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.

Our lab is leading a big effort to get undergrads involved in biodiversity research by transforming the UT turtle pond into a living lab. We’ve involved around 100 students so far!

Last year, students sampled turtles (mostly red-eared sliders) in urban ponds across Austin to ask whether microbiomes were different in turtles from different ponds, or if different body parts of the turtles had different microbial communities.

This year, we’re focusing on the UT turtles, examining microbiomes in the same individuals across seasons and asking whether individuals have specific microbiomes. The turtles were also moved off campus for a short time while the UT ponds were being repaired, so we can ask whether an environmental disturbance caused changes in microbial communities.

Here’s a story from KUT highlighting the turtles’ moving adventure, and another story on our work.

Next year the project will continue in the broad sense, but students will be working with a different PI to address a different question at the ponds.

Almost anyone can get involved in this work! Just email Justin to get started.

Welcome to the lab! We’re in the Integrative Biology Department @ The University of Texas. We study evolution, ecology, and physiology and most of our projects have something to do with mitochondria. Click around to learn more and reach out if you have any questions.