About
Paul Schmidt is a Patricia M. Williams Term Professor of Biology and Undergraduate Chair at the Department of Biology at the University of Pennsylvania. His research interests encompass ecology and biodiversity, evolution, genetics, epigenetics, genomics, and neurobiology, behavior, and physiology. His research group broadly investigates the ecological and evolutionary dynamics of populations experiencing environmental heterogeneity over various spatial and temporal scales. The focus is on understanding the mechanisms of natural selection in heterogeneous environments, the context dependency and constraints on these processes, and how these factors produce adaptive responses. Schmidt's work combines extensive sampling of natural populations with -omics level characterizations, classical and molecular genetics in laboratory settings, and experimentation conducted both in the field and laboratory. A significant aspect of his research involves testing the functional significance of molecular polymorphisms by establishing links between allelic variation, physiological performance, and the differential fitness of genotypes across environments. His contributions include studies on adaptive tracking, seasonal adaptation, and rapid genomic evolution in Drosophila melanogaster, among other topics. He has authored numerous publications in this field and is actively involved in advancing understanding of evolutionary ecology and genetics.
Research topics
- Biology
- Genetics
- Evolutionary biology
- Computer Science
- Statistics
- Ecology
- Demography
Selected publications
Evolution · 2026-03-11
articleOpen accessSenior authorPigmentation has been widely studied by evolutionary biologists due to both ease of measurement and relationship to fitness. Drosophila melanogaster pigmentation has represented a particularly useful avenue of investigation, as extensive genetic tools have enabled the characterization of the trait's complex architecture. Drosophila pigmentation also varies predictably across space and time in wild populations, suggesting pigmentation is a component of adaptation to local environmental conditions. Despite this, the impact of D. melanogaster pigmentation on fitness, and the environmental factors that drive the evolution of pigmentation, are not well understood. To address this gap, we experimentally evolved replicated D. melanogaster populations in field mesocosms to determine whether and how pigmentation evolves in response to environmental variation. We found that pigmentation rapidly and predictably adapted to a direct manipulation of temperature, supportive of melanization playing a role in thermoregulation. However, we also determined that pigmentation responded adaptively to direct manipulations of numerous additional factors, including intraspecific competition, diet, and the microbiome. These findings suggest that the selective landscape acting on pigmentation is complex and multifaceted, and that patterns of melanization may be driven, at least in part, by indirect selection due to correlations with other fitness-related traits.
Seasonal evolution and its effects on competition
Open MIND · 2026-01-21
otherRapid evolution can influence competitive dynamics. While theory and past work have focused on the competitive consequences of rapid evolution in response to competitors (e.g., character displacement), abiotic environmental factors are also responsible for much of the rapid evolution observed in nature. Yet, we lack knowledge of how evolution in response to a variable abiotic environment shapes competition between evolving species. Our knowledge of these effects is limited not only by the absence of direct quantification of environment-driven evolution's effects on competition, but also by the rarity of systems in which environment-driven evolution itself has been measured across multiple competitors. Here, we used an outdoor mesocosm experiment with three species of naturally co-occurring Drosophilid fly competitors to quantify the seasonal evolution of stress tolerance and reproductive traits and the effects of this evolution on demographic performance under competition. We found that rapid seasonal evolution occurred across all three species, across all measured traits, and across every sampling interval. Throughout the course of their growing season, species first converged on similar phenotypic profiles (e.g., high heat tolerance and low fecundity), then evolved in parallel. This seasonal evolution had clear impacts on pairwise competition between species. In competition trials in a common garden greenhouse environment, seasonal evolution had the potential to alter demographic performance by over 30%. Under seasonally varying field conditions over the summer, in one species pair, seasonal evolution had 7x stronger effects on competitive performance than did the changing environmental conditions themselves. Our work highlights that the rapid, environment-driven evolution increasingly documented by evolutionary biologists can have a major, underappreciated influence on ecological competitive dynamics.
Seasonal evolution and its effects on competition
Zenodo (CERN European Organization for Nuclear Research) · 2026-01-21
otherOpen accessRapid evolution can influence competitive dynamics. While theory and past work have focused on the competitive consequences of rapid evolution in response to competitors (e.g., character displacement), abiotic environmental factors are also responsible for much of the rapid evolution observed in nature. Yet, we lack knowledge of how evolution in response to a variable abiotic environment shapes competition between evolving species. Our knowledge of these effects is limited not only by the absence of direct quantification of environment-driven evolution's effects on competition, but also by the rarity of systems in which environment-driven evolution itself has been measured across multiple competitors. Here, we used an outdoor mesocosm experiment with three species of naturally co-occurring Drosophilid fly competitors to quantify the seasonal evolution of stress tolerance and reproductive traits and the effects of this evolution on demographic performance under competition. We found that rapid seasonal evolution occurred across all three species, across all measured traits, and across every sampling interval. Throughout the course of their growing season, species first converged on similar phenotypic profiles (e.g., high heat tolerance and low fecundity), then evolved in parallel. This seasonal evolution had clear impacts on pairwise competition between species. In competition trials in a common garden greenhouse environment, seasonal evolution had the potential to alter demographic performance by over 30%. Under seasonally varying field conditions over the summer, in one species pair, seasonal evolution had 7x stronger effects on competitive performance than did the changing environmental conditions themselves. Our work highlights that the rapid, environment-driven evolution increasingly documented by evolutionary biologists can have a major, underappreciated influence on ecological competitive dynamics.
Microbiota composition of fruit flies and their environments in eastern USA orchards
Microbiology Resource Announcements · 2026-01-12
articleOpen accessWe present a 16S rRNA analysis of the microbiota of fruit flies and their fruit and soil environments collected across a latitudinal gradient in the eastern USA. Collections varied according to fly taxonomy, location, sampling substrate, and starvation condition. These samples reveal variation in microbiota composition with several key variables.
Journal of Magnetic Resonance Imaging · 2026-05-06 · 1 citations
articleOpen accessBACKGROUND: Xenon MRI is increasingly used to evaluate patients with interstitial lung disease (ILD) and pulmonary hypertension (PH), both of which are common manifestations of systemic sclerosis (SSc). As such, Xe-MRI may be suited to interrogate lung function impairment in SSc. PURPOSE: To characterize xenon MRI signatures in SSc, toward evaluating the utility of xenon MRI as a method to elucidate mechanisms of regional lung function impairment in this population. STUDY TYPE: Prospective. POPULATION: Of 25 participants initially imaged, 21 participants (18 females) with SSc were included. Sixteen healthy volunteers (13 females) were enrolled. FIELDSTRENGTH/SEQUENCE: 3 T, 1-point Dixon imaging using xenon MRI. ASSESSMENT: Xenon MRI measures including ventilation defect percent, membrane uptake, red blood cell (RBC) transfer, RBC defect percent, and RBC oscillation amplitude were generated. Measures were compared across healthy and SSc groups and correlated with standard clinical measures, including demographics, pulmonary function tests, CT lung density measures, and pulmonary artery pressure. STATISTICAL TESTS: Due to a small number of male participants, statistical analysis was limited to female participants. Wilcoxon, t-tests, or Fisher's exact tests were used to compare between healthy and SSc groups. Pearson's correlation was used to correlate xenon MRI with clinical measures. p < 0.05 was considered significant. RESULTS: Despite a relatively mild burden of pulmonary disease, SSc participants exhibited significantly lower RBC/Membrane ratio (0.25 [IQR, 0.10] vs. 0.34 [0.05]) and RBC transfer (0.22 ± 0.07 vs. 0.28 ± 0.07), and significantly greater RBC defect percent (22.8 [IQR, 16.9] vs. 11.9 [13.7]) compared to healthy volunteers. DATA CONCLUSION: Xenon MRI measures, including RBC transfer, RBC/Membrane, and RBC defect percent were markedly different in female SSc patients compared to age-matched healthy volunteers, suggesting that xenon MRI may be an effective method for examining regional impairments to pulmonary gas exchange in SSc. EVIDENCE LEVEL: 2. TECHNICAL EFFICACY: Stage 2.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-12 · 1 citations
preprintOpen accessSenior authorDetermining the scale and scope of the predictability of evolution is fundamental to understanding biological processes and to managing biodiversity. Ecological frameworks, including life history theory and ecological stoichiometry, offer testable predictions about the direction of adaptation and trade-offs between traits in response to environmental change. Similarly, well-characterized molecular pathways, genotype phenotype linkages, and prior evolutionary genomic studies could be predictive of the genomic architecture underlying adaptation. We tested whether ecological frameworks and evolutionary genomic data can be used to forecast rapid adaptation in replicated outdoor populations of Drosophila melanogaster evolving in response to natural seasonal fluctuations from summer to late fall. Life history theory predicted the observed pattern of adaptive tracking: in summer, reproductive output increased and stress tolerance decreased, while in fall, this direction reversed, with evolution of increased stress tolerance at the expense of reproduction. Stoichiometric phenotypic evolution was also predictable, with phosphorus and magnesium content, both linked to growth rate, and alkali metal, associated with maintaining homeostasis in response to thermal stress, showing rapid and parallel evolution indicative of adaptation. Temporal genomic data revealed a complex genomic architecture of temporal adaptation and the SNPs and genes involved in adaptation were largely unpredictable. These results demonstrate that ecological frameworks, more than genomic data, have utility in forecasting adaptation in complex and variable environments.
Genetics · 2025-11-27
articleOpen accessTo understand the relative importance of cis and trans effects on regulation, we crossed multi-parent recombinant-inbred lines (RILs) to a common tester and measured allele-specific gene expression in the offspring. Testing the difference of allelic imbalance between two RIL × Tester crosses is a test of cis or trans, depending on the RIL alleles compared. The study design also enables to separation of two sources of trans variation, genetic and environmental, detected via interactions with cis effects. We demonstrate the effectiveness of this approach in a long-read RNA-seq experiment in female abdominal tissue at two time points in Drosophila melanogaster. Among the 40% of all loci that show evidence of genetic variation in cis, trans effects due to environment are detectable in 31% of loci and trans effects due to genetic background in 19%, with little overlap in sources of trans variation. The genes identified in this study are associated with genes previously reported to exhibit genetic variation in gene expression. Eleven genes in a QTL for thermotolerance, previously shown to differ in expression based on temperature, have evidence for regulation of gene expression regardless of the environment, including the cuticular protein Cpr67B, suggesting a functional role for standing variation in gene expression. This study provides a blueprint for identifying regulatory variation in gene expression, as the tester design maximizes cis variation and enables the efficient assessment of all pairs of RIL alleles relative to the tester, a much smaller study compared to the pairwise direct assessment.
Molecular Biology and Evolution · 2025-08-30 · 1 citations
articleOpen accessHow genetic variance for fitness is maintained is incompletely understood. Mutation-selection balance and single-locus overdominance cannot account for the large variance observed. Recent work suggests that antagonistic balancing selection, favoring different alleles in different contexts and involving beneficial dominance reversals, might contribute to maintaining fitness variance. However, while this mechanism is plausible, evidence for dominance reversals remains scarce. Here, we study how In(3R)Payne, a balanced inversion polymorphism in Drosophila melanogaster, affects gene expression and chromatin accessibility by using RNA-seq and ATAC-seq (assay for transposase-accessible chromatin with sequencing). We find that, in embryos, the inverted (INV) arrangement tends to have dominant effects, while the standard (STD) arrangement behaves like a recessive Mendelian allele. Yet, in wing discs, this pattern is reversed: STD has mostly dominant effects, whereas INV behaves recessively. Since this shift in the dominance of the INV "allele" between developmental contexts affects the expression of suites of genes in a concerted manner, it might be mediated by a dominance modifier, for example, a transcription factor. In favor of this idea, 25% of the differentially expressed genes between INV and STD encode transcription factors. Interestingly, while only four differentially expressed genes are shared between embryos and wing discs, one of them is HP1c, a chromatin-binding protein and major transcriptional regulator, and thus a promising candidate for mediating the context-dependent change in dominance. Although the relationship between these patterns and fitness is presently unknown, our observations are consistent with a potential role of reversals (or, more generally, shifts) of dominance in maintaining inversion polymorphism.
Evolution Letters · 2025-09-05 · 3 citations
articleOpen accessSenior authorAbstract Natural populations often experience heterogeneity in the quality and abundance of environmentally acquired resources across both space and time, and this variation can influence population demographics and evolutionary dynamics. In this study, we directly manipulated diet in replicate populations of Drosophila melanogaster cultured in experimental mesocosms in the field. We found no significant effect of resource variation on estimates of adult census size. Resource variation altered patterns of phenotypic and genomic evolution across replicate populations; however, we find that this effect is secondary to selection driven by the fluctuating seasonal environment. Seasonal adaptation was observed for all traits assayed and elicited genome-wide signatures of selection. In contrast, adaptation to the resource environment was trait-specific and exhibited an oligogenic architecture. This illustrates the capacity of populations to adapt to a specific axis of variation (the resource environment) without hindering the adaptive response to seasonal change. This, in turn, suggests that resource variation may be an important force driving fluctuating selection across natural populations, ultimately contributing to the maintenance of genetic and phenotypic variation.
Nature Ecology & Evolution · 2025-09-15 · 9 citations
article
Recent grants
NIH · $3.3M · 2021
NSF · $294k · 2006–2010
NSF · $468k · 2009–2013
Frequent coauthors
- 44 shared
Alan O. Bergland
University of Virginia
- 38 shared
Martin Kapun
Natural History Museum Vienna
- 34 shared
Thomas Flatt
University of Fribourg
- 34 shared
David M. Rand
Providence College
- 34 shared
Dmitri A. Petrov
Stanford University
- 33 shared
Subhash Rajpurohit
- 30 shared
Emily L. Behrman
Dartmouth College
- 23 shared
Josefa González
Institut de Biologia Evolutiva
Labs
Evolutionary change and its impact on ecological interactions
Education
- 1999
PhD, Ecology and Evolutionary Biology
Brown University
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