chemical defense in birds

IN the early 1990s, colleagues and I discovered that several species of New Guinea birds carry potent neurotoxins in their skins and feathers, presumably as a defense against their enemies.  After studying these birds for many years, we have isolated and identified the toxins, described several new chemical structures, studied which tissues contain the toxins, explored their potential uses of toxins, determined the most likely source of the toxins, and significantly revised our understanding of the evolutionary relationships of these birds.  Currently I am working with Megan Kobiela (University of Minnesota) and Butch Brodie (UVa) to study the evolution of sodium channel genes to understand how the birds evolved the capacity to withstand such high levels of these toxins in their tissues.

Selected bibliography:
  1. Dumbacher, J.P., et al., Homobatrachotoxin in the genus Pitohui: Chemical defense in birds? Science, 1992. 258(5083): p. 799-801. (PDF Available)
  2. Dumbacher, J.P., et al., Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds. Molecular phylogenetics and evolution, 2008. 49(3): p. 774-81. (PDF Available)
  3. Dumbacher, J.P. and R.C. Fleischer, Phylogenetic evidence for colour pattern convergence in toxic pitohuis: Müllerian mimicry in birds? Proceedings. Biological sciences / The Royal Society, 2001. 268(1480): p. 1971-6. (PDF Available)
  4. Dumbacher, J.P., G.K. Menon, and J.W. Daly, Skin as a toxin storage organ in the endemic New Guinean genus Pitohui. The Auk, 2009. 126(3): p. 520-530. (PDF Available)
  5. Dumbacher, J.P., T.F. Spande, and J.W. Daly, Batrachotoxin alkaloids from passerine birds: A second toxic bird genus (Ifrita kowaldi) from New Guinea. Proceedings of the National Academy of Sciences, USA, 2000. 97(24): p. 12970-12975. (PDF)
  6. Dumbacher, J.P., et al., Melyrid beetles (Choresine): A putative source for the batrachotoxin alkaloids found in poison-dart frogs and toxic passerine birds. Proceedings of the National Academy of Sciences, USA, 2004. 101(45): p. 15857-15860. (PDF)

Also - check out my recent online "Breakfast Club" presentation of some highlights of this work:
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Galapagos Baselines

We are using data from museums, archives, and the fossil record to document what species used to be on various Galápagos islands.  This is a project that we have just begun (funding just officially came in a couple of months ago) so stay tuned for updates about this exciting research...

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phylogenetics and biogeography

Together with my students and collaborators, we have studied the relationships of many different groups of birds (and now some mammals).  We usually study these animals for specific purposes, to study particular These have revealed interesting relationships that were not appreciated, and have revealed biogeographic patterns that help us identify regions that need more attention of conservation protection.  Our work has led to splitting a couple species and describing one newly discovered mammal species.

Selected Bibliography:
  1. Dumbacher, J.P., T.K. Pratt, and R.C. Fleischer, Phylogeny of the owlet-nightjars (Aves: Aegothelidae) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution, 2003. 29(2003): p. 540-549. (PDF Available)
  2. Dumbacher, J.P., et al., Phylogeny of the avian genus Pitohui and the evolution of toxicity in birds. Molecular Phylogenetics and Evolution, 2008. 49: p. 774-781. (PDF Available)
  3. ​Dumbacher, J.P., et al., Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea). PLOS One, 2012. 7(3): p. e32410. (PDF Available)
  4. Deiner, K., et al., A Passerine Bird's Evolution Corroborates the Geologic History of the Island of New Guinea. PloS one, 2011. 6(5): p. e19479-e19479. (PDF available)
  5. Andersen, M.J., et al., Molecular systematics of the world’s most polytypic bird: the Pachycephala pectoralis/melanura (Aves: Pachycephalidae) species complex. Zoological Journal of the Linnean Society, 2014. (PDF Available)
  6. 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.
  7. Carmi, O., 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.
  8. 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.
  9. 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​

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Barred and Spotted Owls in California

Our team is studying the invasion of the Barred Owl (Strix varia) from eastern US into the west coast states.  In Washington, Oregon, and California, the Barred Owl is clashing with the federally-protected Northern Spotted Owl (Strix occidentalis) and is turning out to be one of the major threats to the Spotted Owls.  Our work is currently focusing on the genetics of both owls and studying the implications of hybrid matings between the two owls.
     To accomplish the work, we are sequencing and assembling the complete Northern Spotted Owl genome.  The owl whose genome is being sequenced is named Sequoia, and she lives at the WildCare center in San Rafael, California.

Selected Bibliography:
  1. 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.
  2. 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/
  3. 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
  4. 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
  5. 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
  6. Courtney, S. P., J. A. Blakesley, R. E. Bigley, M. L. Cody, J. P. Dumbacher, R. C. Fleischer, A. Franklin, J. F. Franklin, R. J. Gutierrez, J. M. Marzluff and L. Sztukowski. Scientific evaluation of the status of the northern spotted owl. 2004. Sustainable Ecosystems Institute, Portland, Oregon. (PDF available)
  7. Diller, L., J. Dumbacher, R. Bosch and R. Brown (2012). The response of Northern Spotted Owls to Barred Owl removal: Implications for additional removal studies based upon preliminary reports. Report to the California Department of Fish and Game and US Fish and Wildlife Service.
  8. Diller, L. V., J. P. Dumbacher, R. P. Bosch, R. R. Bown and R. J. Gutiérrez (2014). Removing Barred Owls From Local Areas: Techniques and Feasibility. Wildlife Society Bulletin 38(1):211-216.
  9. Ishak, H. D., J. P. Dumbacher, N. L. Anderson, J. J. Keane, G. Valkiunas, S. M. Haig, L. A. Tell and R. N. M. Sehgal (2008). Blood Parasites in Owls with Conservation Implications for the Spotted Owl (Strix occidentalis)." PLoS ONE 3(5) e2304.

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Sengi research (AKA elephant-shrews)

Together with Galen Rathbun, we are studying the evolution of sengis, also known as elephant-shrews.  Sengis are neither elephants nor shrews, but members of an ancient group of of mammals that evolved in Africa before the breakup of Gondwana. Our recent work with Galen has been to study the relationships within the round-eared sengis (genus Macroscelides) and the giant sengis (genus Rhynchocyon). 

Selected Bibliography:
  1. 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.
  2. 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.
  3. 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.
  4. Dumbacher, J. P., 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.
  5. Dumbacher, J. P., G. B. Rathbun, H. A. Smit and S. J. Eiseb (2012). "Phylogeny and taxonomy of the round-eared sengis or elephant-shrews, genus Macroscelides (Mammalia, Afrotheria, Macroscelidea)." PLOS One 7(3): e32410.

Avian virus discovery

In collaboration with Joe Derisi's lab at UCSF, we have worked on a couple projects involving the avian microbiome and avian virus discovery. Some of the most productive work has been looking for viruses in birds that have Avian Keratin Disorder (AKD).  

Selected Bibliography:
  1. 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.
  2. 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.
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Forest Resilience 

It is clear that many of California's forests are not resilient to fire and that recent high-severity fires have done tremendous damage to California ecosystems.  There are hundreds of millions of dollars being spent annually to "treat" these forests to make them more resilient to fire and drought,
however there is very little follow-up or critical work being done to assess whether the forests are truly "healthy" after being treated, or whether they are "resilient" to stressors such as fire, disease, drought, etc.

We realized after many meetings and discussions that forest managers are primarily interested in structure (does it look like a forest?) and function (is it producing the required number of board feet of wood? Is there clean water in the watershed? Are people enjoying recreation in the area and not complaining?) but few studies were actually asking whether the forest was healthier after treatments (apart from measuring a small number of human "values" or ecosystem services that humans value.)  So in addition to structure and function, we are also focussing on composition -- that is, what is the biodiversity that composes the forest. We think that biodiversity is a critical component and that it is directly correlated with forest resilience, and not just resilience to today's issues (fire) but to all other potential threats in the future.  I have been involved in a collaborative project with Durrell Kapan (CAS), Peter Roopnarine (CAS), Pat Manley (US Forest Service), Mary Clapp (UC Davis), and several other partners to study how fire and other management schemes affect the biodiversity present in forests, and how biodiversity is directly related to forest resilience to fire and other stressors (climate change, disease, etc.)

Our work is trying to add the biodiversity component, and we are using native biodiversity as a proxy for measuring forest health.  We are also developing tools to directly test whether these forests are resilient in an ecological way (as measured by food-web dynamics and other biodiversity measures).  We hope to use these tools to measure how fire affects forest health and resilience directly, and we hope to ask whether alternative (non-fire) forest management strategies are as effective as fire at maintaining healthy forests.

Stay tuned for publications - we have several projects that are ongoing and just received a sizeable grant to scale our work.