Dr. Makenzie Mabry

@makenziemabryphd.bsky.social

USDA NIFA postdoc 📚💻 • evolutionary biology 🧬🧪 • plant systematics 🌿🥦 #iamabotanist • she/her 👩🏼‍💻

A new method for trimming alignments in #phylogenomics — PhyIN. It identifies and trims regions with high phylogenetic discord. Able to trim well even on single loci — an advantage for gene tree/species tree studies. #evolbiol #phylogeny 🧪http://doi.org/10.7717/peerj.18504 Some backstory... 🧵

PhyIN: trimming alignments by phylogenetic incompatibilities among neighbouring sites

In phylogenomics, regions of low alignment reliability and high noise are typically trimmed from multiple sequence alignments before they are used in phylogenetic inference. I introduce a new trimming...

doi.org

Hello Bluesky! I’m Paul, a Data Scientist and Computational Geneticist. I love programming, analyzing data, and building software tools – which means I spend a lot of my time battling bugs, but even more time battling my cat’s desire to sit on my keyboard

Cat standing on laptop keyboard, asking cheekily for treats.

🥦 Hi! I’m Makenzie, and I study plant biodiversity, focusing on wild relatives of crops in the Brassica family—think cabbages, mustards, and leafy greens. My research explores how these plants adapt to diverse and often challenging environments, revealing insights into resilience and survival. (1/9)

The plants we found were often connected to human habitation. They appeared as weeds in gardens, like Zilla spinosa, or as volunteers in farmers’ fields, where the centuries-old practice of community-coordinated groundwater extraction from oases sustains them and their cousin Brassica oleraceae.

Researcher R. Shawn Abrahams, crouched, attaching a Licor 6400 to a Zilla spinosa volunteer in the pea garden of a local Moroccan hotel. View of an irrigated oasis field in southern Morocco with leafy "collard greens" planted throughout and date palms in the background. Under the canopy of an irrigated oasis palm grove, with a clear view of the pools of water that are filled in around the base of the palms .

To observe this otherwise hidden photosynthetic phenotype, we brought a Licor 6400 to the desert to measure photosynthetic efficiency. Unfortunately, due to an earlier drought, many plants had already activated their avoidance strategies, so we missed the opportunity to observe and measure them.

The Licor 6400 photosynthesis measurement tool is balanced on its carrying case so as to attach to the leaf of a Moricandia suffruticosa that is growing out of the rock wall of a drainage ditch. A dry, dead or dormant plant of the tribe Brassiceae, identified from dried fruit silique, sits amongst stones in a desert landscape.

Some utilize avoidance strategies, like those that go dormant or completely disappear from the landscape, relying on a resilient seed bed to avoid the harshest conditions. Others have evolved a photosynthetic tolerance strategy hidden from the naked eye, allowing them to persist.

The rocky desert landscape of southern Morocco pointed towards a cliff side dotted with little desert plants, primarily brown and dry but a few vibrant greens despite the conditions. A sandy desert landscape in southern Morocco with brown plants sticking up through the dunes.

When people think of the Sahara, they rarely consider the plants or realize how close a thorny desert shrub is to their favorite leafy greens. My field partner, Makenzie Mabry, and I traveled to Morocco with Abderrahim Ouarghidi to uncover the secrets of these desert-adapted Brassiceae species.

Researchers Makenzie Mabry (Left), R. Shawn Abrahams (Middle), and Abderrahim Ouarghidi (right) in the Moroccan desert in search of local plant species.