Data Management Plan for the California LCC project:

Determining Landscape Connectivity and Climate Change Refugia Across the Sierra Nevada

Table of Contents
Data Input - New Collections
  1   Belding's Ground Squirrel Yosemite National Park Surveys

Data Input - Existing Collections
  1   Belding's Ground Squirrel California-wide persistence data
  2   Sierra Nevada Meadows Shapefile
  3   Downscaled Monthly Climate Data and Estimates
  4   Elevation data
  5   Watercourse Information
  6   Roads Dataset

Data Output - Product or Deliverables
  1   Yosemite National Park Meadow Attributes
  2   Belding's Ground Squirrel Genetic Structure Across California
  3   Sierra Nevada Refugial Meadows with Connectivity Rankings.

Not Data - non-data Products
  1   Workshop #1: "Landscape Connectivity and Climate Change Refugia Across the Sierra Nevada: Presentation and Application of Products for Sierra Nevada Decision-makers"
  2   Beyond a global warming fingerprint of climate change: heterogeneous biogeographic responses in California
  3   A test of climate change refugia
  4   Climate Change Refugia website
  5   Meeting #1 with Agency Partners: UC Berkeley, USFS, NPS, CADFW, USGS
  6   Meeting #2 with Agency Partners: UC Berkeley, USFS, NPS, CADFW, USGS
  7   Workshop #2: Climate Adaptation Options for Natural Resource Managers in the Sierra Nevada
  8   Regional Climate Change Refugia Workshop at UC Berkeley
  9   Article in March 2014 Estuary News
  10   Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge
  11   A Ghost Town's Second Life as a Climate Refuge for Rodents
  12   Publication: Managing climate change refugia for climate adaptation
  13   Climate Change Refugia as a Tool for Climate Adaptation
  14   Poster: Climate Change Refugia as a Tool for Climate Adaptation
  15   Connectivity and Refugia in the Sierra Nevada, an article in the Climate Commons
  16   Evil Cannibal Squirrels Could Make California's Drought Less Terrible

Data Input - Existing Collections
1Belding's Ground Squirrel California-wide persistence data
DescriptionThis is a shapefile that shows locations where we resurveyed meadows where Belding's ground squirrels had been originally documented in the first half of the 20th century (primarily in the 1910s and 1920s but as late as 1963). The publication explaining these results in more detail can be found here: 10.1098/rspb.2012.1301 This dataset was used to test the hypothetical connectivity and refugia maps produced by this project.
Formatshapefile
Processing and WorkflowChoice of survey sites and method of surveys is described in Morelli et al 2012, Proceedings of the Royal Society B. Sites were then plotted on a map based on GPS coordinates and labeled as to whether Belding's ground squirrels were found there (persistent) or not (extirpated).
Access and SharingPublic
CitationMorelli, T.L., A.B. Smith, C. Kastely, I. Mastroserio, C. Moritz & S.R. Beissinger. 2012. Anthropogenic refugia ameliorate the severe climate-correlated decline of a montane mammal along its trailing edge. Proceedings of the Royal Society B 279: 4279-4286.
DOI10.1098/rspb.2012.1301
ContactToni Lyn Morelli 313-919-0191 morellitlm@gmail.com

2Sierra Nevada Meadows Shapefile
DescriptionA geodatabase representing meadows across the Sierra Nevada.
SourceInformation Center for the Environment at UC Davis
Processing and WorkflowWe applied post-processing buffer and dissolve methods using ArcGIS 10 to simply the data set.
Quality ChecksWe cross-validated the extent and occurrence using a dataset covering Yosemite National Park and Sequoia National Park
Backup and StorageWe stored data on servers and external drives at the Museum of Vertebrate Zoology at UC Berkeley
Linkhttp://meadows.ucdavis.edu/products/data

3Downscaled Monthly Climate Data and Estimates
DescriptionInterpolations of 20th century climate values from PRISM (monthly precipitation, minimum temperature, & maximum temperature) were downscaled from 4km grid cells to 270m grid cells using methods described in Flint and Flint 2012. These were used, along with other GIS layers (e.g. geology), as input for a version of the Basin Characterization Model (Flint and Flint 2007), to provide additional estimates of Actual Evapotranspiration (AET), Potential Evapotranspiration (PET) , Climatic Water Deficit (CWD) and Snow Water Equivalent (SWE). Furthermore, four projections of monthly 21st century climate based upon two circulation models (NCAR Parallel Climate Model, PCM, and NOAA Geophysical Fluids Dynamics Laboratory model, GFDL) and two scenarios (A2, a higher emission scenario, and B1, an ecological friendly scenario), were available with the same variable suite. The data encompassed the all watersheds associated with California.
SourceWe received the data directly for Alan and Lorraine Flint.
Processing and WorkflowTo speed processing, we clipped the data to a rectangular region that would encompass the Sierra Nevada and surrounding areas. We used two thirty year periods of observed climate, 1910-1939 (historic) and 1970-1999 (modern), and three periods in future estimates, 2010-2039, 2040-2069, and 2070-2099, to summarize trends. For climate information, we constructed bioclimatic variables associated with each time period using the R package raster. We determined the extreme values during the historic time and determined the frequency in which modern and future periods exceeded them. We summarized CWD & AET for each year within the dataset, and then determined the mean for each of the periods.
Backup and StorageData are stored on external drives and on servers at the Museum of Vertebrate Zoology at UC Berkeley.
Volume Estimate2TB
CitationFlint and Flint: Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis. Ecological Processes 1:2. doi:10.1186/2192-1709-1-2

4Elevation data
DescriptionElevation layer for the western United States with estimates at 90m resolution.
FormatRaster GIS Layer
Processing and WorkflowWe resampled the data to 540m resolution.
Backup and StorageData were provided by the Museum of Vertebrate Zoology and are housed on associated servers.

5Watercourse Information
DescriptionLine shapefile representing watercourses for most of the watershed associated with the contiguous United States.
CitationLehner, B., Verdin, K., Jarvis, A. (2006): HydroSHEDS Technical Documentation. World Wildlife Fund US, Washington, DC. Available at http://hydrosheds.cr.usgs.gov.

6Roads Dataset
DescriptionLine shapefile of all Primary and Secondary roads courtesy of U.S. Department of Commerce, U.S. Census Bureau, Geography Division
Linkhttp://www2.census.gov/geo/tiger/TIGER2012/PRISECROADS/tl_2012_41_prisecroads.zip

Data Input - New Collections
1Belding's Ground Squirrel Yosemite National Park Surveys
Deliverable TypeDatasets / Database
DescriptionWe conducted surveys of Belding's ground squirrels in all meadows that we could access in Yosemite National Park in the summer of 2011 as well as a few in 2010.
NCCWSC Collection ProtocolsSites were chosen from Yosemite National Park maps. Larger meadows were prioritized and although most the meadows were within a day's hike from a trailhead, several were tens of kilometers from the nearest road. Previous research (Morelli et al 2012 Proceedings of the Royal Society B) showed that detectability was very high (>95% with only one visit) so most sites were visited only one or two times although always with two experienced observers. Sites were surveyed on foot for at least 30 minutes during morning or evening hours. A site would be considered occupied if only one Belding's ground squirrel was detected but in reality numerous individuals were detected at all occupied sites.
Formatshapefile, PDF map
Volume Estimatesmall (<1 MB)
Access and SharingPDF will be made publicly available. Interested users should contact Toni Lyn Morelli to get access to the shapefile.
Linkhttp://climate.calcommons.org/sites/default/files/reports/YNP%20surveys.jpg
ContactToni Lyn Morelli morellitlm@gmail.com 313-919-0191

Data Output - Product or Deliverables
1Yosemite National Park Meadow Attributes
Deliverable TypeDatasets / Database
DescriptionThis is a table describing information on the majority of meadows in Yosemite National Park. This table includes information that was developed by this project, namely columns describing connectivity value based on different predictors and a measure of whether the meadow is a climate change refugium.
Linkhttp://climate.calcommons.org/sites/default/files/dmpfiles/Yosemite%20Meadow%20Analysis.zip
ContactSean Maher, smaher02@gmail.com

2Belding's Ground Squirrel Genetic Structure Across California
Deliverable TypeDatasets / Database
DescriptionBelding's ground squirrel genetic structure mapped across California with a close-up of sampling in and just east of Yosemite National Park.
NCCWSC Collection ProtocolsWe sampled 187 adult or sub-adult Belding’s ground squirrels at 15 sites across California from Modoc County to the southern Sierra Nevada from 2003 to 2011, with the majority of samples obtained in 2010 and 2011. Ground squirrels were trapped in Sherman or Tomahawk Live Traps. Genetic samples were collected through an ear snip or from a liver biopsy during preparation of museum skins. DNA was extracted using standard methods and amplified using ten polymorphic microsatellite loci optimized from protocols developed based on other sciurid species. We tested for and, where necessary, adjusted for null alleles, as well as Hardy-Weinberg equilibrium, and linkage disequilibrium. To assign individuals to populations, we ran an analysis in STRUCTURE 2.3.4, first across the entire study area based on the 15 sampling sites. Initially we split state-wide samples into four major areas: Northern California, Tahoe area, Yosemite, and southern Sierras. Then these four subpopulations were iteratively run until samples grouped into a single genetic population (i.e., K = 1 had the strongest support based on the method by Evanno et al). Each run was replicated ten times with K set from 1 to 8 populations, with an initial burn-in of 10,000 iterations followed by 106 Markov chain Monte Carlo repetitions.
Formattif or jpg
Volume Estimate<10 MB
Access and SharingPublic, once released.
Exclusive Use EmbargoEmbargoed until July 2014
Linkhttp://climate.calcommons.org/sites/default/files/reports/Beldings%20Ground%20Squirrel%20Genetic%20Structure%20Across%20California.jpg
ContactToni Lyn Morelli morellitlm@gmail.com 313-919-0191

3Sierra Nevada Refugial Meadows with Connectivity Rankings.
Deliverable TypeMap
DescriptionMeadows delineated in the Sierra Nevada wth refugial status and connectivity rankings--WellConnected (WC), ReallyWellConnected (RC), Stable. Satisfies the delivery of "Sierra Nevada Connectivity Maps" and "Sierra Nevada Meadows Map". Maps of the Sierra Nevada Meadows designated by their connectivity classification and whether they are expected to have a climate different than historic (1910-1939). We generated maps for modern climate (1970-1999) and four future climate scenarios, broken down into 30 year intervals, in which we assumed connectivity would not change because resistance and conductance surfaces were static. Data for the map are polygon shapefiles of meadows, processed first by buffer and dissolve in ArcGIS that were overlayed on connectivity surfaces and climate layers. We classified polygons based on connectivity value and the amount of change observed or expected. Refugia definitions depended upon the climate variable (i.e. within 1 degree Celcius in temperature; 10% of precipitation).
FormatRaster layers, generally at 540m resolution. Presented as a ESRI Layer Package in Databasin.
Processing and WorkflowUsing the program Circuitscape, we estimated connectivity between meadows using raster layers representing hypotheses of isolation. Depending upon the values in the raster, they were treated as conductance or resistance surfaces; the output map for each layer represent the sum of connectivity.
Backup and StorageData are stored on portable harddrives and servers at the Museum of Vertebrate Zoology at UC Berkeley
Volume Estimate130MB
Linkhttp://databasin.org/datasets/33035c0f338d40b88ad23de5a10d8842
ContactSean Maher, smaher02@gmail.com

Not Data - non-data Products
1Workshop #1: "Landscape Connectivity and Climate Change Refugia Across the Sierra Nevada: Presentation and Application of Products for Sierra Nevada Decision-makers"
Deliverable TypeTraining / Outreach / Workshop
DescriptionThrough CA LCC funding, researchers at U.C. Berkeley have collaborated with federal and CDFW scientists to develop a map of meadow connectivity and climate change refugia across the Sierra Nevada. The goal of this December 10, 2013 workshop was to create an opportunity for managers to review the results, discuss their options for managing land in the face of climate change, and determine how these products can inform on-the-ground decisions and aid climate adaptation actions.
Access and SharingPublic domain
Linkhttp://californialcc.org/news/workshop-recording-available-landscape-connectivity-and-climate-change-refugia-across-sierra
Contactmorelli@ecs.umass.edu

2Beyond a global warming fingerprint of climate change: heterogeneous biogeographic responses in California
Deliverable TypePublication
DescriptionBeyond a global warming fingerprint of climate change: heterogeneous biogeographic responses in California
CitationRapacciuolo, G., S. P. Maher, A. C. Schneider, T. T. Hammond, M. D. Jabis, R. Walsh, K. J. Iknayan, G. K. Walden, M. F. Oldfather, D. D. Ackerly, & S. R. Beissinger. Accepted. Beyond a global warming fingerprint of climate change: heterogeneous biogeographic responses in California. Global Change Biology
ContactToni Lyn Morelli

3A test of climate change refugia
Deliverable TypePublication
DescriptionMorelli et al., To be submitted in May to Molecular Ecology, "A test of climate change refugia"
Access and SharingPublic, unless Molecular Ecology has a pay-wall.
CitationMorelli et al., To be submitted in May to Molecular Ecology, “A test of climate change refugia”
ContactToni Lyn Morelli

4Climate Change Refugia website
Deliverable TypeWebsite
DescriptionWebsite: "Climate Change Refugia" website will feature a dynamic, interactive refugia map and all deliverables.
Access and SharingPublic
Linkhttp://museum-of-vertebrate-zoology.github.io/MVZ-Web/Grinnell/refugia/index.html
ContactToni Lyn Morelli

5Meeting #1 with Agency Partners: UC Berkeley, USFS, NPS, CADFW, USGS
Deliverable TypeTraining / Outreach / Workshop
Description-Participants: UC Berkeley, USFS, NPS, CADFW, USGS -Objective: Work with scientists and natural resource managers to design the LCC-funded project for maximum impact
Linkhttp://climate.calcommons.org/sites/default/files/dmpfiles/Climate%20Refugia%20Workshop%202014%20-%20Agenda.docx

6Meeting #2 with Agency Partners: UC Berkeley, USFS, NPS, CADFW, USGS
Deliverable TypeTraining / Outreach / Workshop
Description- Participants: UC Berkeley, USFS, NPS, CADFW, USGS -Objective: Work with scientists and natural resource managers to refine the LCC-funded project and share preliminary results for maximum impact
Linkhttp://climate.calcommons.org/sites/default/files/dmpfiles/UCB%20LCC%20Workshop%20Agenda%20-%20March%2021.docx

7Workshop #2: Climate Adaptation Options for Natural Resource Managers in the Sierra Nevada
Deliverable TypeTraining / Outreach / Workshop
DescriptionParticipants: USFS, NPS; Objective: Create an opportunity for managers to review project results, discuss their options for managing land in the face of climate change, and determine how these products can inform on-the-ground decisions and aid climate adaptation actions.
Linkhttp://climate.calcommons.org/sites/default/files/reports/Climate%20Adaptation%20Options%20for%20Natural%20Resource%20Managers%20in%20the%20Sierra%20Nevada_Workshop%20Agenda.docx, http://climate.calcommons.org/sites/default/files/reports/MorelliMaher27MayFresnoPresentation.pdf
ContactToni Lyn Morelli

8Regional Climate Change Refugia Workshop at UC Berkeley
Deliverable TypeTraining / Outreach / Workshop
Description-Participants: Climatologists, hydrologists, ecologists, and other researchers from universities, USGS, and institutions in California and elsewhere in the western U.S. along with natural resource specialist staff at NPS and USFS -Objective: Identify how the climate refugia concept can best be applied in management; produce a review paper focused on the management implications
Linkhttp://climate.calcommons.org/sites/default/files/dmpfiles/Climate%20Refugia%20Workshop%202014%20-%20Agenda.docx
ContactToni Lyn Morelli

9Article in March 2014 Estuary News
Deliverable TypePublication : Article
DescriptionStory in San Francisco Estuary Partnerships' quarterly magazine.
Linkhttp://climate.calcommons.org/sites/default/files/CALCC-Mar2014-EstuaryNews.pdf

10Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge
Deliverable TypePublication
DescriptionWe conducted detailed resurveys of a montane mammal, Urocitellus beldingi, to examine the effects of climate change on persistence along the trailing edge of its range. Of 74 California sites where U. beldingi were historically recorded (1902–1966), 42 per cent were extirpated, with no evidence for colonization of previously unoccupied sites. Increases in both precipitation and temperature predicted site extirpations, potentially owing to snowcover loss. Surprisingly, human land-use change buffered climate change impacts, leading to increased persistence and abundance. Excluding human-modified sites, U. beldingi has shown an upslope range retraction of 255 m. Generalized additive models of past distribution were predictive of modern range contractions (AUC = 0.76) and projected extreme reductions (52% and 99%, respectively) of U. beldingi's southwestern range to 2080 climates (Hadley and CCCMA A2). Our study suggests the strong impacts of climate change on montane species at their trailing edge and how anthropogenic refugia may mitigate these effects.
Access and SharingPublic
RestrictionsNone
CitationMorelli, T. L., A. B. Smith, C. R. Kastely, I. Mastroserio, C. Moritz, and S. R. Beissinger. 2012. Anthropogenic refugia ameliorate the severe climate-related decline of a montane mammal along its trailing edge. Proceedings of the Royal Society B: Biological Sciences. doi: 10.1098/rspb.2012.1301.
DOI10.1098/rspb.2012.1301
Linkhttp://rspb.royalsocietypublishing.org/content/early/2012/08/13/rspb.2012.1301.full
ContactToni Lyn Morelli

11A Ghost Town's Second Life as a Climate Refuge for Rodents
Deliverable TypePublication : Article
DescriptionMedia piece about the project.
Linkhttp://www.psmag.com/environment/ghost-towns-second-life-climate-refuge-rodents-67242/

12Publication: Managing climate change refugia for climate adaptation
Deliverable TypePublication
DescriptionMorelli, Toni Lyn, Christopher Daly, Solomon Z. Dobrowski, Deanna M. Dulen, Joseph L. Ebersole, Stephen T. Jackson, Jessica D. Lundquist, et al. 2016. “Managing Climate Change Refugia for Climate Adaptation.” PLOS ONE 11 (8): e0159909. doi:10.1371/journal.pone.0159909.
DOI10.1371/journal.pone.0159909

13Climate Change Refugia as a Tool for Climate Adaptation
Deliverable TypePublication
DescriptionMaher et al. "Erosion of refugia in the Sierra Nevada meadows network with climate change", Ecography

14Poster: Climate Change Refugia as a Tool for Climate Adaptation
Deliverable TypePresentation : poster
DescriptionThe concept of refugia has been discussed from theoretical and paleontological perspectives to address how populations persisted during periods of unfavorable climate. Recently, several studies have applied the idea to contemporary landscapes to identify locations that are buffered from climate change effects so as to favor greater persistence of valued resources relative to other areas. Refugia are now being discussed among natural resource agencies as a potential adaptation option in the face of anthropogenic climate change. Under funding from the California Landscape Conservation Cooperative, we worked with state and federal scientists and natural resource managers to get closer to developing a process to implement climate change refugia as a tool for climate adaptation. Using survey and genetic data from Belding’s ground squirrel (Urocitellus beldingi) populations in California, we tested whether particular montane meadows are acting as refugia. We also analyzed the connectivity among these sites. At each step of the research, we worked with managers to ensure the research would have the best impact. Although no panacea, climate change refugia could be important tools for prioritizing habitats for management intervention in order to conserve populations, including genetic diversity and evolutionary potential.
CitationClimate Change Refugia as a Tool for Climate Adaptation Morelli, Toni L. Northeast Climate Science Center, University of Massachusetts, Amherst, MA 01003
Linkhttp://climate.calcommons.org/sites/default/files/dmpfiles/NWLLC%20Morelli%20Poster.pdf

15Connectivity and Refugia in the Sierra Nevada, an article in the Climate Commons
Deliverable TypePublication : Article
DescriptionClimate Commons article providing an introduction, overview of results, and access to the products of the project.
Linkhttp://climate.calcommons.org/article/connectivity-and-refugia-sierra-nevada

16Evil Cannibal Squirrels Could Make California's Drought Less Terrible
Deliverable TypePublication : Article
DescriptionArticle in Mother Jones magazine.
Linkhttp://www.motherjones.com/environment/2015/01/beldings-ground-squirrels-californias-drought

This Data Management Plan structure is based on recommendations from the Data Management Plan Guidance document from the National Climate Change and Wildlife Science Center