# Rapid evolution of pigmentation in D. melanogaster: from cis regulation to phenotype

> **NIH NIH R01** · UNIVERSITY OF PENNSYLVANIA · 2021 · $563,316

## Abstract

PROJECT SUMMARY
Rapid evolutionary adaptation is a foundational process in biology and at the core of many issues facing humanity
including cancer, bacterial and viral diseases, evolution of drug and pesticide resistance, and biological response
to global change. Many traits that evolve rapidly are complex and polygenic, and we lack a comprehensive
understanding of the genetic and evolutionary dynamics of rapid evolution in natural populations. Pigmentation
is a complex phenotype determined by many loci. From the peppered moth to the pocket mouse, adaptive
coloration is widely observed and, in many cases, a few large effect loci have been identified and then shown
mechanistically to be responsible. Patterns of pigmentation in Drosophila melanogaster are also thought to be
adaptive, exhibiting clines at multiple scales, yet the genetic architecture and evolutionary dynamics are
substantially more complex: body segments exhibit a variety of colors and patterns, dozens of loci affecting
pigmentation have been verified, and patterns among different segments are not always highly correlated. Our
preliminary data demonstrate that pigmentation can evolve very rapidly and cyclically in natural populations,
fluctuating seasonally between dark coloration post-winter and light coloration post-summer. Hundreds of alleles
change in frequency and are associated with the rapid evolution of pigmentation phenotype. Rapid seasonal
evolution of pigmentation in D. melanogaster is not an example of a few loci of large effect, but represents a
different paradigm underpinning the rapid evolution of complex traits. The need for rapid change is associated
with a plastic response in which temperature causes an immediate change in pigmentation during development,
but thermal plasticity does not explain the seasonal pigmentation response. We observe both durable shifts in
midpoints as well as an increase in the distribution of the extremes. Shifts in population midpoint may not be due
to the same set of loci as those that drive the phenotypic extremes. There are more than 20 known pigmentation
loci controlled by cis regulation and associated with a diverse set of transcription factors. Pigmentation changes
could be a result of shifting frequencies in trans factors that trigger cis regulation among a large number of loci,
or it could be changes in cis effects directly. The targets of selection may be small in number or may represent
a larger mutational target, and testing parallelism will enable us to determine the mutational target size. In this
proposal we survey the genetics of rapid evolution in pigmentation with the goal of answering the following
questions: Are the loci responsible for the average shift in pigmentation the same as loci in phenotypic extremes?
Are the targets of rapid directional selection the same among populations? Are pigmentation traits directly
responsible for rapid adaptation? Are cis regulatory changes occurring in the same set of loci at differe...

## Key facts

- **NIH application ID:** 10133273
- **Project number:** 1R01GM137430-01A1
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** Lauren M. MCINTYRE
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $563,316
- **Award type:** 1
- **Project period:** 2021-01-01 → 2024-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10133273

## Citation

> US National Institutes of Health, RePORTER application 10133273, Rapid evolution of pigmentation in D. melanogaster: from cis regulation to phenotype (1R01GM137430-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10133273. Licensed CC0.

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