DOI: 10.5061/dryad.g4f4qrfv9
title: Data from: The effect of shrub cover on conifer water-use patterns, growth, and response to climate change in the southern Sierra Nevada

description: As wildfire increases in size and severity, large areas of forest are
 undergoing substantial increases in shrub cover. In forests where water is
 the limiting resource, the paritioning of soil water between shrubs and
 trees may determine how shrubs affect tree growth and water-stress. We
 analyzed hydrogen and oxygen isotopes in the xylem water for two conifer
 species and two shrub species to assess how shrub cover affects the
 water-uptake patterns of conifers in the southern Sierra Nevada. Further,
 we analyzed tree growth and stable carbon isotopes in tree rings to assess
 how shrub cover affects tree growth, intrinsic water-use efficiency and
 response to climate change.
description: Xylem samples were collected from two conifer species
 (<em>Abies concolor</em> and <em>Pinus
 jeffreyi</em>) and two shrub species (<em>Arctostaphylos
 patula</em> and <em>Ceanothus cordulatus</em>) in the
 southern Sierra Nevada. Soil samples were collected near a subset of the
 sampled trees. Xylem water and soil water were extracted using a cryogenic
 vacuum distillation and analyzed for hydrogen and oxygen stable
 isotopes. Trees of both conifer species were cored or
 cross-sectioned after xylem samples were collected. Tree-ring analysis was
 used to calculate age and growth for each tree and carbon isotope analysis
 was performed on wood samples obtained from each tree core/cross
 section. 
description: Data and Code for "The effect of shrub cover on conifer water-use
 patterns, growth, and response to climate change in the southern Sierra
 Nevada" Created by Marissa J. Goodwin Code: Shrub-Tree Water Use.Rmd
 = Code for data analysis Dataframes: Raw Soil Data.csv - This dataframe
 contains soil water hydrogen and oxygen data for each growing environment
 and tree species combination at three soil depths (0-10 cm, 10-20 cm,
 20-30 cm). Columns are as follows: "Identifier.1" = unique
 identifier for each soil sample (some soil samples were analyzed twice),
 "d18OVsmow" = oxygen isotope ratio, "d2HVsmow" =
 hydrogen isotope ratio, "Species.Shrub" = Tree Species and
 growing environment combination (AO = white fir-Open, AS= white fir-Shrub,
 PO = Jeffrey pine-Open, PS = Jeffrey pine-Shrub), "Site" =
 Growing Environment (Open = Shrub Absent and Shrub = Shrub Dominant) Xylem
 Water Data.csv - This dataframe contains xylem water hydrgoen and oxygen
 data for all trees and shrubs in each growing environment and at each time
 period. Columns are as follows: "Sample.ID" = unique identifier
 for each sample, "d18O"= oxygen isotope ratio, "dD" =
 hydrogen isotope ratio, "Species" = tree or shrub species (ABCO
 = white fir, PIJE = Jeffrey pine, ARPA = greenleaf manzanita, CECO =
 mountain whitethorn), "Site" = growing environment (Open = Shrub
 Absent and Shrub = Shrub Dominant), "Period" = when the sample
 was taken (Early Summer = Early June, Late Summer = Late August), and
 "Type" = plant type (Tree vs Shrub) averages.csv - This
 dataframe contains average soil water hydrogen and oxygen isotope values
 and their standard deviation for each group (Tree Species, Shrub Species,
 and Soil Depth) by growing environment (Shrub Absent vs. Shrub Dominant)
 and time period (Early Summer vs Late Summer). Columns are as follows:
 "Species" = Tree or Shrub Species (also includes soil since this
 dataframe is used for plotting xylem water values with soil water values),
 "Type" = sample type (Tree, Shrub or Soil water), "
 Site" = growing environment, "Group" = same as Species
 column but with scientific names and soil depths included for plotting,
 "Name" = group and Time period combined (Soil does not have a
 time period associated with is since it was only measured in early
 summer), "Period" = when the sample was taken (Early Summer =
 Early June, Late Summer = Late August), "o.mean" = average
 oxygen isotope ratio by group "o.sd" = standard deviation for
 the oxygen isotope ratio by group, "h.mean" = average hydrogen
 isotope ratio by group, "h.sd" = standard deviation for the
 hydrogen isotope ratio by group. soil.source.csv - This dataframe contains
 average hydrogen and oxygen isotope values and their standard deviation
 for each soil depth by growing environment. This dataframe is used for
 plotting the xylem water values against average soil water values in
 simmr. Columns are as follow: "Means" = Growing environment and
 soil depth, "meand18O" = average oxygen isotope ratio,
 "sdd18O" standard deviation for the oxygen isotope ratio,
 "meand2H" = average hydrogen isotope ratio, "sdd2H" =
 standard deviation for the hydrogen isotope ratio. soil.source.shrub.csv -
 This dataframe is the same as "soil.source" but only contains
 soil water averages for the shrub growing environment. Used for
 calculating source water contributions using the simmer mixing model for
 trees and shrubs in the shrub dominant growing environment.
 soil.source.open.csv - This dataframe is the same as
 "soil.source" but only contains soil water averages for the open
 growing environment. Used for calculating source water contributions using
 the simmer mixing model for trees in the shrub absent growing environment.
 Cores_Tucson_12.7.txt = text file with raw ring width data (unit=mm) for
 each tree and year. RWL file is generated using WinDendro. Only 11 of the
 40 trees were cored (data for the other 29 trees can be found in
 "Cookies_averaged_rwl.txt"). Unique identifiers (ex. AS8)
 include the tree species (A=white fir, P=Jeffrey pine), growing
 environment (S=shrub, O=Open) and tree number. Cookies_averaged_rwl.txt =
 text file with raw ring width data (unit=mm) for each tree and year. RWL
 file is generated using WinDendro. This dataframe contains data for the 29
 out of 40 trees where we collected cross sections. Unique identifiers (ex.
 AS8) include the tree species (A=white fir, P=Jeffrey pine), growing
 environment (S=shrub, O=Open) and tree number. rwi by year.csv - This
 dataframe contains raw ring width data (unit=mm) for each tree and year
 growth (ex. row 1 is the trees first year of growth). Unique identifiers
 (ex. AS8) include the tree species (A=white fir, P=Jeffrey pine), growing
 environment (S=shrub, O=Open) and tree number. carbon.csv - This dataframe
 contains carbon isotope data for each tree and year from 2016 to 2021.
 Columns are as follows: "Sample ID" = unique identifier for each
 sample. The unique identifier contains tree species (A=white fir,
 P=Jeffrey pine), growing environment (S = Shrub, O = Open), tree number,
 and wood type (Earlywood = E, and Latewood = L). Most trees/years had both
 earlywood and latewood sampled, but 27 trees had earlywood and latewood
 sampled together. These are denoted as ".B" for both types of
 wood. Column "d13C" = carbon isotope ratio. SWE.csv - This
 dataframe contains snow water equivalent data for April 1st from 2015 to
 2021 for three different sites in the southern Sierra Nevada located near
 the Teakettle Experimental Forest. Data was obtained from the USDA NRCS
 National Water and Climate Center database. Columns are as follows:
 "Date" = Date of Snow Water Equivalent measurement,
 "Year" = year of snow water equivalent measurement, "TW SWE
 (mm)" = Tamarack Summit SWE in millimeters, "UBC SWE (mm)"
 = Upper Burnt Corral SWE in millimeters, "WWM SWE (mm)" = West
 Woodchuck meadow SWE in millimeters, "Mean.SWE" = average SWE of
 all three sites, "SD.SWE" = SWE standard deviation for all three
 sites. Supplmental PRISM Data.csv - This dataframe contains monthly
 precipitation data (mm) for the Teakettle Experimental Forest from 2000 to
 2021. *Note* - blank cells indicate no data was available for that site
 and time point. There are four sites/time points that do not have data: TS
 (4/1/2015), WWM (4/1/2015), TS (4/1/2020), WWM (4/1/2021). Averages were
 calculated without these points. Supplemental Prism Data.csv - This
 dataframe contains monthly precipitation data (mm) for the Teakettle
 Experimental Forest from 2000 to 2021. Columns are as follows:
 "Date" = year and month, "ppt(mm)" = precipitation
 totals in millimeters, "Water Year" = water year precipitation
 fell during (water year is includes October to September). Blank cells
 mean no data is available for this site.