iiinova — where your digital self keeps evolving

Patrick McKenzie @patrickmckenzie.bsky.social · 03/08/2026

Major #Botany2026 FOMO, but the drive MA->OR starts this week. So, sharing from afar: I’m recruiting grad students for my new lab at OSU! Info: www.mckenzie-lab.org . We're going to have FUN with systematics, speciation genomics, methods, natural history, and more in North Am angiosperms. Reach out!

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Patrick McKenzie @patrickmckenzie.bsky.social · 04/06/2026

Short but awesome trip to Mexico with a great team. Also, success: finding Monarda pringlei! It’s one of two red Monarda species (the other being the Appalachian species M didyma) and it is confined just to a tiny area in the mountains above Monterrey

A bright red Monarda flower (Monarda pringlei)

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Patrick McKenzie @patrickmckenzie.bsky.social · 22/05/2026

I’m starting at Oregon State University this September as Herbarium Director and Assistant Professor in the Department of Botany and Plant Pathology. An absolute dream job and I am so grateful! Looking to grow the lab soon and will update here. In the meantime please don’t hesitate to reach out!

Picture of a person (me) holding a stuffed beaver toy and a laptop that reads “McKenzie Lab at Oregon State University”

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Patrick McKenzie @patrickmckenzie.bsky.social · 06/05/2026

outdoors time today. The birds are moving, the bugs are out, the plants are flowering, and the kids are tired

Small yellow bird with a black eye stripe in the center of a photo, the surrounding filled with foliage

Broad leaves plants (trilliums) with flowers among ferns

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Patrick McKenzie @patrickmckenzie.bsky.social · 06/03/2026

map of overall (radial) avg flowering day across all species, made using PhenoVision-labeled iNat data. Trying to figure out if I should be surprised by this or questioning my data analysis... is the late flowering in the west Sierra Madre well known? Fwiw, corresponds to rainy season there.

a heatmap of average flowering time in North America, with earlier days of year colored in blues and later days as red or orange. General pattern of blue to red from south to north, but with a vertical band of red in western Mexico

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Patrick McKenzie @patrickmckenzie.bsky.social · 05/03/2026

this one started from my living room with an 11:02pm email to colleagues of basically “check out this weird observation” and turned into a super rewarding international collaboration

email screenshot with subject line "interesting Cheilyctis observation" and timestamp 11:02pm. Message begins "Hi y'all, Keeping with my tradition of oversharing random iNaturalist observations, thought y'all might find this one interesting:"

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Patrick McKenzie @patrickmckenzie.bsky.social · 04/03/2026

Successful Ithaca visit looks like 1) time in the Bailey Herbarium, and 2) birding the compost piles

Me in the LH Bailey Herbarium at Cornell, with a bunch of Monarda specimens out on the table

My kid looking out the car window at a bunch of gulls on compost piles

One of the gulls we came for, in the center of the picture: glaucous-winged gull

Four people looking out (birding) at a snowy field

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Patrick McKenzie @patrickmckenzie.bsky.social · 09/01/2026

I wrote in the most recent issue of Arnoldia about using @inaturalist.bsky.social and, more generally, about the continuing role of natural history in motivating questions in evo bio + my excitement about community science for unlocking new scales of analysis: arboretum.harvard.edu/arnoldia-sto...

“Natural History, Crowdsourced,” an article in Arnoldia by Patrick McKenzie. The article begins with an image of a ruby-throated hummingbird visiting Lobelia cardinalis.

Quiet hours in the sun, meditating with the bugs, plants, and birds, are my inspiration as an evolutionary biologist.

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Patrick McKenzie @patrickmckenzie.bsky.social · 08/11/2025

micro-break from paternity leave to catch @martinebotany.bsky.social talk for NEBS. Awesome examples of the value of natural history for generating new questions

Chris Martine presenting in front of a PowerPoint and chalk board

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Patrick McKenzie @patrickmckenzie.bsky.social · 09/10/2025

Fitting in a bit of fall birding at the little park across the street from our apartment. Just in the past couple days: orange-crowned warbler, red-tailed hawk subsp abieticola, purple finch, eastern towhee

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/09/2025

We implement the math in ipcoal, and we validate against coalescent simulations. Finally, we demonstrate that there is information from observed waiting distances alone for fitting MSC parameters (Ne, divergence times, recombination rate).

MS-SMC predictions validated against coalescent simulations. (a) Results are shown for three models containing 1, 2, or 8 populations. For each model, 100K tree sequences were simulated for 10 different constant Ne values between 50K and 500K. (b) The distributions of summed edge lengths of
the first genealogy in each tree sequence. (c-d) The mean frequency (black square) with which the first observed recombination event was a tree-change (c) or topology-change (d) in a simulated tree sequence, and the mean (colored circle) and 95% CI (grey fill) of the predicted probability of tree or topology-change calculated from the first embedded genealogy in each tree sequence. Probabilities are constant with respect to Ne in the single population model but vary in models with population structure (also shown with respect to species tree interval lengths in coalescent units, across the top axis). (e-f) The mean waiting distance (black square) until the first observed tree-change (e) or topology-change (f) in a simulated tree sequence, and the mean (colored circle) and 95% CI (grey fill) of predicted waiting distances calculated using the first embedded genealogy in each tree sequence.

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/09/2025

This *explicitly* links observable turnover in local ancestry to MSC model parameters.

Figure 2. An example genealogy embedded in a species tree and the corresponding embedding table used for MS-SMC calculations. (a) A four tip species tree is composed of seven discrete population intervals separated by speciation events (Wx), each of which can be further dissected by coalescent events (tx).
(b) The probability of coalescence is constant within each discrete interval and is scaled by the number
of lineages (k), the effective population size (n), and the interval length (d). Under the MS-SMC, the probability that a detached lineage will re-coalesce on a specific branch of the genealogy (e.g., branch 7) is calculated using the piecewise constant probabilities from each discrete interval spanning that branch (e.g., rows 1, 6, 7, and 8 in the embedding table).

Figure 4. The MS-SMC is a model of the probability of different categorical event outcomes given recombination occurring uniformly on a genealogy embedded in a parameterized MSC model (a). A recombination event can cause one of three possible recombination event types between two sequential genealogies in a genome: no-change, tree-change, or topology-change. The probability of these event types are calculated by integrating over each branch on the genealogy on which recombination can occur; which in turn is calculated by integrating over each position on a genealogy branch at which recombination can occur. (b-d) The probability that a recombination event causes a no-change, tree-change, or topology- change event, for the example genealogy embedded in a species tree, was calculated for three selected genealogy branches (2: red; 5: blue; and 7: purple), at each position along the branch where recombination could occur.

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/09/2025

alignments are mosaics of autocorrelated genealogies... nearby bases share ancestry until recombination alters the local tree. We derived the distributions of waiting distances for tree-change and topology-change events, extending prior single-population results to arbitrary species tree models.

figure illustrating the concept of an ARG, including recombination events that create no-change, vs. tree-change, vs. topology-change

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Patrick McKenzie @patrickmckenzie.bsky.social · 29/07/2025

Awesome Penstemon genetics work from @trinitydepatie.bsky.social !!! meticulous crossing design and such a clean result 🤯

Trinity showing cross-sections from personate vs open flowers

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Patrick McKenzie @patrickmckenzie.bsky.social · 28/07/2025

Come see me at the poster session tonight (P16) for two separate applications of @inaturalist.bsky.social in Monarda… showcasing iNat’s help for understanding organismal biology at both super broad (thousands of observations) and super targeted (single observation) scales 🙂 #Botany2025

Title of my poster: iNaturalist-facilitate natural history in Monarda

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Patrick McKenzie @patrickmckenzie.bsky.social · 28/07/2025

Awesome (allo)polyploid Phlox presentation from @christeinecke.bsky.social … a ton of fieldwork behind it #Botany2025

Christina presenting on Texas polyploid phlox

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Patrick McKenzie @patrickmckenzie.bsky.social · 28/07/2025

Fun getting to see the live version of my favorite paper title of the year: Deeper Bulbs are Larger. Super fun work by @wile-phylote.bsky.social

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Patrick McKenzie @patrickmckenzie.bsky.social · 28/07/2025

Some great talks in the Botanical Research Across Borders symposium this morning, starting with a broad survey of botanists about equity of US / Mexico collaboration #Botany2025

Title slide of Equitable botanical collaboration USA - Mexico: principles and perceptions

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Patrick McKenzie @patrickmckenzie.bsky.social · 27/07/2025

Not much Monarda in Southern California… so Monardella will have to suffice 🙂 (pretty sure this is Monardella australis but not 100%)

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Patrick McKenzie @patrickmckenzie.bsky.social · 24/07/2025

Poster printed, presentation slides prepared……. Palm Springs tomorrow! #Botany2025

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Patrick McKenzie @patrickmckenzie.bsky.social · 23/07/2025

other species seemed to be more consistent with their behavior in this particular Monarda fistulosa stand. e.g. I saw exclusively nectar-robbing behavior from carpenter bees and honeybees (which struggle to access nectar through the mouth of the flowers)

honeybee nectar-robbing from monarda fistulosa

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Patrick McKenzie @patrickmckenzie.bsky.social · 23/07/2025

even with there only being a couple of them, strategy 3 is super obvious because (a) very small bee, and (b) *usually* highly visible pollen baskets

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Patrick McKenzie @patrickmckenzie.bsky.social · 23/07/2025

strategy 3: pollen collector! again have only seen very small bees do this, but I think still B impatiens... Only a couple bees in the whole Monarda stand doing this. (please forgive my cinematography)

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Patrick McKenzie @patrickmckenzie.bsky.social · 23/07/2025

strategy 2: nectar robber! For B impatiens (again I think this is correct ID but bee people please check me). I see this with especially small bees and assumed it was a different species, but now I think not (tons of lit I don't know well about intraspecific Bombus body size variation)

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Patrick McKenzie @patrickmckenzie.bsky.social · 23/07/2025

spent time today watching different foraging strategies among (I *think?*) the same species of bumblebee (B impatiens), all right next to each other. Starting with the classic nectar dive, which seems to be by far the most common... but notice that the anthers and stigma project way out over the bee

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Patrick McKenzie @patrickmckenzie.bsky.social · 17/07/2025

A distinguishing character of Monarda fistulosa and its close relatives is a fun tuft of hairs at the top of the upper corolla lobe. Endearingly it persists all through flower development (and is arguably even more fun in the early stages)

Tip of the the upper calyx lobe of a mature M fistulosa flower, sporting a tuft of hairs

M fistulosa flower that is just beginning to open - the tuft of hairs on the upper corolla lobe is obvious as it separates from the lower lobe

Closed M fistulosa flower that is a lot of the way through development, which still shows the tuft of hairs on top

Closed M fistulosa flower that is still in the early stages of development but still shows the tuft of hairs

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/07/2025

We visited her burial site (it was lovely) on the way home from seeing family and visiting the JMU herbarium last month. She seems to keep coming up. so it’s extra special to see her Monarda blooming now!

Headstone for Lena Artz alongside her family. She contributed to botanical science around the Shenandoah Valley and - close to my heart - described Monarda brevis

Monarda brevis from the JMU herbarium, collected by Lena Artz

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/07/2025

M brevis was first described by Lena Artz, who contributed a ton to botanical science in Virginia. Andrea Weeks recently wrote an amazing profile about her in Castanea and helped develop an exhibit about her life at Fort Valley Museum: www.winchesterstar.com/winchester_s...

“In Memoriam: Lena Artz (1891-1976), a Hidden Figure of 20th-century Southeastern U.S. Botany” by Andrea Weeks in the journal Castanea

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/07/2025

Monarda brevis finally blooming in the greenhouse!!! My first time ever seeing the flowers on a living plant. This species is endemic to limestone outcrops in a tiny part of West Virginia. one of the coolest Monardas imo with these waxy leaves, creeping habit, and dainty flowers

Monarda brevis showing full inflorescence and vegetative growth

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Patrick McKenzie @patrickmckenzie.bsky.social · 16/06/2025

Father’s Day and sample processing (aka getting tissue into the freezer) after restorative week of family + fieldwork

Plants and supplies spread out on the potting room table

My mother-in-law’s fridge - she took good care of my plants!

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Patrick McKenzie @patrickmckenzie.bsky.social · 13/06/2025

Amazing to visit the JMU herbarium yesterday, graciously hosted by @aeberardi.bsky.social (who also joined me for field collecting earlier in the week!) Got a thorough Virginia Monarda experience on this trip!

Me working at the JMU herbarium (photo by Andrea Berardi)

Annotated Monarda specimens at the JMU herbarium (photo by Andrea Berardi)

Monarda brevis specimen collected by Lena Artz

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/06/2025

Fieldwork in the Allegheny highlands. Perfect weather and successful collecting!

Footbridge crossing the cowpasture river

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Patrick McKenzie @patrickmckenzie.bsky.social · 08/06/2025

More insect diversity at my mother-in-law’s hybrid Monarda

Small carpenter bee (Ceratina) on monarda inflorescence

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Patrick McKenzie @patrickmckenzie.bsky.social · 07/06/2025

Both like the nectar but the halictid bees REALLY focus on anther/stigma part of the flower. But people seem to think bumblebees are still effective pollinators by moving pollen around on their wings (there has been some back and forth about this specifically with M fistulosa).

Halictid bee on monarda (M didyma-derived cultivar) anthers.

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Patrick McKenzie @patrickmckenzie.bsky.social · 07/06/2025

Bumblebee clumsiness vs halictid bee precision!

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Patrick McKenzie @patrickmckenzie.bsky.social · 03/06/2025

Long day driving to and from Cold Spring Harbor, dropping off Monardas for ref genome sequencing. It’s happening!!!!!

Monardas in the back of the car. Stayed safe even without the car seat.

Monardas in front of the cold spring harbor entrance.

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Patrick McKenzie @patrickmckenzie.bsky.social · 27/05/2025

New preprint out today! A really fun collaboration with @shchurch.bsky.social and Robin Hopkins in which we study flower color variation in Monarda fistulosa using iNaturalist data. We process >40,000 images and use them to phenotype flower color in >16,000 observations: doi.org/10.1101/2025...

Figure 1: Steps with representative photographs of the flower color phenotyping pipeline. A) We exported all research-grade iNaturalist observations of Monarda fistulosa from GBIF. B) We used GPT-4o to classify each image as to whether it contained a flower. C) We trained a Roboflow semantic segmentation model on a subset of images and applied the trained model to extract “flower” pixels from each image in the dataset. D) We calculated the geometric median of each set of extracted pixels to represent the flower color phenotype from each image, and we paired this phenotype with the observation’s iNaturalist metadata for spatial analysis.

Figure 2: Spatial summary of Monarda fistulosa flower colors across North America. A) Map of the color of M. fistulosa flowers. Each square is a 200km x 200km cell with the color corresponding to the average median CIELAB color value of each observation in the cell. The dotted line denotes -100° longitude, separating eastern and western regions of the range. B) Boxplots summarizing LCh color components west and east of -100° longitude, with each box showing the median and interquartile range, and with the color of each box reflecting the geometric median CIELAB value from west and east, respectively.

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Patrick McKenzie @patrickmckenzie.bsky.social · 14/04/2025

Hot off the presses and so so thrilled. Thanks to @inaturalist.bsky.social + computer vision we found something beautifully simple: Red and orange flowers bloom later than all the other colors in the eastern United States. Paper here: authors.elsevier.com/a/1kwzh3QW8S...

Visual abstract: “we test hypotheses about floral diversity with community science data and an advanced computer vision model. Red/orange flowers have delayed flowering that matches hummingbird migratory patterns”

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Patrick McKenzie @patrickmckenzie.bsky.social · 14/04/2025

Plant appreciation day? I appreciate them! especially Monarda and Phlox rn 🫣

Two people - me and my spouse - collecting Monarda along the Bluestone River in West Virginia

Close-up of Monarda russeliana flowers, which are bright white with purple-spotted, curled lower lips

Close-up of Monarda stanfieldii, which has yellow flowers with maroon spots on the upper and lower lips

Me collecting Phlox along the roadside in central Texas

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Patrick McKenzie @patrickmckenzie.bsky.social · 11/04/2025

if you know Lamiaceae at all, you probably know that they sort of famously all have opposite leaves. But a single stem of this Monarda in the greenhouse has whorls of three!

Top-down look at Monarda stem with whorls of three leaves

Monarda stem with whorls of three leaves

Monarda stem with whorls of three leaves - you can see more typical opposite-leaved stems surrounding it

Monarda stem with whorls of three leaves, with typical opposite-leaved stems around it

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Patrick McKenzie @patrickmckenzie.bsky.social · 07/04/2025

two nice birds in under 24 hours in the little patch across the street from my apartment: wilson’s snipe and pileated woodpecker!

A Wilson’s snipe. Classic bigfoot-like snipe photo in that it is taken through brush so that the bird is hardly recognizable

A pileated woodpecker clinging to a tree

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Patrick McKenzie @patrickmckenzie.bsky.social · 27/03/2025

picture day! The setup -> the results. (Monarda citriodora from near Monterrey, NL, Mexico)

Cell-phone picture of a simple macro setup with ring light and black screen, with a plant in front of the screen

“Glamor shot” of Monarda citriodora inflorescence taken using the setup in the first picture

“Glamor shot” of a Monarda citriodora flower taken using the setup in the first picture

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Patrick McKenzie @patrickmckenzie.bsky.social · 06/03/2025

Pretty sweet conference birding in Ventura! a selection of lifers shown here 👀

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Patrick McKenzie @patrickmckenzie.bsky.social · 05/03/2025

Beyond birds - another perk of southern California conference… I get to see my sibling!!! Seen here crashing their first speciation conference

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Patrick McKenzie @patrickmckenzie.bsky.social · 05/03/2025

Standing in parking lot, looked up, got my lifer townsend’s warbler 🤠

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Patrick McKenzie @patrickmckenzie.bsky.social · 02/03/2025

1000% exhausted after a full day of travel + the kickoff of the Gordon Speciation seminar & conference in Ventura, CA. But good stuff - airplane views, Popeyes, and LOTS of iNaturalist data annotation on the airplane 🫡

Snowy Rocky Mountain view from an airplane window

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