bioRxiv Science⌕ Search

Biology subjects

Havird, J. C.

Publications and source records attributed to Havird, J. C..

18 recordsLinked to original sources

Adaptation to increasing elevation via metabolic rates and mitochondrial genetics in Andean birds

Closely related species often replace each other at different elevations, a pattern that results in high biodiversity in mountains. Species range limits are set by physiological adaptation to gradients in temperature and oxygen availability as well as by competition with species above and below them on the gradient. As mountains warm due to climate change and many species move upward in elevation it is increasingly important to understand the mechanisms of climatic adaptation and competition that govern where and when species will persist, migrate, or go extinct. We investigated the genetics and physiology of tapaculos (Passeriformes: Rhinocryptidae), a group of small, weakly flying birds known for their narrow elevation ranges across the Andes, where as many as 6 species may replace each other on one transect. We first looked for selection on the mitochondrial genome, which is thought to be important in adaptation to elevation, in 85 members of this clade across South America. We found a signature of intensified positive selection on mitochondrial genes among species with mid-point elevations above 3000 m, suggesting metabolic adaptation to the harsh, high-altitude environment. We then measured metabolic rates and mitochondrial function in the field in four species of the genus Scytalopus that replace each other in a series along the Manu elevation gradient in Southeastern Peru. We found that higher elevation species have higher Basal Metabolic Rates (BMR) and more extreme Lower Critical Temperatures (LCTs), suggesting adaptation to the cold. However, these differences do not have a clear basis in mitochondrial function, which was broadly similar across species. Rather, higher-elevation species are smaller overall but have larger relative organ masses and maintain lower body temperatures, which may be adaptations to meeting the high thermogenic demands of their environment. These four species conform well to expectations of the Competitive-Exclusion Tolerance Rule (Martin & Ghalambor, 2023), with each species up the gradient being a poorer competitor (smaller body size) but having adapted to a harsher part of the gradient that more competitive species cannot occupy. We discuss these results in the context of theories about the importance of climate, competition, and ecotones in the distribution of Andean organisms, predicting that species living in the highest-elevation forests just below the treeline may be at the greatest risk of extinction due to climate change.

evolutionary biology↗

Mitochondrial DNA copy number in neurodegenerative diseases: a global meta-analysis of 156 comparisons across 76 studies

Mitochondria are central hubs for cellular metabolism and mitochondrial dysfunction is a hallmark of many chronic diseases. Consequently, changes in mitochondrial DNA copy number (mtDNA-CN), the number of mtDNA genomes per cell or tissue sample, are associated with diseases ranging from cancer and obesity to psoriasis and all-cause mortality. MtDNA-CN especially holds promise as a biomarker for neurodegenerative diseases, but whether and how mtDNA-CN changes with neurodegeneration is controversial. Here, we performed a systematic review and meta-analysis of 76 studies including 156 comparisons of mtDNA-CN in populations with or without a neurodegenerative disease to identify overall trends and potential moderators that explain variation among studies. Overall, mtDNA-CN was not statistically different with neurodegeneration, but heterogeneity among studies was extreme (I2 = 99.5%). The diagnosed disease explained the most variation. For example, Alzheimer's patients showed a 21% decrease in mtDNA-CN, but there was no change in mtDNA-CN with Parkinson's disease. Decreases in mtDNA-CN during neurodegeneration were also more extreme at older ages. Surprisingly, the tissue sampled for mtDNA-CN was not particularly influential, except for certain diseases. Studies published in earlier years also showed more extreme decreases in mtDNA-CN with neurodegeneration. Excessive heterogeneity persisted even after accounting for all moderators and their interactions (I2 = 85.7%). We conclude that the general perception of decreased mtDNA-CN with neurodegeneration is a vast oversimplification that may stem from legacy effects of early studies. However, mtDNA levels offer great promise as biomarkers for neurodegeneration, other diseases, and general health metrics, assuming appropriate complications can be considered.

neuroscience↗

Coordinated Evolutionary Rates in Oxidative Phosphorylation Complexes of Papilionoid Legumes: Cytonuclear Coevolution and Relaxed Selection

Across eukaryotes, mitochondrial (mt) and nuclear genomes coordinate the expression and interaction of gene products to maintain cellular functions. While mitonuclear coevolution has been widely explored in animals, it remains understudied in plants, despite their utility as model systems due to relatively slow mitochondrial evolutionary rates and the presence of plastids. Plants rely on oxidative phosphorylation (OXPHOS) for ATP conversion, which requires cofunctionality and likely coevolution of mitochondrial and nuclear gene products. Here, we investigated evolutionary rate covariation (ERC) between mitochondrial- and nuclear-encoded OXPHOS genes in papilionoid legumes, where plastid-nuclear coevolution and an inversion in plastid DNA have been documented previously. Using 50 legume species spanning 15 papilionoid clades, we estimated evolutionary rates for five gene sets: mt-encoded OXPHOS genes, nuclear-encoded mitochondrial-targeted (N-mt) OXPHOS genes, and three control nuclear gene sets that lack mitochondrial interactions (glycolysis, cell cycle, and cytosolic ribosomal genes). Both mt and N-mt OXPHOS genes exhibited significantly elevated nonsynonymous (dN) and synonymous substitution rates (dS) in the 50-kb inversion clade relative to other legumes, suggesting accelerated mitochondrial substitution rates. Moreover, elevated dN/dS ratios in mt and N-mt OXPHOS genes in this clade were driven by relaxed purifying, not intensified positive selection. ERCs were highest for OXPHOS complexes and genes with physical mitonuclear interactions, as predicted under mitonuclear coevolution. We discuss how these results compare to other cases of cytonuclear coevolution in plants, including plastid-nuclear coevolution in papilionoids, and why dual-targeted, nuclear-encoded genes that repair mt and plastid DNA may underly patterns of molecular evolution in both organelles. Significance StatementMitonuclear interactions are essential for cellular energy production, yet the evolutionary dynamics of these interactions remain poorly understood in plants. This study highlights papilionoid legumes as an important system for understanding how coordinated evolution between mitochondrial and nuclear genes shapes plant genomes. By identifying signatures of mitonuclear coevolution in the 50-kb inversion clade, this work demonstrates how shifts in selective pressures on mitochondrial processes can influence nuclear gene evolution. These findings advance our understanding of cytonuclear coordination in plants and provide a foundation for future studies exploring how interactions among genomic compartments contribute to plant evolution, adaptation, and resilience in agriculturally important lineages.

evolutionary biology↗

Sensitivity of genome-wide tests for mitonuclear genetic incompatibilities

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 disruptions in mitonuclear coevolution can contribute to reproductive isolation, but whether mitonuclear incompatibilities generate selection that impacts multiple n-mt loci and/or causes broad, genome-wide contributions to speciation is unclear. Here, we leverage a system with several hybridizing species pairs (Xiphophorus fishes) that have known mitonuclear incompatibilities of large effect. We divided nuclear-encoded genes into three classes based on level of interaction with mitochondrial gene products. We found only inconsistent statistical support for a difference between these classes in the degree of positive covariation in mitonuclear ancestry. We discuss evidence that these analyses are sensitive to the amount of non-synonymous divergence between parent species in interacting n-mt genes or the age of the hybridization event. Overall, our results imply that genome-wide scans focused on enrichment of broad functional gene classes may often be insufficient for detecting a history of mitonuclear coevolution, even when strong selection is acting on mitonuclear incompatibilities at multiple loci.

genomics↗

Recombination and retroprocessing in broomrapes reveal a universal roadmap for mitochondrial evolution in heterotrophic plants

The altered life history strategies of heterotrophic organisms often leave a profound genetic footprint on energy metabolism related functions. In parasitic plants, the reliance on host-derived nutrients and loss of photosynthesis in holoparasites have led to highly degraded to absent plastid genomes, but its impact on mitochondrial genome (mitogenome) evolution has remained controversial. By examining mitogenomes from 45 Orobanchaceae species including three independent transitions to holoparasitism and key evolutionary intermediates, we identified measurable and predictable genetic alterations in genomic shuffling, RNA editing, and intracellular (IGT) and horizontal gene transfer (HGT) en route to a nonphotosynthetic lifestyle. In-depth comparative analyses revealed DNA recombination and repair processes, especially RNA-mediated retroprocessing, as significant drivers for genome structure evolution. In particular, we identified a novel RNA-mediated IGT and HGT mechanism, which has not been demonstrated in cross-species and inter-organelle transfers. Based on this, we propose a generalized dosage effect mechanism to explain the biased transferability of plastid DNA to mitochondria across green plants, especially in heterotrophic lineages like parasites and mycoheterotrophs. Evolutionary rates scaled with these genomic changes, but the direction and strength of selection varied substantially among genes and clades, resulting in high contingency in mitochondrial genome evolution. Finally, we describe a universal roadmap for mitochondrial evolution in heterotrophic plants where increased recombination and repair activities, rather than relaxed selection alone, lead to differentiated genome structure compared to free-living species.

evolutionary biology↗

Altered mitochondrial respiration is associated with loss of nuclear-encoded OXPHOS genes in parasitic broomrapes

Parasitic plants, characterized by their dependency on host organisms for nutrients, have displayed far-reaching alterations in physiology and genetics. While significant gene losses and relaxed selection have been documented in the nuclear and plastid genomes, how parasitism impacts the molecular evolution and function of mitochondria has remained controversial. One of the main culprits hindering our understanding in this area is the lack of knowledge on nuclear-encoded mitochondrial-targeted genes (N-mt), which encode most mitochondrial oxidative phosphorylation (OXPHOS) proteins. By conducting a comprehensive survey of N-mt genes across angiosperms, we demonstrated significant gene losses and horizontal transfers associated with relaxed selection unique to holoparasitic Orobanchaceae. These putative losses and transfers have the potential to affect mitochondrial function directly and cause mitonuclear incompatibility because of breakdown between co-evolved protein complexes from mitochondrial and nuclear genomes. Our physiological assessments using high-resolution respirometry revealed that despite genetic alterations, holoparasitic Orobanchaceae maintained robust OXPHOS function but relied more on the fully nuclear-encoded succinate dehydrogenase (complex II). Our results document the first example of significant and biased gene loss in nuclear-encoded mitochondrial OXPHOS genes in parasitic plants, expanding on previous studies focused on mitochondrial-encoded genes and elucidating the mechanisms underlying the preservation of OXPHOS function despite genomic reduction.

evolutionary biology↗

Admixture mapping reveals evidence for multiple mitonuclear incompatibilities in swordtail fish hybrids

How barriers to gene flow arise between closely related species is one of the oldest questions in evolutionary biology. Classic models in evolutionary biology predict that negative epistatic interactions between variants in the genomes of diverged lineages, known as hybrid incompatibilities, will reduce viability or fertility in hybrids. The genetic architecture of these interactions and the evolutionary paths through which they arise have profound implications for the efficacy of hybrid incompatibilities as barriers to gene flow between species. While these questions have been studied using theoretical approaches for several decades, only recently has it become possible to genetically map larger numbers of hybrid incompatibilities. Here, we use admixture mapping in natural hybrid populations of swordtail fish (Xiphophorus) to identify hybrid incompatibilities involving genetic interactions between the mitochondrial and nuclear genomes. We find that at least nine regions of the genome are involved in mitonuclear incompatibilities. These incompatibilities involve interactions between the nuclear genome and the X. malinche mitochondria, the X. birchmanni mitochondria, or both. Moreover, they vary in the strength of selection they experience, and the degree to which they limit gene flow in natural hybrid populations. Our results build a deeper understanding of the complex architecture of selection against incompatibilities in naturally hybridizing species and highlight an important role of mitonuclear interactions in the evolution of reproductive barriers between closely related species.

evolutionary biology↗

An Affordable and Customizable Arduino-based Thermo-controller for Thermal Ecology Experiments

Insight into organismal physiology, evolutionary ecology, and climate change susceptibility all rely on high-quality and easily-obtainable thermal tolerance information. A variety of methods exist for measuring thermal tolerance, and thermal tolerance metrics are highly influenced by small differences in methodology. To promote consistency, reproducibility, and accessibility, we present here instructions for building an Arduino-based thermo-controller for raising, lowering, and holding temperature in a variety of experimental conditions. The setup is affordable ([~]$100), highly customizable, and highly consistent in the outcomes it produces. We include data from real thermal trials demonstrating the ability of the system to meet, hold, and reproduce desired ramping rates and hold temperatures.

physiology↗

Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA

Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.

evolutionary biology↗

Mitonuclear sex determination? Empirical evidence frombivalves

Genetic elements encoded in nuclear DNA determine the sex of an individual in many animals. In bivalves, however, mitochondrial DNA (mtDNA) has been hypothesized to contribute to sex determination in lineages that possess doubly uniparental inheritance (DUI). In these cases, females transmit a female mtDNA (F mtDNA) to all offspring, while male mtDNA (M mtDNA) is transmitted only from fathers to sons. Because M mtDNA is inherited in the same way as Y chromosomes, it has been hypothesized that mtDNA may be responsible for sex determination. However, the role of mitochondrial and nuclear genes in sex determination has yet to be validated in DUI bivalves. In this study, we used DNA, RNA, and mitochondrial short non-coding RNA (sncRNA) sequencing to explore the role of mitochondrial and nuclear elements in the sexual development pathway of the freshwater mussel Potamilus streckersoni (Bivalvia: Unionida). We found that the M mtDNA shed a sncRNA partially within a male-specific mitochondrial gene that targeted pathways hypothesized to be involved in female development and mitophagy. RNA-seq confirmed the gene target was significantly upregulated in females, supporting a direct role of mitochondrial sncRNAs in gene silencing. These findings support the hypothesis that M mtDNA inhibits female development. Genome-wide patterns of genetic differentiation and heterozygosity did not support a nuclear sex determining region, although we cannot reject that nuclear factors are involved with sex determination. Our results provide further evidence that mitochondrial loci contribute to diverse, non-respiratory functions and provide a first glimpse into an unorthodox sex determining system.

evolutionary biology↗

The revised leopard gecko (Eublepharis macularius) reference genome provides insight into the considerations of genome phasing and assembly

Genomic resources across squamate reptiles (lizards and snakes) have lagged behind other vertebrate systems and high-quality reference genomes remain scarce. Of the 23 chromosome-scale reference genomes across the order, only 12 of the ~60 squamate families are represented. Within geckos (infraorder Gekkota), a species-rich clade of lizards, chromosome-level genomes are exceptionally sparse representing only two of the seven extant families. Using the latest advances in genome sequencing and assembly methods, we generated one of the highest quality squamate genomes to date for the leopard gecko, Eublepharis macularius (Eublepharidae). We compared this assembly to the previous, short-read only, E. macularius reference genome published in 2016 and examined potential factors within the assembly influencing contiguity of genome assemblies using PacBio HiFi data. Briefly, the read N50 of the PacBio HiFi reads generated for this study was equal to the contig N50 of the previous E. macularius reference genome at 20.4 kilobases. The HiFi reads were assembled into a total of 132 contigs, which was further scaffolded using HiC data into 75 total sequences representing all 19 chromosomes. We identified that 9 of the 19 chromosomes were assembled as single contigs, while the other 10 chromosomes were each scaffolded together from two or more contigs. We qualitatively identified that percent repeat content within a chromosome broadly affects its assembly contiguity prior to scaffolding. This genome assembly signifies a new age for squamate genomics where high-quality reference genomes rivaling some of the best vertebrate genome assemblies can be generated for a fraction previous cost estimates. This new E. macularius reference assembly is available on NCBI at JAOPLA010000000. The genome version and its associated annotations are also available via this Figshare repository https://doi.org/10.6084/m9.figshare.20069273.

genomics↗

A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance

In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to these assumptions is called doubly uniparental inheritance (DUI): a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluscan class Bivalvia. The phylogenetic distribution of male mitochondrial DNA in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female mitochondrial DNA. In this study, we use phylogenetic methods to test male mitochondrial DNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of male mitochondrial DNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of female and male mitochondrial DNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination may be neutral but could be connected to the role of M mtDNA in sex determination or sexual development. Our results support recombination events in DUI species may occur throughout their genomes. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of male mitochondrial DNA in protein coding genes.

evolutionary biology↗

Disentangling positive vs. relaxed selection in animal mitochondrial genomes

Disentangling different types of selection is a common goal in molecular evolution. Elevated dN/dS ratios (the ratio of nonsynonymous to synonymous substitution rates) in focal lineages are often interpreted as signs of positive selection. Paradoxically, relaxed purifying selection can also result in elevated dN/dS ratios, but tests to distinguish these two causes are seldomly implemented. Here, we reevaluated seven case studies describing elevated dN/dS ratios in animal mtDNA and their accompanying hypotheses regarding selection. They included flightless vs. flighted lineages in birds, bats, and insects, and physiological adaptations in snakes, two groups of electric fishes, and primates. We found that elevated dN/dS ratios were often not caused by the predicted mechanism, and we sometimes found strong support for the opposite mechanism. We discuss reasons why energetic hypotheses may be confounded by other selective forces acting on mtDNA and caution against overinterpreting molecular "spandrels", including elevated dN/dS ratios.

evolutionary biology↗

A Lethal Genetic Incompatibility between Naturally Hybridizing Species in Mitochondrial Complex I

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of "hybrid incompatibilities," where alleles derived from two different species no longer interact properly in hybrids. Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes and that incompatibilities involving multiple genes should be common, but there has been sparse empirical data to evaluate these predictions. Here, we describe a mitonuclear incompatibility involving three genes in physical contact within respiratory Complex I in naturally hybridizing swordtail fish species. Individuals homozygous for specific mismatched protein combinations fail to complete embryonic development or die as juveniles, while those heterozygous for the incompatibility have reduced function of Complex I and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the impacts of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. We document the evolutionary history of the genes involved, showing for the first time that an incompatibility has been transferred between species via hybridization. This work thus provides the first glimpse into the genetic architecture, physiological impacts, and evolutionary origin of a complex incompatibility impacting naturally hybridizing species.

evolutionary biology↗

Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias

Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e. the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG[->]AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Further, we found an excess of G[->]T and C[->]T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.

genetics↗

Temperature-dependence of metabolic rate in tropical and temperate aquatic insects: support for the Climate Variability Hypothesis in mayflies but not stoneflies.

A fundamental gap in climate change vulnerability research is an understanding of the relative thermal sensitivity of ectotherms. Aquatic insects are vital to stream ecosystem function and biodiversity but insufficiently studied with respect to their thermal physiology. With global temperatures rising at an unprecedented rate, it is imperative that we know how aquatic insects respond to increasing temperature and whether these responses vary among taxa, latitudes, and elevations. We evaluated the thermal sensitivity of standard metabolic rate in stream-dwelling baetid mayflies and perlid stoneflies across a ~2,000 m elevation gradient in the temperate Rocky Mountains in Colorado, U.S.A., and the tropical Andes in Napo, Ecuador. We used temperature-controlled water baths and microrespirometry to estimate changes in oxygen consumption. Tropical mayflies generally exhibited greater thermal sensitivity in metabolism compared to temperate mayflies; tropical mayfly metabolic rates increased more rapidly with temperature and the insects more frequently exhibited behavioral signs of thermal stress. By contrast, temperate and tropical stoneflies did not clearly differ. Varied responses to temperature among baetid mayflies and perlid stoneflies may reflect differences in evolutionary history or ecological roles as herbivores and predators, respectively. Our results show that there is physiological variation across elevations and species and that low elevation tropical mayflies may be especially imperiled by climate warming. Given such variation among species, broad generalizations about the vulnerability of tropical ectotherms should be made more cautiously.

ecology↗

CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis

The function and evolution of eukaryotic cells depends upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.

genomics↗

Assessing mitochondrial function in angiosperms with highly divergent mitochondrial genomes

Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large ([~]11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was used to characterize inter-and intraspecific variation in mt function. Contributions of the individual \"classic\" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter-and intraspecific variation, possibly due to local adaptation or environmental effects. Although this study suggests that these Silene species with peculiar mt genomes still show relatively normal mt function, future experiments utilizing the protocol developed here can explore such questions in a more detailed and comparative framework.

plant biology↗