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Blue Oak Ranch Reserve

UC Berkeley Natural Reserve System

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Station Bibliography

Dissertations and Theses


Wommack, E.A. (2014). The Range and Use of Plumage Variation in the American Kestrel (Falco sparverius). Ph.D. Dissertation. University of California, Berkeley. pp. 183.


Richgels, Katherine Lee Dosch, "Parasite Metacommunities across Scales: Trematodes in their Freshwater Mollusk Hosts" (2014). Ecology & Evolutionary Biology Graduate theses & Dissertations. Paper 5. University of Colorado, Boulder.


McCarey, Keegan, "Patterns of Multi-Symbiont Community Interactions in California Freshwater Snails" (2014). Undergraduate Honors theses. Paper 154. University of Colorado, Boulder.


Morgan Murrell. Population Genetics of the Western Toad (Bufo boreas) in the Central Valley of California. Thesis projects. Paper 440. Western Kentucky University. 12-14-2013


Mantor, Margaret. Anti-predator Behavior of California Ground Squirrels (Otospermophilus beecheyi).  Dissertation in Geography. Office of Graduate Studies. UC Davis. 2012. 72 pp.


Stumpf, Ute Erika. 2010. Influence of slope position and mistletoe infestation on water relations of oak trees (Quercus lobata (Nee.)) measured by traditional methods in comparison to aerial SAVI images. A Thesis Presented to The Faculty of the Department of Geobotany, Trier University, Germany. 74 pages.


Huck, Katrina  L.  2010. Reproductive  den  habitat  characterization  of  American badgers (Taxidea  taxus)  in  Central  California.  A Thesis Presented to The Faculty of the Department of Biological  Sciences, San José State University, 2010.  33 pages.  


Padgett-Flohr, Gretchen Elizabeth. 2009. Batrachochytrium dendrobatidis in central California amphibians. Ph.D., Southern Illinois University at Carbondale, 2009 , 148 pages; AAT 3358727


Publications and Presentations


2016

Erika Walther & Gediminas Valkiūnas & Elizabeth A. Wommack & Rauri C. K. Bowie & Tatjana A. Iezhova & Ravinder N. M. Sehgal. Description and molecular characterization of a new Leucocytozoon parasite (Haemosporida: Leucocytozoidae), Leucocytozoon californicus sp. nov., found in American kestrels (Falco sparverius sparverius).  Parasitol Res. DOI 10.1007/s00436-016-4925-5


2015

Breanna J. Putman and Rulon W. Clark. HABITAT MANIPULATION IN HUNTING RATTLESNAKES (CROTALUS SPECIES). 2015. THE SOUTHWESTERN NATURALIST 60(4): 374–377.


Michaella Chung, Carrick Detweiler, Michael Hamilton, James Higgins, John-Paul Ore and Sally Thompson.  Obtaining the Thermal Structure of Lakes from the Air. Water 2015, 7, 6467-6482; doi:10.3390/w7116467.  


Stephen D. Hopper & Fernando A. O. Silveira & Peggy L. Fiedler. Biodiversity hotspots and Ocbil theory. Plant Soil. 2015 DOI 10.1007/s11104-015-2764-2


Fabiana Neves, Joana Abrantes, Tereza Almeida, Paulo P. Costa, and Pedro J. Esteves, “Evolutionary Insights into IL17A in Lagomorphs,” Mediators of Inflammation, vol. 2015, Article ID 367670, 7 pages, 2015. doi:10.1155/2015/367670


Breanna J. Putman & Richard G. Coss & Rulon W. Clark. The ontogeny of antipredator behavior: age differences in California ground squirrels (Otospermophilus beecheyi) at multiple stages of rattlesnake encounters. Behav Ecol Sociobiol (2015) 69:1447–1457.

Breanna J. Putman and Rulon W. Clark. CROTALUS OREGANUS (Northern Pacific Rattlesnake). NON- RATTLING TAIL DISPLAY.  Herpetological Review 46(2), 2015.



2014

Liman, Noura and Malek Naouach. Scheduled sampling for robust sensing. Proceedings of the 10th International Conference on Network and Service Management, Rio de Janeiro, Brazil, November 17-21, 2014. page 224-229.


Ana Lemos de Matos & Grant McFadden & Pedro J. Esteves.  Evolution of viral sensing RIG-I-like receptor genes in Leporidae genera Oryctolagus , Sylvilagus , and Lepus. Immunogenetics (2014) 66:43–52.


Breanna J. Putman and Rulon W. Clark. The fear of unseen predators: ground squirrel tail flagging in the absence of snakes signals vigilance.  Behavioral Ecology (2014), 00(00), 1–9. doi:10.1093/beheco/aru176.


B. C. McLaughlin, C. N. Morozumi, J. Mackenzie, A. Cole, and S. Gennet.  Demography linked to climate change projections in an ecoregional case study: integrating forecasts and field data. Ecosphere. July 2014. Vol:5(7). article 85.


Fabiana Neves, Joana Abrantes, Andrey A Lissovsky and Pedro Jose ́ Esteves.  Pseudogenization of CCL14 in the Ochotonidae (pika) family. Innate Immunity

0(0) 1–8.


Pieter T. J. Johnson and Jason T. Hoverman.  Heterogeneous hosts: how variation in host size, behaviour and immunity affects parasite aggregation.  Journal of Animal Ecology 2014, 83, 1103–1112.


Michael P. Hamilton. Drones, Nodes, and Apps: perspectives and prospects for the next generation of ecological applications using Micro Aerial Vehicles. Workshop on Robotic Monitoring at Robotics: Science and Systems 2014 Conference, Berkeley, California


Pieter T. J. Johnson and Jason T. Hoverman. 2014. Heterogeneous hosts: how variation in host size, behavior, and immunity affect parasite aggregation in an experimental system. Parasite and Disease Ecology. doi: 10.1111/1365-2656.12215.


Pieter T. J. Johnson, Daniel L. Preston, Jason T. Hoverman, and Bryan E. LaFontea. 2014. Host and parasite diversity jointly control disease risk in complex communities. PNAS. www.pnas.org/cgi/doi/10.1073/pnas.1310557110


Mantor, M., Krause, S. and Hart, L. A. (2014), Trapping and handling squirrels: Trap modification and handling restraint to minimize injuries and stress. Wildlife Society Bulletin, 38: 152–159. doi: 10.1002/wsb.371


Ana Lemos de Matos & Grant McFadden & Pedro J. Esteves (2014). Evolution of viral sensing RIG-I-like receptor genes in Leporidae genera Oryctolagus , Sylvilagus , and Lepus. Immunogenetics (2014) 66:43–52.


2013

PAUL F. GUGGER, MAKIHIKO IKEGAMI and VICTORIA L. SORK. Influence of late Quaternary climate change on present patterns of genetic variation in valley oak, Quercus lobata. Molecular Ecology (2013) 22, 3598–3612


Snelling RR, Borowiec ML, Prebus MM (2013) Studies on California ants: a review of the genus Temnothorax (Hymenoptera, Formicidae). ZooKeys 372: 27–89. doi: 10.3897/zookeys.372.6039 Specimen data associated with the new species. doi: 10.3897/zookeys.372.6039.app


Korrodi-Gregório L, Margarida Lopes A, Esteves SLC, Afonso S, Lemos de Matos A, et al. 2013. An Intriguing Shift Occurs in the Novel Protein Phosphatase 1 Binding Partner, TCTEX1D4: Evidence of Positive Selection in a Pika Model. PLoS ONE 8(10): e77236. doi:10.1371/journal.pone.0077236


Lemos de Matos, D. K. Lanning & P. J. Esteves. Genetic characterization of CCL3, CCL4 and CCL5 in leporid genera Oryctolagus, Sylvilagus and Lepus. International Journal of Immunogenetics, 2013, 0, 1–5


Blair C. McLaughlin and Erika S. Zavaleta. (2013). Regional and temporal patterns of natural recruitment in a California endemic oak and a possible ‘research reserve effect’. Diversity and Distributions, 19, 1440–1449.


McLaughlin, B. C., Zavaleta, E. S. (2013). Regional and temporal patterns of natural recruitment in a California endemic oak and a possible ‘research reserve effect’. Diversity and Distributions 19: 1440–1449.


Mantor, M., Krause, S. and Hart, L. A. (2013). Trapping and handling squirrels: Trap modification and handling restraint to minimize injuries and stress. Wildlife Society Bulletin. doi: 10.1002/wsb.371.


J. Lambden, Peter T. J. Johnson. (2013). Quantifying the biomass of parasites to understand their role in aquatic communities. Ecology and Evolution 3(7): 2310–2321.


Joel A. Granados, Eric A. Graham, Philippe Bonnet, Eric M. Yuen, Michael Hamilton. (2013). EcoIP: An open source image analysis toolkit to identify different stages of plant phenology for multiple species with pan–tilt–zoom cameras. Ecological Informatics 15:58–65.


Pieter T. J. Johnson, Daniel L. Preston, Jason T. Hoverman & Katherine L. D. Richgels. (2013). Biodiversity decreases disease through predictable changes in host community competence. Nature 494: 230–233.


Peggy L. Fiedler, Susan Gee Rumsey, Kathleen M. Wong. (2013). The Environmental Legacy of the UC Natural Reserve System. University of California Press. 286 pages. eISBN: 978-0-520-95364-2



2012

Pontailler, Jean-yves, and Kamel Soudani. 2012.  "Tracking canopy phenology and structure using ground-based remote sensed NDVI measurements." In: Sensors for ecology: 243. (F. Gaill, Y. Lagadeuc and J-F. Le Galliard eds).



2011

Ana Lemos de Matos, Wessel van der Loo, Helena Areal, Dennis K Lanning, and Pedro J Este- ves. 2011. Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha. BMC Evolutionary Biology 2011, 11:294


Goodman, B. A. and P. T. J. Johnson. 2011. Ecomorphology and disease: understanding the cryptic effects of parasitism on host habitat use, thermoregulation, and predator avoidance. Ecology 92:542-548.


Goodman, B. A. and P. T. J. Johnson (2011). Disease and the extended phenotype: parasites control host performance and survival through induced changes in body plan. PLoS ONE 6: e20193.


Michael Hamilton, Todd Dawson, Sally Thompson. 2011. The Very Large Ecological Array. Paper presented at the annual meeting of the American Geophysical Union, December 4-9, 2011, Moscone Conference Center, San Francisco, California.


Barbour MA, Clark RW. In review. Field videography reveals chemosensory behaviors of ambush foraging Crotalus species lying in wait for prey. Submitted to Ethology October 2011.


Clark RW, Tangco S, Barbour MA, 2011. Strike behavior of free-ranging rattlesnakes. Joint Annual Meeting of Ichthyology and Herpetology, Minneapolis MN.


Clark RW, Tangco S, Barbour MA, 2011. Predator-prey interactions between rattlesnakes and ground squirrels. Biology of the Rattlesnakes Conference, Tuscon, AZ.


Clark RW, Tangco S, Barbour MA. In review. Field recordings reveal factors that influence predatory strike success of free-ranging rattlesnakes (Crotalus spp.). Submitted to Animal Behavior, September 2011.


Ana Lemos de Matos, Wessel van der Loo, Helena Areal, Dennis K Lanning, and Pedro J Esteves. Study of Sylvilagus rabbit TRIM5α species-specific domain: how ancient endoviruses could have shaped the antiviral repertoire in Lagomorpha. BMC Evolutionary Biology 2011, 11:294


Goodman, B. A. and P. T. J. Johnson. Ecomorphology and disease: understanding the cryptic effects of parasitism on host habitat use, thermoregulation, and predator avoidance. 2011. Ecology 92:542-548.


Goodman, B. A. and P. T. J. Johnson (2011). Disease and the extended phenotype: parasites control host performance and survival through induced changes in body plan. PLoS ONE 6: e20193.



2010

Hamilton, M., Dawson, T., Stewart-Frey, I., and Gomez, J. July 8-10, 2010. The Very Large Ecological Array. Society for Conservation GIS Annual Meeting, Asilomar Conference Center, Pacific Grove, Ca.


Johnson, P. T. J. and I. D. Buller. Parasite competition hidden by correlation coinfections: using field studies and experiments to understand parasite interactions. 2010. Ecology 92: 535-541.


Johnson, P. T. J., M. K. Reeves, S. K. Krest, and A. E. Pinkney. 2010. A decade of deformities: advances in our understanding of amphibian malformations and their implications.in Sparling, Linder, Bishop, and Krest, editors. Ecotoxicology of amphibians and reptiles, 2nd edition. SETAC Press, Pensacola, FL


Johnson, P. T. J., and D. W. Thieltges 2010. Diversity, decoys and the dilution effect: how ecological communities affect disease risk.  Journal of Experimental Biology 213: 961-970.


Barbara J Benson, Barbara J Bond, Michael P Hamilton, Russell K Monson, and Richard Han. 2010. Perspectives on Next Generation Technology for Environmental Sensor Networks. Front Ecol Environ; 8(4): 193–200.


Eric A Graham; Eric M Yuen; Geoff F Robertson; William J Kaiser; Michael P Hamilton; Philip W Rundel. 2010. Budburst and leaf area expansion measured with a novel mobile camera system and simple color thresholding. Environmental and Experimental Botany. 65: 238–244.


Padgett-Flohr, G.E. and R. L. Hopkins, II. 2010. Landscape epidemiology of Batrachochytrium dendrobatidis in Central California. Ecography 33:1-1


Michael P. Hamilton, Todd Dawson, Iris Stewart-Frey, and Joseph Gomez. 2010. The Very Large Ecological Array. Poster presented at the 13th annual meeting of the Society for Conservation GIS, July 8-11, 2010, ASILOMAR Conference Center, Pacific Grove, California.


Teresa Ko, Shaun Ahmadian, John Hicks, Mohammad Rahimi, Deborah Estrin, Stefano Soatto, Sharon Coe, and Michael Hamilton. 2010. Heartbeat of a Nest: Using imagers as biological sensors. ACM Transaction on Sensor Networks, Vol. 6, Issue 3, Article 19.


Wilcox, Jeffery. 2010. Actinemys Marmorata (Western Pond Turtle) Predation. Herpetological Review. 41(2).



2009

Jeffery T. Wilcox and Brendan N. Larsen. 2009. A Group Defense Incident Involving Juvenile Striped Skunks, Mephitis mephitis. The Canadian Field-Naturalist. Vol. 122:80-82.


Jeffery T. Wilcox and Dirk H. Van Vuren . 2009. Wild Pigs as Predators in Oak Woodlands of California. Journal of Mammalogy, 90(1):114–118.


Priya Gupta, Michael E. Loik, Gregor Hsiao, Randy Apodaca, Michael P. Hamilton, Sharon J. Martinson, Iain Green, and Todd Dawson. 2009. Capturing small-scale variations of water isotopes in ambient air and natural waters of California: Results of field measurements using Wavelength Scanned Cavity Ring-Down Spectroscopy. Poster presented at AGU Chapman Conference, 4-8 October, 2009, Boise, Idaho.


Padgett-Flohr, G.E. and R. L. Hopkins, II. 2009. Batrachochytrium dendrobatidis: A Novel Pathogen Approaching Endemism in Central California. Diseases of Aquatic Organisms 83(1):1-9.



2008

Padgett-Flohr, G.E. 2008. Pathogenicity of Batrachochytrium dendrobatidis in two threatened California amphibians: Rana draytonii and Ambystoma californiense. Herpetological Conservation and Biology 3(2):182-191.


Danny L. Fry. 2008. Prescribed Fire Effects on Deciduous Oak Woodland Stand Structure, Northern Diablo Range, California. Rangeland Ecology & Management, 61(3):294-301.


2007


Gretchen E. Padgett-Flohr,1,3 and Molly E. Goble. 2007. Evaluation of tadpole mouthpart depigmentation as a diagnostic test for infections by Batrachochytrium Dendrobadids for four California Anurans. Journal of Wildlife Diseases, 43(4), pp. 690–699.