David B. Stern

Research

Areas of Investigation

Mechanisms of repeated evolution

Convergent and parallel evolution is among the strongest evidence for the power of natural selection, yet the mechanisms that promote repeated evolution remain poorly understood. My research integrates evolutionary genetics, population genomics, and bioinformatics to understand how organisms adapt to novel environments. Using evolve-and-resequence experiments, comparative genomics, and computational approaches, I investigate the genomic basis of parallel adaptation in both macro- and microorganisms, including how balancing selection and epistasis promote parallel genomic responses, and how cave-adapted organisms repeatedly lose complex traits like vision. My goal is to uncover generalizable mechanisms of adaptation to enable effective prediction of evolution in changing environments.

Biosurveillance and bioforensics

Much of my recent work involves developing bioinformatics tools for biosurveillance and bioforensics. This includes population genetics from complex samples, characterizing novel genomic elements, and large-scale whole-genome phylogenetics. Current interests include developing methods to benchmark protein structure-based phylogeny inference, using genomic foundation models to detect anomalous sequence in genome assemblies, and benchmarking scientific reasoning in AI systems.

Manhattan plot showing genome-wide parallel selection signals in copepods

Mechanisms of Parallel Adaptation

Selected Publications

Genome-wide signatures of synergistic epistasis during parallel adaptation in a Baltic Sea copepod. Stern DB, Anderson NW, Diaz JA, Lee CE. Nature Communications, 2022.

Evolutionary origins of genomic adaptations in an invasive copepod. Stern DB, Lee CE. Nature Ecology & Evolution, 2020.

The evolution of gene expression underlying vision loss in cave animals. Stern DB, Crandall KA. Molecular Biology & Evolution, 2018.

Microbial Genomics

Selected Publications

Novel toxin biosynthetic gene cluster in harmful algal bloom-causing Heteroscytonema crispum. Stern DB, Raborn RT, Lovett SP, Boise NR, et al. Genome Biology and Evolution, 2025.

Hybridization capture sequencing for Vibrio spp. and associated virulence factors. Brumfield KD, Enke S, Swan BK, ..., Stern DB, et al. mBio, 2025.

Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection. Nashed L, Mani J, Hazrati S, Stern DB, et al. Gut, 2022.

Ecological Genomics

Selected Publications

Local adaptation despite gene flow in copepod populations across salinity and temperature gradients in the Baltic and North Seas. Diaz JA, Stern DB, Lee CE. Diversity and Distributions, 2026.

Phototransduction gene expression and evolution in cave and surface crayfishes. Stern DB, Crandall KA. Integrative and Comparative Biology, 2018.

Phylogenetic evidence from freshwater crayfishes that cave adaptation is not an evolutionary dead-end. Stern DB, Breinholt J, Pedraza-Lara C, ..., Crandall KA. Evolution, 2017.

Bioinformatics Resources

Selected Publications

A phylogenetic framework to simulate synthetic interspecies RNA-Seq data. Bastide P, Soneson C, Stern DB, Lespinet O, Gallopin M. Molecular Biology and Evolution, 2023.

Hemiptera phylogenomic resources: tree-based orthology prediction and conserved exon identification. Owen CL, Stern DB, Hilton SK, Crandall KA. Molecular Ecology Resources, 2020.

Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions. Tonini J, Moore A, Stern DB, Shcheglovitova M, Ortí G. PLoS currents, 2015.

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