Zachary R. Hanna

Zachary R. Hanna, Ph.D.
Email

Education

• Ph.D., Integrative Biology, University of California, Berkeley 2017
• B.S., Molecular Environmental Biology, University of California, Berkeley 2008

Publications

• Hanna ZR, Dumbacher JP, Bowie RCK, Henderson JB, Wall JD. 2018. Whole-genome analysis of introgression between the spotted owl and barred owl (Strix occidentalis and Strix varia, respectively; Aves: Strigidae) in western North America. G3: Genes, Genomes, Genetics 8, no. 12: 3945–52. DOI:10.1534/g3.118.200754. Available here or Download PDF

• Hanna ZR, Cicero C, Bowie RCK. 2018. Molecular evidence that the Channel Islands populations of the orange-crowned warbler (Oreothlypis celata; Aves: Passeriformes: Parulidae) represent a distinct evolutionary lineage. PeerJ Preprints 6: e27418v1. DOI:10.7287/peerj.preprints.27418v1. Available here or Download PDF

• Hanna ZR, Dumbacher JP, Bowie RCK, Wall JD. 2018. Whole-genome sequences suggest long term declines of spotted owl (Strix occidentalis) (Aves: Strigiformes: Strigidae) populations in California. bioRxiv 343434. DOI:10.1101/343434. Available here or Download PDF

• Hanna ZR, Henderson JB, Sellas AB, Fuchs J, Bowie RCK, Dumbacher JP. 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. DOI: 10.7717/peerj.3901. Available here or Download PDF

• Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. 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 9(10):2522-2545. DOI: 10.1093/gbe/evx158. Available here or Download PDF

• Bowie RCK, Feldheim KA, Hanna ZR, Sellas AB, Cicero C. 2017. Development of Polymorphic Tetranucleotide Microsatellite Markers for New World Warblers (Aves: Passeriformes: Parulidae) with Broad Cross-species Utility. The Wilson Journal of Ornithology 129:401–407. DOI: 10.1676/16-110.1. Available here or Download PDF

• Linck EB, Hanna ZR, Sellas A, Dumbacher JP. 2017. Evaluating hybridization capture with RAD probes as a tool for museum genomics with historical bird specimens. Ecology and Evolution 7:4755–4767. DOI: 10.1002/ece3.3065. Available here or Download PDF

• Hanna ZR, Ortiz-Ramírez MF, Ríos-Muñoz CA, Cayetano-Rosas H, Bowie RCK, Navarro-Sigüenza AG. 2016. Phylogenetic and morphologic evidence confirm the presence of a new montane cloud forest associated bird species in Mexico, the Mountain Elaenia (Elaenia frantzii; Aves: Passeriformes: Tyrannidae). PeerJ 4:e1598. DOI: 10.7717/peerj.1598. Available here or Download PDF

• Hanna ZR, Runckel C, Fuchs J, DeRisi JL, Mindell DP, Hemert CV, Handel CM, Dumbacher JP. 2015. Isolation of a Complete Circular Virus Genome Sequence from an Alaskan Black-Capped Chickadee (Poecile atricapillus) Gastrointestinal Tract Sample. Genome Announcements 3:e01081-15. DOI: 10.1128/genomeA.01081-15. Available here or Download PDF

Electronic Resources and Datasets

• Hanna ZR, Henderson JB, Wall JD, Emerling CA, Fuchs J, Runckel C, Mindell DP, Bowie RCK, DeRisi JL, Dumbacher JP. 2017. Supplemental dataset for Northern Spotted Owl (Strix occidentalis caurina) genome assembly version 1.0. Zenodo. DOI: 10.5281/zenodo.822859.

• Hanna ZR, Sellas AB. 2017. hyRADccg Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.268048.

• Henderson JB, Hanna ZR. 2016. scafSeqContigInfo. Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.163748.

• Henderson JB, Hanna ZR. 2016. BLATq. Version 1.0.2. Zenodo. DOI: 10.5281/zenodo.61136.

• Henderson JB, Hanna ZR. 2016. excerptByIDs. Version 1.0.2. Zenodo. DOI: 10.5281/zenodo.61134.

• Henderson JB, Hanna ZR. 2016. dupchk. Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.163722.

• Henderson JB, Hanna ZR. 2016. GItaxidIsVert. Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.163737.

• Henderson JB, Hanna ZR. 2016. scafN50. Version 1.0.0. Zenodo. DOI: 10.5281/zenodo.163739.

Presentations

• Hanna ZR 2018. Extent of Introgression Detected in Spotted Owls and Western Barred Owls. Invited presentation at the “Extinction or management of owls: the dilemma of the barred owl invasion in California” symposium at the Western Section of the Wildlife Society annual meeting, Santa Rosa, California

• Hanna ZR, Dumbacher JP, Wall JD, Bowie RCK. 2017. Genomics of the Spotted and Barred Owls. Presented by Z.R. Hanna at the MVZ Lunch Seminar - Topics in Evolutionary Biology, Museum of Vertebrate Zoology, UC Berkeley, California

• Hanna ZR, Dumbacher JP, Wall J. 2016. Extent of Introgression Detected in Spotted Owls and Western Barred Owls. Presented by Z.R. Hanna at the North American Ornithological Conference, Washington, D.C.

• Hanna ZR, Dumbacher JP, Henderson JB. 2015. Genome of the northern spotted owl and its use in studying the genetic relationships of barred and spotted owls. Presented by Z.R. Hanna at The Wildlife Society Western Section annual meeting, Santa Rosa, California

• Hanna ZR, Bowie RCK, Cicero C. 2008. Phylogeography of the Orange-crowned Warbler (Vermivora celata). Presented by Z.R. Hanna at the American Ornithologists Union conference, Portland, Oregon

Teaching Experience

• Graduate Student Instructor, Ornithology Laboratory and Field (IB 174), UC Berkeley. January-May 2017
• Graduate Student Instructor, Natural History of the Vertebrates Laboratory and Field (IB 104), UC Berkeley. January-May 2016
• Graduate Student Instructor, Introduction to Biology Laboratory (Bio 1B), UC Berkeley. January-May 2012

Professional Employment

• Postdoctoral Researcher, University of California, San Francisco. January-October 2018
• Graduate Student Curatorial Assistant, Museum of Vertebrate Zoology, UC Berkeley. August-December 2015
• Laboratory and Field Research Technician, California Academy of Sciences. September 2010 – December 2011
• Laboratory and Field Research Technician, Museum of Vertebrate Zoology. May 2006 – January 2010
• Laboratory Research Technician, Department of Environmental Science, Policy, and Management, UC Berkeley. 2005
• Environmental Eco-label Research Technician, Department of Environmental Science, Policy, and Management, UC Berkeley. June-September 2004

Mentoring Experience

• 2012 May-2017 May.Genetics laboratory and data analysis advising. I trained 3 UC Berkeley undergraduate students in laboratory and data analysis techniques and guided them in designing and conducting independent research projects.
• 2012 October-December. Genetics laboratory and data analysis advising. I instructed two Guatemalan licenciatura students in laboratory and data analysis techniques to produce genetics data for their theses projects as part of a collaboration between the Museum of Vertebrate Zoology (MVZ), UC Berkeley and the Museo de Historia Natural de la Universidad de San Carlos (MUSHNAT), Guatemala.
• 2012 June. Field survey and museum collecting techniques instruction. During a collecting expedition to Mexico, I instructed undergraduate students in bird capture using mistnets as well as techniques of tissue sampling and museum study skin preparation as part of a collaboration between the MVZ and the Museo de Zoología “Alfonso L. Herrera” (MZFC), Mexico.
• 2009 April-2011 May. Field survey and museum collecting techniques instruction. During a collecting expedition to Guatemala, I instructed Guatemalan licenciatura students in bird capture using mistnets as well as techniques of tissue sampling and museum study skin preparation as part of a collaboration between the MVZ and the MUSHNAT.

Expedition and Field Work

• 2013-2015. Barred Owl specimen collection for Ph.D. research, Northern California.
• 2014 June. Grinnell Resurvey Project, Museum of Vertebrate Zoology (MVZ), UC Berkeley. Avian specimen collections in Lassen National Forest, California.
• 2013 August. Mexico, Chiapas. Avian and herpetofauna collections in collaboration between the MVZ and the Museo de Zoología “Alfonso L. Herrera” (MZFC), Mexico.
• 2012 June. Mexico, Chiapas. Avian and herpetofauna collections in collaboration between the MVZ and the MZFC, Mexico.
• 2011 September- November. Papua New Guinea, Milne Bay Islands. Avian collections and metagenomic collections with Dr. John Dumbacher, California Academy of Sciences.
• 2011 May. Guatemala. Avian, mammal, and herpetofauna collections in collaboration between the MVZ and the Museo de Historia Natural de la Universidad de San Carlos (MUSHNAT), Guatemala.
• 2009 June. Grinnell Resurvey Project, MVZ, UC Berkeley. Avian specimen collection and curation of associated data under Dr. Carla Cicero.
• 2009 April. Guatemala. Avian, mammal, and herpetofauna collections in collaboration between the MVZ and the MUSHNAT.
• 2009 January. Guatemala. Avian, mammal, and herpetofauna collections in collaboration between the MVZ and the MUSHNAT.
• 2008 May-August. Grinnell Resurvey Project, MVZ, UC Berkeley. Avian and mammal specimen collections with Dr. Carla Cicero.
• 2008 May. Orange-crowned Warbler specimen collection in southern California.
• 2007 June-August. Research Experience for Undergraduates (REU) Summer Research in Peru. Avian specimen collection under Dr. Christopher Witt.
• 2007 May. Grinnell Resurvey Project, MVZ, UC Berkeley. Avian specimen collections with Dr. Carla Cicero.
• 2007 May. Orange-crowned Warbler collections at Hastings Natural History Reservation, California with Prof. Rauri Bowie.
• 2006 May-September. Grinnell Resurvey Project, MVZ, UC Berkeley. Avian, mammal, and herpetofaunal specimen collection and curation of associated data under Dr. Carla Cicero.
• 2006 August-December. UC Berkeley field course in the Biology and Geomorphology of Tropical Islands, Moorea, French Polynesia.
• 2005 October-December. UC Education Abroad Tropical Biology & Conservation Field Course, Monteverde Institute, Costa Rica.
• 2005 June-August. UC Berkeley Summer Field Program at Baker Forest.

Grants, Fellowships, and Awards

• 2017. Semester Fellowship, UC Conservation Genomics Consortium, UC President’s Research Catalyst Award
• 2016. American Ornithologists’ Union Travel Award
• 2016. Museum of Vertebrate Zoology Travel Funds Award
• 2016. Graduate Student Conference Travel Award, Integrative Biology, UC Berkeley
• 2016. Summer Research Award, Integrative Biology, UC Berkeley
• 2016. Graduate Student Research Funds Award, Integrative Biology, UC Berkeley
• 2016. Joseph Mailiard Fellowship, Museum of Vertebrate Zoology, UC Berkeley
• 2016. Ned K. Johnson Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2016. Doctoral Dissertation Improvement Grant, National Science Foundation
• 2015. Summer Research Award, Integrative Biology, UC Berkeley
• 2015. Graduate Student Research Funds, Integrative Biology, UC Berkeley
• 2015. Martens Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2014. Graduate Student Research Funds, Integrative Biology, UC Berkeley
• 2014. Ned K. Johnson Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2013. Outstanding Graduate Student Instructor Award, UC Berkeley
• 2013. Graduate Student Research Funds, Integrative Biology, UC Berkeley
• 2013. Louise Kellogg Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2012. Graduate Division Summer Grant, UC Berkeley
• 2012. Louise Kellogg Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2012. Jerry O. Wolff Research Fund Award, Museum of Vertebrate Zoology, UC Berkeley
• 2012-2015. Graduate Research Fellowship, National Science Foundation
• 2008. American Ornithologists’ Union Travel Award
• 2007. Sponsored Projects for Undergraduate Research Grant, College of Natural Resources, UC Berkeley
• 2006. Fellowship with the Exploring California Biodiversity Project, UC Berkeley. Prepared skins and skeletons for a teaching collection used for K-12 education.
• 2000. Eagle Scout, Boy Scouts of America