Google Scholar Profile
In revision/review:
Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W. & Bowie, R.C.K. Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery. in review. Genome Biology and Evolution. Preprint on bioRxiv: https://doi.org/10.1101/2023.10.26.564301
2024
Benham, P.M., Walsh, J. & Bowie, R.C.K. Spatial variation in population genomic responses to 125 years of anthropogenic change within a tidal marsh songbird. 30, e17126. Open access:
https://doi.org/10.1111/gcb.17126
Press: The Wildlife Society, Berkeley News, Phys.org, EurekAlert, earth.com
2023
Mikles, C.S., Arcese, P., I.J., Lovette, Aguillon, S.M., Chan, Y.L., , Benham, P.M., Carbeck, K., & Walsh, J. 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
DeRaad, D.A., Escalona, M., Benham, P.M., Marimuthu, M.P.A., Sahasrabudhe, R.M., Nguyen, O., Chumchim, N., Beraut, E., Fairbairn, C.W., Seligmann, W., Bowie, R.C.K., Cicero, C., McCormack, J.E., Wayne, R.K. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. Journal of Heredity, 114, 669-680. Open access: https://doi.org/10.1093/jhered/esad047
Benham, P.M., Cicero, C., DeRaad, D.A., McCormack, J.E., Wayne, R.K., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri). Journal of Heredity, 114, 549-560. Open Access: https://doi.org/10.1093/jhered/esad042
Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. A highly contiguous genome assembly for the California quail (Callipepla californica). Journal of Heredity, 114, 418-427. https://doi.org/10.1093/jhered/esad008
Benham, P.M. & Bowie, R.C.K. 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
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. Blood variation implicates respiratory limits on elevational ranges of Andean birds. American Naturalist. 201: 741-754.
2022
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 PDF
Clark, J.D., P.M. Benham, J.E. Maldonado, D.A. Luther, & H.C. Lim. Genomic patterns of incipient ecological speciation in a locally adapted songbird subspecies. Evolution, 76: 1481-1494. https://doi.org/10.1111/evo.14538 PDF
2021
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. PDF
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. PDF
Featured in The Scientist Magazine
2020
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. PDF
Sweazea, K.L., Tsosie, K., Beckman, E.J., Benham, P.M. & C.C. Witt. Seasonal and elevational variation in glucose and glycogen in two songbird species. Comparative Biochemistry and Physiology, Part A, 245: 1-6. PDF
Benham, P.M. & Cheviron, Z.A. Variation in demographic history and the selective landscape shape nonparallel patterns of functional divergence in tidal marsh Savannah Sparrows (Passerculus sandwichensis). Evolution, 74: 57-72. PDF
2019
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. PDF
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. Genomics of rapid ecological divergence and parallel adaptation in songbirds. Evolution Letters, 4: 324-338. Open Access PDF
Benham, P.M. & Cheviron, Z.A. Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah Sparrow (Passerculus sandwichensis). Moleculary Ecology, 28: 1765-1783. PDF
2018
Beckman, L., P.M. Benham, Z.A. Cheviron, & C.C. Witt. Detecting introgression despite persistent phylogenetic uncertainty: the case of the South American siskins. Molecular Ecology, 27: 4350-4367. PDF
2016
Benham, P.M & Witt, C.C. The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC Evolutionary Biology. DOI: 10.1186/s12862-016-0595-2. Open Access. PDF
2015
Galen, S.C., Natarajan, C., Moriyama, H., Weber, R.E., Fago, A., Benham, P.M., Chavez, A.N., Cheviorn, Z.A., Storz, J.F. & Witt, C.W. Contribution of a mutational hotspot to the functional evolution of avian hemoglobin. Proceedings of the National Academy of Sciences USA, 112: 13958-13963. DOI: 10.1073/pnas.150730011 PDF
Stager, M., Pollock, H.S., Benham, P.M., Sly, N.D., Brawn, J.D. & Cheviron, Z.A. Disentangling environmental drivers of metabolic flexibility in birds: the importance of temperature extremes versus temperature variability. Ecography. DOI: 10.1111/ecog.01465. PDF
Benham, P.M., A.M. Cuervo, J.A. McGuire & C.C. Witt. Biogeography of the Andean metaltail hummingbirds: contrasting evolutionary histories of treeline-specialist and habitat-generalist clades. Journal of Biogeography 42: 763-777. PDF
2014
Lim, H.C., Chua, V.L., Benham, P.M., Oliveros, C.H., Rahman, M.A., Moyle, R.G. & Sheldon, F.H. 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. PDF
2012
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. PDF
2011
Gibbons, R.E., P.M. Benham & J. M Maley. Notes on birds of the high Andes of Peru. Ornitología Colombiana, 11: 76-86. PDF
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. Satellite imagery reveals new critical habitat for endangered bird species in the high Andes of Peru. Endangered Species Research 13: 145-157. PDF
2008
Hallworth, M.T., P.M. Benham, J.D. Lambert & L. R. Reitsma. 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. PDF
Reitsma, L.R, M.T. Hallworth & P.M. Benham. 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. PDF
Book chapters:
Benham, P.M. 2022. Plain Xenops (Xenops minutus). In: Elusive birds of the tropical understory. Edited by J.P. Whitelaw, J.D. Brawn, H.S. Pollock & J.W. Fitzpatrick. Cornell University Press, Ithaca, NY.
Benham, P.M. 2022. Russet Antshrike (Thamnistes anabatinus). In: Elusive birds of the tropical understory. Edited by J.P. Whitelaw, J.D. Brawn, H.S. Pollock & J.W. Fitzpatrick. Cornell University Press, Ithaca, NY.
In revision/review:
Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Fairbairn, C., Marimuthu, M.P.A., Nguyen, O., Sahasrabudhe, R., King, B.L., Thomas, W.K., Kovach, A.I., Nachman, M.W. & Bowie, R.C.K. Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery. in review. Genome Biology and Evolution. Preprint on bioRxiv: https://doi.org/10.1101/2023.10.26.564301
2024
Benham, P.M., Walsh, J. & Bowie, R.C.K. Spatial variation in population genomic responses to 125 years of anthropogenic change within a tidal marsh songbird. 30, e17126. Open access:
https://doi.org/10.1111/gcb.17126
Press: The Wildlife Society, Berkeley News, Phys.org, EurekAlert, earth.com
2023
Mikles, C.S., Arcese, P., I.J., Lovette, Aguillon, S.M., Chan, Y.L., , Benham, P.M., Carbeck, K., & Walsh, J. 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
DeRaad, D.A., Escalona, M., Benham, P.M., Marimuthu, M.P.A., Sahasrabudhe, R.M., Nguyen, O., Chumchim, N., Beraut, E., Fairbairn, C.W., Seligmann, W., Bowie, R.C.K., Cicero, C., McCormack, J.E., Wayne, R.K. De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica. Journal of Heredity, 114, 669-680. Open access: https://doi.org/10.1093/jhered/esad047
Benham, P.M., Cicero, C., DeRaad, D.A., McCormack, J.E., Wayne, R.K., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri). Journal of Heredity, 114, 549-560. Open Access: https://doi.org/10.1093/jhered/esad042
Benham, P.M., Cicero, C., Escalona, M., Beraut, E., Marimuthu, M.P.A., Nguyen, O., Nachman, M.W., & Bowie, R.C.K. A highly contiguous genome assembly for the California quail (Callipepla californica). Journal of Heredity, 114, 418-427. https://doi.org/10.1093/jhered/esad008
Benham, P.M. & Bowie, R.C.K. 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
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. Blood variation implicates respiratory limits on elevational ranges of Andean birds. American Naturalist. 201: 741-754.
2022
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 PDF
Clark, J.D., P.M. Benham, J.E. Maldonado, D.A. Luther, & H.C. Lim. Genomic patterns of incipient ecological speciation in a locally adapted songbird subspecies. Evolution, 76: 1481-1494. https://doi.org/10.1111/evo.14538 PDF
2021
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. PDF
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. PDF
Featured in The Scientist Magazine
2020
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. PDF
Sweazea, K.L., Tsosie, K., Beckman, E.J., Benham, P.M. & C.C. Witt. Seasonal and elevational variation in glucose and glycogen in two songbird species. Comparative Biochemistry and Physiology, Part A, 245: 1-6. PDF
Benham, P.M. & Cheviron, Z.A. Variation in demographic history and the selective landscape shape nonparallel patterns of functional divergence in tidal marsh Savannah Sparrows (Passerculus sandwichensis). Evolution, 74: 57-72. PDF
2019
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. PDF
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. Genomics of rapid ecological divergence and parallel adaptation in songbirds. Evolution Letters, 4: 324-338. Open Access PDF
Benham, P.M. & Cheviron, Z.A. Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah Sparrow (Passerculus sandwichensis). Moleculary Ecology, 28: 1765-1783. PDF
2018
Beckman, L., P.M. Benham, Z.A. Cheviron, & C.C. Witt. Detecting introgression despite persistent phylogenetic uncertainty: the case of the South American siskins. Molecular Ecology, 27: 4350-4367. PDF
2016
Benham, P.M & Witt, C.C. The dual role of Andean topography in primary divergence: functional and neutral variation among populations of the hummingbird, Metallura tyrianthina. BMC Evolutionary Biology. DOI: 10.1186/s12862-016-0595-2. Open Access. PDF
2015
Galen, S.C., Natarajan, C., Moriyama, H., Weber, R.E., Fago, A., Benham, P.M., Chavez, A.N., Cheviorn, Z.A., Storz, J.F. & Witt, C.W. Contribution of a mutational hotspot to the functional evolution of avian hemoglobin. Proceedings of the National Academy of Sciences USA, 112: 13958-13963. DOI: 10.1073/pnas.150730011 PDF
Stager, M., Pollock, H.S., Benham, P.M., Sly, N.D., Brawn, J.D. & Cheviron, Z.A. Disentangling environmental drivers of metabolic flexibility in birds: the importance of temperature extremes versus temperature variability. Ecography. DOI: 10.1111/ecog.01465. PDF
Benham, P.M., A.M. Cuervo, J.A. McGuire & C.C. Witt. Biogeography of the Andean metaltail hummingbirds: contrasting evolutionary histories of treeline-specialist and habitat-generalist clades. Journal of Biogeography 42: 763-777. PDF
2014
Lim, H.C., Chua, V.L., Benham, P.M., Oliveros, C.H., Rahman, M.A., Moyle, R.G. & Sheldon, F.H. 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. PDF
2012
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. PDF
2011
Gibbons, R.E., P.M. Benham & J. M Maley. Notes on birds of the high Andes of Peru. Ornitología Colombiana, 11: 76-86. PDF
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. Satellite imagery reveals new critical habitat for endangered bird species in the high Andes of Peru. Endangered Species Research 13: 145-157. PDF
2008
Hallworth, M.T., P.M. Benham, J.D. Lambert & L. R. Reitsma. 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. PDF
Reitsma, L.R, M.T. Hallworth & P.M. Benham. 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. PDF
Book chapters:
Benham, P.M. 2022. Plain Xenops (Xenops minutus). In: Elusive birds of the tropical understory. Edited by J.P. Whitelaw, J.D. Brawn, H.S. Pollock & J.W. Fitzpatrick. Cornell University Press, Ithaca, NY.
Benham, P.M. 2022. Russet Antshrike (Thamnistes anabatinus). In: Elusive birds of the tropical understory. Edited by J.P. Whitelaw, J.D. Brawn, H.S. Pollock & J.W. Fitzpatrick. Cornell University Press, Ithaca, NY.