Cellular Machinery

Cellular machinery of energy generation: It is fundamental to all complex lifeforms, but encoded by two different genomes. mtDNA encoded residues are in greennucDNA encoded residues are in yellow, and residues encoded by one genome that physically interact with the other are in red


Most complex lifeforms - humans, animals, plants, and even unicelluar eukaryotes - generate a majortiy of their cellular energy through passing electrons down the electron transport chain, which is composed of protein complexes located in the inner mitochondrial membrane. However, these complexes, and the cellular machinery that is responsible for their transcription and translation, is encoded by two different genomes: the mitochondrial genome, derived from a bacterial progenitor, and the nuclear genome, derived from a different prokaryotic precursor. It is absolutely essential that the intricate interactions between gene products encoded by these two genomes remain in sync. Otherwise, organismal health and fitness decreases drastically.

​Exploring the evolution of such cytonuclear interactions has implications for a wide range of topics that are of general interest to biologists. These include the origin of the eukaryotes, endosymbiosis, the ultimate cause of sexual reproduction, why organisms age, how speciation occurs, and environmental adaptation, to name a few. 

​Ongoing projects -

Cytonuclear coevolution
Cytonuclear coevolution is expected to be common in eukaryotes because any changes in a cytoplasmic genome must be complemented by appropriate changes in the nuclear genome to maintain proper cytonuclear interactions and function. We are using molecular data from a wide range of eukaryotes to test predictions of cytonuclear coevolution. We are also interested in what specific forms cytonuclear coevolution takes when it is found - one notable hypothesis is nuclear compensation, in which slightly deleterious mutations in cytoplasmic genomes are offset by compensatory changes in nuclear-encoded genes. 

​Some publications describing this work:

Causes and consequences of mito mutations
Mito mutations and speciation
Plastid-nuclear coevolution
Evolution in mito vs. nuclear genomes
Nuclear compensation for mito mutations

Mutation rates and causes in cytoplasmic genomes

We are interested in why mitochondrial and other cytoplasmic genomes show a wide variety in mutation rates and what types of mutations are most common in these genomes. These areas have implications for human health as well as ecology and evolution. Recent projects along these lines include quantifying mitochondrial mutation rates and characterizing mitochondrial mutation spectra in C. elegans nematodes and the PolG mouse (which has a faulty polymerase and high mutation rates). We're using deep, high-fidelity sequencing approaches to characterize mutations in different eukaryotic lineages and correlate mutation rates and types with mitochondrial function.


Roles of cytoplasmic genomes during speciation
If mutations in cytoplasmic genomes cause the fixation of mutations in the nuclear genome, then cytoplasmic and nuclear genomes might be coadapted to one another within an evolutionary lineage. Hybridization between species or populations might break up these coadapted genomes, leading to hybrid breakdown and reproductive isolation between lineages. Paradoxically, cytoplasmic genomes are especially prone to cross species boundaries via introgression. To resolve these conflicting observations, we are using large, publicly available datasets and targeted experiments in Xiphophorus to reconcile the contradictory roles for cytoplasmic genomes at species boundaries. 

​Some publications describing this work:

The paradoxical roles of cytoplasmic genomes in speciation
Cytonuclear linkage disequilibrium in humans

​Mitochondrial function and environmental adaptation

Because mitochondria provide the majority of cellular energy in eukaryotes, mitochondrial function is critical for adaptation to novel environments. We're doing detailed wet lab experiments looking at mitochondrial function in different systems and in different environments. For example, we previously examined how mitochondrial respiration and whole animal metabolism phenotypes may change in mountain aquatic insects during acclimation to different thermal environments. We also showed that Silene angiosperms with high mitochondrial mutation rates show increased reliance on nuclear-encoded components for mitochondrial function. We're exploring mitochondrial respiration, membrane potential, and ROS production in a variety of systems. We're also examining signatures of selection on mitochondrial genes from animals living across different environments.

​Some publications describing this work:

Thermal responses of mitochondrial respiration in montane mayflies
Thermal responses of whole animal respiration across elevation and latitudes
How to measure thermal acclimation in biological rates
Differences in thermal responses across organizational levels
Silene angiosperms with different mt mutation rates have different mt physiology


Anchialine ecology and evolution

Anchialine habitats are another focus of the lab. Anchialine habitats are coastal water bodies influenced by both seawater and freshwater that have high levels of endemism. We are currently examining the physiological and genetic basis for red coloration in anchialine shrimps. These shrimps also have high rates of mitochondrial mutation and strong population structure across the islands where they're found, both considerations for future work. We were also recently funded to examine the formation of microbial communities during the early creation of anchialine habitats by examining anchialine ponds created in 2018 by lava flows in Hawaii (NSF DEB2020099).  

​Some publications describing this work:

Carotenoid variation in red coloration across anchialine shrimp lineages
Microbial community structure in anchialine habitats
Seasonality in anchialine microbial communities
Microbial communities and vertical stratification in anchialine habitats






Some publications describing previous work in the anchialine ecosystem and other interesting projects: 

​​Salinity responses and RNA-Seq across anchialine shrimps

Metabolic rates in anchialine shrimps

Sex, mitochondria, and genetic rescue

Mitochondria and the evolution of sex


Word Cloud
Word cloud summarizing research themes from recent publications



Silene angiosperms with variable rates of mtDNA evolution are a natural model to investigate consequences of mtDNA mutations.


Anchialine organisms and habitats. A) The endemic Hawaiian anchialine shrimp Halocaridina rubra (B) is found in distinct genetic lineages across Hawaii. C) Anchialine habitats harbor distinct microbial communities.


Click herehere, and here for some popular press coverage of our mito-mutation and sex hypothesis