• Intro

    The short version

    Over the 20 years of experience of natural history research, I’ve worn many hats— student of comparative anatomy, paleontology, physical anthropology, and more recently herpetologist and GIS/ data scientist. In my current role at the Museum of Vertebrate Zoology (UC Berkeley) I oversee museum informatics and GIS technologies and provide training, infrastructure support and analyses in GIS, spatial and distributional modeling and other research-based activities. My research integrates biocollections and fieldwork to answer questions in phylogeography: for example, our Evolutionary Hotspots work, which modeled areas conducive to the processes of speciation by identifying regions of high endemic diversification; or the Grinnell Resurvey Project, an effort to resurvey 80 year old sites in California to document changes in species distribution and through modeling analyze the impact of climate change. Along the way, I collaborate with experts to build tools that try to make workflows more elegant and data more beautiful.

    I contend that there's really nothing you cannot map: amphibian biodiversity, the flow of wind*, or even the seven deadly sins*! (*favorites that are not my work)

  • Informatics Projects

    Major Project work as PI or Informatic strategist.

    Holos: Berkeley Ecoinformatics Engine

    A collaborative biodiversity informatics project borne from the need to integrate diverse data sets from natural history museums and field stations to address how species respond to global change. Built by researchers and technologists in biological, ecological, geospatial and informatic sciences, we created an open web service or API (ecoengine.berkeley.edu) made accessible through web-based tools (holos.berkeley.edu).

     

    Explore tool - discover data by faceted searches on geography, taxonomy or decades, and more.

     

    Compare tool - compare more than one query easily and dynamically

     

    ROpenSci package - use the ecoengine package to access data

    • PI

    VertNet

    VertNet is a NSF-funded collaborative project that makes biodiversity data free and available on the web. VertNet is a tool designed to help people discover, capture, and publish species data from biocollections around the world. VertNet is a community for training current and future professionals to use and build upon best practices in data quality, curation, research, and data publishing. The VertNet team are collaborators from the Universities of California, Colorado, Kansas, and Tulane, and partners from a wide-range of biodiversity projects, who work to build upon the successes of four classic vertebrate networks (FishNet, MaNIS, HerpNET, ORNIS) to combine them into a single
    integrated data portal, and solve the problems that these networks face.

    • Sr.Personnel and Trainer

    AmphibiaWeb

    AmphibiaWeb is an online system that synthesizes and disseminates information on amphibian natural history, conservation, taxonomy, and global decline. The website integrates contributions from scientists and experts with the latest in biodiversity informatics. Features include: up-to-date tracking of newly described amphibian species, expert-based species accounts for over 30% of the world’s amphibians, some in multiple languages; dynamic species range and occurrence mapping; detailed pages on amphibian declines and its causes with ongoing literature updates; community- contributed multimedia files (sound, video and photos); and a community of scientists responsive to the latest taxonomic and research developments in amphibian biology and conservation to any inquiries from the public.

    • Associate Director

     

  • Publications

    Peer-reviewed (since 2007)

    Kelly, M, K J Easterday, MS Koo, J H Thorne, S Mukythar, and B Galey. 2017. Geospatial informatics key to recovering and sharing historical ecological data for modern use. Photogrammetric Engineering and Remote Sensing 18(11): 779-786 doi: 10.14358/PERS.83.10.779

     

    Cicero, C., CL Spencer, DA Bloom, RP Guralnick, MS Koo, J Otegui, L Russell, and JR Wieczorek. 2017. Biodiversity informatics and data quality on a global scale. In M. S. Webster, ed. Emerging Frontiers in Collections-based Ornithological Research: The Extended Specimen. Studies in Avian Biology (no. 50), CRC Press, Boca Raton, FL.

     

    Kelly, M, K Easterday, G Rapacciuolo, MS. Koo, P Mcintyre, and J Thorne. 2016. Rescuing and sharing historical vegetation data for ecological analysis: The California Vegetation Type Mapping project. Biodiversity Informatics 11: 40-62

     

    Yap, T, L Gillespie, S Ellison, SV Flechas, MS Koo, AE Martinez, and VT Vredenburg. 2016. Invasion of the fungal pathogen Batrachochytrium dendrobatidis on California Islands. EcoHealth 13(1):145-150. DOI:10.1007/s10393-015-1071-y

     

    Yap TA, MS Koo, RF Ambrose, DB Wake, and VT Vredenburg. 2015. Averting a North American biodiversity crisis. Science 349 (6247), 481-482. DOI:10.1126/science.aab1052

     

    Rowe, K.C., K.BC Rowe, M.W. Tingley, M.S. Koo, J.L. Patton, C.J. Conroy, S. Beissinger, and C. Moritz. 2015. Spatially heterogeneous impact of climate change on small mammals of montane California. Proceedings of the Royal Society B: Biological Sciences 282(1799): 20141857.
     
    Davies, N., et al. 2014. Founding Charter of the Genomic Observatories Network. GigaScience 2014, 3:2 doi:10.1186/2047-217X-3-2.

    Reilly, S.B., D. Portik, M.S. Koo, D.B. Wake. 2013. Discovery of a New, Disjunct Population of a Narrowly Distributed Salamander (Taricha rivularis) in California Presents Conservation Challenges. Journal of Herpetology. Early Online: December 18, 2013; September 2014: 48(3):371-379.
     
    Smith, A.B., M.J. Santos, M.S. Koo, K.M.C. Rowe, K.C. Rowe, J.L. Patton, J.D. Perrine, S.R. Beissinger, C. Moritz. 2013. Evaluation of species distribution models by resampling of sites surveyed a century ago by Joseph Grinnell. Ecography. 36(9):1017-1031. doi: 10.1111/j.1600-0587.2013.00107.x
     
    Tingley, M., M.S. Koo, C. Moritz, A.C. Rush, S. Beissinger. 2012. The push and pull of climate change causes heterogeneous shifts in avian elevational ranges. Global Change Biology 18(11):3279-3290.
     
    Cicero, C. and M.S. Koo 2012. The role of niche divergence and phenotypic adaptation in promoting lineage diversification of the Sage Sparrow (Artemisiospiza belli, Aves: Emberizidae). Biological Journal of the Linnean Society 107(2):332-354.
     
    Leaché, A.D., M.S. Koo, C.L. Spencer, T.J. Papenfuss, R.N. Fisher and J.A. McGuire. 2009. Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma). Proceedings of the National Academy of Sciences 28 July 2009. 106(30): 12418-12423.

     

    Davis, E. B., M.S. Koo, C. Conroy, J.L. Patton, C. Moritz. 2008. The California Hotspots Project: Identifying regions of rapid
    diversification of mammals. Molecular Ecology. 17(1):120-138. doi:10.1111/j.1365-294X.2007.03469.x
     
    Wogan, G.O.U., J.V. Vindum, J.A. Wilkinson, M.S. Koo, J.B. Slowinski, Htun Win, Thin Thin, Sai Wunna Kyi, San Lwin Oo, Kyi Sow Lwin, and Awan Khwi Shein. 2008. New country records and range extensions for Myanmar amphibians and reptiles. Hamadryad. 33(1):83-96.
     
    Fellers, G.M., K.L. Pope, J.E. Stead, M.S. Koo, H.H. Welsh, Jr. 2007. Turning population trend monitoring into active conservation: Can we save the Cascades frog (Rana cascadae) in the Lassen region of California? Herpetological Conservation and Biology 3(1):28-39.


    McGuire, J.A., C.W. Linkem, M.S. Koo, D.W. Hutchison, A.K. Lappin, D.I. Orange, J. Lemos-Espinal, B.R. Riddle, J.R. Jaeger. 2007. Mitochondrial introgression and incomplete lineage sorting through space and time: phylogenetics of crotaphytid lizards. Evolution 61 (12): 2879–2897.


    Zug, G.R., J.V. Vindum, M.S. Koo. 2007. Burmese Hemidactylus (Reptilia, Squamata, Gekkonidae): Taxonomic Notes on Tropical Asian Hemidactylus. Proceedings of the California Academy of Sciences 58: 387 - 405.


    Pawar, S., M.S. Koo, C. Kelly, M.F. Ahmed, S. Choudhury, S. Sarkar. 2007. Conservation assessment and prioritization of areas in Northeast India: Priorities for amphibians and reptiles. Biological Conservation. 136: 346 - 361.

    Technical Reports/ Other

    9. Smith, A.B., M.S. Koo, K.C. Rowe, J. Patton, S. Beissinger, and C. Moritz 2011. Testing methods for predicting mammalian species responses to 20th century climate change in California. Report to California Energy Commission, Public Interest Energy Research Program, 65 pp.
     
    8. Loarie, S., T.R. Kahn, B. Gratwicke, K. Johnson, M.S. Koo, G.A. Chaves Portilla, B. Tapley, K. Ueda. 2011. The Global Amphibian Bioblitz. FrogLog 97:48-50.
     
    7. Koo, M.S., J.V. Vindum and D.G. Mulcahy. 2007. Herpetological Baseline Survey of the Presidio of San Francisco. Report to National Park Service, Dept. of Interior, San Francisco, CA. 56 pp.
     
    6. Perrine, J., C. Conroy, C. Cicero, M.S. Koo, and M. Tingley. Lassen Transect Resurvey 2006 Annual Report. 83 pp.
     
    5. Koo, M.S., J.V. Vindum, and M. McFarland. 2004. Amphibians and Reptiles of the Lassen National Forest: Results of 02-CS-11050650-029 The 2003 California Academy of Sciences Survey. Report to US Forest Service, Dept. of Agriculture, Susanville, CA. 175 pp.
     
    4. Koo, M.S. and J.V. Vindum 2003. Amphibians and Reptiles of the Sierra and Sequoia National Forests. Report to the US Forest Service, Dept. of Agriculture, Porterville, CA, xxx pp.
     
    3. Koo, M.S. and J.V. Vindum 2001. Amphibians and Reptiles of the Sequoia National Forest: Results of CCS-00-CC-11051322-034, the 2000 California Academy of Sciences Survey. Report to the US Forest Service, Dept. of Agriculture, Porterville, CA.
     
    2. Koo, M.S. and J.V. Vindum 1999. Amphibians and Reptiles of the Mendocino National Forest: Results of the 2000 California Academy of Sciences Survey. Report to the US Forest Service, Dept. of Agriculture, Willows, CA.
     
    1. Koo, M.S. and J.V. Vindum 1998. Amphibians and Reptiles of the Tahoe and Plumas National Forests. Report to the US Forest Service, Dept. of Agriculture, Quincy, CA, 164 pp.
     

    Books

    Whittaker, K., M.S. Koo, V. T. Vredenburg and D. B. Wake. 2011 Global Declines of Amphibians In Levin SA (ed) Encyclopedia of Biodiversity Online Update 2. pp. 1-9. Oxford: Elsevier Ltd.
     
    Vredenburg, V.T., M.S. Koo, and D.B. Wake. 2008. Declines of amphibians in California. In Hoffman, M. et al. (Ed.), Threatened Amphibians of the World. Lynx Ediciones, Barcelona, Spain. 776 pp.
     
    Koo, M.S. 2001. California Academy of Sciences’ Herpetology project and GIS. In Convis, C.L. (Ed.), Conservation Geography. Case Studies in GIS, Computer Mapping, and Activism. ESRI Press, Redlands, California. pp. 107 – 109.

  • Skills

    20+ years

    GIS experience using ArcGIS, Quantum GIS and R Stats. Includes teaching and consultations, freelance cartography and data visualizations.

    Regular user of

    Adobe Creative Suite: Photoshop, Illustrator

    R Statistics

    ESRI ArcGIS, Quantum GIS

    Google Maps, Earth Engine

    CartoDB

    HTML, CSS, SQL

    Grant writing success

    --> $1.5M Keck Foundation

    --> $482k Mellon Foundation

    --> 4 NSF grants as co-PI, 3 NSF grants as Sr. Personnel

    --> 13 US Forest Service Challenge Cost-share Agreements for biotic survey work (over $176k total)

    Workshop Teaching

    GIS, and Georeferencing biodiversity records

    Informatics tools in R

    Species distribution modeling

    Database fundamentals for natural history museums

    Herpetology

    Project Management

    Oversees personnel (IT, Application programmers, archivists and informaticists) in both grant-funded efforts and daily maintenance.

    Bonus domains

    Herpetology, especially North America

    Graphic design

    Cartography

     

  • Experience

    Biodiversity Informatics and GIS Staff Curator

    Museum of Vertebrate Zoology, UC Berkeley, 2006 - present

     

    Research focuses on spatial modeling of species distributions and biodiversity informatics tools. Worked on the Grinnell Resurvey Project, an NSF grant to resurvey 100-year-old sites in California to document and analyze species changes over time and assess the factors that contribute to both local and broad extirpations and expansions of vertebrate species. For the California Evolutionary Hotspots project, mapped and modeled areas conducive to the processes of speciation by identifying regions of high endemism in mammals and amphibians to help with conservation prioritization. As a staff curator, responsibilities include curation and management of the MVZ’s collection database (Arctos), MVZ’s Archives, and teaching specialized workshops in GIS, cartography, modeling and informatics. A member of the Arctos Steering Committee, and Chair of the Berkeley Natural History Museum IT & Informatics Committee.

     

    Biogeographic Systems Manager

    California Academy of Sciences, 1996 - 2006

    Conducted biodiversity surveys focusing on amphibians and reptiles on US Forest Service and US National Park Service lands with federal funding including: Tahoe, Plumas, Lassen, Mendocino, Sierra, Sequoia National Forests and the Presidio of San Francisco. Provided research and public exhibit support for several biodiversity efforts around the world, including Burma/Myanmar, Yunnan, Sao Tome and Principe, Eastern Africa, Western North America. Honed map-making and herpetological specimen prepping skills.

    GIS Consultant

    American Museum of Natural History, 2000

    GIS and archival work to georeference historic specimens from the Chapin and Lang expeditions to the Congo basin from 1909-1915 for the AMNH Digital Library.

    Research intern

    Center for Reproduction of Endangered Wildlife, Cincinnati Zoo, 1995

    Independently tested cryopreservation methods for amphibian embryos and gametes. Coined 'frog-sicles' and created recipes of glucose treatment for gray treefrog eggs and embryos.

  • Map

    Hike with a view