Philosophical Transactions of the Royal Society B Biological Sciences

Abstract Human mitochondrial DNA (mtDNA) contains 13 protein-coding subunits of the oxidative phosphorylation pathway, 22 tRNA and two rRNA genes. However, accumulating evidence suggests that mtDNA encodes additional overlapping genetic elements, including mitochondrial-derived peptides (MDPs) and alternative reading frames. Here, we assessed signatures of selection across 66 328 human mtDNAs and…

Abstract Mitochondrial genomes (mtDNA) have distinct evolutionary trajectories owing to their inheritance, ploidy and underlying mutation rates, making them prone to accumulate slightly deleterious mutations. Positive selection on mtDNA has been suggested to be important during adaptation to ‘high-energy’ lifestyles and environments. Disentangling positive versus relaxed selection in molecular mt…

Abstract 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 mitocho…

Abstract The link between longevity and mitochondrial function has been documented; therefore, we suspect that the evolution of mitochondrial DNA (mtDNA) is linked to the evolution of longevity. We selected 128 fish species with a wide range of longevity and inhabiting habitats with differing temperatures and examined their association with dN/dS ratios of mtDNA genes. Our findings (i) rule out e…

Abstract The evolution of sexes is closely tied to uniparental inheritance (UPI) of mitochondrial DNA (mtDNA), where only females transmit mtDNA. Unlike nuclear DNA, mtDNA is highly polyploid and never evolved to be part of meiotic sex. Modelling shows that UPI increases mtDNA mutational variance, enhancing selection for high-quality mtDNA and promoting the emergence of sexes from mating types in…

Abstract Eukaryotes likely originated from an endosymbiosis between an α-protobacterium and an Asgard archaeal host. Although endosymbiosis was followed by massive gene transfer from the mitochondrial DNA (mtDNA) to the nuclear genome, mtDNA was retained in most eukaryotes. Since the early 1980s, the genetic variation, species diversity and functional implications of mtDNA’s genetic content have …

Abstract Mismatches between interacting mitochondrial and nuclear gene products in hybrids have been proposed to disproportionately contribute to early species boundaries. Under this model, genetic incompatibilities emerge when mitochondrial haplotypes are in a cellular context without their coevolved nuclear-encoded mitochondrial (n-mt) proteins. Some case studies have shown that such disruption…

Abstract 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 pot…

Abstract Sexual reproduction is a widely spread feature of eukaryotes and was already present in the last eukaryotic common ancestor. While most extant eukaryotes inherit mitochondria from a single parent, the mechanisms enforcing uniparental inheritance vary widely. The first eukaryotes likely would not have evolved such mechanisms yet, so cellular fusion would have led to mitochondrial mixing (…

Abstract Mitochondrial genomes (mt-genomes) of calcaronean sponges are among the most unusual in Metazoa. They are fragmented into multiple linear chromosomes (mt-chromosomes) and often rely on insertional mRNA editing to generate functional transcripts. These unusual features have precluded complete characterization of calcaronean mt-genomes using short-read sequencing technologies. Here, we ass…

Abstract The origin of eukaryotic cells remains a highly contested problem. While eukaryotes arose from the merger of a bacterial and an archaeal partner giving rise to mitochondria and the cell proper, the order of steps is not known, nor is it understood why it was a singular event. Prokaryotes engage in various cooperative interactions everywhere, yet there is no evidence that they could estab…

Abstract Mitochondrial alternative open reading frames (ORFs) substantially broaden the functional scope traditionally attributed to mitochondrial DNA, encoding peptides and proteins that participate in diverse cellular processes. These newly identified ORFs are embedded within annotated sequences, both coding and non-coding, and reveal layers of overlapping genetic information. We report the dis…

Abstract Mitochondrial DNA (mtDNA) encodes essential bioenergetic and metabolic machinery across eukaryotes, but it is susceptible to mutational damage. The high copy number, physical location and inheritance patterns of mtDNA mean that specialist approaches to mitigate such damage are needed. A common theme across many species is segregation or ‘sorting out’ of different mtDNA types—generating v…

The performance of an individual has remained at the heart of evolutionary biology since the time of Darwin. Physiologists are equally drawn to the implications of individual variation for health and sporting endeavours, and specifically, whether or not a physiological trait is repeatable within an individual. Experimental biologists are especially interested in temporally stable physiological tr…

Animal personality, also sometimes called temperament, has been investigated in domesticated and non-domesticated species, mammal and non-mammal animals, from foxes and marsupials to horses and sheep. Standardized behavioural tests can be used to assess the phenotype of temperament and have identified large variability within populations of many species. Here, we present three examples that illus…

Differences in growth rate and metabolism between individual animals can influence survival, reproduction and competitive social dynamics during vulnerable life stages. Acknowledging this, among-individual variability has received growing research attention. Less attention has been given to temporal variability within individuals, which can also be substantial and influence individual-level perfo…

Inter-individual variability is the range of phenotypes within a population and can shape adaptive responses to environmental change. However, how temperature influences this variability remains unclear despite its importance for predicting population resilience to warming. We tested how rearing temperature (15°C and 22°C) affects both trait means and variability in time to stage, size, oxygen co…

Body size is a key trait that influences ecological processes such as metabolism, abundance and species interactions. While the metabolic theory of ecology (MTE) proposes a universal scaling of metabolic rate with body mass, recent evidence shows that this relationship is not fixed. Environmental factors like temperature and predation can alter the metabolic scaling exponent, potentially reshapin…

Our understanding of how environmental variability shapes animal physiology and behaviour is rapidly evolving. This is largely facilitated by a new wave of physiology research that has embraced environmental variability by simulating real-world conditions in experimental designs. While the move away from classical static holding conditions offers promising insights into environmental physiology, …