Justin Conover

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!

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

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)

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

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)

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.

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...

Oh this is really fun!

Logo for the Genomic History Inference Strategies Tournament.

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

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.

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!

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

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...

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

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.

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!

Congrats Dior!!

Congrats Kevin!

Many ferns images from the paper.

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

Century-old genetics mystery of Mendel’s peas finally solved Researchers pinpoint the genes responsible for the final three pea traits studied by the famed citizen scientist.

Researchers pinpoint the genes responsible for the final three pea traits studied by Gregor Mendel more than 160 years ago

https://go.nature.com/3EC3eqT

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...

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...

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?

Internationally recognized plant scientist named next President of the Danforth Plant Science Center - Danforth Plant Science Center After an extensive international search, the Donald Danforth Plant Science Center has named Giles Oldroyd, PhD, as its next President.

After an extensive search, the Danforth Center has named Giles Oldroyd, PhD, its next President.

@gilesoldroyd.bsky.social is a renowned plant geneticist & one of only a few hundred scientists elected to both the UK @royalsociety.org & the US @nasonline.org.
www.danforthcenter.org/news/interna...

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

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...

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

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

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

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...

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.

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

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

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...

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

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

Order of amino acid recruitment into the genetic code resolved by last universal common ancestor’s protein domains | PNAS The current “consensus” order in which amino acids were added to the genetic code is based on potentially biased criteria, such as the absence of s...

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

Final version of this out now in that beautiful Amnat typesetting! www.journals.uchicago.edu/doi/10.1086/...