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I’m excited about this new special issue in Philosophical Transactions B on the evolutionary genetics of mitochondria. Organized by Venkatesh Nagarajan-Radha and others, this issue brings together a large group of diverse biologists studying the mechanistic basis of mitochondrial evolution, including early endosymbiosis, mitochondrial mRNA editing, sex, uniparental inheritance, heteroplasmy and mitochondrial-nuclear coevolution. The papers span a diverse set of methods, organisms, and scales, with some of the leading scientists across mitochondrial evolution and ecology.

Our lab was involved with 3 papers in this special issue:

1. In Havird et al., we collaborated with Bo Zhang to again look at mtDNA evolution in mites – this time seeing whether parasitic mites had mtDNA evolving under relaxed selection compared to predatory mites. We generally found the opposite, predatory mites had mtDNA with relatively relaxed selection, which we think is related to life-history traits and is supported by much higher rates of genome rearrangements in some predatory groups. This was a fun example of how to examine evolutionary processes in mtDNA and disentangle signatures of relaxed vs. positive selection.
2. In Klabacka et al., we review how mitonuclear interactions play out in asexual vertebrates. Because asexual vertebrates generally show features of clonality and hybridity, they have some unusual predictions for mitonuclear interactions and coevolution between the two genomes. We review these possibilities and offer some outlines for future experimental work to test these predictions.
3. In Kuster et al., we ask whether the common approach to break up the nuclear genome into genes that are vs. aren’t interacting with mitochondrial-encoded gene products is powerful enough to detect signatures of mitonuclear coevolution and incompatibilities. We generally find that genome-wide scan approaches where the genome is broken into these simple gene categories are likely underpowered to detect incompatibilities with even drastic fitness effects.

Tons of other great papers are also included in this special issue, check it out!

Huge congrats to Jess Sterling, who just successfully defended her PhD!

Jess has been a great lab member and researcher, who has made superb progress over the last 5 years. She joined the lab to work on immunity in marine systems, but ended up getting excited about how mitochondria might contribute to aging. She’s done side projects on bacterial communities in anchialine ecosystems, population genetics, and mitochondrial evolution of different animals, but her dissertation is titled “Discerning Mechanisms of Mitochondrial DNA (mtDNA) Mutation through Sequence Analysis”.

In her first chapter, she examined patterns of mtDNA sequence evolution in 4 groups of animals with quite variable lifespans to see if any mtDNA evolutionary patterns correlated with lifespan. She supported some previous findings showing that vertebrates with longer lifespans might have decreased mtDNA mutation rates, but ultimately she concluded that this was probably a methodological artifact and the pattern disappears when taking generation time into account. This story (and more) is in review now and should be published soon.

Her other projects made use of the model nematode C. elegans and several naturally occuring strains with variable lifespans. She characterized mitochondrial physiology among the strains and performed duplex sequencing to ask how mitochondrial mutations accumulated throughout the life of different strains. She’s wrapping up this work now and finding some really interesting conclusions, suggesting what’s been described in mammals might not apply to animals at large.

Finally, Jess has secured her “dream job” which she’ll be starting next Spring, working for the Boston Consulting Group (and staying based in Austin!).

Congrats again Jess!!!

Congrats to Reuben Matthews, an undergrad in the lab who is attending the Society for Neuroscience and presenting a poster on mitochdonrial DNA copy number and neurodegenerative diseases. Reuben has been in the lab for about a year and has driven a new collaboration between us and Jennifer Donegan’s lab here at UT who is interested in neurodegeneration.

Reuben and Jennifer’s student Sifallah have been working together on a meta-analysis asking whether patients with neurodegenerative diseases have different numbers of mtDNA genome copies compared to a control population. So far, they’ve found a weak signal for lower mtDNA CN associated with neurodegeneration, but lots of heterogeneity among studies. Some of that variation can be explain by which disease was being investigated, which tissue was used for sampling, and which geographic location the population came from. But, lots of variation remain and we’re not sure why some studies find a big effect and others don’t.

Reuben will be following up on this with a lab experiment using mice genetic models for different neurodegenerative diseases and examining mt CN in different tissues.

PhD candidate Mariangel Correa-Orellana was just awarded a prestigious HHMI Gilliam Fellowship! This is a very competitive award (>800 applicants this year and only 30 fellows) designed to launch promising young scientists into a scientific career. In addition to 3 years of fellowship support, Mariangel receives a yearly allowance for travel and professional development. This is also the first time anyone from UT has received this award.

This award also provides a great opportunity to get connected with the HHMI community through yearly conferences and meetings with other HHMI fellows.

Finally, as her adviser, I also get to benefit from this award as it includes a serious mentorship development component. I get to attend monthly online mentorship meetings as well as an in-person workshop to enhance my mentorship next Spring.

Mariangel’s dissertation focuses on microbial ecology of anchialine habitats in Hawaii. She’s interested in what these microbes are doing and will be applying metagenomics to ask what metabolic functions different members of these communities are performing, as well as whether these functions are different across different habitat types (for example, habitats with a distinct orange crust community vs. those with mud substrates or green algal mats). She’s also interested in animal-microbe interactions in these habitats and will be taking a deep dive into the gut microbiomes of the main shrimp species that is endemic to these habitats (opae ula, Halocaridina rubra).

Huge congrats to Kendra Zwonitzer, who just successfully defended her PhD!

Kendra is a stellar scientist that has been a blast to work with over the past 5 years. She has been incredibly productive, authoring several papers and appearing as a co-author on several more. She is an absolute wizard at the lab bench and when it comes to bioinformatics – and has a skillset that everybody in the lab likes to parasitize (especially me).

Kendra’s dissertation is titled “Discerning Mechanisms of Mitochondrial DNA (mtDNA) Mutation through Sequence Analysis” and she’s been excited about mtDNA mutations even since before she joined the lab.

Her first chapter explores how homologous recombination may shape mtDNA mutation rates in plants. This entailed analyzing dozens of plant genomes from diverse species and leading an international research team. The paper was published in PNAS last year.

Her next chapter explores mtDNA substitutions across all animals, with a goal to undercover the diversity and drivers of mtDNA mutation mechanisms. She analyzed >16,000 animal mtDNAs for this work, and found that the well-known stories presented from model systems do not apply to many animals (although mostly do to vertebrates). She’s currently writing up this publication.

He last chapter is an experimental approach to understand how different putative mutation mechanisms affect what types of mtDNA mutations are generated and their effects on fitness. This involved raising tons of different strains and treatments for the model nematode C. elegans, measuring different phenotypes, and ultimately generating duplex sequencing data to examine mutations as they arise. She’s currently finishing up this story as well, adding a few more strains.

Kendra has been a fantastic student and is a rising star in mtDNA evolution. She will go on to do great things, but luckily for me, she’s agreed to stay on for a few months as a postdoc. I was dreading her leaving, so this will help ease the lab into a post-Kendra era.

We just published a study in Ecology and Evolution, led by former postdoc Liming Cai, now at the University of Florida, examining mitochondrial respiration and mitochdonrial gene content in a family of parasitic plants, Orobanchaceae. This family has been a great model in Liming’s research because it contains closely related free-living, hemiparasitic (like the cancer roots pictured above), and holoparasitic species (including some independent origins of holoparasitism).

Here, Liming took a look at the nuclear-encoded genes targeted to the mitochdonria (N-mt) genes, which are often ignored in similar studies on parasitic plants. Although the parasitic species had a complete component of genes encoded in their mitochondrial genomes (coming out soon in a companion paper), there was one parasitic group that lost a significant number of N-mt genes, especially in Complex I. See the left hand columns in Fig. 1 of the paper:

Despite this, we found that even these parasitic plants with unusual N-mt gene loss maintained proper mitochondrial respiration. Things like maximum respiration and Complex I driven respiration were similar between these parasitic species and non-parasitic relatives, although there was a lot of variation. However, there was a trend for parasitic species to rely more on OXPHOS complexes that were made up of entirely nuclear-encoded proteins – CII, AOX, and alternative NADHs. This was only statistically significant for CII, but we think it might indicate some shift in mitochondrial function in parasitic plants.

Check out the respiration data in Fig. 2 from the paper here:

See the paper for more of our thoughts, but this adds to a complex body of literature that’s emerging on parasitic plants and mitochondrial evolution/function. Some parasitic species seem to have drastic changes in their mtDNA-encoded proteins, others are fairly normal. Some have lost Complex I completely, others still have a fully-functional version. This is in contrast to the plastid genome, which is almost universally degraded across parasitic plants.

By taking a look at the N-mt genes in this interesting family, Liming has provided a new avenue for examining these awesome, weird plants.

Stay tuned to her for more research on parasitic plants and mitochdonria!

A huge congratulations to Erik Iverson, who successfully defended his PhD dissertation last week. Erik was the first PhD student to join the lab and is also the first one to successfully defend. He has been incredibly productive during his time in the lab, authoring over a dozen publications, receiving multiple grants/fellowships, and mentoring a score of successful undergraduates. I am so proud of him!!!

Erik’s dissertation is titled “Implications of mitochondrial genetics and physiology for biogeography and conservation” and focuses on how processes in the mitochondria influence environmental adaptation, speciation, and responses to a changing world. His four main chapters include:

*An analysis of whether mtDNA has undergone adaptive changes in high elevation animals – published in Molecular Biology and Evolution

*A perspective piece on using mitochondrial replacement techniques and gene-editing technology in order to “pre-adapt” animals to climate change – published in Evolutionary Applications

*An experiment in natural populations of swordtail fishes with known mitonuclear incompatibilities that asks how fishes with different genetic backgrounds respond to changes in temperature – publication is in prep

*A field experiment on tapaculos birds in the Andes that demonstrates how mitochondrial and whole-organism physiology changes across species that replace each other with elevation – publication is in prep

Although I could go on and on about Erik, I’ll just end by mentioning how independent he’s been throughout his dissertation. He’s done projects in three new experimental systems (tapaculos, swordtail fishes, and tit mice), got funds to largely support his entire dissertation, and brought several undergrads into the field with him for a crazy-hard amount of fieldwork.

He’ll be acting as a field instructor for Wildlands Studies over the next year before moving onto a postdoc and hopefully starting his own lab eventually.

Our new paper describing thermal biology of Halocaridina rubra, a small shrimp endemic to anchialine habitats of Hawaii, is now available online @ Journal of Thermal Biology.

In this work, led by PhD student Mariangel Correa-Orellana, we examined how different populations/genetic lineages of H. rubra (known in Hawaii as opae ula) respond to changes in temperature. We were especially focused on populations from new habitats created during 2018 lava flows that continue to experience high temperatures due to geothermal activity.

Here’s 5 cool things we found:

1. Critical thermal limits, the upper and lower temperatures at which shrimp can continue to function, seem to be mainly determined by the temperatures shrimp are acclimated to. In other words, if they are kept at higher temps, they can tolerate higher temps. Genetics might play influence this a little, but it mostly seems to be nurture, not nature. Here’s Fig. 2 from the paper showing some data:

2. Even though the shrimp from the new, hot habitats are living at high temps (e.g., ~40 C), they can’t tolerate much higher temps. They are basically living at their maximum limit. We also never see shrimp in habitats that are much hotter than the maximum limits we measured, so we think these limits are ecologically important.

3. We also measured metabolic rates of shrimps from across the islands at room temperature. We found there was significant variability among genetic lineages, suggesting their might be a genetic component for baseline metabolic rates in this species. Here’s our data:

4. We also measured metabolic rates of different lineages that were acclimated to either a relatively warm or cool temperature. Importantly, we tested the shrimp from the different acclimation temperatures at either the cool or warm temp, so we could determine whether test or acclimation temperature was driving variation in metabolic rates. We found that metabolic rates in opae ula are almost entirely determined by test, not acclimation temperature. In other words, metabolic rates scale really fast with temperature and do not rebound if the animal is allowed to acclimate to that temperature (at least for 4 weeks). We call this a “no acclimation” response, which is fairly common across ectothermic animals, but not as common as a “partial acclimation” response where rates rebound somewhat with acclimation. Here’s the relevant figure:

5. If you look closely at the above figure, there’s no much difference among the different genetic lineages (HM, EP, P1, and SPAG) as to how their metabolic rates change with temperature. Our hypothesis was that shrimp from the new, warm habitats would show a stronger warm acclimation response – in other words their rates would not be as affected by warm temperatures as those from the old, cool habitats. But, this wasn’t really what we saw. Instead, we saw that rates were determined mostly by test temperature in all populations – none of them really showed much acclimation response.

Check out the paper if you want to learn more!

Congrats to Mariangel Correa-Orellana, a second year PhD student in our EEB program, for passing her qualifying exams and advancing to becoming a PhD candidate! Mariangel’s dissertation focuses on microbial ecology of anchialine habitats in Hawaii. She’s interested in what these microbes are doing and will be applying metagenomics to ask what metabolic functions different members of these communities are performing, as well as whether these functions are different across different habitat types (for example, habitats with a distinct orange crust community vs. those with mud substrates or green algal mats). She’s also interested in animal-microbe interactions in these habitats and will be taking a deep dive into the gut microbiomes of the main shrimp species that is endemic to these habitats (opae ula, Halocaridina rubra).

We’re all interested to see how her work turns out over the next few years!

We had a great time hosting my postdoc adviser Dan Sloan for a lab BBQ outing in the Texas Hill country! Dan was in town to celebrate his postdoc adviser, Nancy Moran, and Howard Ochman, along with ~50 other of their lab alumni. It was great catching up and seeing some academic relatives.