iiinova — where your digital self keeps evolving

Justin Conover @conjustover.bsky.social · 25/06/2026

By far, the best acknowledgements slide I saw at Evolution this year came from @swsschaeffer.bsky.social, professor emeritus at Penn State University. “Thank you to Penn State for still giving me an office space. And I thank Social Security for my salary support.”

Stephen Schaeffer, professor emeritus at Penn State, stands at a podium to the right during a talk at the Evolution Conference. On the left, a slide is shown with a list of acknowledgements, including “Funding: Social Security Administration.”

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Reposted by Justin Conover

Kyle T David @kylethedavid.bsky.social · 21/06/2026

@conjustover.bsky.social explaining why all polyploid researchers are masochists at #Evol2026

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Justin Conover @conjustover.bsky.social · 21/06/2026

I just enjoy challenges that most others are fearful of 😊 But also, did this have to be a photo of me yelling into the void?? 🤣🤣🤣

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Joel Sharbrough @jsharbro.bsky.social · 03/11/2025

I am looking for a PhD student to start in my lab at UCSB in Fall 2026, studying evolutionary biology. See attached flyer for more information. Please also share with potentially interested students. Thanks!

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Justin Conover @conjustover.bsky.social · 02/09/2025

And as always, I'm happy to answer any questions or receive any feedback on this work!

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Justin Conover @conjustover.bsky.social · 02/09/2025

I hope Sam (who is a math/economics major, and had never taken a genetics class before this project) learned as much about polyploids as I learned from him about math. Thanks also to @ryangutenkunst.bsky.social and @barkerms.bsky.social for overseeing this project as well

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Justin Conover @conjustover.bsky.social · 02/09/2025

Overall, I'm super excited about this paper, as it is one of the first pieces of theory based on tetraploids with disomic inheritance, without treating the subgenomes independently. I think there is still lots to learn on this front, and hope that other will help push this field forward

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Justin Conover @conjustover.bsky.social · 02/09/2025

Here, we can directly measure additive genetic variance and the change in allele freq and pop fitness. When the population is in the bistability regime, Fisher's Fundamental Theory of Natural Selection does not hold, and there are subtle differences between disomic and polysomic inheritance patterns

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Justin Conover @conjustover.bsky.social · 02/09/2025

Finally, we wanted to see if there was a difference to how polyploid populations might approach these equilibrium points based on segregation patterns. For this, we developed a forward-in-time 1 locus simulation for disomic and polysomic inheritance.

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Justin Conover @conjustover.bsky.social · 02/09/2025

The ability for a population to remove this is totally dependent on whether the initial allele frequency is higher or lower than the unstable equil point. Also, because this model assumes infinite population sizes, there is no influence of drift in this model.

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Justin Conover @conjustover.bsky.social · 02/09/2025

This is a classic example of a saddle node bifurcation in nonlinear dynamics. Meaning, a population may be completely unable to purge a deleterious mutation, despite it being dominant and at high/intermediate frequency, depending on the initial allele frequency. Exactly the opposite of masking.

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Justin Conover @conjustover.bsky.social · 02/09/2025

When the deleterious mutation rate is higher than the back-mutation rate (in this case, 40x greater), then we see a totally different dynamic for dominant muts - for some selection coefficients, there is no single equilibrium point - there are three points! Two are stable points, one is unstable

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Justin Conover @conjustover.bsky.social · 02/09/2025

This 'bump' appears to coincide with the point at which the distribution of genotype frequencies is the farthest from Hardy-Weinberg Equilibrium - suggesting another avenue in which the allele frequency is insufficient to describe population dynamics in polyploid populations

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Justin Conover @conjustover.bsky.social · 02/09/2025

First, we found that our results are quite sensitive to mutation rates. If the deleterious mutation rate = back mutation rate, then this is the plot of the equilibrium allele frequency and load of the populations. Nothing surprising here, except there is a 'bump' in the load for the dominant case

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Justin Conover @conjustover.bsky.social · 02/09/2025

These PDEs are not easy to analytically understand, and are surprisingly much much more complex than the diploid ODEs (it's not just a factor of two difference!). This is just one of the entries of the Jacobian for a tetraploid with polysomic inheritance - don't stare at this for too long, I beg you

A mathematical equation that represents the first order partial differential equation for the change in gamete frequencies for a tetraploid with polysomic inheritance. The expression is long, and is in a tiny text, to highight that it is impossible to intuit anything from this expression alone.

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Justin Conover @conjustover.bsky.social · 02/09/2025

In order to probe this question, Sam had to approach it using a nonlinear dynamics framework. Although mut-sel equilibrium is easy in diploids (and can be analyzed using a simple ODE), for polyploids, Sam had to develop a framework to numerically estimate equilbria points with a series of PDEs

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Justin Conover @conjustover.bsky.social · 02/09/2025

And, the only theory work that has been done for any tetraploid is for very idealistic and convenient dominance relationships (completely recessive, perfectly additive) that make the math simpler. We wanted to look at arbitrary dominance relationships, to see if any interesting patterns arose

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Justin Conover @conjustover.bsky.social · 02/09/2025

Although mut-sel equilibria has been estimated for tetraploids with polysomic inheritance, very little theory has been developed for tetraploids with disomic inheritance. We wanted to see if segregation differences changed these mut-sel equilibrium points, or how populations approach these points

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Justin Conover @conjustover.bsky.social · 02/09/2025

New Preprint! This one led by Sam Gibbon, an outstanding undergrad I've worked with for the past year. We take a look at whether segregation patterns in tetraploids (disomic v polysomic) affects mut-sel dynamics. We found some surprising results, and some subtleties: www.biorxiv.org/content/10.1...

biorxiv.org

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics

Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of ...

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Justin Conover @conjustover.bsky.social · 21/08/2025

That's true, with a strong enough drawl, there's no confusing the two. There is a flow cytometer here that is part of the center's shared equipment, it's currently not being used. So it'll migrate down the hallway into my space as soon as I get it ready

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Justin Conover @conjustover.bsky.social · 21/08/2025

Annie Mae might evolve into Anime by accident? Or on purpose, your choice

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Justin Conover @conjustover.bsky.social · 21/08/2025

Oh I'm stealing this for the flow cytometer my lab is inheriting!

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Justin Conover @conjustover.bsky.social · 13/08/2025

Overall, I'm excited to see future broader sampling of high-quality genomes refine the story we've shown here, arguably one of the most complicated polyploid histories in plants. And, there's a ton to be learned about how this ancient polyploid history influences modern biological processes, too!

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Justin Conover @conjustover.bsky.social · 13/08/2025

We found a bunch of traits are associated with this ancient polyploid history, and especially with the rate at which chromosome number (and gene content) is reduced, suggesting that the 'recovery' that lineages much endure from this massive ploidy increase also leads to, e.g., higher speciation rate

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Justin Conover @conjustover.bsky.social · 13/08/2025

And yet, one of the genomes assembled for this paper (Reevisia pubescens) has a totally different polyploid history, even though it is nestled in the middle of this polyploid rich family (it was in the same subfamily as Durio! This is also the reason we suggest a new subfamily designation for Durio)

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Justin Conover @conjustover.bsky.social · 13/08/2025

In this new paper, which has a genome from every subfamily, we discovered that the polyploid history looks to be one giant mess - All three subgenomes of the hexaploid Durio are found in the decaploid cotton, and 2 of the 3 subgenomes in Durio can be found in subfamilies that only have a duplication

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Justin Conover @conjustover.bsky.social · 13/08/2025

When the Durio zibethinus genome came out in 2017, it showed evidence of a whole genome triplication. So not the exact same history as cotton, but we couldn't rule out if that hexaploidy was a stepping stone on the same path that cotton took on its way to become decaploid (10N) or dodecaploid (12N)

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Justin Conover @conjustover.bsky.social · 13/08/2025

When the first diploid cotton genome was published in 2013, there was evidence of an ancient 5- or 6-fold multiplication that wasn't shared by the chocolate genome (one of the early-diverging lineages to the rest of the family). But it wasn't known whether this was a singular or multiple events.

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Justin Conover @conjustover.bsky.social · 13/08/2025

New Paper! In 2019, my first dissertation chapter revealed complicated polyploidies in the cotton family (Malvaceae) but we lacked the tools and genomes to truly understand it. Now with better genomes and improved methods, it's much more complicated than we thought. www.nature.com/articles/s41...

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Ryan Gutenkunst @ryangutenkunst.bsky.social · 05/08/2025

If you're new to demographic history inference from population genomics, try this webapp I created to illustrate how dadi fits bottleneck models to site frequency spectra: ryangutenkunst-dadi-two-epoch.hf.space . It even outputs files for submitting to the GHIST competition! ghi.st

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Justin Conover @conjustover.bsky.social · 01/07/2025

The Conover Lab is open! I am so excited to join a group of talented, caring, and creative folks at the @danforthcenter.bsky.social, all in service of improving the human condition through plant science.

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Justin Conover @conjustover.bsky.social · 12/06/2025

All you need is read counts for positions you want to call SNPs for. We used GATK for this, but any program that can give allele counts for read mapping works. Feel free to reach out and I'm happy to help debug!

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Justin Conover @conjustover.bsky.social · 12/06/2025

We're writing up the paper now, but all of the code is publicly available on the rm branch of the github repo, and works for any even-ploidy population. github.com/dcgerard/upd...

github.com

GitHub - dcgerard/updog at rm

Flexible Genotyping of Polyploids using Next Generation Sequencing Data - GitHub - dcgerard/updog at rm

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Justin Conover @conjustover.bsky.social · 12/06/2025

I haven't used freebayes, so not totally sure what the memory issue might be. But I would also recommend updog - and I've been working with David on a new prior that can genotype autos and allos (without knowing which fits your system a priori) much better than the other priors that are available

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Justin Conover @conjustover.bsky.social · 01/05/2025

Thanks for everything, Tucson! I arrived in St. Louis today, and am incredibly excited to see what this city has in store for me. Only one month until the Conover Lab officially opens at the Donald Danforth Plant Science Center!

Shadowy silhouettes of several tall saguaro cacti, backlit by a beautiful Arizona sunset. The sky is painted with oranges and yellows, juxtaposed against the Sonoran desert flora.

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Nature Plants @natplants.nature.com · 23/04/2025

New Article: "Comparative transcriptomics in ferns reveals key innovations and divergent evolution of the secondary cell walls" rdcu.be/eiWNF Fern transcriptomes reveal repeated whole-genome duplications, unique gene families and distinct lignocellulosic evolution... #PlantScience

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Bethany Brookshire @beebrookshire.bsky.social · 01/04/2025

The tragic irony of nearly 2000 scientists, members of the National Academies, coming together to write a letter condemning the attacks on science: docs.google.com/document/d/1... www.nytimes.com/2025/03/31/s... And then today: Mass cuts to federal health www.nytimes.com/live/2025/04...

docs.google.com

Public Statement on Supporting Science for the Benefit of All Citizens

TO THE AMERICAN PEOPLE We all rely on science. Science gave us the smartphones in our pockets, the navigation systems in our cars, and life-saving medical care. We count on engineers when we drive acr...

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Ryan Gutenkunst @ryangutenkunst.bsky.social · 28/03/2025

Brilliant idea from a colleague. We need the NCAA to advocate on behalf of higher ed in America, b/c they can reach people suspicious of "elites" in higher ed. Imagine March Madness ending with a message about how admin is threaten unis and thus college sports... Any ideas how to make this happen?

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Ryan Gutenkunst @ryangutenkunst.bsky.social · 24/01/2025

Our paper on fitting population genetic models to low-pass sequencing data is now out in Molecular Biology and Evolution! doi.org/10.1093/molb...

Comparison of allele frequency spectra for 3x coverage, with and without our bias model.

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Justin Conover @conjustover.bsky.social · 21/01/2025

If you get the change to try it, any and all feedback would be appreciated!

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Justin Conover @conjustover.bsky.social · 21/01/2025

Yes pSONIC is based on pairwise syntenic relationships, so it'll perform best on short phylogenetic depths. One other option would be edgeHOG (github.com/DessimozLab/...), which attempts to reconstruct ancestral syntenic blocks along the way, although I don't have much experience working with it yet

github.com

GitHub - DessimozLab/edgehog: Infering ancestral synteny with hierarchical orthologous groups

Infering ancestral synteny with hierarchical orthologous groups - DessimozLab/edgehog

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Reposted by Justin Conover

David Castellano @castellanoed.bsky.social · 09/01/2025

Short thread on my updated work with @gutengroup.mcb.arizona.edu "Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects", latest version at: www.biorxiv.org/content/10.1... Here we simulate a kind of canonical and idealised domestication process.

biorxiv.org

Detection of Domestication Signals through the Analysis of the Full Distribution of Fitness Effects

Domestication is a process marked by complex interactions between demographic changes and selective pressures, which together shape genetic diversity. While the phenotypic outcomes of domestication ar...

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Justin Conover @conjustover.bsky.social · 07/01/2025

First statistical test of the year was p=0.053. It's going to be a good year.

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Dan Sloan @sloanevolab.bsky.social · 18/12/2024

Second paper from the lab out today (woohoo!). This one led by Rachael DeTar. Check out what happens to mito+plastid translation machinery in plants that have lost photosynthesis! Published in @pnas.org: www.pnas.org/doi/10.1073/... Also available on bioRxiv: www.biorxiv.org/content/10.1...

Fluorescence microscopy of plant leaf cells showing mitochondrial and chloroplast targeting of proteins.

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Shelly Gaynor @shellygaynor.bsky.social · 18/12/2024

If you happen to be interested in the coexistence of diploids and tetraploids given modern coexistence theory and stochastic population dynamics - Check out our #JustAccepted paper at @asn-amnat.bsky.social doi.org/10.1086/734411

doi.org

Dynamics of mixed-ploidy populations under demographic and environmental stochasticities | The American Naturalist: Vol 0, No ja

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