About

Todd Oakley is an evolutionary biologist and a professor in the EEMB Department at the University of California, Santa Barbara. He earned a Bachelor of Science and a Master of Science from the University of Wisconsin-Milwaukee, followed by a PhD in Biological Sciences from Duke University. Dr. Oakley was an NIH-NRSA postdoctoral fellow at the University of Chicago. He joined the faculty of the EEMB Department in 2003. Currently, he serves as Vice Chair of resources for EEMB and is a member of UCSB’s Marine Science Institute. His research involves evolution, ecology, and genomics, and he is the principal investigator or co-principal investigator on multiple federally funded research projects.

Research topics

• Biology
• Ecology
• Evolutionary biology
• Computational biology
• Genetics
• Biochemical engineering
• Economics
• Engineering
• Biological system
• Zoology

Selected publications

• Competitive environment predicts weaponry in an intertidal sea anemone

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-20

  articleSenior author

  Abstract Animal weapons are ecologically important traits that mediate contests over limiting resources and can strongly influence survival and reproduction. Weapon traits often exhibit substantial intraspecific morphological diversity, raising questions about the ecological drivers of this variation. Acrorhagi are weapons produced by sea anemones that are used in intraspecific territorial encounters. Although acrorhagial morphology varies widely within species, patterns of intraspecific variation remain poorly characterized, and the extent to which such variation reflects differences in local intraspecific competition is unclear. Here, we conduct morphometric analyses to characterize within-population variation and allometry in acrorhagial traits of the solitary anemone Anthopleura sola . We show that these traits covary with habitats differing in conspecific density. The number of acrorhagi scaled positively with body size, and individuals occupying a high-density habitat tended to possess more acrorhagi than did similar sized individuals from a low-density habitat. In addition, anemones from high-density habitats exhibited longer acrorhagial cnidae, a pattern that was not explained by differences in body size or acrorhagial density. Together, these results suggest that competitive context influences weapon-related traits at multiple levels of biological organization, potentially via phenotypic plasticity or selective processes. More broadly, our findings highlight how fine-scale ecological variation may contribute to the maintenance of trait diversity within and across species.

  PublisherDOI

• Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-24

  articleOpen accessSenior authorCorresponding

  Researchers often infer evolutionary repeatability when selection scans implicate homologous genes in repeatedly evolved traits or ecologies. However, the causes and frequency of genome-scale molecular convergence remain unresolved, particularly over deep time. We show that adaptive molecular convergence— excess convergence of nonsynonymous substitutions, consistent with positive selection—is pervasive across Medusozoa. Molecular convergence declines over time but persists among lineages separated by > 600 million years, exceeding null expectations based on random overlap. However, lineages sharing repeatedly evolved phenotypes (eyes, medusa loss, upright colonies) do not exhibit elevated molecular convergence relative to other comparisons. Instead, convergence is non-randomly distributed across genes and enriched for environment-facing functions, including metabolism, immunity, and xenobiotic processing, suggesting that widespread reuse of genes reflects multifaceted organism-environment interactions.

  PublisherOA PDFDOI

• Genome assembly of <i>Bougainvillia</i> cf. <i>muscus</i> (Cnidaria: Hydrozoa)

  G3 Genes Genomes Genetics · 2025-05-19 · 2 citations

  articleOpen accessSenior author

  As one of just a handful of nonbilaterian animal phyla, Cnidaria are key to understanding genome evolution across Metazoa. Despite their importance and diversity, the genomes of most species in the phylum are unsequenced, due in large part to difficulties cultivating them in a laboratory. Here, we present a genome sequence of Bougainvillia cf. muscus, a hydrozoan with 4 marginal bulbs each containing 7 simple eyes (ocelli). This species appeared in our tanks from contamination. While we lacked sufficient samples for transcriptomic or functional studies, we were able to expand our knowledge of how the genome of this species compares to the few, better studied members of hydrozoans by investigating synteny to other cnidarians, repetitive element content, and phylogenetics and synteny of vision-related genes in this eyed species compared to eyeless relatives. The genome sequence consists of 350 contigs with an N50 of 10 Mb, a total genome length of 375.328 Mb, a BUSCO score of 90.1%, and predicted protein coding genes totaling 46,431. We found a high degree of macrosynteny conservation with Hydra vulgaris, Hydractinia symbiolongicarpus, and Turritopsis rubra. Repetitive elements make up 62% of this Bougainvillia genome. For vision-related genes, we identified 20 cnidarian opsins (cnidops) in Bougainvillia and found instances of gene duplication and loss in families associated with bilaterian eye development, phototransduction, and visual cycling. This high-quality, contiguous genome in an eyed hydrozoan will be a valuable resource for additional comparative genomic studies.

  PublisherOA PDFDOI

• Comparative Analysis of Convergent Jellyfish Eyes Reveals Extensive Differences in Expression of Vision‐Related Genes

  Ecology and Evolution · 2025-07-01 · 2 citations

  articleOpen accessSenior authorCorresponding

  Quantifying gene expression across convergent origins of traits clarifies the degree to which those traits arise from shared versus distinct genetic programs, revealing how gene reuse relates to the repeatability of evolution. Eyes are important traits that evolved in many distantly related lineages, including at least nine times within cnidarians. Here, we investigate gene expression in eye-bearing and nonvisual tissues from three cnidarian species representing long-diverged lineages where eyes evolved convergently (Cubozoa, Scyphozoa, and Hydrozoa). We find gene expression in eye-bearing tissues to be mostly lineage-specific, with only a small proportion of genes having convergent expression across species. Nevertheless, all species express homologs of deeply conserved vision-related genes known from Bilateria, which likely reflects deep homology (parallel evolution across vast phylogenetic distances) of a metazoan phototransduction toolkit. A gene tree analysis of opsins-the prototypical animal photosensors-shows that convergent eyes recruited different opsin paralogs, with the potential exception of an opsin ortholog shared between scyphozoan and cubozoan eyes. Our results suggest that eyes have mostly lineage-specific patterns of gene expression, yet some key phototransduction components are repeatedly recruited across multiple independent eye origins in Medusozoa.

  PublisherOA PDFDOI

• Shedding light on patterns of unconventional expression of opsin genes in <i>Hydra vulgaris</i>

  Integrative and Comparative Biology · 2025-06-23

  articleOpen accessSenior author

  Opsins are G-protein-coupled receptors often expressed in neuronal photoreceptor cells and used for light detection in most animals, including cnidarians like corals, jellyfish, and anemones. Opsins may also be expressed in non-neuronal cell types, where they may confer light sensitivity. For example, opsins might be involved in pre-neural phototaxis of larval box jellyfish. However, the overall extent of non-neuronal expression of opsins is not well understood, despite the potential for identifying additional light or opsin-mediated organismal functions. To investigate the prevalence of non-neuronal opsin expression in a cnidarian, we analyzed published data from Hydra vulgaris, a freshwater hydroid that responds to light despite lacking distinct photosensory structures such as eyes. We quantified opsin expression across Hydra cell types and states of cell differentiation using published single-cell RNA sequencing (scRNA-seq) data and assay for transposase-accessible chromatin sequencing data. We identified 45 opsin transcripts in Hydra expressed in neuronal and non-neuronal cell types, as well as across inferred states of cell differentiation. We found a wider diversity of opsin gene transcripts in neuronal cell types, predominantly in fully differentiated cells. In contrast, we detected fewer opsin transcripts in non-neuronal cell types, and they were expressed from stem cell to progenitor cell to fully differentiated cell state-all within the same inferred cell type. These opsin transcripts appear to be expressed at higher levels in ectodermal epithelial cells near the head organizer of Hydra (a key developmental patterning region) and share transcription factor binding motifs with development genes such as Six, Otx, Ptx, Rfx4, and Hxa. Overall, we outline an array of opsin gene transcripts, their expression, and open chromatin patterns across cell type diversity in Hydra, and highlight potential co-regulatory relationships that may pave the way for future work on unconventional roles for opsin genes in Hydra.

  PublisherOA PDFDOI

• Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-27 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract Predicting phenotypes from genetic variation is a central challenge in biology. Linking genotypes and phenotypes using machine learning (ML) offers great promise, but its use is limited by poor accessibility, overestimated performance, and a “data-cliff”—a gap between abundant sequences and scarce functional measurements. To develop more robust methods for genotype–phenotype prediction, an outstanding model system is opsin genes, visual pigments with extensive phenotypic information that strongly influence animal spectral sensitivity. Here we advance ML characterization of the opsin genotype–phenotype map through four main contributions. First, we introduce the Opsin Phenotype Tool for Inference of Color Sensitivity (OPTICS), a user-friendly platform for predicting maximum wavelength sensitivity (λ max ) from amino-acid sequences. Second, we show that encoding sequences with amino-acid physicochemical properties improves predictive performance and reveals mechanistic relationships. Third, we develop Phylogenetically Weighted Cross-Validation (PW-CV), a method that accounts for non-independence among related sequences, providing more realistic assessments of model generalizability. Finally, we present the Mine-N-Match (MNM) pipeline, which systematically links published opsin sequences to compiled in-vivo λ max data, expanding genotype–phenotype coverage and improving prediction, especially for invertebrate opsins with undersampled heterologous data. By integrating accessible software, biologically informed encoding, phylogeny-aware evaluation, and data harmonization, our framework improves confidence, accuracy, and interpretability of genotype–phenotype prediction. An accurate genotype-phenotype map allows simulating molecular evolution of function, reconstructing the history of visual phenotypes, designing functional proteins, and generating new hypotheses that can be tested with heterologous phenotyping.

  PublisherOA PDFDOI

• deepBreaks identifies and prioritizes genotype–phenotype associations using machine learning

  Scientific Reports · 2025-11-07

  articleOpen access

  Sequence data, such as nucleotides or amino acids, are crucial in advancing our understanding of biology. However, investigating and analyzing sequencing data and genotype-phenotype associations present several challenges, including noise components that arise from the sequencing, nonlinear genotype-phenotype associations, collinearity between input features, and high dimensionality of the input data. Machine learning (ML) algorithms have proven to be effective in detecting intricate and nonstructural patterns, making them a valuable tool for studies focused on genotype-phenotype associations. Yet, there needs to be more user-friendly ML implementations that leverage the unique features of high-volume DNA sequence data. Here, we introduce deepBreaks, a generic approach that detects important positions (genotypes) in sequence data that are associated with phenotypic traits. deepBreaks compares the performance of multiple ML algorithms and prioritizes positions based on the best-fit models. It is open-source software with online documentation and examples available at https://github.com/omicsEye/deepBreaks .

  PublisherOA PDFDOI

• Genome assembly of <i>Bougainvillia</i> cf. <i>muscus</i> (Cnidaria: Hydrozoa)

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-27

  preprintOpen accessSenior author

  Abstract Background As one of just a handful of non-Bilaterian animal phyla, Cnidaria are key to understanding genome evolution across Metazoa. Despite their importance and diversity, the genomes of most species in the phylum are unsequenced, due in large part to difficulties cultivating them in a laboratory. Here, we present a genome sequence of Bougainvillia cf. mucus , a hydrozoan with four marginal bulbs each containing seven simple eyes (ocelli). This species appeared in our tanks from contamination. While we lacked sufficient samples for transcriptomic or functional studies, we were able to expand our knowledge of how the genome of this species compares to the few, better studied members of hydrozoans by investigating synteny to other cnidarians, repetitive element content, and phylogenetics and synteny of vision-related genes in this eyed species compared to eyeless relatives. Results The genome sequence consists of 350 contigs with an N50 of 10 Mb, a total genome length of 375.328 Mb, a BUSCO score of 90.1%, and predicted protein coding genes totaling 46,431. We found a high degree of macrosynteny conservation with Hydra vulgaris and Hydractinia symbiolongicarpus . Repetitive elements make up 62% of this Bougainvillia genome. For vision-related genes, we identified 20 cnidarian opsins (cnidops) in Bougainvillia and found instances of gene duplication and loss in families associated with bilaterian eye development, phototransduction, and visual cycling. Conclusions This high-quality, contiguous genome in an eyed Hydrozoan will be a valuable resource for additional comparative genomic studies.

  PublisherOA PDFDOI

• Comparative analysis of convergent jellyfish eyes reveals extensive differences in expression of vision-related genes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-17 · 1 citations

  preprintOpen accessSenior author

  Abstract Quantifying gene expression across convergent origins of traits clarifies the degree to which those traits arise from shared versus distinct genetic programs, revealing how gene re-use relates to the repeatability of evolution. Eyes are important traits that evolved in many distantly related lineages, including at least nine times within cnidarians. Here, we investigate gene expression in eye-bearing and non-visual tissues from three cnidarian species representing long-diverged lineages where eyes evolved convergently (Cubozoa, Scyphozoa, and Hydrozoa). We find gene expression in eye-bearing tissues to be mostly lineage-specific, with only a small proportion of genes having convergent expression across species. Nevertheless, all species express homologs of deeply conserved vision-related genes known from Bilateria, which likely reflects deep homology (parallel evolution across vast phylogenetic distances) of a metazoan phototransduction toolkit. A gene tree analysis of opsins—the prototypical animal photosensors—shows that convergent eyes recruited different opsin paralogs, with the potential exception of an opsin ortholog shared between scyphozoan and cubozoan eyes. Our results suggest that eyes have mostly lineage-specific patterns of gene expression, yet some key phototransduction components are repeatedly recruited across multiple independent eye origins in Medusozoa.

  PublisherOA PDFDOI

• Cnidarian Eyes as a Meta-Model to Explore Evolutionary Repeatability Over Deep Time

  Integrative and Comparative Biology · 2025-07-19

  article1st authorCorresponding

  Understanding the extent and nature of evolutionary repeatability is a fundamental goal in biology, with broad relevance to fields including protein engineering, macroevolution, and climate change biology. Studies of evolutionary repeatability often capitalize on convergent evolution as a source of natural replication to examine which genes are recruited or reused in similar traits or adaptations in different lineages. At least two key questions remain: First, how often are the same genes reused across convergent lineages; i.e., what is the extent of gene reuse? Second, what properties make genes more likely to be reused; i.e., what is the nature of gene reuse? An emerging hypothesis is that the overall extent of gene reuse declines with increasing divergence time between converged lineages. While this prediction is supported over shorter timescales, it remains insufficiently tested on deeper times. In this review, I argue that functional compatibility-the degree to which a gene's capabilities align with the functional demands of convergent traits-is a critical factor governing both the extent and nature of gene reuse. I also examine how definitions of gene reuse, ranging from identical substitutions in orthologs to recruitment of paralogs from the same gene families, might affect interpretations and quantification of gene reuse. To explore these ideas, I compare results from the fields of comparative genomics and evo-devo, highlighting possible tension between studies of shorter (<100 MY) versus longer timescales. I also present animal eyes-especially eyes of Medusozoa (Cnidaria)-as a compelling meta-model for studying evolutionary repeatability. Animal eyes have well characterized genetic and functional bases in model organisms and they evolved convergently many times, including at least nine times in cnidarians, spanning a wide range divergence times. Therefore animals eyes, especially when including Medusozoa, will have the potential to test the extent and nature of gene reuse across a wide range of divergence times, providing a more comprehensive understanding of the interplay between constraint, innovation, and divergence time across the history of life.

  PublisherDOI

Recent grants

• Collaborative Research: Phylogeny of Cnidaria - Convergent Evolution of Eyes, Gene Expression, and Cell Types

  NSF · $727k · 2022–2025

• CAREER: Exploring Congruence of Fossil and Molecular Estimates of Macroevolutionary Divergence Times in Ostracoda (Crustacea)

  NSF · $637k · 2007–2014

• RUI: Collaborative Research: Timing and Molecular Origins of Recently Evolved Chiton Shell-Eyes: Phylogenomics of Chitonina

  NSF · $350k · 2014–2018

• Dimensions: Collaborative Research: Can Evolutionary History Predict How Changes in Biodiversity Impact the Productivity of Ecosystems?

  NSF · $682k · 2010–2015

• DISSERTATION RESEARCH: Tracing the Origins and History of Animal Phototransduction using Phylogenetic Approachs

  NSF · $12k · 2007–2009

Frequent coauthors

• Daniel I. Speiser

  University of South Carolina Sumter

  42 shared

• Alexander K. Zaharoff

  University of California, Santa Barbara

  28 shared

• Thomas M. Cronin

  26 shared

• Megan L. Porter

  University of Hawaiʻi at Mānoa

  26 shared

• Roy L. Caldwell

  25 shared

• E. Ann Ellis

  University of Surrey

  22 shared

• Bradley J. Cardinale

  Pennsylvania State University

  18 shared

• Markos A. Alexandrou

  Bangor University

  17 shared

Education

• B.S.

  University of Wisconsin-Milwaukee

• M.S.

  University of Wisconsin-Milwaukee

• Ph.D., Biological Sciences

  Duke University