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Patrick McKenzie @patrickmckenzie.bsky.social · 2h

Family of four 🏡

Reposted by Patrick McKenzie

Brian O'Meara @omearabrian.bsky.social · 6d

Webpage on the hidden curriculum of applying to ecology and evolution grad programs in the US (a lot of the info applies to other fields too, but perhaps less well): applyingtoeeb.info

#AcademicSky 🧪

Applying to US Graduate School in Ecology, Evolution, and Related Fields

applyingtoeeb.info

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Reposted by Patrick McKenzie

Dr. Hilary Rose Dawson @hilaryrosed.bsky.social · 20d

I just passed my 50,000th identification on @inaturalist.bsky.social! Identifying is a huge but often ignored part of the #iNaturalist community and dataset so I wanted to share why and how I identify. 1/14

🧪 #ecology #taxonomy #botany #CommunityScience

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Patrick McKenzie @patrickmckenzie.bsky.social · 20d

super helpful guide!!!! and congrats on the milestone!

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Patrick McKenzie @patrickmckenzie.bsky.social · 27d

super grateful to colleagues and reviewers who greatly improved early versions of this manuscript. We're really proud of it.

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Patrick McKenzie @patrickmckenzie.bsky.social · 27d

there's value in leveraging linked genomic signals (vs. just unlinked gene trees) to learn about species history and demography. In the future we're hoping to see this plugged into species-tree inference and/or ARG inference pipelines.

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Patrick McKenzie @patrickmckenzie.bsky.social · 27d

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 · 27d

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 · 27d

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 · 27d

super excited to share this big project with @daeaton.bsky.social out now in Systematic Biology! We derived distributions for -- given an arbitrary species tree model -- how far you have to move along a genome before observing a change in the underlying genealogy: doi.org/10.1093/sysb...

Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent

Abstract. Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genea

doi.org

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Reposted by Patrick McKenzie

Christopher Krieg 🌿 @ckrieg.bsky.social · 27d

🌱 Calling all mentors!
The BSA Early Career Committee is bringing back the NSF GRFP Workshop. Sign up to be a mentor if you are a:

✅ Grad student who already received a GRFP or
✅ PI, postdoc, senior researcher

Sign up here 👉 forms.gle/sQUwhVryYHJK...

#NSFGRFP #botany

Mentor Registration Form — GRFP Workshop

Are you interested in helping students write a stronger NSF GRFP application? We hope you will join us as a mentor in this BSA-organized GRFP workshop, where you will work with 4-6 applicants to help ...

forms.gle

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Reposted by Patrick McKenzie

Casey Dunn @caseywdunn.bsky.social · 27d

Interested in joining our lab (dunnlab.org) as a postdoc to work on siphonophores, processes that structure diversity in the open ocean, or natural history? If so, please reach out to discuss a nomination for the Donnelley Postdoctoral Fellowship - yibs.yale.edu/donnelley-fe...

The Dunn Lab

Casey Dunn's laboratory in the Department of Ecology and Evolutionary Biology at Yale University.

dunnlab.org

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Reposted by Patrick McKenzie

Nate Upham @n8upham.bsky.social · Sep 8

When & where have species of bats, rodents, & shrews been collected across the 54 mountains of the Madrean Sky Islands?

Damien Rivera in our lab led this effort to find out!

New preprint "Uncovering historical small mammal biodiversity among the Madrean Sky Islands" www.biorxiv.org/content/10.1...

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Patrick McKenzie @patrickmckenzie.bsky.social · Aug 29

Really sorry to hear this. good thoughts your way.

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Reposted by Patrick McKenzie

Samuel Church @shchurch.bsky.social · Aug 28

The Church Evolution Laboratory (CEL@NYU) will be official as of Sep 1st: shchurch.github.io. We are recruiting at all levels, including a postdoc to work on evolutionary patterns and processes via comparative genomics in Hawaiian Drosophila. Please share widely!

Church Evolution Laboratory

Department of Biology, New York City

shchurch.github.io

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Reposted by Patrick McKenzie

Casey Dunn @caseywdunn.bsky.social · Aug 28

I hope to take a PhD student in 2026 to study siphonophores. Please reach out if you are interested in applying this fall. For examples of recent lab projects see www.sciencedirect.com/science/arti... and academic.oup.com/gbe/article/...

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Reposted by Patrick McKenzie

Seema Sheth @seemasheth.bsky.social · Aug 22

Responses to climate change – insights and limitations from herbaceous plant model species

Herbaceous plant species have been the focus of extensive, long-term research into climate change responses, but there has been little effort to synthesize results and predicted outlooks. This primer....

nph.onlinelibrary.wiley.com

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Reposted by Patrick McKenzie

Mark Hibbins, Great Lakes Swashbuckler @rejectresubmit.bsky.social · Aug 21

I'm hiring a postdoc to work in theoretical / computational phylogenomics! More info at tinyurl.com/63hb5ew8. Please share!

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Patrick McKenzie @patrickmckenzie.bsky.social · Aug 21

felt really lucky to be sitting in the room during Andrew's incoming president's lecture at Botany - really glad to see it preserved here!

Andrew Hipp @andrewlhipp.bsky.social · Aug 21

As incoming president of @amsocplanttaxon.bsky.social (ASPT), I am excited to see how societies can work together with practictioners & academics to support & grow the natural history community.

Incoming president's lecture linked here; comments & discussion welcome!

ecoevorxiv.org/repository/v...

Fostering a natural history community

ecoevorxiv.org

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Reposted by Patrick McKenzie

River B Abedon @rbabedon.bsky.social · Aug 19

Check out our preprint 🧪 on the origin & dispersal dynamics of a sailing ⛵ #siphonophore! We use #iNaturalist and particle tracking simulations to show that juvenile man o' war surface in the Gulf of Mexico & Straits of FL and disperse rapidly along the Gulf Stream 🌊

www.biorxiv.org/content/10.1...

From surfacing to stranding: The origins and dispersal dynamics of a neustonic siphonophore

The siphonophore Physalia physalis regularly strands along the US East Coast, yet the dynamics driving its seasonal and geographic distribution in this region remain poorly understood. Building on a n...

www.biorxiv.org

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Reposted by Patrick McKenzie

Aidan Short @aidanwshort.bsky.social · Aug 3

Just want to shoutout a new study from the Wessinger Lab by my colleague @trinitydepatie.bsky.social. bsapubs.onlinelibrary.wiley.com/doi/10.1002/.... She investigated the repeated evolution of personate flowers within Penstemon by examining patterns of introgression, topological discordance, and

bsapubs.onlinelibrary.wiley.com

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Reposted by Patrick McKenzie

Carrie Wessinger @carriewessi.bsky.social · Aug 4

This is an awesome summary of @trinitydepatie.bsky.social 's new paper!!! Thanks @aidanwshort.bsky.social ! Check it out folks!!!!

Aidan Short @aidanwshort.bsky.social · Aug 3

Just want to shoutout a new study from the Wessinger Lab by my colleague @trinitydepatie.bsky.social. bsapubs.onlinelibrary.wiley.com/doi/10.1002/.... She investigated the repeated evolution of personate flowers within Penstemon by examining patterns of introgression, topological discordance, and

bsapubs.onlinelibrary.wiley.com

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Reposted by Patrick McKenzie

Laura Lagomarsino, PhD @tropicalbotany.bsky.social · Jul 30

What a night for #Rubiaceae! I’m so proud of my student @laymonstera.bsky.social for taking home the American Society of Plant Taxonomist’s Cooley Award for best talk, and my colleague and dear friend Charlotte Taylor for receiving the lifetime achievement Asa Gray Award. #Botany2025 #LagoLab

Laymon receives the award from Dave Tank.

Charlotte gives the her statement after the award is announced.

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