Research Overview

For nearly two decades, our research has focused on understanding the origin and maintenance of biological diversity in the tropics, the cradle of our planet’s diversity. Our work explores how populations change to adapt to their physical and social environments, and how these changes, in turn, can result in reproductive barriers. To this end, my research group explores two major foci. First, we explore how changes in the ways animals communicate can lead to reproductive barriers between populations — the hallmark of biological species. For instance, we explore how changes in plumage color and song in birds, which are traits used in choosing and competing for mates, can result in premating reproductive barriers between populations. Second, we explore how populations change to more effectively exploit their biotic and abiotic environments, and how these changes can likewise lead to reproductive barriers and the maintenance of species boundaries. We explore, for example, how novel environments, including urbanization, drive changes for more efficient feeding and communication.

For both foci, we take advantage of species with populations currently adapting to their environment and/or are on the verge of becoming new species. In these projects, we use an integrative approach to determine the molecular basis and genomic consequences of adaptive change by combining long-term field observations and experiments with cutting-edge approaches in genomics, proteomics, and developmental biology.

Speciation in Birds

Our long-term work in the Solomon Islands takes advantage of a single species of bird with populations on the verge of splitting into several species. Described by Ernst Mayr in his foundational book on evolution as an exemplar case of incipient speciation (Systematics & the Origin of Species, 1942), populations of the Monarcha castaneiventris vary in plumage color and song throughout the Solomon Islands. For the past ten years, we have explored the ecology and genetics of plumage and song divergence, using a combination of genomic, and long-term field approaches. Thus far, we have found that 1) the differences in  plumage color and song among populations are indeed used in recognizing conspecifics and thus may result in reproductive barriers (i.e., incipient species), 2) simple point mutations mediate the significant differences in plumage color among islands, 3) convergent plumage color across islands are mediated by unique mutations in different genes, and 4) strong disruptive selection keeps the populations distinct in plumage color despite substantial gene flow between islands. These results suggest that the origin of species can be initiated by intense selection acting on simple point mutations. Ongoing long-term work builds on these results to further explore 1) the ecology and population genomics of adaptive changes, 2) the genetic basis of diverse plumage patterns, and 3) the consequences of divergent female choice.

To learn more about our research, please visit our lab website.

Research Interests

• Evolutionary Ecology
• Behavioral Ecology
• Evolutionary Genetics
• Speciation
• Conservation

Selected Publications

• Campagna, L., Z. Mo, A. Siepel & J.A.C. Uy. 2022. Selective sweeps on different pigmentation genes mediate convergent evolution of island melanism in two incipient bird species. PLoS Genetics. 18(11): e1010474. 
• Ocampo, D., K. Winker, M.J. Miller, L. Sandoval & J.A.C. Uy. 2022. Rapid diversification of the Variable Seedeater superspecies complex despite widespread gene flow. Molecular Phylogenetics & Evolution 173: 107510. 
• Cowles, S.A. & J.A.C. Uy. 2019. Rapid, complete reproductive isolation in two closely related Zosterops White‐eye bird species despite broadly overlapping ranges. Evolution 73:1647-1662. 
• Uy, J.A.C., D.E. Irwin & M. Webster. 2018. Behavioral isolation and incipient speciation in birds. Annual Review of Ecology, Evolution & Systematics 49: 1-24.  
• Uy, J.A.C., E.A. Cooper, S. Cutie, M.R. Concannon, J. Poelstra, R.G. Moyle & C.E. Filardi.  2016. Mutations in different genes mediate convergent melanism between isolated populations of an island flycatcher. Proceedings of the Royal Society of London, Series B 283: 20160731.  
• Sardell, J.M. & J.A.C. Uy. 2016. Hybridization following recent secondary contact results in asymmetric genotypic and phenotypic introgression between island species of Myzomela honey-eaters. Evolution, 70: 257-269. 
• Chaves, J.A., E. A. Cooper, A.P. Hendry, J. Podos, L.F. De León,J.A.M. Raeymaekers, O.W. McMillan & J.A.C. Uy. 2016. Genomic variation at the tips of the adaptive radiation of Darwin’s finches. Molecular Ecology 25: 5282-5295.  
• Uy, J.A.C., R.G. Moyle, C.E. Filardi & Z.A. Cheviron. 2009. Difference in plumage color used in species recognition between incipient species is linked to a single amino acid substitution in the melanocortin-1 receptor. American Naturalist. 174: 244-254. [Chosen by Faculty of 1000].