Justin Conover
@conjustover.bsky.social
Assistant Member and Principal Investigator
Donald Danforth Plant Science Center, St. Louis MO
Interested in plants, popgen, polyploidy, and puns.
Donald Danforth Plant Science Center, St. Louis MO
Interested in plants, popgen, polyploidy, and puns.
And as always, I'm happy to answer any questions or receive any feedback on this work!
September 2, 2025 at 6:32 PM
And as always, I'm happy to answer any questions or receive any feedback on this work!
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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.
September 2, 2025 at 6:32 PM
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.
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.
September 2, 2025 at 6:32 PM
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.
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.
September 2, 2025 at 6:32 PM
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.
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
September 2, 2025 at 6:32 PM
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
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
August 21, 2025 at 1:10 PM
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
Annie Mae might evolve into Anime by accident? Or on purpose, your choice
August 20, 2025 at 11:13 PM
Annie Mae might evolve into Anime by accident? Or on purpose, your choice
Oh I'm stealing this for the flow cytometer my lab is inheriting!
August 20, 2025 at 11:12 PM
Oh I'm stealing this for the flow cytometer my lab is inheriting!
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!
August 13, 2025 at 8:31 PM
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
August 13, 2025 at 8:31 PM
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)
August 13, 2025 at 8:31 PM
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
August 13, 2025 at 8:31 PM
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)
August 13, 2025 at 8:31 PM
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.
August 13, 2025 at 8:31 PM
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.