Publications

Original Papers: (Names of our lab group members are highlighted in bold)
  1. David J. Anchundia, Athena W. Lam, James B. Henderson, Matthew H. Van Dam, and John P. Dumbacher.  2024. Genome Assembly of Pyrocephalus nanus: A Step Toward the Genetic Conservation of the Endangered Little Vermilion Flycatcher of the Galapagos Islands. Genome Biology and Evolution.  165(5):1-8. https://doi.org/10.1093/gbe/evae083
  2. Ingo A Müller, Filip Thörn, Samyuktha Rajan, Per GP Ericson, John P Dumbacher, Gibson Maiah, Mozes PK Blom, Knud A Jønsson, Martin Irestedt. 2024. Species-specific dynamics may cause deviations from general biogeographical predictions–evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae). Public Library of Science. 19(5)e0293715: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0293715 
  3. Dumbacher, J.P., J. Chaves. 2023. The Role for Scientific Collections and Public Museums in Island Conservation. In S.J. Walsh et al. (eds.), Island Ecosystems, Social and Ecological Interactions in the Galapagos Islands. Springer Nature; Switzerland. https://doi.org/10.1007/978-3-031-28089-4_25.
  4. Michael W Nachman, Elizabeth J Beckman, Rauri CK Bowie..., John P Dumbacher, et al. 2023. Specimen collection is essential for modern science. Public Library of Science biology. 21(11)e3002318: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0293715 
  5. Niedringhaus K.D., J.P. Dumbacher, F. Dunker, S. Medina, B. Lawson, H.M.A. Fenton, J. M. Higley, M.J. Yabsley. 2023. Apparent prevalence, diversity, and associated lesions of peri-orbital nematodes in a population of barred owls (Strix varia) from Northern California, USA. Journal of Wildlife Diseases. 59(2): 299-309. https://doi.org/10.7589/JWD-D-21-00186
  6. Klicka L.B., Campillo L.C., Manthey J.D., Andersen M.J., Dumbacher J.P., Filardi C.E., Joseph L., Uy J.A.C., Weidemann D.E. and Moyle R.G. 2023. Genomic and geographic diversification of a “great-speciator” (Rhipidura rufifrons). Ornithology: ukac049. https://doi.org/10.1093/ornithology/ukac049
  7. Kryshak N.F., Fountain E.D., Hofstadter D.F., Dotters B.P., Roberts K.N., Wood C.M., Kelly K.G., Schwarcz I.F., Kulzer P.J., Wray A.K., Kramer H.A., Dumbacher J.P., Keane J.J., Shaklee P.A., Gutiérrez R.J. and Peery M.Z. (2022) DNA metabarcoding reveals the threat of rapidly expanding barred owl populations to native wildlife in western North America. Biological Conservation 273: 109678.
  8. Amaya-Mejia W., Dodge M., Morris B., Dumbacher J.P. and Sehgal R.N.M. (2022) Prevalence and diversity of avian haemosporidian parasites across islands of Milne Bay Province, Papua New Guinea. Parasitology Research 121: 1621-1630.
  9. Devon A. DeRaad, Joseph D. Manthey, Emily N. Ostrow, Lucas H. DeCicco, Michael J. Andersen, Peter A. Hosner, Hannah T. Shult, Leo Joseph, John P. Dumbacher, Robert G.Moyle. Population connectivity across a highly fragmented distribution: Phylogeography of the Chalcophaps doves.  Molecular Phylogenetics and Evolution Volume 166, January 2022, 107333. Online here https://doi.org/10.1016/j.ympev.2021.107333.
  10. Abderemane-Ali, F., Rossen, N.D., Kobiela, M.E., Craig, R.A., Garrison, C.E., Chen, Z., Colleran, C.M., O'Connell, L.A., du Bois, J., Dumbacher, J.P., and Minor, D.L. (2021). Evidence that toxin resistance in poison birds and frogs is not rooted in sodium channel mutations and may rely on “ toxin sponge ” proteins. Journal of General Physiology 153, e202112872. Online and open access here: ​https://doi.org/10.1085/jgp.202112872
  11. Abderemane-Ali, F., Rossen, N.D., Kobiela, M.E., Craig, R.A., Garrison, C.E., O’Connell, L.A., Du Bois, J., Dumbacher, J.P., and Minor, D.L. (2020). Sodium channel toxin-resistance mutations do not govern batrachotoxin (BTX) autoresistance in poison birds and frogs. bioRxiv, 2020.2010.2029.361212.
  12. Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A.H., Xie, D., Chen, G., Guo, C., Faircloth, B.C., et al. (2020). Dense sampling of bird diversity increases power of comparative genomics. NATURE 587, 252-257. 
  13. Ethan Linck, Benjamin G. Freeman, John P. Dumbacher. 2020. Speciation and gene flow across an elevational gradient in New Guinea kingfishers. Journal of Evolutionary Biology 33(11), 1643-1652. https://onlinelibrary.wiley.com/doi/abs/10.1111/jeb.13698
  14. Naoko T. Fujito, Zachary R. Hanna, Michal Levy-Sakin, Rauri C. K. Bowie, Pui-Yan Kwok, John P. Dumbacher, Jeffrey D. Wall. 2020. Genomic variation and population histories of spotted (Strix occidentalis) and barred (S. varia) owls. BioRxiv doi: https://doi.org/10.1101/2020.02.18.954685.
  15. Zachary R. Hanna, John P. Dumbacher, Rauri C. K. Bowie, James B. Henderson and Jeffrey D. Wall. 2018. Whole-Genome Analysis of Introgression Between the Spotted Owl and Barred Owl (Strix occidentalisand Strix varia, Respectively; Aves: Strigidae) in Western North America. G3: GENES, GENOMES, GENETICS December 1, 2018 vol. 8 no. 12 3945-3952; https://doi.org/10.1534/g3.118.200754
  16. Zachary R. Hanna, John P. Dumbacher, Rauri C. K. Bowie, Jeffrey D. Wall. 2018. Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California. Preprint published in BioRxiv doi: https://doi.org/10.1101/343434. Currently in review for another journal.
  17. G. Geupel, M. E. Flannery, and J. P. Dumbacher. Chapter 31: Fundamental Methods in Ornithology.  2018.  In Ornithology: Foundation, Critique, and Application. Editors M. L. Morrison, A. D. Rodewald, G. Voelker, J. F. Prather, and M. R. Colón. Johns Hopkins University Press, Baltimore, MD.
  18. Shelby L. Medina, Mark Higley, and John P. Dumbacher. 2018. Rough-skinned newt (Taricha granulosa) predation by Barred Owls (Strix varia). The Wilson Journal of Ornithology 130(3): 780-783.
  19. Galen Rathbun, Jack Dumbacher, and Robert Nyirenda. 2018. A Traditional Method of Hunting Dusky Sengis in Southern Malawi. Afrotherian Conservation, number 14: 51-55.
  20. Thomson, Scott A., Richard L. Pyle, Shane T. Ahyong, et. al. 2018. Taxonomy based on science is necessary for global conservation. PLoS Biology 16(3):e2005075. doi: 10.1371/journal.pbio.2005075
  21. Gabriel, M. W., L. V. Diller, J. P. Dumbacher, G. M. Wengert, J. M. Higley, R. H. Poppenga and S. Mendia. 2018. Exposure to rodenticides in Northern Spotted and Barred Owls on remote forest lands in northwestern California: evidence of food web contamination. Avian Conservation and Ecology 13 (1):2. [online] URL: http://www.ace-eco.org/vol13/iss1/art2/
  22. Zachary R. Hanna​,James B. Henderson, Anna B. Sellas, Jérôme Fuchs, Rauri C.K. Bowie, John P. Dumbacher. 2017. Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region. PeerJ 5:e3901. https://doi.org/10.7717/peerj.3901
  23. Zachary R. Hanna, James B. Henderson, Jeffrey D. Wall, Christopher A. Emerling, Jérôme Fuchs  Charles Runckel, David P. Mindell, Rauri C. K. Bowie, Joseph L. DeRisi, John P. Dumbacher. 2017. Northern spotted owl (Strix occidentalis caurina) genome: divergence with the barred owl (Strix varia) and characterization of light-associated genes. Genome Biology and Evolution evx158, https://doi.org/10.1093/gbe/evx158
  24. Zachary R. Hanna, James B. Henderson, Jeffrey D. Wall, Christopher A. Emerling, Jérôme Fuchs  Charles Runckel, David P. Mindell, Rauri C. K. Bowie, Joseph L. DeRisi, John P. Dumbacher. 2017. Supplemental dataset for Northern Spotted Owl (Strix occidentalis caurina) genome assembly version 1.0. Zenodo. http://doi.org/10.5281/zenodo.822859. DOI:10.5281/zenodo.822859
  25. E. J. Carlen, G. B. Rathbun, L. E. Olson, C. A. Sabuni, W. T. Stanley, and J. P. Dumbacher.2017. Reconstructing the molecular phylogeny of giant sengis (Macroscelidea; Macroscelididae; Rhynchocyon). Molecular Phylogenetics and Evolution 113:150-160. http://dx.doi.org/10.1016/j.ympev.2017.05.012.
  26. E.B. Linck, Z.R. Hanna, A. Sellas, J.P. Dumbacher. 2017. Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecology and Evolution. 2017;00:1–13. https://doi.org/10.1002/ece3.3065
  27. T. J. O'Shea,C. Klinger, L. Smythe, L. Wilkinson, and J. P. Dumbacher. 2016. Survey of the bat fauna, Desert National Wildlife Refuge. Western North American Naturalist 76(4): 501-508.
  28. M. Zylberberg, C. Van Hemert, J. P. Dumbacher, C. M. Handel, T. Tihand, J. L. DeRisi. 2016. Novel picornavirus associated with avian keratin disorder in Alaskan birds. doi: 10.1128/mBio.00874-16 26 July 2016 mBio vol. 7 no. 4e00874-16.
  29. J. P. Dumbacher, E. J. Carlen, and G. B. Rathbun. 2016. Petrosaltator gen. nov., a new genus replacement for the North African sengi Elephantulus rozeti (Macroscelidea; Macroscelididae). Zootaxa 4136(3): 567-579.
  30. O. Carmi, C. C. Witt, A. Jaramillo, and J. P. Dumbacher. 2016. Phylogeography of the Vermilion Flycatcher species complex: Multiple speciation events, shifts in migratory behavior, and an apparent extinction of a Galápagos-endemic bird species. Molecular Phylogenetics and Evolution 102 (2016) 152-173.
  31. L. Q. Kahle, M. E. Flannery, and J. P. Dumbacher. 2016. Bird-Window Collisions at a West-Coast Urban Park Museum: Analyses of Bird Biology and Window Attributes from Golden Gate Park, San Francisco. PLoS One 11(1): e0144600. DOI: 10.1371/journal.pone.0144600
  32. E. Linck, S. Schaack and J. P. Dumbacher. 2016. Genetic differentiation within a widespread “supertramp” taxon: molecular phylogenetics of the Louisiade White-eye (Zosterops griseotinctus). Molecular Phylogenetics & Evolution 94(A): 113-121.
  33. G. B. Rathbun and J. P. Dumbacher. 2015. Home range and habitat use by the Etendeka Round-eared Sengi (Macroscelides micus), a Namibian endemic desert mammal. PeerJ 3:e1302 https://dx.doi.org/10.7717/peerj.1302.
  34. Z. R. Hanna, C. Runckel, J. Fuchs, D. P. Mindell, C. v. Hemmert, C. Handel, J. L. DeRisi, and J. P. Dumbacher. 2015. Isolation of a Complete Circular Virus Genome from an Alaskan Black-capped Chickadee (Poecile atricapillus). Genome Announcements 3(5): e01081-15.
  35. J. P. Dumbacher, G. B. Rathbun, T. O. Osborne, M. Griffin, and S. J. Eiseb.  2014.  A new species of round-eared sengi (genus Macroscelides) from Namibia.  Journal of Mammalogy, 95(3) 443-454.
  36. L. Rocha, et al. 2014. Specimen collection: An essential tool.  Science 344(6186):814-815.
  37. J. P. Dumbacher. 2014. Batrachotoxin. In: Wexler, P. (Ed.), Encyclopedia of Toxicology, 3rd edition vol 1. Elsevier Inc., Academic Press, pp. 371–373. ISBN: 9780123864543
  38. G. Menon and J. P. Dumbacher.  2014. A “toxin mantle “ as defensive barrier in a tropical bird: evolutionary exploitation of the basic permeability barrier forming organelles.  Experimental Dermatology 23(4): 288-290.
  39. J. P. Dumbacher.  2014. A taxonomic revision of the genus Pitohui, with historical notes on names.  Bulletin of the British Ornithologists Club 134(1): 19-22.
  40. M. J. Andersen, Á. S. Nyári, I. Mason, L. Joseph, J. P. Dumbacher, C. E. Filardi, and R. G. Moyle. 2014.  Molecular systematics of the world’s most polytypic bird: the Pachycephala pectoralis/melanura (Aves: Pachycephalidae) species complex.  Zoological Journal of the Linnean Society. 170(3): 566-588 (Cover article).
  41. L. V. Diller, J. P. Dumbacher, R. P. Bosch, R. R. Bown, R. J. Gutiérrez. 2014. Removing Barred Owls From Local Areas: Techniques and Feasibility. Wildlife Society Bulletin 38(1): 211-216.
  42. J. P. Dumbacher, H. S. Smit, S. Eiseb, and G. B. Rathbun. (2012). Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea). PLoS One 7(3): e32410.
  43. K. Deiner, A. R. Lemmon, A. L. Mack, R. C. Fleischer, and J. P. Dumbacher. 2011. A passerine bird’s evolution corroborates the geologic history of New Guinea. PLoS One 6(5): e19479.
  44. J. P. Dumbacher, M. Flannery, J. Miller, Y. Xiaojun. 2011. The avifauna of the Gaoligongshan Mountains of western China: A hotspot of avian species diversity. In S. C. Renner, Ed., The Avifauna of the Eastern Himalayas and Southeastern Sub-Himalayan Mountains. Ornithological Monographs, No. 70: 30-63.
  45. H. K. M. M. Thwin, J. P. Dumbacher, K. S. Lwin, and S. C. Renner. 2011. Ornithology of Northern Myanmar. In S. C. Renner, Ed., The Avifauna of the Eastern Himalayas and Southeastern Sub-Himalayan Mountains. Ornithological Monographs, No. 70:109-142.
  46. J. P. Dumbacher and B. West. 2010. Collecting Galapagos and the Pacific: How Rollo Howard Beck shaped our understanding of evolution. Proceedings of the California Academy of Sciences, Series 4, Vol 61, Supplement II, No. 13: pp 211-243. (Low resolution version 1.5Mb; high resolution version 25Mb)
  47. K. P. Johnson, D. H. Clayton, J. P. Dumbacher, and R. C. Fleischer. 2010. The flight of the Passenger Pigeon: Phylogenetics and biogeographical history of an extinct species. Molecular Phylogenetics and Evolution 57: 455-458.
  48. J. P. Dumbacher, G. K. Menon, and J. W. Daly.  2009.  Skin as toxin storage organ in the endemic New Guinea genus Pitohui. The Auk 126(3) 520-530.
  49. J. P. Dumbacher, K. Deiner, L. Thompson, and R. C. Fleischer. 2008. Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds.  Molecular Phylogenetics and Evolution 49: 774-781.
  50. S. C. Renner, J. H. Rappole, P. C. Rasmussen, T. Aung, M. Aung, N. M. Shwe, J. P. Dumbacher, and R. C. Fleischer.  2008.  A new subspecies of Tesia olivea (Sylviidae) from Chiang Mai province, northern Thailand. J. Ornithol. 149: 439-450.
  51. H. D. Ishak, J. P. Dumbacher, N. L Anderson, J. J. Keane, G. Valkiūnas, S. M. Haig ,  L. A. Tell, R. N. M. Sehgal. 2008.  Blood Parasites in Owls with Conservation Implications for the Spotted Owl (Strix occidentalis).  PLoS One 3(e2304): 1-9.
  52. A. Mack, Dumbacher, J. P. Chapter 4.9: Birds of Papua. 2007. In Beehler, B.M. ed., The Ecology of Papua. Volume IX in the Ecology of Indonesia series.  Oxford University Press, UK.
  53. B. S. Arbogast, J. P. Dumbacher, S. J. Steppan, S. P. Courtney, and L. A. Sztukowski. 2006. Evaluation of scientific information regarding Preble's meadow jumping mouse. Sustainable Ecosystems Institute, Portland, Oregon. (Report submitted by Sustainable Ecosystems Institute to US Fish and Wildlife Service, July 20, 2006.)
  54. R. C. Fleischer, J. J. Kirchman, J. P. Dumbacher, et al. 2006. Mid-Pleistocene divergence of Cuban and North American ivory-billed woodpeckers. Biology Letters 2(3) 466-469.
  55. A. L. Töpf, M. T. Gilbert, J. P. Dumbacher, and A. R. Hoelzel. 2006. Tracing the phylogeography of human populations in Britain based on 4th-11th century mtDNA genotypes. Mol. Biol. Evol. 23(1): 152-161.
  56. J. P. Dumbacher. 2005. "Batrachotoxin" in  Encyclopedia of Toxicology (Wexler P), 2nd edition. Oxford. Elsevier.  pp. 215-17.
  57. Beadell, J. S., E. Gering, J. Austin, J. P. Dumbacher, M. A. Peirce, T. K. Pratt, C. A. Atkinson, and R. C. Fleischer.  2004.  Prevalence and differential host-specificity of two avian blood parasite genera in the Australo-Papuan region.  Molecular Ecology 13:3829-3844.
  58. J. P. Dumbacher, A. Wako, S. R. Derrickson, A. Samuelson, T. F. Spande, and J. W. Daly. 2004. Melyrid beetles ( Choresine): A putative source for the batrachotoxin alkaloids found in poison-dart frogs and toxic passerine birds. Proc. Natl. Acad. Sci. USA, 101(45): 15857-15860.
  59. S. P. Courtney, J. A. Blakesley, R. E. Bigley, M. L. Cody, J. P. Dumbacher, R. C. Fleischer, A. B. Franklin, J. F. Franklin, R. J. Gutiérrez, J. M. Marzluff, L. Sztukowski. 2004. Scientific evaluation of the status of the Northern Spotted Owl. Sustainable Ecosystems Institute, Portland, Oregon. (Available online.)
  60. J. P. Dumbacher, T. K. Pratt, and R. C. Fleischer.  2003. Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence.  Molecular Phylogenetics and Evolution 29: 540-549.
  61. J. P. Dumbacher and R. C. Fleischer.  2001. Phylogenetic evidence for colour-pattern convergence in toxic pitohuis: Müllerian mimicry in birds?  Proceedings of the Royal Society of London: Biology, 268: 1971-1976.
  62. L. Shapiro and J. P. Dumbacher.  2001.  Adenylate kinase intron 5: A new nuclear locus for avian systematics. The Auk, 118(1): 248-255.
  63. J. P. Dumbacher, T. Spande, and J. W. Daly.  2000.  Batrachotoxin alkaloids from passerine birds: A second toxic bird genus (Ifrita kowaldi). Proc. Natl. Acad. Sci. USA, 97(24): 12970–12975.
  64. J. P. Dumbacher.  1999.  The evolution of toxicity in Pitohuis: I. Effects of homobatrachotoxin on chewing lice (Order Phthiraptera). The Auk 116(4): 957-963.
  65. R. Visnak and J. P. Dumbacher.  1999.  Comparison of four fumigants for removing avian lice.  Journal of Field Ornithology, 70(1): 42-48.
  66. J. P. Dumbacher.  1997.  The ecology and evolution of chemical defense in the avian genus Pitohui.  Ph.D. Thesis.  University of Chicago.
  67. J. P. Dumbacher and S. Pruett-Jones.  1996.  Avian chemical defense.  Current Ornithology, 13: 137-174.
  68. B. M. Beehler and J. P. Dumbacher.  1996.  More examples of fruiting trees visited predominantly by birds of paradise.  Emu, 96: 81-88.
  69. J. P. Dumbacher, B. M. Beehler, T. F. Spande, H. M. Garraffo, and J. W. Daly.  1993.  Pitohui: How toxic and to whom?  Science, 259: 582-583.
  70. J. P. Dumbacher, B. M. Beehler, T. F. Spande, H. M. Garraffo, and J. W. Daly.  1992.  Homobatrachotoxin in the genus Pitohui: Chemical defense in birds? _Science, 258: 799-801.
  71. J. P. Dumbacher.  1991.  Bird life of Kagi, Central Province.  Muruk (Journal of the Papua New Guinea Bird Society), 5(1): 19-21.
  72. B. M. Beehler and J. P. Dumbacher.  1990.  Interesting observations of birds at Varirata National Park, June - July 1990.  Muruk, 4(3): 111.
 
Book Reviews:

  1. J.P. Dumbacher. 2018. [review of] Birds of New Guinea: Distribution, Taxonomy, and Systematics by Bruce M. Beehler and Thane K. Pratt, Princeton University Press. The Condor, Ornithological Applications 120(1): 245-246.
  2. J.P. Dumbacher. 2017. [review of] Cat Wars: The Devastating Consequences of a Cuddly Killer, By Peter P. Marra and Chris Santella, Princeton University Press. Journal of Field Ornithology 88(1):95-97.
  3. J.P Dumbacher. 2014. [review of] A Feathered River Across the Sky, by Joel Greenberg, Journal of Field Ornithology, 85(3): 340-342.
  4. J.P Dumbacher. 2004. [review of] My Family Album, by Franz de Waal, and Animal Social Complexity, edited by Franz de Waal and Peter Tyack.  California Wild Magazine.
  5. J. P. Dumbacher.  2002.  [review of] The Birds of Paradise, by Clifford Frith and Bruce M. Beehler.  The Auk 119(3): 880-881.
  6. J. P. Dumbacher.  1991.  [review of] The Ruff, by Johan G. Van Rhijn.  The Auk 108(4): 1007.
  7. J. P. Dumbacher.  1991.  [review of] Social, Sexual, and Pseudosexual Behavior of the Blue-bellied Roller, Coracias cyanogaster: The Consequences of Crowding or Concentration, by Martin Moynihan.  Auk 108(2): 457.

Popular writing:
  1. J. P. Dumbacher. 2012. [Appreciation] in Tiffany Bozic: Drawn By Instinct. Selected Works from 2003-2011. Gingko Press: Berkeley, CA. 
  2. J. P. Dumbacher. 2011. [Forward] in Nests: Fifty Nests and the Birds that Built Them, by Sharon Beals. Chronicle Books: San Francisco.