mitochondrial respiration at different steps of the electron transport system (ETS) and related the results to citrate synthase activity in the liver of non-reproductive and reproductive (two and eight pups) female house mice at peak lactation. Whereas we did not find differences between females having different litter sizes, liver mitochondria of reproductive females showed lower ETS activity and an increase in mitochondrial density when compared with the non-reproductive females. Although it is possible that these changes were due to combined processes involved in reproduction and not to the relative investment in lactation, we propose that the mitochondrial adjustment in liver might help to spare substrates and therefore energy for milk production in the mammary gland. Moreover, our results suggest that these changes lead to an increase in ROS production that subsequently upregulates antioxidant defence activity and decreases oxidative stress.

Wolbachia gonadal density in female and male Drosophila vary with laboratory adaptation and respond differently to physiological and environmental challenges

In symbiotic associations such as those between Wolbachia and insects, the within-host symbiont density plays an important role in the maintenance of the infection in natural populations, as it relates to transmission fidelity and pathogenicity of the symbiont. Within-host density is speculated to be the result of complex interactions between the bacterial genotype, the host genotype and the environment, which may account for the substantial variation in Wolbachia titres among wild collected individuals compared to laboratory lines. Using quantitative PCR, we screened the Wolbachia gonadal density of individuals from 50 isofemale Drosophila simulans lines raised in standard conditions for at least two generations after collection from the wild. Although these newly collected lines displayed significant variation of ovarian Wolbachia titres, such variation was lost by F(19). Assaying these flies at different ages and under different environmental conditions indicated that symbiont titres in female gonads were not affected by the conditions tested. However, Wolbachia density in male gonads was consistently affected by these treatments in a line-specific way. We propose that the differences in Wolbachia densities among ovaries of F(4) flies are the consequence of large differences in the field-collected females caused by the variable environment, and carried over for at least four generations. In addition, we provide evidence of sex-specific dynamics of Wolbachia in gonads of females and males. In combination, our results support the view of sex-specific Wolbachia evolutionary interactions for males and females, which has been predicted by theory and observed experimentally.

Naturally occurring mitochondrial DNA haplotypes exhibit metabolic differences: insight into functional properties of mitochondria

Linking the mitochondrial genotype and the organismal phenotype is of paramount importance in evolution of mitochondria. In this study, we determined the differences in catalytic properties of mitochondria dictated by divergences in the siII and siIII haplogroups of Drosophila simulans using introgressions of siII mtDNA type into the siIII nuclear background. We used a novel in situ method (permeabilized fibers) that allowed us to accurately measure the consumption of oxygen by mitochondria in constructed siII-introgressed flies and in siIII-control flies. Our results showed that the catalytic capacity of the electron transport system is not impaired by introgressions, suggesting that the functional properties of mitochondria are tightly related to the mtDNA haplogroup and not to the nuclear DNA or to the mito-nuclear interactions. This is the first study, to our knowledge, that demonstrates a naturally occurring haplogroup can confer specific functional differences in aspects of mitochondrial metabolism. This study illustrates the importance of mtDNA changes on organelle evolution and highlights the potential bioenergetic and metabolic impacts that divergent mitochondrial haplogroups may have upon a wide variety of species including humans.

Females with a mutation in a nuclear-encoded mitochondrial protein pay a higher cost of survival than do males in Drosophila

Males and females age at different rates in a variety of species, but the mechanisms underlying the difference is not understood. In this study, we investigated sex-specific costs of a naturally occurring mildly deleterious deletion (DTrp85, DVal86) in cytochrome c oxidase subunit 7A (cox7A) in Drosophila simulans. We observed that females and males homozygous for the mutation had 30% and 26% reduced Cox activity, respectively, compared with wild type. Furthermore, 4-day-old females had 34%-42% greater physical activity than males. Greater physical activity in mutant females was correlated with a 19% lower 50% survival compared with wild-type females. Mutant and wild-type males had equal survival. These data suggest that females paid a higher cost of the mutation than did males. The data demonstrate linking population genetics and structural modeling to experimental manipulations that lead to functional predictions of mitochondrial bioenergetics and organism aging.

Thermal sensitivity of mitochondrial functions in permeabilized muscle fibers from two populations of Drosophila simulans with divergent mitotypes

In ectotherms, the external temperature is experienced by the mitochondria, and the mitochondrial respiration of different genotypes is likely to change as a result. Using high-resolution respirometry with permeabilized fibers (an in situ approach), we tried to identify differences in mitochondrial performance and thermal sensitivity of two Drosophila simulans populations with two different mitochondrial types (siII and siIII) and geographical distributions. Maximal state 3 respiration rates obtained with electrons converging at the Q junction of the electron transport system (ETS) differed between the mitotypes at 24°C. Catalytic capacities were higher in flies harboring siII than in those harboring siIII mitochondrial DNA (2,129 vs. 1,390 pmol O(2)·s(-1)·mg protein(-1)). The cytochrome c oxidase activity was also higher in siII than siIII flies (3,712 vs. 2,688 pmol O(2)·s(-1)·mg protein(-1)). The higher catalytic capacity detected in the siII mitotype could provide an advantage in terms of intensity of aerobic activity, endurance, or both, if the intensity of exercise that can be aerobically performed is partly dictated by the aerobic capacity of the tissue. Moreover, thermal sensitivity results showed that even if temperature affects the catalytic capacity of the different enzymes of the ETS, both mitotypes revealed high tolerance to temperature variation. Previous in vitro study failed to detect any consistent functional mitochondrial differences between the same mitotypes. We conclude that the in situ approach is more sensitive and that the ETS is a robust system in terms of functional and regulatory properties across a wide range of temperatures.

Temporal and geographical genetic variation in the amphipod Melita plumulosa (Crustacea: Melitidae): Link of a localized change in haplotype frequencies to a chemical spill

Anthropogenic effects such as contamination affect the genetic structure of populations. This study examined the temporal and geographical patterns of genetic diversity among populations of the benthic crustacean amphipod Melita plumulosa in the Parramatta River (Sydney, Australia), following an industrial chemical spill. The spill of an acrylate/methacrylate co-polymer in naphtha solvent occurred in July 2006. M. plumulosa were sampled temporally between December 2006 and November 2009 and spatially in November 2009. Genetic variation was examined at the mitochondrial cytochrome c oxidase subunit I locus. Notably, nucleotide diversity was low and Tajima's D was significantly negative amongst amphipods collected immediately downstream from the spill for 10 months. We hypothesize that the spill had a significant localized effect on the genetic diversity of M. plumulosa. Alternate explanations include an alternate and unknown toxicant or a localized sampling bias. Future proposed studies will dissect these alternatives.

Cost of a naturally occurring two-amino acid deletion in cytochrome c oxidase subunit 7A in Drosophila simulans

This study aimed to determine whether a naturally occurring (DeltaTrp85, DeltaVal86) deletion from a protein subunit of cytochrome c oxidase (complex IV) influenced cytochrome c oxidase activity, mRNA expression levels of electron transport chain genes, and aspects of adult female fitness in the fly Drosophila simulans. We modeled the tertiary structure of D. simulans cox7A containing the deletion by homology to the bovine cox7A structure and predicted that it would decrease the function of complex IV. This prediction led to the hypothesis that flies with the deletion would have lower cytochrome c oxidase activity and higher levels of mRNA expression from cox7A. This result was observed, but unexpectedly, elevated levels of mRNA expression were also observed in genes encoding subunits of complexes I, III, and IV. Together these data suggest that the deletion causes a high bioenergetic cost to the organism. To investigate the predicted cost at a physiological level, we assayed aspects of adult female fitness. Starvation sensitivity but not feeding rate was significantly influenced by the two-amino acid deletion. Further, we observed that carbohydrate and protein levels but not lipid levels were higher in the mutant flies. Together, these data show that quaternary structure modeling and biochemistry can be used to link the genotype with the organismal phenotype.

Early life benefits and later life costs of a two amino acid deletion in Drosophila simulans

Linking naturally occurring genotypic variation to the organismal phenotype is critical to our understanding of, and ability to, model biological processes such as adaptation to novel environments, disease, and aging. Rarely, however, does a simple mutation cause a single simple observable trait. Rather it is more common for a mutation to elicit an entangled web of responses. Here, we employ biochemistry as the thread to link a naturally occurring two amino acid deletion in a nuclear encoded mitochondrial protein with physiological benefits and costs in the fly Drosophila simulans. This nuclear encoded gene produces a protein that is imported into the mitochondrion and forms a subunit of complex IV (cytochrome c oxidase, or cox) of the electron transport chain. We observe that flies homozygous for the deletion have an advantage when young but pay a cost later in life. These data show that the organism responds to the deletion in a complex manner that gives insight into the mechanisms that influence mitochondrial bioenergetics and aspects of organismal physiology.

Thermal sensitivity of mitochondrial metabolism in two distinct mitotypes of Drosophila simulans: evaluation of mitochondrial plasticity

The overall aim of this study was to (1) evaluate the adaptive value of mitochondrial DNA by comparing mitochondrial performance in populations possessing different haplotypes and distribution, and to (2) evaluate the sensitivity of different enzymes of the electron transport system (ETS) during temperature-induced changes. We measured the impact of temperature of mitochondrial respiration and several key enzymes of mitochondrial metabolism in two mitotypes (siII and siIII) of Drosophila simulans. The temperature dependencies of oxygen consumption for mitochondria isolated from flight muscle was assessed with complex I substrates (pyruvate + malate + proline) and with sn glycerol-3-phosphate (to reduce complex III via glycerophosphate dehydrogenase) in both coupled and uncoupled states. Activities of citrate synthase, cytochrome c oxidase (COX), catalase and aconitase, and the excess capacity of COX at high convergent pathway flux were also measured as a function of temperature. Overall, our results showed that functional differences between the two mitotypes are few. Results suggest that differences between the two mitotypes could hardly explain the temperature-specific differences measured in mitochondria performances. It suggests that some other factor(s) may be driving the maintenance of mitotypes. We also show that the different enzymes of the ETS have different thermal sensitivities. The catalytic capacities of these enzymes vary with temperature changes, and the corresponding involvement of the different steps on mitochondrial regulation probably varies with temperature. For example, the excess COX capacity is low, even non-existent, at high and intermediate temperatures (18°C, 24°C and 28°C) whereas it is quite high at a lower temperature (12°C), suggesting release of respiration control by COX at low temperature.

Evidence of recent population expansion in the field cricket Teleogryllus commodus

The patterns of intraspecific genetic variation can be driven by large-scale environmental events or smaller-scale phenomena such as land clearing. In Australia, European farming techniques have altered the landscape by increasing the amount of arable farmland. We hypothesised that this increase in farmland would result in a concomitant increase in the effective population size of the black field cricket (Teleogryllus commodus). To test our hypothesis, we investigated genetic variation in 1350 bp of mitochondrial mtDNA and in two nuclear encoded loci, hexokinase and elongation factor 1-α, from 20 crickets collected at Smiths Lake, New South Wales. Molecular variation in T. commodus was characterised by an over-representation of singleton mutations (negative Tajima’s D and Fu and Li’s D) in all loci studied. Further, HKA tests do not suggest that selection is acting on any one gene. Combined, these data support the hypothesis that population expansion is the force driving molecular variation in T. commodus. If an increase in agricultural habitats is the cause of population expansion in T. commodus we hypothesise greater genetic subdivision in natural than farmland habitats. An alternative possibility is that the effective geographical range of the species has increased but the density at a given site remains unchanged.