Leonardo Campagna
Assistant Director, Fuller Evolutionary Biology Program
Expertise
Evolutionary Biology • Genomics • Speciation • Phylogeography • Neotropical Ornithology
I use genomic tools, like obtaining the DNA sequences from entire genomes of many species, to study the evolution of avian systems, generally in the early stages of speciation. I use this and similar strategies to understand the evolutionary processes that generate differences among species.
I’m particularly interested in exploring how changes in genomic DNA sequences lead to differences in the general appearance (e.g., morphology or coloration) and behavior of the incredible diversity of birds. One example is finding the genes that are responsible for the different coloration patterns among male capuchino seedeaters (genus Sporophila).
A part of my work also focuses on studying the patterns of genetic differentiation among individuals and populations across landscapes, with the objective to uncover the geological and demographic processes that contribute to genetic differentiation.
Education
Ph.D., University of Buenos Aires
Recent Publications
2804417
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https://www.birds.cornell.edu/home/wp-content/plugins/zotpress/
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Sutter, S. M., O. G. Rogers, D. L. Bilezikian, C. B. Dillman, T. J. Porri, L. F. Silveira, S. P. Turbek, L. A. Estroff, and L. Campagna (2025). A multiscale physicochemical characterization of melanin-based feather coloration in the rapid capuchino seedeater radiation. [Online.] Available at
Recuerda, M., S. Kraemer, J. R. R. Rosoni, M. Repenning, M. Browne, J. F. Cataudela, A. S. Di Giacomo, C. Kopuchian, and L. Campagna (2025). A pangenomic approach reveals the sources of genetic variation fueling the rapid radiation of capuchino seedeaters. Evolution:qpaf188.
Céspedes Arias, L. N., A. M. Cuervo, C. D. Cadena, E. Bonaccorso, C. Witt, I. Lovette, and L. Campagna (2025). History of divergence and gene flow shaping geographic variation in Andean warblers ( Myioborus ). [Online.] Available at
Arias, L. C., K. F. P. Bennett, L. Campagna, A. W. Wood, E. Bonaccorso, A. M. Cuervo, C. D. Cadena, I. J. Lovette, and D. P. L. Toews (2025). Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics. [Online.] Available at
Lavinia, P. D., L. Campagna, M. Carboni, A. S. Barreira, S. C. Lougheed, P. L. Tubaro, and D. A. Lijtmaer (2025). Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow ( Zonotrichia capensis ). Evolution 79:1310–1321.
Bonar, M., A. J. Blumenfeld, N. A. Fusco, L. Campagna, A. Timpson, M. G. Thomas, B. J. Cosentino, J. P. Gibbs, and A. Caccone (2025). Natural selection beyond city limits. [Online.] Available at
Bukowski, B., L. Campagna, G. S. Cabanne, P. L. Tubaro, and D. A. Lijtmaer (2024). Genetic and phenotypic differentiation in Thamnophilus ruficapillus , a Neotropical passerine with disjunct distribution in the Andean and Atlantic forests. Journal of Avian Biology:e03293.
Recuerda, M., and L. Campagna (2024). How structural variants shape avian phenotypes: Lessons from model systems. Molecular Ecology:e17364.
Kasinsky, T., N. Rosciano, J. A. Vianna, P. Yorio, and L. Campagna (2024). Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia. PLOS ONE 19:e0301004.
Nguyen, T. N., M. Repenning, C. Suertegaray Fontana, and L. Campagna (2024). Genomic islands of speciation harbor genes underlying coloration differences in a pair of Neotropical seedeaters. Evolution:qpae051.
Taff, C. C., S. M. McNew, L. Campagna, and M. N. Vitousek (2024). Corticosterone exposure is associated with long‐term changes in DNA methylation, physiology and breeding decisions in a wild bird. Molecular Ecology 33:e17456.
Bukowski, B., L. Campagna, M. J. Rodríguez‐Cajarville, G. S. Cabanne, P. L. Tubaro, and D. A. Lijtmaer (2023). The role of glaciations in the evolutionary history of a widely distributed Neotropical open habitat bird. Journal of Biogeography:jbi.14738.
García, N. C., L. Campagna, A. C. Rush, R. C. K. Bowie, and I. J. Lovette (2023). Comparative genomics of two Empidonax flycatchers reveal candidate genes for bird song production. Evolution 77:1818–1828.
Palacios, C., L. Campagna, J. L. Parra, and C. D. Cadena (2023). Mito-nuclear discordance in the phenotypically variable Andean hummingbirds Coeligena bonapartei and Coeligena helianthea (Trochilidae). Biological Journal of the Linnean Society 139:145–157.
Di Giacomo, A. S., C. Kopuchian, and L. Campagna (2023). Los enigmáticos capuchinos. Aves Argentinas 66:10–19.
Campagna, L., Z. Mo, A. Siepel, and 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:e1010474.
Rohwer, S., C. S. Wood, J. L. Peters, E. T. Miller, D. Cagley, B. G. Butcher, K. L. Epperly, and L. Campagna (2022). Interspecific forced copulations generate most hybrids in broadly sympatric ducks. PLOS ONE 17:e0274059.
Rojas Ripari, J. M., L. Campagna, B. Mahler, I. Lovette, J. C. Reboreda, and M. C. De Mársico (2022). Family ties in a neotropical cooperative breeder: within‐group relatedness and fine‐scale genetic structure in the greyish Baywing ( Agelaioides badius ). Ibis:ibi.13108.
Arrieta, R. S., L. Campagna, B. Mahler, I. Lovette, and P. E. Llambías (2022). Local male breeding density affects extra‐pair paternity in a south temperate population of grass wrens Cistothorus platensis. Journal of Avian Biology. https://doi.org/10.1111/jav.02887
de Freitas, E. L., L. Campagna, B. Butcher, I. Lovette, and R. Caparroz (2022). Ecological traits drive genetic structuring in two open‐habitat birds from the morphologically cryptic genus Elaenia (Aves: Tyrannidae). Journal of Avian Biology:jav.02931.
Estalles, C., S. P. Turbek, M. José Rodríguez-Cajarville, L. F. Silveira, K. Wakamatsu, S. Ito, I. J. Lovette, P. L. Tubaro, D. A. Lijtmaer, and L. Campagna (2022). Concerted variation in melanogenesis genes underlies emergent patterning of plumage in capuchino seedeaters. Proceedings of the Royal Society B: Biological Sciences 289:20212277.
Hejase, H. A., Z. Mo, L. Campagna, and A. Siepel (2022). A deep-learning approach for inference of selective sweeps from the ancestral recombination graph. Molecular Biology and Evolution 39:msab332.
Arrieta, R. S., L. Campagna, B. Mahler, and P. E. Llambías (2022). Neither paternity loss nor perceived threat of cuckoldry affects male nestling provisioning in grass wrens. Behavioral Ecology and Sociobiology 76:147.
Campagna, L., and D. P. L. Toews (2022). The genomics of adaptation in birds. Current Biology 32:R1173–R1186.
Rodríguez‐Cajarville, M. J., L. Campagna, C. A. Lima‐Rezende, M. Carboni, P. L. Tubaro, and G. S. Cabanne (2022). Genomic and phenotypic divergence‐with‐gene‐flow across an ecological and elevational gradient in a neotropical bird. Journal of Biogeography 49:1535–1548.
Turbek, S. P., G. A. Semenov, E. D. Enbody, L. Campagna, and S. A. Taylor (2021). Variable signatures of selection despite conserved recombination landscapes early in speciation. Journal of Heredity:esab054.
Hejase, H. A., Z. Mo, L. Campagna, and A. Siepel (2021). SIA: Selection Inference Using the Ancestral Recombination Graph. bioRxiv.
Arrieta, R. S., L. Campagna, B. Mahler, I. Lovette, and P. E. Llambías (2021). Double-digest RAD sequencing reveals low rates of conspecific brood parasitism and no cases of quasi-parasitism in a Neotropical passerine. The Wilson Journal of Ornithology 132.
Turbek, S. P., M. Browne, A. S. Di Giacomo, C. Kopuchian, W. M. Hochachka, C. Estalles, D. A. Lijtmaer, P. L. Tubaro, L. F. Silveira, I. J. Lovette, R. J. Safran, et al. (2021). Rapid speciation via the evolution of pre-mating isolation in the Iberá Seedeater. Science 371:eabc0256.
Walsh, J., L. Campagna, W. E. Feeney, J. King, and M. S. Webster (2021). Patterns of genetic divergence and demographic history shed light on island-mainland population dynamics and melanic plumage evolution in the white-winged Fairywren. Evolution. https://doi.org/https://doi.org/10.1111/evo.14185
Berv, J. S., L. Campagna, T. J. Feo, I. Castro-Astor, C. C. Ribas, R. O. Prum, and I. J. Lovette (2021). Genomic phylogeography of the White-crowned Manakin Pseudopipra pipra (Aves: Pipridae) illuminates a continental-scale radiation out of the Andes. Molecular Phylogenetics and Evolution 164:107205.
Rabinowicz, S., N. García, T. Herwood, A. Lazar, B. Hein, E. Miller, and L. Campagna (2020). An avian dominance hierarchy at a supplemental water source in the Patagonian steppe. PLOS ONE 15:e0244299.
Hejase, H. A., A. Salman-Minkov, L. Campagna, M. J. Hubisz, I. J. Lovette, I. Gronau, and A. Siepel (2020). Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences 117:30554–30565.
Palacios, C., L. Campagna, J. L. Parra, and D. Cadena (2020). Complete mitochondrial genomes do not distinguish phenotypically distinct lineages of Andean Coeligena hummingbirds. biorxiv.
Kopuchian, C., L. Campagna, D. A. Lijtmaer, G. S. Cabanne, N. C. García, P. D. Lavinia, P. L. Tubaro, I. Lovette, and A. S. Di Giacomo (2020). A test of the riverine barrier hypothesis in the largest subtropical river basin in the Neotropics. Molecular Ecology 29:2137–2149.
Lois, N. A., L. Campagna, U. Balza, M. J. Polito, K. Pütz, J. A. Vianna, A. Morgenthaler, E. Frere, R. Sáenz‐Samaniego, A. Raya Rey, and B. Mahler (2020). Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the Southern Rockhopper Penguin. Ecology and Evolution 10:3346–3355.
Poblete, Y., G. E. Soto, L. Campagna, M. E. Ávila, C. Fernández, C. R. Flores, and A. D. Rodewald (2020). Deforestation patterns shape population structure of the Magellanic Woodpecker (Campephilus magellanicus) in southern Chile. Avian Conservation and Ecology 15:art19.
Baldassarre, D. T., L. Campagna, H. A. Thomassen, J. W. Atwell, M. Chu, L. H. Crampton, R. C. Fleischer, and C. Riehl (2019). GPS tracking and population genomics suggest itinerant breeding across drastically different habitats in the Phainopepla. The Auk 136:ukz058.
Campagna, L., K. G. McCracken, and I. J. Lovette (2019). Gradual evolution towards flightlessness in steamer ducks. Evolution 73:1916–1926.
Lavinia, P. D., A. S. Barreira, L. Campagna, P. L. Tubaro, and D. A. Lijtmaer (2019). Contrasting evolutionary histories in Neotropical birds: divergence across an environmental barrier in South America. Molecular Ecology. https://doi.org/10.1111/mec.15018
Taff, C. C., L. Campagna, and M. N. Vitousek (2019). Genome‐wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird. Molecular Ecology 28:3722–3737.
Cabanne, G. S., L. Campagna, N. Trujillo-Arias, K. Naoki, I. Gómez, C. Y. Miyaki, F. R. Santos, G. P. M. Dantas, A. Aleixo, S. Claramunt, A. Rocha, et al. (2019). Phylogeographic variation within the Buff-browed Foliage-gleaner (Aves: Furnariidae: Syndactyla rufosuperciliata) supports an Andean-Atlantic forests connection via the Cerrado. Molecular Phylogenetics and Evolution 133:198–213.
Campagna, L., and T. D. Price (2019). Flying up the bird tree. Trends in Ecology & Evolution 34:1–2.
Campagna, L., P. Rodriguez, and J. C. Mazzulla (2018). Transgressive phenotypes and evidence of weak postzygotic isolation in F1 hybrids between closely related capuchino seedeaters. PLOS ONE 13:e0199113.
Campagna, L. (2018). Among Ruffs, Some “Fight-Loving Fighters” Don’t Like to Fight. Living Bird.
Aguillon, S. M., L. Campagna, R. G. Harrison, and I. J. Lovette (2018). A flicker of hope: Genomic data distinguish Northern Flicker taxa despite low levels of divergence. The Auk 135:748–766.
Thrasher, D. J., B. G. Butcher, L. Campagna, M. S. Webster, and I. J. Lovette (2018). Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: A proof of concept in a highly promiscuous bird. Molecular Ecology Resources 18:953–965.
Toews, D. P. L., J. Walsh, and L. Campagna (2018). Population Genomics of Birds: Evolutionary History and Conservation. In Population Genomics: Wildlife. Springer International Publishing, Cham.
Van Doren, B. M., L. Campagna, B. Helm, J. C. Illera, I. J. Lovette, and M. Liedvogel (2017). Correlated patterns of genetic diversity and differentiation across an avian family. Molecular Ecology 26:3982–3997.
Campagna, L., M. Repenning, L. F. Silveira, C. S. Fontana, P. L. Tubaro, and I. J. Lovette (2017). Repeated divergent selection on pigmentation genes in a rapid finch radiation. Science Advances 3:e1602404.
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