Publications

Have a look at our work on Google Scholar.

Rick, J.A., C.D. Brock, A.L. Lewanski, J. Golcher Benavides, C.E. Wagner. 2023. Reference genome choice and filtering thresholds jointly influence phylogenomic analyses. In press, Systematic Biology.

Meier, J.M, M.D. McGee, D.A. Marques, S. Mwaiko, M. Kishe, S. Wandera, D. Neumann, H. Mrosso, L.J. Chapman, C.A. Chapman, L. Kaufman, A. Taabu-Munyaho, C.E. Wagner, R. Bruggmann, L. Excoffier, O. Seehausen. 2023. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science, 38, eade2833.

Rolland, J., Henao-Diaz, L.F., Doebeli, M., R. Germain, L.J. Harmon, L.L. Knowles, L.H. Liow, J.E. Mank, A. Machac, S.P. Otto, M. Pennell, N. Salamin, D. Silvestro, M. Sugawara, J. Uyeda, C.E. Wagner, D. Schluter. Conceptual and empirical bridges between micro- and macroevolution. Nature Ecology Evolution 7, 1181–1193 (2023).  

Combrink, L., W.C. Rosenthal, L. Boyle, J. Rick, A. Krist, A. Walters, C.E. Wagner. 2023. Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments. Evolution, 77(7): 1522–1538. See media coverage on Science Friday, Wyoming Public Media, The Washington Post, Jackson Hole News & Guide, and more!

Lewanski, A.L, J. Golcher Benavides, J.A. Rick, C.E. Wagner. 2022. Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact. Molecular Ecology 31(16):5041–5059.

Rosenthal, W.C., J.M. Fennell, E.G. Mandeville, J.C. Burckhardt, A.W Walters and C.E. Wagner. 2022. Hybridization decreases native cutthroat trout reproductive fitness. Molecular Ecology 31(16):4224-4241.

J.M. Fennell, W.C. Rosenthal, C.E. Wagner, J.C. Burckhardt, A.W. Walters. 2022. Temporal segregation in spawning between native Yellowstone cutthroat trout and introduced rainbow trout. Ecology of Freshwater Fish, 32, 94–106.

J.A. Rick, J. Junker, I.A. Kimirei, E.A. Sweke, J.B. Mosille, C. Dinkel, S. Mwaiko, O. Seehausen, C.E. Wagner. 2022. The genetic population structure of Lake Tanganyika’s Lates species flock, an endemic radiation of top predators. Journal of Heredity 113(2): 145-159.

L.J.M. Milec, M.P.M. Vanhove, F.M. Bukinga, E.L.R. De Keyzer, V.L. Kapepula, P.M. Masilya, N. Mulimbwa, C.E. Wagner, J.A.M. Raeymaekers. 2022. Complete mitochondrial genomes and updated divergence time of the two freshwater clupeids endemic to Lake Tanganyika (Africa) suggest intralacustrine speciation. BMC Ecology and Evolution 22(1): 1-17.

Wagner, C.E. 2021. Ecological opportunity, genetic variation, and the origins of African cichlid radiations. In: M.E. Abate and D.L.G. Noakes, editors, The behavior, ecology and evolution of cichlid fishes. Springer.

Overcast, I, M. Ruffley, J. Rosindell, L. Harmon, P.A.V. Borges, B.C. Emerson, R.S. Etienne, R. Gillespie, H. Krehenwinkel, D.L. Mahler, F. Massol, C.E. Parent, J. Patiño, B. Peter, B. Week, C.E. Wagner, M.J. Hickerson, A. Rominger. 2021. A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities. Mol. Ecol. Resources 21(8):2782-2800.

Nordberg, B.J., E.G. Mandeville, A.W. Walters, J.C. Burckhardt, C.E. Wagner. 2021. Historical data provide important context for understanding declines in cutthroat trout. North American Journal of Fisheries Management 41:809-819.

Klobucar, S.L., J.A. Rick, E.G. Mandeville, C.E. Wagner, P. Budy. 2021. Investigating the morphological and genetic divergence of arctic char (Salvelinus alpinus) populations in lakes of arctic Alaska. Ecology and Evolution 11 (7), 3040-3057. Link.

Junker, J., J. Rick, P.B. McIntyre, I. Kimirei, E.A. Sweke, J.B. Mosille, B. Wehrli, C. Dinkel, S. Mwaiko, O. Seehausen, C.E. Wagner. 2020. Sex differentiation and a chromosomal inversion lead to cryptic diversity in Lake Tanganyika sardines. Molecular Ecology 29 (17), 3277-3298. Link.

Gillespie, R.G., G.M. Bennett, L. De Meester, J.L. Feder, R.C. Fleischer, L.J. Harmon, A.P. Hendry, M.L. Knope, J. Mallet, C. Martin, C.E. Parent, A.H. Patton, K.S. Pfennig, D. Rubinoff, D. Schluter, O. Seehausen, K.L. Shaw, E. Stacy, M. Stervander, J.T. Stroud, C.E. Wagner, Guinevere O.U. Wogan. 2019. Comparing adaptive radiations across space, time, and taxa. Journal of Heredity, in press. doi:10.1093/jhered/esz064. Link.

McGill, B.J., J.M. Chase, J. Hortal, I. Overcast, A.J. Rominger, J. Rosindell, P.A.V. Borges, B.C. Emerson, R. Etienne, M.J. Hickerson, D.L. Mahler, F. Massol, A. McGaughran, P. Neves, C. Parent, J. Patiño, M. Ruffley, C.E. Wagner, R. Gillespie. 2019. Unifying macroecology and macroevolution to answer fundamental questions about biodiversity. Global Ecology and Biogeography, 29(6):1095.

Meier, J.I., R.B. Stelkens, D.A. Joyce, S. Mwaiko, N. Phiri, U.K. Schliewen, O.M. Selz, C.E. Wagner, C. Katongo, O. Seehausen. 2019. The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlids. Nature Communications, 10(1):1-11.

Mandeville, E.G., A.W. Walters, B.J. Nordberg, K.H. Higgins, J.C. Burckhardt, and C.E. Wagner. 2019. Variable hybridization outcomes in trout are predicted by historical fish stocking and environmental context. Molecular Ecology, 28: 3738-3755

Golcher-Benavides, J. and C.E. Wagner. 2019. Playing out Liem’s paradox: opportunisitic piscivory across Lake Tanganyikan cichlids. American Naturalist, 194(2):260-267. (See also News & Views piece on this work in Nature)

Brock, C.D., and C.E. Wagner. 2018. The smelly path to sympatric speciation? Molecular Ecology, 27:4153–4156. Link.

Dönz, C., D. Bittner, P Vonlanthen, C.E. Wagner, O. Seehausen. 2018. Rapid buildup of sympatric species diversity in Alpine whitefish. Ecology & Evolution 8:9398–9412. Link.

Karvonen, A., C.E. Wagner, O.M. Selz, O. Seehausen. 2018. Divergent parasite infections in sympatric cichlid species in Lake Victoria. Journal of Evolutionary Biology 31:1313-1329. Link.

Meier, J.I., D.A. Marques, C.E. Wagner, L. Excoffier, O. Seehausen. 2018. Genomics of parallel ecological speciation in Lake Victoria cichlids. Molecular Biology and Evolution 35(6):1489-1506. Link.

Wagner, C.E.. 2018. Improbable big birds. Science 359:157-159. Link.

Wagner, C.E. and E.G. Mandeville. 2017. Speciation, species persistence and the goals of studying genomic barriers to gene flow. Journal of Evolutionary Biology 30:1512-1515. Link.

Mahler, D.L., M.G. Weber, C.E. Wagner, T. Ingram. 2017. Pattern and process in the comparative study of convergent evolution. The American Naturalist, 190(S1):S13-S28. Link.

Meier, J.I., D.A. Marques, S. Mwaiko, C.E. Wagner, L. Excoffier, O. Seehausen. 2017. Ancient hybridization fuels cichlid fish adaptive radiations. Nature Communications, 8:14363. Link. *Recommended by Faculty of 1000

Weber, M.G., C.E. Wagner, R.G. Best, L.J. Harmon, B. Matthews. 2017. Evolution in a community context: On integrating ecological interactions and macroevolution. Trends in Ecology and Evolution, 32(4): 291-304. Link.

Meier, J.I., V.C. Sousa, D.A. Marques, O.M. Selz, C.E. Wagner, L. Excoffier, O. Seehausen. 2017. Demographic modeling with whole genome data reveals parallel origin of similar Pundamilia cichlid species after hybridization. Molecular Ecology, 26: 123-141. Link.

Marques, D.A., K. Lucek, M.P. Haesler, A.F. Feller, J.I. Meier, C.E. Wagner, L. Excoffier, O. Seehausen. 2017. Genomic landscape of early ecological speciation initiated by selection on nuptial color. Molecular Ecology, 26: 7-24. Link.

Marques, D.A., K. Lucek, J.I. Meier, S. Mwaiko, C.E. Wagner, L. Excoffier, O. Seehausen. 2016. Genomics of rapid incipient speciation in sympatric threespine stickleback. PLoS Genetics 12(2): e1005886. Link.

Seehausen, O., and C.E. Wagner. 2014. Speciation in freshwater fishes. Annual Review of Ecology, Evolution, and Systematics. 45: 621-651. Link.

Brawand, D.*, C.E. Wagner*, Y. Li*, et al. 2014. The genomic substrate for adaptive radiation in African cichlid fish. Nature, 513: 375-381. Link.  (*these authors contributed equally)

Wagner, C.E., L.J. Harmon, and O. Seehausen. 2014. Cichlid species-area relationships are shaped by adaptive radiations that scale with area. Ecology Letters, 17: 583-592. Link.
*Recommended by Faculty of 1000

Seehausen, O., R.K. Butlin, I. Keller, C.E. Wagner, et al. 2014. Genomics and the origin of species. Nature Reviews Genetics, 15: 176-192. Link.

Wagner, C.E., I. Keller, S. Wittwer, O.M. Selz, S. Mwaiko, L. Greuter, A. Sivasundar, O. Seehausen. 2013. Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation. Molecular Ecology, 22:787-798. Link.

Keller, I., C.E. Wagner, L. Greuter, S. Mwaiko, O.M. Selz, A. Sivasundar, S. Wittwer, O. Seehausen. 2013. Population genomic signatures of divergent adaptation, gene flow, and hybrid speciation in the rapid radiation of Lake Victoria cichlid fishes. Molecular Ecology, 22:2848-2863. Link.

Wagner, C.E., L.J. Harmon, and O. Seehausen. 2012. Ecological opportunity and sexual selection together predict adaptive radiation. Nature, 487:366-369. Link.

Wagner, C.E., A.R. McCune, I.J. Lovette. 2012. Recent speciation between sympatric Tanganyikan cichlid color morphs. Molecular Ecology, 21:3283-3292. Link.

Junker, J., A. Peter, C.E. Wagner, S. Mwaiko, B. Germann, O. Seehausen, I. Keller. 2012. River fragmentation increases localized population genetic structure and enhances asymmetry of dispersal in bullhead (Cottus gobio). Conservation Genetics,13:545-556. Link.

Wagner, C.E. and A.R. McCune. 2009. Contrasting patterns of spatial genetic structure in sympatric rock-dwelling cichlid fishes. Evolution 63:1312-1326. Link.

Wagner, C.E.*, P.B. McIntyre*, K. Smith and E. Michel. 2009. Diet predicts intestine length in Lake Tanganyika’s cichlid fishes. Functional Ecology 23:1122-1131. Link. (*these authors contributed equally)

Capps, K. A., M. A. Davison, Y. A. Kapetanakos, J. M. Moslemi, C.E. Wagner and A. Flecker. 2009. Crossing borders: promoting graduate research in the developing world. Frontiers in Ecology and the Environment 7:333-334.