About
In the Hopkins Lab, we believe the strength and excellence of our community stems from our diversity of identities, experiences, and perspectives. STEM, and specifically the field of evolutionary biology, suffer from systematic prejudices and lack of diversity. In our lab, we actively work to create an anti-racist, feminist, anti-discriminatory community that values and empowers our unique and diverse voices. We strive to achieve scientific excellence through respectfully communicating, supportively collaborating, and actively listening. Our motivation to study evolutionary biology comes, in part, from the need for conservation and environmental justice, which we see as intimately tied to social justice. We believe understanding the evolution and ecology of biological diversity requires valuing diversity in our community.
Research topics
- Biology
- Evolutionary biology
- Computer Science
- Zoology
- Ecology
- Botany
- Physics
Selected publications
A lectin receptor-like kinase controls self-pollen recognition in <i>Phlox</i>
Proceedings of the National Academy of Sciences · 2026-02-13
articleOpen accessSenior authorCorrespondingSelf-incompatibility (SI) describes a widespread collection of genetic mechanisms in flowering plants used to specifically recognize and reject self-pollen. These mechanisms are fundamental to plant sexual reproduction and offer valuable insight into the molecular basis of cell–cell communication and self-recognition more broadly. Here, we leverage an independent evolution of SI in the lineage containing Phlox (Polemoniaceae) to identify the gene causing self-pollen recognition which we name Phlox drummondii Pistil Identity Receptor Kinase (PdPIRK) . Recognition of self-pollen associates with a single genomic region containing the Phlox S -locus. We generate predictions regarding how S -loci must function and evolve to identify a single candidate gene within this S -associated region. This gene, PdPIRK , is highly and specifically expressed in the pistil and has exceptionally high polymorphism maintained by negative frequency-dependent selection, two hallmarks of self-pollen recognition genes. Functional validation with gene silencing confirms that PdPIRK is necessary for self-incompatibility, and we further demonstrate allele-specific activity, confirming its role in self-pollen recognition per se. PdPIRK encodes a G-type lectin receptor-like kinase, which is a member of the same gene family as SRK , the gene controlling self-pollen recognition in the distantly related Brassicaceae. Our findings suggest the presence of genetic constraints or paths of least resistance governing how S -loci evolve and add to our understanding of the diverse molecular mechanisms through which organisms achieve self-recognition.
Genomics highlight an underestimation of phenology sensitivity to the urban heat island effect
Proceedings of the National Academy of Sciences · 2025-03-18 · 5 citations
articleOpen accessThe phenological timing of leaf out in temperate forests is a critical transition point each year that alters the global climate system, which in turn, feeds back to plants, driving leaf out to occur nearly 3 d earlier per decade as temperatures rise. To improve predictions of leaf out timing, urban heat islands (UHIs) or densely developed areas that are hotter than surrounding undeveloped regions are often used to approximate warming via space-for-time substitutions (i.e., rural-to-urban temperature gradients). However, more than just environment changes along these gradients—urban regions are highly managed systems with limited-to-no within species diversity. We demonstrate here that recent observations that UHI gradients underpredict leaf out response to temperature when compared to temperature gradients through time is likely because both genetics and environment are changing across rural-to-urban gradients, whereas only environment is changing through time. We tested this hypothesis using genomic, phenological, and temperature data of northern red oak ( Quercus rubra ) over several years between an urban and rural site. Across our gradient, models that included just temperature predicted moderate advancement of leaf out. However, if we account for the genetic diversity of our trees in our model, leaf out phenology is predicted to advance significantly more in response to temperature. We demonstrate that this stronger relationship between phenological timing and climate is because urban trees have reduced genetic diversity as they are planted from limited stock by humans and, moreover, are most closely related to individuals at the rural site that leaf out later on average.
Variation in Response to Water Availability Across <i>Phlox</i> Species
Plant-Environment Interactions · 2025-11-08
articleOpen accessSenior authorABSTRACT Plants adapt to environmental variation both by evolving divergent trait means and by plastically adjusting trait expression in response to local conditions. While these dual strategies are essential for persistence in diverse environments, there are still outstanding questions about how they interact and vary across closely related species. For plants, water availability is a particularly important selective force that shapes species distributions, selects for growth habit and life history strategy, and can dictate individuals' plastic expressions of trait values and reproductive success. Here, we use ecological niche modeling, field soil characterization, and a controlled dry‐down experiment to understand how geographic distribution and evolutionary background among three closely related Phlox wild flower species and their F1 hybrids explain their responses to water availability. We infer that the species occupy distinct niches that diverge along a primary axis of water availability and soil moisture. Each species has a distinct growth habit that does not match broad predictions of divergence in response to water availability. Nevertheless, we find that all the species show a significant morphological response to controlled soil dry down with reduced biomass, smaller leaves, and fewer flowers, as would be predicted in a response to drought. We find that Phlox drummondii , which occupies intermediate habitats, exhibits the strongest plastic response to water limitation, despite it not having the broadest environmental niche. Additionally, most hybrids involving P. drummondii display intermediate phenotypes in both wet and dry treatments, while hybrids between P. cuspidata and P. roemeriana show phenotypes consistent with hybrid vigor. These results challenge the hypothesis that species from broader environments evolve greater plasticity. Instead, the most plastic species did not have the broadest niche, suggesting plasticity and niche breadth may evolve independently.
The American Naturalist · 2025-11-11
articleSenior authorGenetics · 2025-07-14 · 1 citations
articleOpen accessSenior authorFlowering plants display extensive variation in selfing rate, a trait with significant ecological and evolutionary consequences. Many species use genetic mechanisms to recognize and reject self-pollen (termed self-incompatibility or SI), and the loss of SI is one of the most common evolutionary transitions among flowering plants. Despite the ubiquity of transitions to self-compatibility (SC), little is known about the genetic architecture through which SC evolves. Specifically, it is important to determine if SC has a simple or polygenic basis and if variation localizes to the self-pollen recognition locus (the "S-locus"). Phlox drummondii (Polemoniaceae) is a model system for exploring mating system evolution and expresses range-wide variation in SI. Here, we investigate the genetic architecture of SC variants segregating within this otherwise SI species. Using multiple independent crosses, we uncover numerous QTLs associated with intraspecific SI variation, consistent with a polygenic genetic architecture. While some QTLs overlap across mapping experiments, other QTLs are unique, suggesting that multiple genetic routes to SC exist. We demonstrate that P. drummondii has a sporophytic SI system, revealing an independent evolution of SI within the Phlox lineage. We map this novel S-locus and find that the genomic region containing the S-locus is associated with intraspecific variation in SI in one of the 3 mapping populations. Although further work is necessary to clarify the conditions under which quantitative variation in SI represents a transitional pathway to complete SC, our study reveals the genetic architecture upon which selection could act to drive this frequent and evolutionarily significant transition.
Delayed flowering phenology of red-flowering plants in response to hummingbird migration
Current Biology · 2025-04-14 · 3 citations
articleOpen accessSenior authorbioRxiv (Cold Spring Harbor Laboratory) · 2025-05-26
preprintOpen accessSenior authorAbstract Characterizing patterns of trait variation across widespread species is a fundamental goal of natural history. Here we create a pipeline to analyze a large community science dataset and test hypothesized flower color divergence across the range of a widespread wildflower. Monarda fistulosa is a North American perennial that produces showy lavender inflorescences. Although previous literature suggests that the flowers of western M. fistulosa might display a deeper purple color than the eastern varieties, this divergence has not been assessed at scale. We process over 40,000 community science photographs of M. fistulosa to identify flowers and extract color. We demonstrate that the flowers of the montane western variety have lower lightness and higher chroma, corresponding to a deeper violet color, than those of eastern M. fistulosa . Our approach and validation provides a scalable framework for phenotyping community science images and enables analysis of geographic color variation in other widespread species.
A lectin receptor-like kinase controls self-pollen recognition in <i>Phlox</i> (Polemoniaceae)
bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-21 · 1 citations
preprintOpen accessSenior authorAbstract Self-incompatibility (SI) describes a widespread collection of genetic mechanisms in flowering plants used to specifically recognize and reject self-pollen. These mechanisms are fundamental to plant sexual reproduction and offer valuable insight into the molecular basis of cell-cell communication and self-recognition more broadly. Here, we leverage an independent evolution of SI in the lineage containing Phlox (Polemoniaceae) to characterize a novel gene causing self-pollen recognition which we name Phlox drummondii Pistil Identity Receptor Kinase ( PdPIRK ). Recognition of self-pollen associates with a single genomic region containing the Phlox S -locus. We generate predictions regarding how S -loci must function and evolve to identify a single candidate gene within this S -associated region. This gene, PdPIRK , is highly and specifically expressed in the pistil and has exceptionally high polymorphism maintained by negative frequency dependent selection, two hallmarks of self-pollen recognition genes. Functional validation with gene silencing confirms that PdPIRK is necessary for self-incompatibility, and we further demonstrate allele specific activity, confirming its role in self-pollen recognition per se. PdPIRK encodes a G-type lectin receptor-like kinase, which is a member of the same gene family as SRK , the gene controlling self-pollen recognition in the distantly related Brassicaceae. Our findings suggest the presence of genetic constraints or paths of least resistance governing how S -loci evolve and add to our understanding of the diverse molecular mechanisms through which organisms achieve self-recognition.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-30 · 1 citations
preprintOpen accessSenior authorCorrespondingAbstract Flowering plants display extensive variation in selfing rate, a trait with significant ecological and evolutionary consequences. Many species use genetic mechanisms to recognize and reject self-pollen (termed self-incompatibility or SI), and the loss of SI is one of the most common evolutionary transitions among flowering plants. Despite the ubiquity of transitions to self-compatibility (SC), little is known about the genetic architecture through which SC evolves. Specifically, it is important to determine if SC has a polygenic or simple genetic basis and if variation in compatibility localizes to the genomic locus causing self-pollen recognition (the “ S -locus”). Phlox drummondii (Polemoniaceae) has been a model system for exploring mating system evolution and expresses extensive range-wide variation in the SI response. Here we investigate the genetic architecture of SC variants segregating within this otherwise SI species. Using multiple independent crosses, we uncover numerous QTLs associated with intraspecific variation in SI, consistent with a polygenic genetic architecture. While some QTLs overlap across mapping experiments, other QTLs are unique, suggesting that multiple genetic routes to SC exist. Through these crossing experiments, we demonstrate that P. drummondii has a sporophytic SI system, suggesting that an independent evolution of SI occurred in the lineage containing Phlox . We map this novel S -locus and find that the genomic region containing the S -locus is associated with intraspecific variation in SI in one of the three mapping populations. Although further work is necessary to clarify the conditions under which quantitative variation in SI represents a transitional pathway to complete SC, our study reveals the underlying genetic architecture upon which selection could act to drive this frequent and evolutionarily significant transition.
Variation in response to water availability across <i>Phlox</i> species
bioRxiv (Cold Spring Harbor Laboratory) · 2025-06-20
preprintSenior authorABSTRACT Plants adapt to environmental variation both by evolving divergent trait means and by plastically adjusting trait expression in response to local conditions. While these dual strategies are essential for persistence in diverse environments, how they interact and vary across closely related species is understudied. For plants, water availability is a particularly important selective force that shapes species distributions, selects for growth habit and life history strategy, and can dictate individuals’ plastic expressions of trait values and reproductive success. Here, we use ecological niche modeling, field soil collections, and a controlled drought experiment to test how biogeography and evolutionary history influence responses to limited water availability in three closely related Texas annual Phlox species and their F1 hybrids. We infer that the species occupy distinct niches that diverge along a primary axis of water availably and soil moisture. Each species has a distinct vegetative growth habit that does not match broad predictions of divergence in response to water availability. Nevertheless, we find that all the species show a significant morphological response to controlled soil dry down with reduced biomass, smaller leaves, and fewer flowers, as would be predicted in a response to drought. We find that Phlox drummondii , which occupies intermediate habitats, exhibits the strongest plastic response to water limitation, despite it not having the broadest environmental niche. Additionally, most hybrids involving P. drummondii display intermediate phenotypes in both wet and dry treatments, while hybrids between P. cuspidata and P. roemeriana show phenotypes consistent with hybrid vigor. These results challenge the hypothesis that species from broader environments evolve greater plasticity. Instead, the most plastic species did not have the broadest niche, suggesting plasticity and niche breadth may evolve independently.
Recent grants
Frequent coauthors
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Meghan Blumstein
Harvard University Press
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Jon Runyeon
- 28 shared
Katie Morrison-Graham
- 28 shared
Mike LeMaster
- 28 shared
Amy Harwell
- 28 shared
Devon Quick
- 28 shared
Sierra Dawson
- 28 shared
Philip Matern
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