DOI: 10.5061/dryad.hdr7sqvws
title: Ephemeral vegetation drivers of occupancy dynamics of Mojave desert tortoises (Gopherus agassizii)

description: Understanding the factors associated with the probability of a species
 occurring across the landscape has become a foundational component of
 wildlife management and monitoring. Static factors (e.g., plot
 characteristics that are consistent across time, such as topography or
 permanent woody vegetation)are often investigated, but dynamic vegetation
 factors may also drive apparent occupancy dynamics as energy-minimizing
 species respond to ephemeral changes in food resources. We analyzed the
 role of ephemeral forbs and grasses in the occupancy dynamics of Mojave
 desert tortoises (Gopherus agassizii), expecting higher occupancy when
 food plants (forbs) were abundant and lower occupancy when non-food plants
 (grasses) were widespread. We found that none of the static plot-level
 factors explained initial occupancy in the first year, but vegetation
 factors did influence interannual occupancy dynamics. Plots that were
 unoccupied in a given year were 14.4% less likely to become occupied in
 the following year for every 1% point increase in grass cover within the
 plot (i.e., a negative effect of grass cover on annual plot occupancy).
 Conversely, occupied plots were 72.5% less likely to become unoccupied in
 the subsequent year for every 1% point increase in the cover of forbs and
 we unexpectedly found that occupied plots were 76.9% less likely to become
 unoccupied for every additional grass species present in the plot.
 However, credible intervals were wide, indicating strong but inconsistent
 patterns of ephemeral vegetation driving occupancy dynamics of Mojave
 desert tortoises.
description: # Ephemeral vegetation drivers of occupancy dynamics of Mojave desert
 tortoises (Gopherus agassizii) Dataset DOI:
 [10.5061/dryad.hdr7sqvws](10.5061/dryad.hdr7sqvws) ## Description of the
 data and file structure ### Files and variables #### File:
 OpenResearchData__vegannual_longformat.csv **Description:**  #####
 Variables * Plot: The 4-ha survey plot * Year: The year of the vegetation
 survey * Value: The value of the 'community metric'. * Community
 metric: Derived metric; Species richness = number of unique species across
 all quadrats within the plot, Plant abundance = number of individual
 plants of each 'plant group' across all quadrats within the
 plot, and Percent cover = the mean percent cover of each plant group
 across all quadrats within the plot * Plant group: Forb (herbaceous)
 versus grass species #### File: OpenResearchData__occupancy_vegetation.csv
 **Description:**  ##### Variables * site: Simple integer identifier for
 each Plot * Plot: Alphanumeric identifier for each occupancy sampling plot
 * yvis1.1: Yes(1)/No(0) of whether a Mojave desert tortoise was observed
 in year one, survey one at the plot. * yvis1.2: Yes/No of observing Mojave
 desert tortoise in year one, survey two * yvis1.3: Same as preceding,
 subsequent survey * yvis1.4: Same as preceding, subsequent survey *
 yvis1.5: Same as preceding, subsequent survey * yvis1.6: Same as
 preceding, subsequent survey * yvis1.7: Same as preceding, subsequent
 survey * yvis2.1: Yes(1)/No(0) of whether a Mojave desert tortoise was
 observed in year two, survey one at the plot. * yvis2.2: Same as
 preceding, subsequent survey * yvis2.3: Same as preceding, subsequent
 survey * yvis2.4: Same as preceding, subsequent survey * yvis2.5: Same as
 preceding, subsequent survey * yvis2.6: Same as preceding, subsequent
 survey * yvis2.7: Same as preceding, subsequent survey * yvis3.1:
 Yes(1)/No(0) of whether a Mojave desert tortoise was observed in year
 three, survey one at the plot. * yvis3.2: Same as preceding, subsequent
 survey * yvis3.3: Same as preceding, subsequent survey * yvis3.4: Same as
 preceding, subsequent survey * yvis3.5: Same as preceding, subsequent
 survey * yvis3.6: Same as preceding, subsequent survey * yvis3.7: Same as
 preceding, subsequent survey * Vegetative %: Total percent vegetative
 cover across the Plot * Veg_area_creosote: Total percent creosote cover
 (Larrea tridentata) across the Plot * Veg_area_bursage: Total percent
 bursage cover (Ambrosia dumosa) across the Plot * visit1.1.day: Calendar
 day-of-year for first year, first survey of the Plot * visit1.2.day: Same
 as preceding, subsequent survey * visit1.3.day: Same as preceding,
 subsequent survey * visit1.4.day: Same as preceding, subsequent survey *
 visit1.5.day: Same as preceding, subsequent survey * visit1.6.day: Same as
 preceding, subsequent survey * visit1.7.day: Same as preceding, subsequent
 survey * visit2.1.day: Calendar day-of-year for second year, first survey
 of the Plot * visit2.2.day: Same as preceding, subsequent survey *
 visit2.3.day: Same as preceding, subsequent survey * visit2.4.day: Same as
 preceding, subsequent survey * visit2.5.day: Same as preceding, subsequent
 survey * visit2.6.day: Same as preceding, subsequent survey *
 visit2.7.day: Same as preceding, subsequent survey * visit3.1.day:
 Calendar day-of-year for third year, first survey of the Plot *
 visit3.2.day: Same as preceding, subsequent survey * visit3.3.day: Same as
 preceding, subsequent survey * visit3.4.day: Same as preceding, subsequent
 survey * visit3.5.day: Same as preceding, subsequent survey *
 visit3.6.day: Same as preceding, subsequent survey * visit3.7.day: Same as
 preceding, subsequent survey * visit1.1.temp: Ambient temperature (C) at
 the start of the occupancy survey, first year and first survey *
 visit1.2.temp: Same as preceding, subsequent survey * visit1.3.temp: Same
 as preceding, subsequent survey * visit1.4.temp: Same as preceding,
 subsequent survey * visit1.5.temp: Same as preceding, subsequent survey *
 visit1.6.temp: Same as preceding, subsequent survey * visit1.7.temp: Same
 as preceding, subsequent survey * visit2.1.temp: Ambient temperature (C)
 at the start of the occupancy survey, second year and first survey *
 visit2.2.temp: Same as preceding, subsequent survey * visit2.3.temp: Same
 as preceding, subsequent survey * visit2.4.temp: Same as preceding,
 subsequent survey * visit2.5.temp: Same as preceding, subsequent survey *
 visit2.6.temp: Same as preceding, subsequent survey * visit2.7.temp: Same
 as preceding, subsequent survey * visit3.1.temp: Ambient temperature (C)
 at the start of the occupancy survey, third year and first survey *
 visit3.2.temp: Same as preceding, subsequent survey * visit3.3.temp: Same
 as preceding, subsequent survey * visit3.4.temp: Same as preceding,
 subsequent survey * visit3.5.temp: Same as preceding, subsequent survey *
 visit3.6.temp: Same as preceding, subsequent survey * visit3.7.temp: Same
 as preceding, subsequent survey * stationppt.2014: Total precipitation
 (mm) at nearest weather station from preceding Oct2013-Jan2014 *
 stationppt.2015: Total precipitation (mm) at nearest weather station from
 preceding Oct2014-Jan2015 * stationppt.2016: Total precipitation (mm) at
 nearest weather station from preceding Oct2015-Jan2016 *
 2014.forb.spprich: Plot-level forb species richness from
 'OpenResearchData_vegannual longformat.csv' * 2015.forb.spprich:
 Plot-level forb species richness from 'OpenResearchData_vegannual
 longformat.csv' * 2016.forb.spprich: Plot-level forb species richness
 from 'OpenResearchData_vegannual longformat.csv' *
 2014.grass.spprich: Plot-level grass species richness from
 'OpenResearchData_vegannual longformat.csv' *
 2015.grass.spprich: Plot-level grass species richness from
 'OpenResearchData_vegannual longformat.csv' *
 2016.grass.spprich: Plot-level grass species richness from
 'OpenResearchData_vegannual longformat.csv' *
 2014.nativeforb.abund: Plot-level native forb abundance from
 'OpenResearchData_vegannual longformat.csv' *
 2015.nativeforb.abund: Plot-level native forb abundance from
 'OpenResearchData_vegannual longformat.csv' *
 2016.nativeforb.abund: Plot-level native forb abundance from
 'OpenResearchData_vegannual longformat.csv' *
 2014.nativegrass.abund: Plot-level native grass abundance from
 'OpenResearchData_vegannual longformat.csv' *
 2015.nativegrass.abund: Plot-level native grass abundance from
 'OpenResearchData_vegannual longformat.csv' *
 2016.nativegrass.abund: Plot-level native grass abundance from
 'OpenResearchData_vegannual longformat.csv' * 2014.forb.cover:
 Plot-level percent forb cover from 'OpenResearchData_vegannual
 longformat.csv' * 2015.forb.cover: Plot-level percent forb cover from
 'OpenResearchData_vegannual longformat.csv' * 2016.forb.cover:
 Plot-level percent forb cover from 'OpenResearchData_vegannual
 longformat.csv' * 2014.grass.cover: Plot-level percent grass cover
 from 'OpenResearchData_vegannual longformat.csv' *
 2015.grass.cover: Plot-level percent grass cover from
 'OpenResearchData_vegannual longformat.csv' * 2016.grass.cover:
 Plot-level percent grass cover from 'OpenResearchData_vegannual
 longformat.csv' ## Access information Other publicly accessible
 locations of the data: * None Data was derived from the following sources:
 * Field observations and measurements