Jess Smiley-Rhodes
@j-smiley-rhodes.bsky.social
PhD candidate in Dmitri Petrov's lab @ Stanford
This was an enormous amount of work from everyone involved, and I’m so grateful to all my collaborators! I truly grew as a scientist throughout this project and learned so much. If you have any thoughts about this work, please reach out! I’d love to talk about it more or answer any questions!
November 18, 2025 at 12:15 AM
This was an enormous amount of work from everyone involved, and I’m so grateful to all my collaborators! I truly grew as a scientist throughout this project and learned so much. If you have any thoughts about this work, please reach out! I’d love to talk about it more or answer any questions!
I can’t emphasize enough how impossible this study would have been without Dr. Paul Schmidt's mesocosm system – without the ability to take longitudinal samples, to control for demography/linkage, and to create many replicate populations, we wouldn’t have had the power to tease apart these factors.
November 18, 2025 at 12:15 AM
I can’t emphasize enough how impossible this study would have been without Dr. Paul Schmidt's mesocosm system – without the ability to take longitudinal samples, to control for demography/linkage, and to create many replicate populations, we wouldn’t have had the power to tease apart these factors.
However, if we did have that decreased power, we would still have a stable map, but our ability to make phenotypic predictions would be severely hampered by pleiotropy. The key to predicting evolution from genetic data alone is a complete, well-powered genotype-phenotype map.
November 18, 2025 at 12:15 AM
However, if we did have that decreased power, we would still have a stable map, but our ability to make phenotypic predictions would be severely hampered by pleiotropy. The key to predicting evolution from genetic data alone is a complete, well-powered genotype-phenotype map.
This stability supports recent work that suggests that fine-mapped & high-powered genotype-phenotype maps are portable between populations. This is great news, because without this stability, we’d have to uncover all non-additive epistatic interactions to predict phenotype! doi.org/10.1038/s415...
Fine-scale population structure and widespread conservation of genetic effect sizes between human groups across traits - Nature Genetics
This study introduces the concept of Ancestry Components and shows that they can offer improved population stratification correction for geographically correlated traits. By using ancestry-aware polyg...
doi.org
November 18, 2025 at 12:15 AM
This stability supports recent work that suggests that fine-mapped & high-powered genotype-phenotype maps are portable between populations. This is great news, because without this stability, we’d have to uncover all non-additive epistatic interactions to predict phenotype! doi.org/10.1038/s415...
I also didn’t expect the mapping to be so stable across time and environment! Based on portability studies from the past decade, I thought that we would see widespread epistasis, but even if we had less power, we would still be identifying the same handful of major loci across conditions.
November 18, 2025 at 12:15 AM
I also didn’t expect the mapping to be so stable across time and environment! Based on portability studies from the past decade, I thought that we would see widespread epistasis, but even if we had less power, we would still be identifying the same handful of major loci across conditions.
I didn’t expect the importance of our minor loci for trait prediction! I assumed that tan, ebony, and bab would explain most of the evolution. This really shows the importance of power – with just major loci, we can predict indoor trait change, but in the complex outdoors, we need all loci!
November 18, 2025 at 12:15 AM
I didn’t expect the importance of our minor loci for trait prediction! I assumed that tan, ebony, and bab would explain most of the evolution. This really shows the importance of power – with just major loci, we can predict indoor trait change, but in the complex outdoors, we need all loci!
However, when we use all loci identified via mapping (and not just our “big three”), we correctly predict that both the indoor and outdoor cages become lighter! The trait change is explainable – with all loci, we can understand & explain how we observed this shift in pigmentation.
November 18, 2025 at 12:15 AM
However, when we use all loci identified via mapping (and not just our “big three”), we correctly predict that both the indoor and outdoor cages become lighter! The trait change is explainable – with all loci, we can understand & explain how we observed this shift in pigmentation.
The comparatively simpler selective landscape of the indoor environment leads to less pleiotropic constraint, and thus overall more predictable behavior of our trait-associated loci.
November 18, 2025 at 12:15 AM
The comparatively simpler selective landscape of the indoor environment leads to less pleiotropic constraint, and thus overall more predictable behavior of our trait-associated loci.
This is exactly what we would expect in a system constrained by pleiotropy! The disparate behavior of loci between environments suggests that the other traits under selection influence the seasonal change of these major pigmentation-associated loci and create misleading patterns in outdoor cages.
November 18, 2025 at 12:15 AM
This is exactly what we would expect in a system constrained by pleiotropy! The disparate behavior of loci between environments suggests that the other traits under selection influence the seasonal change of these major pigmentation-associated loci and create misleading patterns in outdoor cages.
Using only tan, ebony, and bab to predict trait evolution, we correctly predict that indoor cages become lighter, but we incorrectly predict that the outdoor cages get darker (positive = light, negative = dark).
November 18, 2025 at 12:15 AM
Using only tan, ebony, and bab to predict trait evolution, we correctly predict that indoor cages become lighter, but we incorrectly predict that the outdoor cages get darker (positive = light, negative = dark).
bab’s strong “counter-gradient” behavior in the outdoor cages was unexpected, but makes sense since bab is a TF and impacts multiple traits, including reproductive development. bab’s pleiotropic constraints are likely much greater than for the enzymes tan and ebony.
November 18, 2025 at 12:15 AM
bab’s strong “counter-gradient” behavior in the outdoor cages was unexpected, but makes sense since bab is a TF and impacts multiple traits, including reproductive development. bab’s pleiotropic constraints are likely much greater than for the enzymes tan and ebony.
But the biggest surprise was at our largest effect locus, around bab, where dark alleles strongly increase in frequency as the population lightens. This counter-gradient behavior was strong in the outdoor cages, but much more moderate in indoor cages, where there are likely fewer constraints.
November 18, 2025 at 12:15 AM
But the biggest surprise was at our largest effect locus, around bab, where dark alleles strongly increase in frequency as the population lightens. This counter-gradient behavior was strong in the outdoor cages, but much more moderate in indoor cages, where there are likely fewer constraints.
For example, if we look at our “big three” genes, tan, ebony, and bab, light-associated SNPs near ebony increase in frequency as expected, but to a much greater degree in the indoor cages. Our tan locus is seasonally neutral outdoors, but light alleles surprisingly slightly decrease in indoor cages.
November 18, 2025 at 12:15 AM
For example, if we look at our “big three” genes, tan, ebony, and bab, light-associated SNPs near ebony increase in frequency as expected, but to a much greater degree in the indoor cages. Our tan locus is seasonally neutral outdoors, but light alleles surprisingly slightly decrease in indoor cages.
Given our well-resolved map, we next aimed to evaluate whether we could use this map to correctly infer the evolution of pigmentation in our mesocosms through time. First looking at our large-effect loci, we found a strong divergence in seasonal behavior between outdoor and indoor environments.
November 18, 2025 at 12:15 AM
Given our well-resolved map, we next aimed to evaluate whether we could use this map to correctly infer the evolution of pigmentation in our mesocosms through time. First looking at our large-effect loci, we found a strong divergence in seasonal behavior between outdoor and indoor environments.
Our mapping is in fact stable enough that we can very accurately predict the relative phenotypes across our genetically diverged populations evolved in a different environment or sampled at different times. (Here we’re using week 8, outdoor mapping – positive = light, negative = dark).
November 18, 2025 at 12:15 AM
Our mapping is in fact stable enough that we can very accurately predict the relative phenotypes across our genetically diverged populations evolved in a different environment or sampled at different times. (Here we’re using week 8, outdoor mapping – positive = light, negative = dark).
The resulting genotype-phenotype map re-identifies large-effect loci near tan, ebony, and bab, and also identifies novel loci, with a range of effect sizes. The mapping was remarkably stable across both time and environment, as can be seen in this Miami plot. (outdoor = top, indoor = bottom)
November 18, 2025 at 12:15 AM
The resulting genotype-phenotype map re-identifies large-effect loci near tan, ebony, and bab, and also identifies novel loci, with a range of effect sizes. The mapping was remarkably stable across both time and environment, as can be seen in this Miami plot. (outdoor = top, indoor = bottom)
To map the pigmentation-associated SNPs, we fit a generalized linear model to allele frequency variation across trait value groups. Our model specifically accounted for the impact of ancestry to identify SNPs with effects on pigmentation that go above and beyond haplotype association.
November 18, 2025 at 12:15 AM
To map the pigmentation-associated SNPs, we fit a generalized linear model to allele frequency variation across trait value groups. Our model specifically accounted for the impact of ancestry to identify SNPs with effects on pigmentation that go above and beyond haplotype association.
To map pigmentation in both environments, before and after the trait evolved, we used a tail-based approach. Specifically, after 2 generations of common garden, we segregated individuals from each sample into dark, midpoint, and light fractions for pooled sequencing.
November 18, 2025 at 12:15 AM
To map pigmentation in both environments, before and after the trait evolved, we used a tail-based approach. Specifically, after 2 generations of common garden, we segregated individuals from each sample into dark, midpoint, and light fractions for pooled sequencing.
In both environments, we see lighter pigmentation evolution, although to a greater degree in the outdoor cages. Given that we observe this across environments, this evolution is likely driven by shifts in population density, with some contribution from abiotic factors in the outdoor environment.
November 18, 2025 at 12:15 AM
In both environments, we see lighter pigmentation evolution, although to a greater degree in the outdoor cages. Given that we observe this across environments, this evolution is likely driven by shifts in population density, with some contribution from abiotic factors in the outdoor environment.
The mesocosm system, while controlling for demography & linkage, also provides the ecological realism needed to solve this mystery. We seeded 10 indoor & 10 outdoor cages with replicate populations derived from a single outbred population (started from inbred lines collected in local orchards).
November 18, 2025 at 12:15 AM
The mesocosm system, while controlling for demography & linkage, also provides the ecological realism needed to solve this mystery. We seeded 10 indoor & 10 outdoor cages with replicate populations derived from a single outbred population (started from inbred lines collected in local orchards).
Can this at-first-glance mysterious pattern be explained by epistasis and/or pleiotropy? And if yes, then what is the underlying genetic basis of these seasonal shifts to lighter pigmentation? Can smaller loci explain this?
November 18, 2025 at 12:15 AM
Can this at-first-glance mysterious pattern be explained by epistasis and/or pleiotropy? And if yes, then what is the underlying genetic basis of these seasonal shifts to lighter pigmentation? Can smaller loci explain this?
Interestingly, recent work headed by @skylerberardi.bsky.social and me demonstrated that mapped pigmentation-associated variants don’t display the predicted clinal and seasonal behavior (e.g., darker alleles sometimes increased from north to south). doi.org/10.1093/evle...
Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism over multiple spatiotemporal scales
Defining the predictability and pace of adaptation in wild populations are key aims of evolutionary biology, and we explored these dynamics using Drosophil
doi.org
November 18, 2025 at 12:15 AM
Interestingly, recent work headed by @skylerberardi.bsky.social and me demonstrated that mapped pigmentation-associated variants don’t display the predicted clinal and seasonal behavior (e.g., darker alleles sometimes increased from north to south). doi.org/10.1093/evle...
D. melanogaster exhibit clinal patterns in pigmentation whereby northern populations are darker relative to southern populations, and populations within a single location evolve from darker pigmentation in the spring to lighter pigmentation through fall.
November 18, 2025 at 12:15 AM
D. melanogaster exhibit clinal patterns in pigmentation whereby northern populations are darker relative to southern populations, and populations within a single location evolve from darker pigmentation in the spring to lighter pigmentation through fall.
Additionally, there have been several associative trait mapping studies in the past decade that found a handful of these genes to be large-effect loci across populations, namely tan, ebony, and bric-a-brac (bab), all key components of the network above. (Figure from Bastide et. al, 2013)
November 18, 2025 at 12:15 AM
Additionally, there have been several associative trait mapping studies in the past decade that found a handful of these genes to be large-effect loci across populations, namely tan, ebony, and bric-a-brac (bab), all key components of the network above. (Figure from Bastide et. al, 2013)