Birds are where we connect molecules to whole-animal outcomes. Using genomics, transcriptomics (including single-cell), metabolomics, and peptidomics, we trace how the reproductive and stress axes — and the gut–brain–microbiome network around them — shape fertility, health, and resilience in poultry.
Fertility
Broiler-breeder fertility is declining, and both the industry and global protein supply feel it — we’ve made the case for treating it as an urgent research priority (Cash, Witherspoon & Athrey, Poultry Science 2025). Our experiments map how it declines: in breeder males, sperm morphology deteriorates along rapid, non-linear trajectories across the productive period (Witherspoon et al., Poultry Science 2026) — work aimed at turning these patterns into early biomarkers producers can act on.
Gut–brain & circadian biology
We trace the gut–microbiome–brain–immune conversation from the environment inward: photoperiod and circadian disruption reshape the microbiota chicks acquire (Hieke, Hubert & Athrey, PeerJ 2019), and early-life light during incubation reprograms the immune transcriptome (Ibrahim et al., Frontiers in Genetics 2021). Most recently we resolved the circadian regulation of gut-microbiome–brain crosstalk in early life (Gupta et al., Microorganisms 2025), alongside work on how stress and diet move the microbiome, plasma chemistry, and cytokine and antioxidant status of broilers (Nelson et al., Poultry Science 2020) and the sampling rigor it demands (Williams & Athrey, Microorganisms 2020).
Comparative & population genomics
Before form can be connected to function, the genome has to be read accurately and its variation understood. Comparative and population genomics are the foundation the interaction-network work is built on — the map that makes the fertility and gut–brain questions tractable. We build reference-scale resources, including a pangenome graph of 30 chicken genomes that captures the large structural variants standard references miss (Rice et al., BMC Biology 2023), and study how domestication reshapes genomes — for example, increasing interspecific hybrid compatibility across landfowl (Alfieri et al., Journal of Heredity 2024). The same lens runs through our wild-bird work, from peregrine-falcon diversity and inbreeding across subspecies (Johnson et al., Ecology & Evolution 2023) to effective population size in captive flocks (Athrey et al., PeerJ 2018), grounded in a long line of conservation genetics beginning with the endangered black-capped vireo (Athrey et al., Evolutionary Applications 2012). And because these questions increasingly demand cellular resolution, we wrote the playbook for single-cell sequencing in non-model organisms (Alfieri et al., Genes 2022). Quantify variation and understand form — and the networks above become interpretable.