About

Gregory Allan Wray is a Professor of Biology at Duke University, with appointments also in Evolutionary Anthropology and Cell Biology. His research focuses on the evolution of genes and genomes, aiming to understand the origins of biological diversity. He studies changes in gene expression using empirical and computational approaches, spanning scales from single nucleotides to entire genomes. His work includes understanding the functional consequences and fitness components of specific genetic variants within regulatory sequences of genes related to ecologically relevant traits. Additionally, he develops molecular and analytical methods to detect changes in gene function across genomes, including statistical frameworks for detecting natural selection on regulatory elements and empirical approaches to identify functional variation in transcriptional regulation. His research investigates functional variation within gene networks in wild populations and natural perturbations, primarily focusing on model systems such as sea urchins and primates, including humans.

Research topics

• Biology
• Genetics
• Computer Science
• Neuroscience
• Machine Learning
• Medicine
• Virology
• Demography
• Immunology
• Zoology
• Pathology
• Cell biology
• Evolutionary biology
• Computational biology

Selected publications

• HiFi-Helper: A reproducible workflow for genome assembly from HiFi reads alone

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-14

  articleOpen accessSenior author

  Abstract The PacBio Revio simplifies genome assembly by generating very long reads with very few errors at an affordable price point. Comparative ease of assembly is democratizing access, leading to a larger niche for assembly workflows. HiFi-Helper is a user-friendly snakemake workflow designed to facilitate genome assembly from HiFi data alone. This tool produces a visual summary that provides intuitive feedback on the quality of the resulting assembly and guides assembly parameter optimization. The case studies presented here confirm that HiFi-only assemblies produced by HiFi-helper can meet or exceed the quality of genomes assembled in prior decades with a much lower investment of time and resources.

  PublisherOA PDFDOI

• Wnt dynamics at the blastopore and stomodeum during sea urchin gastrulation

  Development · 2026-04-01

  article

  In the sea urchin embryo, as many as ten Wnts are expressed by cells that undergo gastrulation movements. Here, Wnt1, 5, 6, 7, 8 and 16 are examined to learn details of expression and function over time using results from a temporal scRNA-seq analysis coupled with hybridization chain reaction in situ analysis in which multiple wnt genes are localized simultaneously in the same embryo. The data reveal that many cells express two or three wnt genes at the same time. A single sharp boundary of expression is seen just lateral to the blastopore. Other boundaries of expression are graded and change over developmental time. Functionally, experiments show that Wnts control expression and/or patterning of other wnt genes, and they control expression of marker genes during and following invagination of the archenteron. Stomodeum formation also requires Wnt signaling, indicating that the entire gut uses Wnt signaling for diversification of endodermal fates.

  PublisherDOI

• Genome Mountaineering: Expanding Horizons of the 3D Genome for the Intrepid Evolutionary Adventurer

  Genome Biology and Evolution · 2025-05-30 · 1 citations

  reviewOpen accessSenior author

  The physical positioning of DNA in 3D space within the nucleus can be important for understanding how genetic changes influence gene regulation and consequently phenotype. The costs of 3D genomic assays are falling, concomitant with the rapid innovation of newer, more customizable methods. Thus, evolutionary researchers are increasingly able to engage with these approaches as barriers diminish. As we apply these methods to a broader range of organisms, we learn more about principles governing genome structure and regulatory evolution in 3D space. Here, we use recent studies in primarily nonmodel organisms to illustrate how these approaches can provide novel insights into evolutionary processes. We focus on these cases as motivation for further research into evolutionary conservation and change in 3D organization; the relationship between 3D organization and structural changes in the genome; and the impact of 3D organization in the evolution of gene regulation and organismal traits. We argue that 3D genomic information can help resolve a wide range of outstanding questions in evolutionary biology, particularly as technologies improve and become more accessible in nonmodel systems.

  PublisherOA PDFDOI

• Genetically tractable embryonic cell lines from sea urchins Lytechinus variegatus and Strongylocentrotus purpuratus

  Communications Biology · 2025-10-14 · 1 citations

  articleOpen access

  Sea urchins have been valuable research models for over a century, advancing our understanding of fundamental biological processes like cell cycle regulation and developmental gene regulatory networks. While an increasing number of functional genomic resources are being developed for sea urchins, in vitro cell culture tools and methods for scalable transgenesis have remained elusive. Here, we successfully established embryonic cell lines from sea urchins (Lytechinus variegatus and Strongylocentrotus purpuratus) which recapitulated aspects of the developmental program in vitro, generating 3D structures and diverse cell types representing all three germ layers. Single-cell transcriptomics revealed signatures of naive stem-like cells and distinct cell clusters expressing markers of neurons, myocytes, skeletogenic, endodermal, and pigment cells. Integration of the single-cell RNA sequencing data from L. variegatus cell cultures and the single-cell developmental atlas revealed that, while most cultured cells were notably distinct from cells in vivo, some cell-types were remarkably similar to their corresponding in vivo counterparts. The ability to genetically manipulate the cultured cells was demonstrated using a lentiviral vector, providing a scalable platform for mechanistic studies. These advances expand the utility of this classic model organism and provide a framework for developing similar tools for other non-model marine invertebrates.

  PublisherOA PDFDOI

• Head start: fossil clues about how bodies evolved from two-fold to five-fold symmetry

  Nature · 2025-09-09

  article1st authorCorresponding
  PublisherDOI

• A human-specific enhancer fine-tunes radial glia potency and corticogenesis

  Nature · 2025-05-14 · 20 citations

  articleOpen access
  PublisherOA PDFDOI

• Lepidopteran scale cells derive from sensory organ precursors through a canonical lineage

  Development · 2025-03-01 · 9 citations

  articleOpen access

  The success of butterflies and moths is tightly linked to the origin of scales within the group. A long-standing hypothesis postulates that scales are homologous to the well-described mechanosensory bristles found in the fruit fly Drosophila melanogaster, as both derive from an epithelial precursor. Previous histological and candidate gene approaches identified parallels in genes involved in scale and bristle development. Here, we provide developmental and transcriptomic evidence that the differentiation of lepidopteran scales derives from the sensory organ precursor (SOP). Live imaging in lepidopteran pupae shows that SOP cells undergo two asymmetric divisions that first abrogate the neurogenic lineage, and then lead to a differentiated scale precursor and its associated socket cell. Single-nucleus RNA sequencing using early pupal wings revealed differential gene expression patterns that mirror SOP development, suggesting a shared developmental program. Additionally, we recovered a newly associated gene, the transcription factor pdm3, involved in the proper differentiation of butterfly wing scales. Altogether, these data open up avenues for understanding scale type specification and development, and illustrate how single-cell transcriptomics provide a powerful platform for understanding evolution of cell types.

  PublisherDOI

• Genetically tractable embryonic cell lines from sea urchins

  Research Square · 2025-01-15

  preprintOpen access
  PublisherOA PDFDOI

• Single-nucleus transcriptomics of wing sexual dimorphism and scale cell specialization in sulphur butterflies

  PLoS Biology · 2025-06-18 · 4 citations

  articleOpen accessCorresponding

  The evolution of sexual secondary characteristics necessitates regulatory factors that confer sexual identity to differentiating tissues and cells. In Colias eurytheme butterflies, males exhibit two specialized wing scale types-ultraviolet-iridescent (UVI) and spatulate scales-which are absent in females and likely integral to male courtship behavior. This study investigates the regulatory mechanisms and single-nucleus transcriptomics underlying these two sexually dimorphic cell types during wing development. We show that Doublesex (Dsx) expression is itself dimorphic and required to repress the UVI cell state in females, while unexpectedly, UVI activation in males is independent from Dsx. In the melanic marginal band, Dsx is required in each sex to enforce the presence of spatulate scales in males, and their absence in females. Single-nucleus RNAseq reveals that UVI and spatulate scale cell precursors each show distinctive gene expression profiles at 40% of pupal development, with marker genes that include regulators of transcription, cell signaling, cytoskeletal patterning, and chitin secretion. Both male-specific cell types share a low expression of the Bric-a-brac (Bab) transcription factor, a key repressor of the UVI fate. Bab ChIP-seq profiling suggests that Bab binds the cis-regulatory regions of gene markers associated to UVI fate, including potential effector genes involved in the regulation of cytoskeletal processes and chitin secretion, and loci showing signatures of recent selective sweeps in a UVI-polymorphic population. These findings open new avenues for exploring wing patterning and scale development, shedding light on the mechanisms driving the specification of sex-specific cell states and the differentiation of specialized cell ultrastructures.

  PublisherDOI

• Single-Cell Transcriptomics Reveals Evolutionary Reconfiguration of Embryonic Cell Fate Specification in the Sea Urchin <i>Heliocidaris erythrogramma</i>

  Genome Biology and Evolution · 2024-11-26 · 6 citations

  articleOpen accessSenior author

  Altered regulatory interactions during development likely underlie a large fraction of phenotypic diversity within and between species, yet identifying specific evolutionary changes remains challenging. Analysis of single-cell developmental transcriptomes from multiple species provides a powerful framework for unbiased identification of evolutionary changes in developmental mechanisms. Here, we leverage a "natural experiment" in developmental evolution in sea urchins, where a major life history switch recently evolved in the lineage leading to Heliocidaris erythrogramma, precipitating extensive changes in early development. Comparative analyses of single-cell transcriptome analysis (scRNA-seq) developmental time courses from H. erythrogramma and Lytechinus variegatus (representing the derived and ancestral states, respectively) reveal numerous evolutionary changes in embryonic patterning. The earliest cell fate specification events and the primary signaling center are co-localized in the ancestral developmental gene regulatory network; remarkably, in H. erythrogramma, they are spatially and temporally separate. Fate specification and differentiation are delayed in most embryonic cell lineages, although in some cases, these processes are conserved or even accelerated. Comparative analysis of regulator-target gene co-expression is consistent with many specific interactions being preserved but delayed in H. erythrogramma, while some otherwise widely conserved interactions have likely been lost. Finally, specific patterning events are directly correlated with evolutionary changes in larval morphology, suggesting that they are directly tied to the life history shift. Together, these findings demonstrate that comparative scRNA-seq developmental time courses can reveal a diverse set of evolutionary changes in embryonic patterning and provide an efficient way to identify likely candidate regulatory interactions for subsequent experimental validation.

  PublisherDOI

Recent grants

• Evolutionary Rewiring of a Developmental Gene Regulatory Network

  NSF · $500k · 2015–2018

• Collaborative Research: Assembling the Echinoderm Tree of Life

  NSF · $174k · 2011–2015

• Collaborative Research: Genetic Bases for the Evolution of Human Diet

  NSF · $1.6M · 2008–2014

• DISSERTATION RESEARCH: Selection, drift, and constraint in the evolution of a developmental regulatory gene network

  NSF · $14k · 2009–2012

• Evolution of a developmental gene regulatory network during a life history switch in Heliocidaris

  NSF · $800k · 2019–2025

Frequent coauthors

• Sudhir Kumar

  Malaviya National Institute of Technology Jaipur

  164 shared

• Pamela S. Soltis

  Florida Museum of Natural History

  164 shared

• Chris Henze

  Ames Research Center

  100 shared

• Michael J. Sanderson

  Georgia State University

  100 shared

• James S. Farris

  Gothenburg Botanic Garden

  100 shared

• Victor A. Albert

  University at Buffalo, State University of New York

  100 shared

• David M. Hillis

  The University of Texas at Austin

  100 shared

• Billie J. Swalla

  University of Washington

  85 shared

Education

• Ph.D., Biology

  Duke University

  1987

• B.S.

  College of William and Mary

  1981

Awards & honors

• Embryonic Cell Recognition: Specificity Determinants Researc…
• Roles for uniquely human enhancers in brain development and…