Climate‐driven mitochondrial selection: A test in Australian songbirds

Diversifying selection between populations that inhabit different environments can promote lineage divergence within species and ultimately drive speciation. The mitochondrial genome (mitogenome) encodes essential proteins of the oxidative phosphorylation (OXPHOS) system and can be a strong target for climate‐driven selection (i.e., associated with inhabiting different climates). We investigated whether Pleistocene climate changes drove mitochondrial selection and evolution within Australian birds. First, using phylogeographic analyses of the mitochondrial ND2 gene for 17 songbird species, we identified mitochondrial clades (mitolineages). Second, using distance‐based redundancy analyses, we tested whether climate predicts variation in intraspecific genetic divergence beyond that explained by geographic distances and geographic position. Third, we analysed 41 complete mitogenome sequences representing each mitolineage of 17 species using codon models in a phylogenetic framework and a biochemical approach to identify signals of selection on OXPHOS protein‐coding genes and test for parallel selection in mitolineages of different species existing in similar climates. Of 17 species examined, 13 had multiple mitolineages (range: 2–6). Climate was a significant predictor of mitochondrial variation in eight species. At least two amino acid replacements in OXPHOS complex I could have evolved under positive selection in specific mitolineages of two species. Protein homology modelling showed one of these to be in the loop region of the ND6 protein channel and the other in the functionally critical helix HL region of ND5. These findings call for direct tests of the functional and evolutionary significance of mitochondrial protein candidates for climate‐associated selection.     

Episodes of adaptive evolution of mitochondrial genome in asiatic salamanders (Amphibia,Caudata, Hynobiidae)

To elucidate the effect of natural selection on the evolution of mitochondrial DNA (mtDNA) in Asiatic salamanders of the family Hynobiidae, nucleotide sequences of 12 protein-coding genes were analyzed. Using a mixed effects model of evolution, it was found that, in spite of the pronounced effect of negative selection on the mtDNA evolution in Hynobiidae (which is typical for the animals in general), two phylogenetic clusters, the West Asian one, represented by the genera Ranodon and Paradactylodon, and North Eurasian one, represented by the genus Salamandrella, were formed under the influence of episodic positive selection. Analysis of protein sequences encoded by the mitochondrial genome also supported the influence of positive selection on the evolution of Hynobiidae at some stages of their cladogenesis. It is suggested that the signatures of adaptive evolution detected in the mtDNA of Hynobiidae were determined by the complex and long-lasting history of their formation, accompanied by adaptation to the changing environment.     

Mitochondrial rate variation among lineages of passerine birds

The order Passeriformes comprises the majority of extant avian species. Analyses of molecular data have provided important insights into the evolution of this diverse order. However, molecular estimates of the evolutionary and demographic timescales of passerine species have been hindered by a lack of reliable calibrations. This has led to a reliance on the application of standard substitution rates to mitochondrial DNA data, particularly rates estimated from analyses of the gene encoding cytochrome b (CYTB). To investigate patterns of rate variation across passerine lineages, we used a Bayesian phylogenetic approach to analyse the protein‐coding genes of 183 mitochondrial genomes. We found that the most commonly used mitochondrial marker, CYTB, has low variation in rates across passerine lineages. This lends support to its widespread use as a molecular clock in birds. However, we also found that the patterns of among‐lineage rate variation in CYTB are only weakly related to the evolutionary rate of the mitochondrial genome as a whole. Our analyses confirmed the presence of mutational saturation at third codon positions across the protein‐coding genes of the mitochondrial genome, reinforcing the view that these sites should be excluded in studies of deep passerine relationships. The results of our analyses have provided information that will be useful for molecular‐clock studies of passerine evolution.     

Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis

The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be selected to best infer the evolutionary history of the mitochondria within a group of organisms, and what properties of a gene determine its phylogenetic performance? The current study addresses these questions in a Bayesian phylogenetic framework with reference to a phylogeny of plethodontid and related salamanders derived from 27 complete mitochondrial genomes; this topology is corroborated by nuclear DNA and morphological data. Evolutionary rates for each mitochondrial gene and divergence dates for all nodes in the plethodontid mitochondrial genome phylogeny were estimated in both Bayesian and maximum likelihood frameworks using multiple fossil calibrations, multiple data partitions, and a clock-independent approach. Bayesian analyses of individual genes were performed, and the resulting trees compared against the reference topology. Ordinal logistic regression analysis of molecular evolution rate, gene length, and the G-shape parameter a demonstrated that slower rate of evolution and longer gene length both increased the probability that a gene would perform well phylogenetically. Estimated rates of molecular evolution vary 84-fold among different mitochondrial genes and different salamander lineages, and mean rates among genes vary 15-fold. Despite having conserved amino acid sequences, cox1, cox2, cox3, and cob have the fastest mean rates of nucleotide substitution, and the greatest variation in rates, whereas rrnS and rrnL have the slowest rates. Reasons underlying this rate variation are discussed, as is the extensive rate variation in cox1 in light of its proposed role in DNA barcoding.     

The role of mitochondrial respiration in physiological and evolutionary adaptation

Aerobic mitochondria serve as the power sources of eukaryotes by producing ATP through oxidative phosphorylation (OXPHOS). The enzymes involved in OXPHOS are multisubunit complexes encoded by both nuclear and mitochondrial DNA. Thus, regulation of respiration is necessarily a highly coordinated process that must organize production, assembly and function of mitochondria to meet an organism's energetic needs. Here I review the role of OXPHOS in metabolic adaptation and diversification of higher animals. On a physiological timescale, endocrine-initiated signaling pathways allow organisms to modulate respiratory enzyme concentration and function under changing environmental conditions. On an evolutionary timescale, mitochondrial enzymes are targets of natural selection, balancing cytonuclear coevolutionary constraints against physiological innovation. By synthesizing our knowledge of biochemistry, physiology and evolution of respiratory regulation, I propose that we can now explore questions at the interface of these fields, from molecular translation of environmental cues to selection on mitochondrial haplotype variation.     

Fast molecular evolution associated with high active metabolic rates in poison frogs

Molecular evolution is simultaneously paced by mutation rate, genetic drift, and natural selection. Life history traits also affect the speed of accumulation of nucleotide changes. For instance, small body size, rapid generation time, production of reactive oxygen species (ROS), and high resting metabolic rate (RMR) are suggested to be associated with faster rates of molecular evolution. However, phylogenetic correlation analyses failed to support a relationship between RMR and molecular evolution in ectotherms. In addition, RMR might underestimate the metabolic budget (e.g., digestion, reproduction, or escaping predation). An alternative is to test other metabolic rates, such as active metabolic rate (AMR), and their association with molecular evolution. Here, I present comparative analyses of the associations between life history traits (i.e., AMR, RMR, body mass, and fecundity) with rates of molecular evolution of and mitochondrial loci from a large ectotherm clade, the poison frogs (Dendrobatidae). My results support a strong positive association between mass-specific AMR and rates of molecular evolution for both mitochondrial and nuclear loci. In addition, I found weaker and genome-specific covariates such as body mass and fecundity for mitochondrial and nuclear loci, respectively. No direct association was found between mass-specific RMR and rates of molecular evolution. Thus, I provide a mechanistic hypothesis of the link between AMRs and the rate of molecular evolution based on an increase in ROS within germ line cells during periodic bouts of hypoxia/hyperoxia related to aerobic exercise. Finally, I propose a multifactorial model that includes AMR as a predictor of the rate of molecular evolution in ectothermic lineages.     

Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity,neutral theory,and phylogenetic relationships within the order Passeriformes

We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald–Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza.     

You are where you live: parasitic nematode mitochondrial genome size is associated with the thermal environment generated by hosts

There exists remarkable interspecific variation in mitochondrial sequence evolution rates and in mitochondrial genome sizes. A number of hypotheses based on the forces of mutation and selection have been proposed to explain this variation. Among such hypotheses, we test three: 1) the ‘longevity‐dependent selection’, 2) the ‘functional constraints’ and 3) the ‘race for replication’ hypotheses, using published mtDNA genomic sequences of 47 Nematoda species. We did not find any relationship between body size (used as a proxy for longevity) and genome size or the substitution rate of protein sequences, providing little evidence for the first hypothesis. Parasitic species from different thermal habitats, as determined by their definitive host type (ectothermal vs. endothermal), did not differ in their rates of protein evolution. Therefore, little support was obtained for the second hypothesis. However, we revealed that mitogenomes of parasites of endotherms were significantly smaller than those of parasites of ectotherms, supporting the race for replication hypothesis. As mitochondrial genomes of endothermal animals are usually more compact than those of ectothermal animals, intriguingly, nematode parasites of endotherms and ectotherms exhibit similar patterns of mtDNA length variation to their hosts.     

Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression

Introgression is the effective exchange of genetic information between species through natural hybridization. Previous genetic analyses of the Drosophila yakuba—D. santomea hybrid zone showed that the mitochondrial genome of D. yakuba had introgressed into D. santomea and completely replaced its native form. Since mitochondrial proteins work intimately with nuclear‐encoded proteins in the oxidative phosphorylation (OXPHOS) pathway, we hypothesized that some nuclear genes in OXPHOS cointrogressed along with the mitochondrial genome. We analyzed nucleotide variation in the 12 nuclear genes that form cytochrome c oxidase (COX) in 33 Drosophila lines. COX is an OXPHOS enzyme composed of both nuclear‐ and mitochondrial‐encoded proteins and shows evidence of cytonuclear coadaptation in some species. Using maximum‐likelihood methods, we detected significant gene flow from D. yakuba to D. santomea for the entire COX complex. Interestingly, the signal of introgression is concentrated in the three nuclear genes composing subunit V, which shows population migration rates significantly greater than the background level of introgression in these species. The detection of introgression in three proteins that work together, interact directly with the mitochondrial‐encoded core, and are critical for early COX assembly suggests this could be a case of cytonuclear cointrogression.     

Eusociality Shapes Convergent Patterns of Molecular Evolution across Mitochondrial Genomes of Snapping Shrimps

Eusociality is a highly conspicuous and ecologically impactful behavioral syndrome that has evolved independently across multiple animal lineages. So far, comparative genomic analyses of advanced sociality have been mostly limited to insects. Here, we study the only clade of animals known to exhibit eusociality in the marine realm—lineages of socially diverse snapping shrimps in the genus Synalpheus. To investigate the molecular impact of sociality, we assembled the mitochondrial genomes of eight Synalpheus species that represent three independent origins of eusociality and analyzed patterns of molecular evolution in protein-coding genes. Synonymous substitution rates are lower and potential signals of relaxed purifying selection are higher in eusocial relative to noneusocial taxa. Our results suggest that mitochondrial genome evolution was shaped by eusociality-linked traits—extended generation times and reduced effective population sizes that are hallmarks of advanced animal societies. This is the first direct evidence of eusociality impacting genome evolution in marine taxa. Our results also strongly support the idea that eusociality can shape genome evolution through profound changes in life history and demography.     

Mitochondrial genome primers for Lake Malawi cichlids

Resolving the evolutionary history of rapidly diversifying lineages like the Lake Malawi Cichlid Flock demands powerful phylogenetic tools. Although this clade of over 500 species of fish likely diversified in less than two million years, the availability of extensive sequence data sets, such as complete mitochondrial genomes, could help resolve evolutionary patterns in this group. Using a large number of newly developed primers, we generated whole mitochondrial genome sequences for 14 Lake Malawi cichlids. We compared sequence divergence across protein‐coding regions of the mitochondrial genome and also compared divergence in the mitochondrial loci to divergence at two nuclear protein‐coding loci, Mitfb and Dlx2. Despite the widespread sharing of haplotypes of identical sequences at individual loci, the combined use of all protein‐coding mitochondrial loci provided a bifurcating phylogenetic hypothesis for the exemplars of major lineages within the Lake Malawi cichlid radiation. The primers presented here could have substantial utility for evolutionary analyses of mitochondrial evolution and hybridization within this diverse clade.     

Molecular Evolution of Cytochrome c Oxidase in High-Performance Fish (Teleostei: Scombroidei)

The 13 peptides encoded by vertebrate mitochondrial DNA (mtDNA) are essential subunits of oxidative phosphorylation (OXPHOS) enzymes. These genes normally experience purifying selection and also coevolve with nuclear-encoded subunits of OXPHOS complexes. However, the role of positive selection on mtDNA evolution is still unclear, as most examples of intergenomic coevolution appear to be the result of compensation by nuclear-encoded genes for mildly deleterious mtDNA mutations, and not simultaneous positive selection in both genomes. Organisms that have experienced strong selective pressures to increase aerobic capacity or adapt to changes in thermal environment may be better candidates in which to examine the impact of positively selected changes on mtDNA evolution. The tuna (suborder Scombroidei, family Scombridae) and billfish (suborder Scombroidei, families Xiphiidae and Istiophoridae) are highly aerobic fish with multiple specializations in muscle energetics, including a high mitochondrial content and regional endothermy. We examined the role of positively selected mtDNA substitutions in the production of these unique phenotypes. Focusing on a catalytic subunit of cytochrome c oxidase (COX II), we found that the rate ratio of nonsynonymous (d(N); amino acid changing)-to-synonymous (d(S); silent) substitutions was not increased in lineages leading to the tuna but was significantly increased in the lineage preceding the billfish. Furthermore, there are a number of individual positively selected sites that, when mapped onto the COX crystal structure, appear to interact with other COX subunits and may affect OXPHOS function and regulation in billfish.     

Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747‐Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.     

Complex mitonuclear interactions and metabolic costs of mating in male seed beetles

The lack of evolutionary response to selection on mitochondrial genes through males predicts the evolution of nuclear genetic influence on male‐specific mitochondrial function, for example by gene duplication and evolution of sex‐specific expression of paralogs involved in metabolic pathways. Intergenomic epistasis may therefore be a prevalent feature of the genetic architecture of male‐specific organismal function. Here, we assess the role of mitonuclear genetic variation for male metabolic phenotypes [metabolic rate and respiratory quotient (RQ)] associated with ejaculate renewal, in the seed beetle Callosobruchus maculatus, by assaying lines with crossed combinations of distinct mitochondrial haplotypes and nuclear lineages. We found a significant increase in metabolic rate following mating relative to virgin males. Moreover, processes associated with ejaculate renewal showed variation in metabolic rate that was affected by mitonuclear interactions. Mitochondrial haplotype influenced mating‐related changes in RQ, but this pattern varied over time. Mitonuclear genotype and the energy spent during ejaculate production affected the weight of the ejaculate, but the strength of this effect varied across mitochondrial haplotypes showing that the genetic architecture of male‐specific reproductive function is complex. Our findings unveil hitherto underappreciated metabolic costs of mating and ejaculate renewal, and provide the first empirical demonstration of mitonuclear epistasis on male reproductive metabolic processes.     

Recruitment of healthy mitochondria fuels transmissible cancers

The replication of mitochondrial DNA (mtDNA) is not under strict control of the nucleus. Therefore, within-cell selection can favour mtDNA variants with a replication or survival advantage even if deleterious for the cell. Here, we consider how the balance between selection within and among cells is shifted in cancer cell lineages, and how this affects the somatic evolution of mitochondria. Cancer cell lineages are known to be prone to mitochondrial genetic erosion. Nevertheless, some cancer lineages are long lived and a few exceptional lineages even can survive their host because of horizontal transmission to other individuals. Recent work now shows that such transmissible cancer cell lineages occasionally secondarily recruit the mitochondrial genome of their host, which we propose as a means to replace genetically eroded mitochondrial genomes. Studying the dynamics of the horizontal exchange of mtDNA between somatic cells may provide important insight into the evolution of mitochondria during somatic growth and in mitochondrial diseases.     

Signatures of natural selection in the mitochondrial genomes of Tachycineta swallows and their implications for latitudinal patterns of the ‘pace of life’

Latitudinal variation in avian life histories can be summarized as a slow–fast continuum, termed the ‘pace of life’, that encompasses patterns in life span, reproduction, and rates of development among tropical and temperate species. Much of the variation in avian pace of life is tied to differences in rates of long-term metabolic energy expenditure. Given the vital role of the mitochondrion in metabolic processes, studies of variation in the mitochondrial genome may offer opportunities to establish mechanistic links between genetic variation and latitudinal ‘pace of life’ patterns. Using comparative genomic analyses, we examined complete mitochondrial genome sequences obtained from nine, broadly distributed Tachycineta swallow species to test for signatures of natural selection across the mitogenome within a phylogenetic framework. Our results show that although purifying selection is the dominant selective force acting on the mitochondrial genome in Tachycineta, three mitochondrial genes (ND2, ND5, and CYTB) contain regions that exhibit signatures of diversifying selection. Two of these genes (ND2 and ND5) encode interacting subunits of NADH dehydrogenase, and amino residues that were inferred to be targets of positive selection were disproportionately concentrated in these genes. Moreover, the positively selected sites exhibited a phylogenetic pattern that could be indicative of adaptive divergence between “fast” and “slow” lineages. These results suggest that functional variation in cytochrome b and NADH dehydrogenase could mechanistically contribute to latitudinal ‘pace of life’ patterns in Tachycineta.     

The mitonuclear compatibility hypothesis of sexual selection

Why females assess ornaments when choosing mates remains a central question in evolutionary biology. We hypothesize that the imperative for a choosing female to find a mate with nuclear oxidative phosphorylation (OXPHOS) genes that are compatible with her mitochondrial OXPHOS genes drives the evolution of ornaments. Indicator traits are proposed to signal the efficiency of OXPHOS function thus enabling females to select mates with nuclear genes that are compatible with maternal mitochondrial genes in the formation of OXPHOS complexes. Species-typical pattern of ornamentation is proposed to serve as a marker of mitochondrial type ensuring that females assess prospective mates with a shared mitochondrial background. The mitonuclear compatibility hypothesis predicts that the production of ornaments will be closely linked to OXPHOS pathways, and that sexual selection for compatible mates will be strongest when genes for nuclear components of OXPHOS complexes are Z-linked. The implications of this hypothesis are that sexual selection may serve as a driver for the evolution of more efficient cellular respiration.     

Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA: new data and reappraisal

Aim We aimed to examine the phylogeographical structure and demographic history of domestic and wild yaks (Bos grunniens) based on a wide range of samples and complete mitochondrial genomic sequences. Location The Qinghai‐Tibetan Plateau (QTP) of western China. Methods All available D‐loop sequences for 405 domesticated yaks and 47 wild yaks were examined, including new sequences from 96 domestic and 34 wild yaks. We further sequenced the complete mitochondrial genomes of 48 domesticated and 21 wild yaks. Phylogeographical analyses were performed using the mitochondrial D‐loop and the total genome datasets. Results We recovered a total of 123 haplotypes based on the D‐loop sequences in wild and domestic yaks. Phylogenetic analyses of this dataset and the mitochondrial genome data suggested three well‐supported and divergent lineages. Two lineages with six D‐loop haplogroups were recovered for all morphological breeds of domestic yaks across their distributions in the QTP, while one more lineage and more endemic haplogroups or haplotypes were found for wild yaks. Based on the mitochondrial genome data, the divergences of the three lineages were estimated to have occurred around 420,000 and 580,000 years ago, consistent with the geological records of two large glaciation events experienced in the QTP. Main conclusions There are distinct phylogeographical differences between wild and domestic yaks. However, there is no apparent geographical correlation between identified haplogroups and distributions of domestic yaks. Three differentiated lineages of yaks probably evolved allopatrically in different regions during the Pleistocene glaciation events, then reunited into a single gene pool during post‐glacial population expansion and migrations before the start of the domestication of yaks in the Holocene.     

Positive selection on the mitochondrial ATP synthase 6 and the NADH dehydrogenase 2 genes across 22 hare species (genus Lepus)

Amino acid changes in mitochondrial (mt) oxidative phosphorylation (OXPHOS) genes have been suggested as a key adaptation to environmental variation. Here, we analyzed 416 sequences of ATPase synthase 6 (MT‐ATP6) and NADH dehydrogenase 2 (MT‐ND2) in 22 different hare (Lepus) species from across a wide range of habitats and climates. We used site‐ and branch‐based methods to test for positive selection on specific codons and lineages. We found four codons in MT‐ATP6 and five in MT‐ND2 under positive selection, affecting several species lineages. We investigated the association of protein variants at each locus with climate zone, using multinomial generalized linear models (glm), including species, regions, historical introgression events, and the co‐occurring protein variant at the other locus as additional explanatory variables. A significant climate effect as based on the “Köppen climate classification” was observed for MT‐ND2 protein variants as translated from our nucleotide sequences. Moreover, MT‐ND2 protein variants were significantly affected by the co‐occurring MT‐ATP6 protein variant in the same mtDNA molecule. Contrary to the expectation for non‐recombining mitochondrial DNA molecules, the presence of an evolutionarily relatively ancestral protein variant at one locus was associated with a relatively derived protein at the other locus in the same mitochondrial molecule, respectively. The relative evolutionary status of a protein variant was evaluated according to its positions relative to the respective out‐group protein variant in a network analysis of nucleotide sequences. All our results suggest a complex effect of various climatic parameters acting on multiple mtOXPHOS genes in a co‐adaptive way, favoring combinations of ancestral and derived variants.