Using Anuran community diversity and Pseudacris crucifer to predict landscape quality across a land use gradient
Data files
Apr 29, 2025 version files 215.70 KB
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Master_Collapsed_Data_21-23_for_R_analysis.csv
132.09 KB
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Mini_Collapsed_Data_21-23_for_R_for_avg_spp_survey_only.csv
61.78 KB
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README.md
21.84 KB
Abstract
As human-modified landscapes and climate changes proliferate, maintaining biodiversity and understanding the function and quality of available habitat is imperative. As anurans (frogs/toads) such as Pseudacris crucifer, can be an indicator species of habitat quality and ecosystem productivity, studying the anuran community in a mixed-land use region provides an opportunity to better understand the relationship between species and landscape modification. We explored the relationship between anurans and ecosystem productivity by assessing the effects of spatial and temporal heterogeneity on the presence of anurans across a land use gradient. Within the Toledo Metropolitan Area, including the biodiversity hotspot Oak Openings Region, we surveyed 67 different wetlands (N=1800) over three years. There was a difference in community assemblage between rural and suburban/urban habitats driven by human modification (impervious surface), composition (landcover type), and productivity (NDVI). The variation in spatial structure but lack of variation in temporal variables suggests that spatial factors explain differences in the anuran community among sites. Areas with more impervious surfaces, lower amounts of swamp forest, and lower NDVI generally had significantly fewer anuran species (p < 0.001, p = 0.001, p = 0.013), significantly lower average species per survey (p < 0.001, p = 0.011, p = 0.005), and lower relative abundance of anurans. Utilizing Generalized Linear Mixed Modeling, we found that P. crucifer relative abundance (p = 0.006) and greater species richness (p = 0.021) were the best predictors of ecosystem productivity. Our research demonstrates the value of non-invasive anuran call surveys to assess ecosystem productivity and species richness on a large scale, while also offering a method to evaluate conservation efforts internationally. This scalable approach can be applied anywhere with available environmental data, and we recommend utilizing anurans as indicator taxa for understanding ecosystem function, especially in human-modified landscapes.
Dataset DOI: 10.5061/dryad.6q573n68m
Description of the data and file structure
This data was collected over three field seasons (1 March through 1 August) from 2021-2023, assessing the relationship between anthropogenic land use change and anuran species diversity/density.
Within sheet 1 (Master Collapsed Data 21-23 for R analysis):
Cells in columns A through E display data about the sites surveyed, the year of the survey, and the number of surveys conducted. Within the "Class" column (D), Class #1 = rural sites, #2 = suburban, #3 = urban.
Columns H through BE display data regarding anuran species surveyed, with WCHF = Western chorus frog, NSPP = Northern spring peeper, NOLF = Northern leopard frog, WOOF = wood frog, EAMT = Eastern American toad, GRTF = gray tree frog complex, FOWT = Fowler's toad, BCRF = Blanchard's cricket frog, GREF = green frog, and BULF = bullfrog. In species "intensity" columns, 0 values were replaced by 1e-14.
Columns BF through FX display habitat and environmental data for each site across the three years of surveying. Columns BG through BL, BN, BO, BS, and BT are averages taken from several measurements at the beginning and end of each field season. BY through EW are values drawn from spatial analysis based on a 250-meter or 1km buffer surrounding the survey point. EX through FX display either averages or single values regarding many weather variables taken from the nearest weather station to the survey point across the time period indicated (February = 2, March = 3, August = 8, September = 9).
Files and variables
File: Master_Collapsed_Data_21-23_for_R_analysis.xls
Description: NA cell values coded as "-"
Class #1 = rural sites, #2 = suburban, #3 = urban
WCHF = Western chorus frog, NSPP = Northern spring peeper, NOLF = Northern leopard frog, WOOF = wood frog, EAMT = Eastern American toad, GRTF = gray tree frog complex, FOWT = Fowler's toad, BCRF = Blanchard's cricket frog, GREF = green frog, and BULF = bullfrog.
February = 2, March = 3, August = 8, September = 9
Variables
Site = Name of site
Year = year of survey
SiteNum = number assigned to each site
Class = urbanization class (1 = rural, 2 = suburban, 3 = urban)
NumSurv = number of surveys at the site during the survey year
TotalRichness = number of species recorded at that site during the survey year
AvgSppsurvey = average species per survey
WCHF (or other species abbreviation) = species presence
WCHFIntensity (or other species abbreviation) = species calling intensity, on a scale of 1 to 3
WCHFavg = percentage of surveys a species was detected
WCHFIntAvg = average intensity of a species over all surveys
WCHFRelative = relative abundance of a species detected, based on the species' calling intensity and percentage of surveys encountered
Elev = elevation (in meters)
ChngLitDep = change in litter depth from March to July (centimeters)
ChngGrsHi = change in grass height from March to July (cm)
ChngLitCov = change in litter cover from March to July (cm)
ChngGrsCov = change in grass cover from March to July (cm)
ChngBgCov = change in bare ground cover from March to July (cm)
ChngOthCov = change in other cover from March to July (cm)
NumCoarseWoody = number of coarse woody debris encountered
ChngEmVeg = change in emergent vegetation from March to July (percentage, estimated by surveyor)
ChngFloVeg = change in floating vegetation from March to July (percentage, estimated by the surveyor)
NumSnags = number of snags encountered
NumShrbs = number of shrubs encountered
NumTrees = number of trees encountered
ChngCanCov = change in canopy cover from March to July (percentage)
ShrubCover = shrub cover (percentage, calculated based on the diameter of the shrub)
FineWoody = number of fine woody debris encountered
TrafficCount = raw number of cars passing in the test time period (from Ohio Department of Transportation (ODOT) data during the most recent traffic survey period)
AADT = Annual Average Daily Traffic (from ODOT data)
6to6Traffic Count = traffic count between 6 pm and 6 am (from ODOT data)
PercentImp = percent impervious surface within a 250m (meter) circle of the survey point, from the US Geological Survey (USGS) impervious surface raster
AvgNDVI250m = average NDVI (normalized difference vegetation index) within a 250m circle of the survey point from March through July, from the USGS' EarthExplorer tool
EarlyNDVI250m = NDVI within a 250m circle of the survey point in March, from the USGS' EarthExplorer tool
LateNDVI250m = NDVI within a 250m circle of the survey point in July, from the USGS' EarthExplorer tool
PercentTurf = percentage of turf within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Percent2Wp = percentage of wet prairie within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc3RMX = percentage of residential/mixed use within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Percent4PerPns = percentage of perennial ponds within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc5UpSav = percentage of upland savanna within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc6Wtshr = percentage of wet shrubland within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc7SwmpFor = percentage of swamp forest within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc8UpCon = percentage of upland coniferous within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc9UpDec = percentage of upland deciduous within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc10FldFrst = percentage of floodplain forest within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc11SandBarrens = percentage of sand barrens within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc12EurM = percentage of Eurasian meadow within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc13Upprair = percentage of upland prairie within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc14Urb = percentage of urban within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc60Cropland = percentage of cropland within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
PercOtB, PercTdA, PercOaC, PercGr, PercCoB, PercSh, PercW, PercGF, PercRnA, PercSo, PercOaB, PercMf, PercUo, PercByA, PercSdB, PercOuB, PercCe, PercSuE3, PercEe, PercDdA, PercBxA, PercCo, PercUn, PercBxB, PercDsA, PercSmC, PercPq, PercSmB, PercWt, PercDcA, PercSmD, PercLf, PercDgB, PercHoA, PercDgA, PercSnB, PercCp, PercDtA, PercDoA - percentage of soil values within a 250m circle from survey point (not used in this analysis)
PercImp1km = percentage of impervious surface within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
AvgNDVI1km = average NDVI (normalized difference vegetation index) within a 1km circle of the survey point from March through July, from the USGS' EarthExplorer tool
EarlyNDVI1km = early NDVI within a 1km circle of the survey point in March, from the USGS' EarthExplorer tool
LateNDVI1km = late NDVI within a 1km circle of the survey point in July, from the USGS' EarthExplorer tool
PercTurf1km = percentage of turf within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc2WP1km = percentage of wet prairie within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc3RMX1km = percentage of residential/mixed-use land within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc4PerP1km = percentage of perennial ponds within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc5UpSav1km = percentage of upland savanna within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc6Wtshr1km = percentage of wet shrubland within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc7SwmpFor1km = percentage of swamp forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc8UpCon1km = percentage of upland coniferous forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc9UpDec1km = percentage of upland deciduous forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc10FldFrst1km = percentage of floodplain forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc11SandBarrens1km = percentage of sand barrens within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc12EurM1km = percentage of Eurasian meadow within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc13Upprair1km = percentage of upland prairie within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc14Urbkm = percentage of urban area within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc60Cropland1km = percentage of cropland within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
PrevYr3to8avgprecip = average precipitation from March through August in centimeters during the year before the survey
PrevYr3to8numdayswithprecip = number of days with precipitation from March through August during the year before the survey
PrevYr3to8totalprecip = total precipitation from March through August in centimeters during the year before the survey
PrevYr3to8avgtemp = average temperature from March through August in Celsius during the year before the survey
PrevYr3to8avgMintemp = average minimum temperature from March through August in Celsius during the year before the survey
Prevyr3to8avgMaxtemp = average maximum temperature from March through August in Celsius during the year before the survey
PrevYr3to8avgwindspd = average wind speed from March through August in miles per hour during the year before the survey
PrevWinter9to2avgprecip = average precipitation from September through February in centimeters during the winter before the survey
PrevWint9to2Numdayswprecip = number of days precipitation from September through February in centimeters during the winter before the survey
PrevWint9to2totalprecip = total precipitation from September through February in centimeters during the winter before the survey
PrevWint9to2avgtemp = average temperature from September through February in Celsius during the winter before the survey
PrevWint9to2Avgmintemp = average minimum temperature from September through February in Celsius during the winter before the survey
PrevWint9to2Avgmaxtemp = average maximum temperature from September through February in Celsius during the winter before the survey
PrevWint9to2avgwindspeed = average wind speed from September through February in miles per hour during the winter before the survey
Inyear3to8avgprecip = average precipitation from March through August in centimeters during the year of the survey
Inyear3to8numprecipdays = number of days with precipitation from March through August in centimeters during the year of the survey
Inyear3to8totalprecip = total precipitation from March through August in centimeters during the year of the survey
Inyear3to8Avgtemp = average temperature from March through August in Celsius during the year of the survey
Inyear3to8avglowtemp = average temperature from March through August in Celsius during the year of the survey
Inyear3to8averagehitemp = average high temperature from March through August in Celsius during the year of the survey
Inyear3to8avgwindspeed = average wind speed from March through August in miles per hour during the year of the survey
NumD1Weekinyear3to8 = number of weeks under D1 drought conditions (moderate drought) from March through August during the year of the survey
NumD1WeeksPrevWinter9to2 = number of weeks under D1 drought conditions (moderate drought) from September through February during the previous winter of the survey
NumD1weeksPrevBreedingseason3to8 = number of weeks under D1 drought conditions (moderate drought) from March through August during the year before the survey
NumD0Weeksinyear3to8 = number of weeks under D0 drought conditions (abnormally dry) from March through August during the year of the survey
NumD0weeksPrevWinter9to2 = number of weeks under D0 drought conditions (abnormally dry) from September through February during the previous winter
NumD0weeksPrevBreedingSeason3to8 = number of weeks under D0 drought conditions (abnormally dry) from March through August during the year before the survey
File: Mini_Collapsed_Data_21-23_for_R_for_avg_spp_survey_only.xls
Description: Within sheet 2 (Mini collapsed data 21-23 for R for avg spp survey only):
These data were used only for the analysis of factors that may have influenced the average species heard per survey.
Cells in columns A through E display data about the sites surveyed, the year of survey, and the number of surveys conducted. Within the "Class" column (D), Class #1 = rural sites, #2 = suburban, #3 = urban.
Columns F and G display data regarding anuran species detected during the surveys across each year.
Columns H through BL include many of the same habitat data measurements as in sheet 1. Columns I-N, P, Q, U, V are averages of several measures taken at both the beginning and end of the field season. Columns H, O, R-T, and W-Y display single values or averages. AA through BL are values drawn from spatial analysis based on a 250-meter buffer surrounding the survey point.
NA cell values coded as "-"
Class #1 = rural sites, #2 = suburban, #3 = urban
February = 2, March = 3, August = 8, September = 9
Variables
Site = Name of site
Year = year of survey
SiteNum = number assigned to each site
Class = urbanization class (1 = rural, 2 = suburban, 3 = urban)
NumSurv = number of surveys at the site during the survey year
TotalRichness = number of species recorded at that site during the survey year
AvgSppsurvey = average species per survey
Elev = elevation (in meters)
ChngLitDep = change in litter depth from March to July (centimeters)
ChngGrsHi = change in grass height from March to July (cm)
ChngLitCov = change in litter cover from March to July (cm)
ChngGrsCov = change in grass cover from March to July (cm)
ChngBgCov = change in bare ground cover from March to July (cm)
ChngOthCov = change in other cover from March to July (cm)
NumCoarseWoody = number of coarse woody debris encountered
ChngEmVeg = change in emergent vegetation from March to July (percentage, estimated by surveyor)
ChngFloVeg = change in floating vegetation from March to July (percentage, estimated by the surveyor)
NumSnags = number of snags encountered
NumShrbs = number of shrubs encountered
NumTrees = number of trees encountered
ChngCanCov = change in canopy cover from March to July (percentage)
ShrubCover = shrub cover (percentage, calculated based on the diameter of the shrub)
FineWoody = number of fine woody debris encountered
TrafficCount = raw number of cars passing in the test time period (from Ohio Department of Transportation data during the most recent traffic survey period)
AADT = Annual Average Daily Traffic (from ODOT data)
6to6Traffic Count = traffic count between 6 pm and 6 am (from ODOT data)
PercentImp = percent impervious surface within a 250m (meter) circle of the survey point, from the US Geological Survey impervious surface raster
AvgNDVI250m = average NDVI (normalized difference vegetation index) within a 250m circle of the survey point from March through July, from the USGS' EarthExplorer tool
EarlyNDVI250m = NDVI within a 250m circle of the survey point in March, from the USGS' EarthExplorer tool
LateNDVI250m = NDVI within a 250m circle of the survey point in July, from the USGS' EarthExplorer tool
PercentTurf = percentage of turf within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Percent2Wp = percentage of wet prairie within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc3RMX = percentage of residential/mixed use within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Percent4PerPns = percentage of perennial ponds within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc5UpSav = percentage of upland savanna within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc6Wtshr = percentage of wet shrubland within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc7SwmpFor = percentage of swamp forest within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc8UpCon = percentage of upland coniferous within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc9UpDec = percentage of upland deciduous within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc10FldFrst = percentage of floodplain forest within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc11SandBarrens = percentage of sand barrens within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc12EurM = percentage of Eurasian meadow within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc13Upprair = percentage of upland prairie within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc14Urb = percentage of urban within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
Perc60Cropland = percentage of cropland within a 250m circle of the survey point, based on landcover data from Martin and Root (2020)
PercImp1km = percentage of impervious surface within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
AvgNDVI1km = average NDVI (normalized difference vegetation index) within a 1km circle of the survey point from March through July, from the USGS' EarthExplorer tool
EarlyNDVI1km = early NDVI within a 1km circle of the survey point in March, from the USGS' EarthExplorer tool
LateNDVI1km = late NDVI within a 1km circle of the survey point in July, from the USGS' EarthExplorer tool
PercTurf1km = percentage of turf within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc2WP1km = percentage of wet prairie within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc3RMX1km = percentage of residential/mixed-use land within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc4PerP1km = percentage of perennial ponds within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc5UpSav1km = percentage of upland savanna within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc6Wtshr1km = percentage of wet shrubland within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc7SwmpFor1km = percentage of swamp forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc8UpCon1km = percentage of upland coniferous forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc9UpDec1km = percentage of upland deciduous forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc10FldFrst1km = percentage of floodplain forest within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc11SandBarrens1km = percentage of sand barrens within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc12EurM1km = percentage of Eurasian meadow within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc13Upprair1km = percentage of upland prairie within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc14Urbkm = percentage of urban area within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Perc60Cropland1km = percentage of cropland within a 1km circle of the survey point, based on landcover data from Martin and Root (2020)
Code/software
R v. 4.3.2, with the packages lme4, conflicted, dplyr, emmeans, coda, reshape2, lattice, car, ggpubr, unmarked, lme4, Matrix, nlme, glmm, reshape, MASS, DHARMa, performance, glmmTMB, bbmle, readxl
