Publications

†: Undergraduate author

  • (35) Cramer, E.R.A., Grønstøl, G., Benham, P.M., Cicero, C. Bowie, R.C.K, Tobiansky, D.J., & Lifjeld, J.T. Unusualsperm morphology in two sedentary songbird species with long-term pair bonds. In press. Ecology & Evolution.

  • (34) Benham, P.M., Cicero, C., Smith, L.L., Davila, M.M., Enbody, E.D., Shultz, A.J., Miller, K., Nachman, M.W. & Bowie, R.C.K. Genetic diversity patterns within three California quail species best explained by historical climate and landscape changes. In revision Molecular Ecology. Preprint: 10.22541/au.174465589.92389898/v1

  •  (33) Curti, J.N., MacDonald, Z.G., Benham, P.M., Bowie, R.C.K., Delaney, K.S., Harrigan, R.J., Lohmueller, K.E., Riley, S.P.D, Shultz, A.J., Wayne, R.K. & Shaffer, B.H. Why didn’t the quail cross the road? Using whole- genome data to evaluate roadways as barriers to gene flow in a North American ground-dwelling bird. In revision. Preprint: 10.22541/au.174387447.73877055/v1

  •  (32) Mateo, M.L.G.†, Benham, P.M., Bowie, R.C.K. 2025. Evidence for temporal morphological change in northern but not southern breeding Zonotrichia sparrows. Evolutionary Ecology. https://doi.org/10.1007/s10682-025-10345-4

  •  (31) Krugler, J.†, Benham, P.M., Bowie, R.C.K. 2025. Shared temporal increases in bill size among songbirds of the San Francisco Bay area are due to different seasonal selective pressures. Ecography, e07494.https://doi.org/10.1002/ecog.07494

  • (30) Benham, P.M. & Beckman, E.J. 2024. Integrating spatial analyses of genomic and physiological data to understand avian responses to environmental change. Integrative and Comparative Biology, 64: 1792–1810.https://doi.org/10.1093/icb/icae059

  • (29) Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., Nachman, M.W. & Bowie, R.C.K. 2024. Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element         discovery. Genome Biology and Evolution, 16: evae067, https://doi.org/10.1093/gbe/evae067

  •  (28) Benham, P.M., Walsh, J. & Bowie, R.C.K. 2024. Spatial variation in population genomic responses to 125 years of anthropogenic change within a tidal marsh songbird. Global Change Biology. 30: e17126, Open Access: https://doi.org/10.1111/gcb.17126

  • (27) DeRaad, D.A., Escalona, M., Benham,P.M., Marimuthu,M.P.A., Sahasrabudhe, R.M., Nguyen,O.,   Chumchim, N., Beraut,E., Fairbair, C.W., Seligmann, W., Bowie, R.C.K., Cicero,C., McCormack, J.E., Wayne, R.K. 2023. De novo assembly of a chromosome-level reference genome for the California      Scrub-Jay, Aphelocoma californica. Journal of Heredity, 114: 669-680. https://doi.org/10.1093/jhered/esad047

  • (26) Mikles, C.S.†, Arcese, P., I.J., Lovette, Aguillon, S.M., Chan, Y.L., , Benham, P.M., Carbeck, K., & Walsh, J. 2023. Evolutionary divergence and adaptive capacity in morphologically distinct Song Sparrow subspecies. Conservation Genetics, 24: 921-932. https://doi.org/10.1007/s10592-023-01547-w

  • (25) Benham, P.M., Cicero, C., DeRaad, D., McCormack, J., Wayne, R., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. 2023. A highly contiguous genome assembly for the Steller's Jay (Cyanocitta stelleri). Journal of Heredity, 114: 549-560. https://doi.org/10.1093/jhered/esad042.

  • (24) Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. 2023 A highly contiguous genome assembly for the California quail (Callipepla californica). Journal of Heredity, 114: 418-427. https://doi.org/10.1093/jhered/esad008

  • (23) Benham, P.M. & Bowie, R.C.K. 2023 Natural history collections as a resource for conservation genomics: understanding the past to preserve the future. Invited contribution to Journal of Heredity president's symposium special issue, 114: 367-384. https://doi.org/10.1093/jhered/esac066

  • (22) Linck, E.B., Williamson, J.L., Bautista, E., Beckman, E.J., Benham, P.M., DuBay, S.G., Flores, L.M., Gadek, C.R., Johnson, A.B., Jones, M.R., Núñez-Zapata, J., Quiñonez, A., Schmitt, C.J., Susanibar, D., Tiravanti C., J., Verde-Guerra, K., Wright, N.A., Valqui, T., Storz, J.F., & C.C. Witt. 2023. Blood variation implicates respiratory limits on elevational ranges of Andean birds. American Naturalist, 201: 741-754.

  • (21) Beckman, E.J., Campos, W.V., Benham, P.M., Schmitt, C.J., Cheviron, Z.A. & Witt, C.C. 2022. Selection on embryonic hemoglobin in an elevational generalist songbird. Biology Letters, 18: 20220105. https://doi.org/10.1098/rsbl.2022.0105

  • (20) Clark, J.D., P.M. Benham, J.E. Maldonado, D.A. Luther, & H.C. Lim. 2022. Genomic patterns of incipient ecological speciation in a locally adapted songbird subspecies. Evolution, 76: 1481-1494.

  • (19) Walsh, J., A.I. Kovach, P.M. Benham, G.V. Clucas, V.L. Winder, & I.J. Lovette. 2021. Genomic data reveal the biogeographic and demographic history of Ammospiza sparrows in northeast tidal marshes. Journal of Biogeography, 48: 2360-2374. https://doi.org/10.1111/jbi.14208

  • (18) Benham, P.M. & Bowie, R.C.K. 2021. The influence of spatially heterogenous anthropogenic change on bill size evolution in a coastal songbird. Evolutionary Applications, 14: 607-624. Open access: https://doi.org/10.1111/eva.13144.

  • (17) Mikles, C.S.†, Walsh, J., Aguillon, S.M., Chan, Y., Arcese, P., Benham, P.M. & I.J., Lovette. 2020. Genomic differentiation of threatened song sparrows on a microgeographic scale. Molecular Ecology, 29: 4295-4307.

  • (16) Sweazea, K.L., Tsosie, K., Beckman, E.J., Benham, P.M. & C.C. Witt. 2020 Seasonal and elevational variation in glucose and glycogen in two songbird species. Comparative Biochemistry and Physiology Part A, 245: 110703.

  • (15) Benham, P.M. & Cheviron, Z.A. 2020. Population history and the selective landscape shape patterns of     osmoregulatory trait divergence in tidal marsh Savannah sparrows (Passerculus sandwichensis). Evolution, 74: 57-72.

  • (14) Sheldon, F.H., Lim, H.C., Benham, P.M., Brady, M.L., Brown, C.E., Burner, R.C., Chua, V.L., Mittermeier, J.C., Shakya, S.B., Van Els, P., Rahman, M.A., Gawin, D.F., Rahim, Z.A., Setia, L.D., & Moyle, R.G. 2019. Ornithological expeditions to Sarawak, Malaysian Borneo, 2007-2017. Occasional Papers of the Museum of Natural Science, Louisiana State University, 90: 1-11.

  • (13) Walsh, J., Benham, P.M., Deane-Coe, P.E., Arcese, P., Butcher, B.G., Chan, Y.L., Cheviron, Z.A., Elphick, C.S., Kovach, A.I., Olsen, B.J., Shriver, W.G., Winder, V.L., & Lovette, I.J. 2019. Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows. Evolution Letters, 3: 324-338. Open access: https://doi.org/10.1002/evl3.126.

  •  (12) Benham, P.M. & Cheviron, Z.A. 2019. Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah Sparrow (Passerculus sandwichensis). Molecular Ecology, 28: 1765-1783.

  • (11) Beckman, L., Benham, P.M., Cheviron, Z.A. & Witt, C.C. 2018. Detecting introgression despite persistent phylogenetic uncertainty: the case of the South American siskins. Molecular Ecology, 27: 4350-4367.

  • (10) Stager, M., Pollock, H.S., Benham, P.M., Sly, N.D., Brawn, J.D. & Cheviron, Z.A. 2016. Disentangling environmental drivers of metabolic flexibility in birds: the importance of temperature extremes versus temperature variability. Ecography, 39: 787-795.

  •  (9) Benham, P.M & Witt, C.C. 2016 The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC Evolutionary Biology, 16:22. Open access: https://doi.org/10.1186/s12862-016-0595-2.

  •  (8) Galen, S.C., Natarajan, C., Moriyama, H., Weber, R.E., Fago, A., Benham, P.M., Chavez, A.N., Cheviron, Z.A., Storz, J.F. & Witt, C.C. 2015 Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens. Proceedings of the National Academy of Sciences, 112: 13958-    13963.

  • (7) Benham, P.M., A.M. Cuervo, J.A. McGuire & C.C. Witt. 2015. Biogeography of the Andean metaltail hummingbirds: contrasting evolutionary histories of treeline-specialist and habitat-generalist clades. Journal of Biogeography, 42: 763-777.

  • (6) Lim, H.C., Chua, V.L., Benham, P.M., Oliveros, C.H., Rahman, M.A., Moyle, R.G. & Sheldon, F.H. 2014.Divergence history of the Rufous-tailed Tailorbird (Orthotomus sericeus) in eastern Sundaland: Implications for the biogeography of Palawan and the taxonomy of island species in general. The                     Auk, 131: 629-642.  

  • (5) Sanchez, C., J. Saucier, P.M. Benham, D.F. Lane, R.E. Gibbons, T. Valqui, S. Figueroa, C.J. Schmitt, C. Sánchez, C.M. Milenski, A.G. Bravo, D.G. Olaechaea. 2012. New and noteworthy records from northwestern Peru, Dpto. Tumbes. El boletín de la Unión de Ornitólogos del Perú, 7: 18-36.

  • (4) Gibbons, R.E., P.M. Benham & J. M Maley. 2011. Notes on birds of the high Andes of Peru. Ornitología Colombiana, 11: 76-86.

  • (3) Benham, P.M., E.J. Beckman, S.G. DuBay, M. Flores, A.B. Johnson, M.J. Lelevier, C.J. Schmitt, N.A. Wright & C.C. Witt. 2011. Satellite imagery reveals new critical habitat for endangered bird species in the high Andes of Peru. Endangered Species Research, 13: 145-157.

  • (2) Hallworth, M.T., P.M. Benham, J.D. Lambert & L.R. Reitsma. 2008. Canada Warbler (Wilsonia canadensis) breeding ecology in young forest stands compared to a Red Maple (Acer rubrum) swamp. Forest Ecology and Management, 255, 1353-1358.

  • (1) Reitsma, L.R, M.T. Hallworth & P.M. Benham. 2008. Does age influence territory size, habitat selection, and reproductive success of male Canada Warblers in Central New Hampshire? Wilson Journal of Ornithology, 120, 446-454.