Data from: Structural diversity shifts from negative to positive associations with forest productivity via basal area, stand age, and precipitation thresholds
Data files
Nov 04, 2025 version files 6.29 MB
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Code_JE.R
99.69 KB
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FIA_Shade_Tolerance.xlsx
10.35 KB
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README.md
8.10 KB
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tbl.fig.RData
2.27 KB
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tbl.growth.Norm.DmgTree.Rdata
1.24 MB
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tbl.site.growth.site.dmgTree.Rdata
816.64 KB
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tbl.tree.MrgSbPlt.Rdata
4.11 MB
Abstract
Understanding the relationship between biological diversity and ecosystem productivity is a central challenge in ecology. Structural diversity—the variation in size, height, and spatial arrangement of individuals within communities—has been proposed as a key driver of productivity, yet previous studies have reported mixed results, leaving its role in ecosystem functioning unclear. Clarifying the structural diversity and productivity relationship (SDPR) is essential not only for advancing ecological theory but also for informing biodiversity conservation, resource management, and climate adaptation strategies across ecosystems. Here, we utilized the USDA Forest Service Forest Inventory and Analysis (FIA) database, encompassing 95,602 trees within 3,307 plots throughout most types of forest ecosystems in the contiguous U.S. We investigated the variation of SDPR by analyzing the growth of existing trees under the main and interactive effects of structural diversity with basal area, stand age, and annual precipitation, with other factors. We also compiled the studies of SDPR published during 1974 - 2022 and compared the mean annual precipitation between studies showing the negative and positive SDPR. We found that: 1) SDPR was negative under the low range of structural diversity, but became positive under the high range; 2) SDPR was more positive with greater basal areas; 3) SDPR was more positive with stand development, and 4) SDPR was more positive with greater annual precipitation in the range of low structural diversity but switched to be more negative in the high range, and the negative SDPR with greater precipitation aligns with the analysis of published studies showing greater precipitation in studies with negative SDPR than the positive ones.
Dataset DOI: 10.5061/dryad.0gb5mkmdq
Description of the data and file structure
We have five datasets for the analysis.
FIA_Shade_Tolerance.xlsx, a shade-tolerance metrics, ranging from 1-5 for the species in FIA data.
tbl.fig.RData, RData for figures.
tbl.growth.Norm.DmgTree.Rdata, Plot-level data w/o standardized variables.
tbl.site.growth.site.dmgTree.Rdata, Plot-level data w/ standardized variables.
tbl.tree.MrgSbPlt.Rdata, tree-level data after data curation in raw FIA data. Note that this tree-level data were aggregated to create plot-level data.
Descriptions
Code_JE.R: Code that includes GAM developments and figures.
FIA_Shade_Tolerance.xlsx
- SpcsNm: Species Name (scientific names)
- Shade tolerance: degree of the shade-tolerance, ranging from 1 (shade intolerant) to 5 (shade tolerant)
tbl.fig.RData: This just rData that includes the components to draw the figures.
tbl.growth.Norm.DmgTree.Rdata (Note that the value was standardized, so it's unitless)
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PlotID: PlotID
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LAT: Latitude
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LON: Longitude
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StartDate: Measurement Starting date
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EndDate: Measurement Ending date
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Bomsclass: Biomass class: Ingrowth; Growth; and Mortality
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ASPECT.factor: aspect (East, West, South, and North)
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Aspect.East: indicator variables if Aspect is East = 1; otherwise = 0
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Aspect.West: indicator variables if Aspect is West= 1; otherwise = 0
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Aspect.South: indicator variables if Aspect is South = 1; otherwise = 0
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Aspect.North: indicator variables if Aspect is North = 1; otherwise = 0
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BIO1: Annual Mean Temperature defined in WorldClim:
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BIO2: Mean Diurnal Range (Mean of monthly (max temp - min temp))
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BIO3 = Isothermality (BIO2/BIO7) (×100)
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BIO4 = Temperature Seasonality (standard deviation ×100)
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BIO5 = Max Temperature of Warmest Month
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BIO6 = Min Temperature of Coldest Month
BIO7 = Temperature Annual Range (BIO5-BIO6)
BIO8 = Mean Temperature of Wettest Quarter
BIO9 = Mean Temperature of Driest Quarter
BIO10 = Mean Temperature of Warmest Quarter
BIO11 = Mean Temperature of Coldest Quarter
BIO12 = Annual Precipitation
BIO13 = Precipitation of Wettest Month
BIO14 = Precipitation of Driest Month
BIO15 = Precipitation Seasonality (Coefficient of Variation)
BIO16 = Precipitation of Wettest Quarter
BIO17 = Precipitation of Driest Quarter
BIO18 = Precipitation of Warmest Quarter
BIO19 = Precipitation of Coldest Quarter
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AWS: Available water storage
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CEC: Cation Exchange Capacity
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OM: Organic matter
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PC: Percentage of clay
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PS: Percentage of sand
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DTW: Depth to water
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ELEV: Elevation
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Slope: slope
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STDAGE: Stand age
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ASPECT: aspect
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COSASP: Cosine of aspect
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SSD: Structural diversity
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FD: Functional diversity
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SLA: Specific leaf area
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LfCN: Leaf C:N ratio
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WD: Wood density
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HT90: 90th percentile tree height
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NumFixer: Number of N-fixed tree number in a plot
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PcntNFixer: Percentage of N-fixed tree number
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BAperha: Basal area per ha
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SSDperha: SSDperha
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SRperha: species richness per ha
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PcntRtDmgTree: percentage of root-damaged trees
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NumDmgTreeperha: Number of damaged trees per ha
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PcntDmgperha: Percentage of damaged trees
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Boms.YrRtperha: Biomass growth rate per ha
tbl.growth.Norm.DmgTree.Rdata,
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PlotID: PlotID
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LAT: Latitude
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LON: Longitude
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Biomass: summation of the biomss of individuals
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TreeNum: Number of trees in a plot
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Boms.YrRt: growth of the biomass (plot-level)
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StartDate: Measurement Starting date
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EndDate: Measurement Ending date
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Bomsclass: Biomass class: Ingrowth; Growth; and Mortality
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ASPECT.factor: aspect (East, West, South, and North)
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Aspect.East: indicator variables if Aspect is East = 1; otherwise = 0
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Aspect.West: indicator variables if Aspect is West= 1; otherwise = 0
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Aspect.South: indicator variables if Aspect is South = 1; otherwise = 0
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Aspect.North: indicator variables if Aspect is North = 1; otherwise = 0
-
BIO1: Annual Mean Temperature defined in WorldClim:
-
BIO2: Mean Diurnal Range (Mean of monthly (max temp - min temp))
-
BIO3 = Isothermality (BIO2/BIO7) (×100)
-
BIO4 = Temperature Seasonality (standard deviation ×100)
-
BIO5 = Max Temperature of Warmest Month
-
BIO6 = Min Temperature of Coldest Month
BIO7 = Temperature Annual Range (BIO5-BIO6)
BIO8 = Mean Temperature of Wettest Quarter
BIO9 = Mean Temperature of Driest Quarter
BIO10 = Mean Temperature of Warmest Quarter
BIO11 = Mean Temperature of Coldest Quarter
BIO12 = Annual Precipitation
BIO13 = Precipitation of Wettest Month
BIO14 = Precipitation of Driest Month
BIO15 = Precipitation Seasonality (Coefficient of Variation)
BIO16 = Precipitation of Wettest Quarter
BIO17 = Precipitation of Driest Quarter
BIO18 = Precipitation of Warmest Quarter
BIO19 = Precipitation of Coldest Quarter
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AWS: Available water storage
-
CEC: Cation Exchange Capacity
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OM: Organic matter
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PC: Percentage of clay
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PS: Percentage of sand
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DTW: Depth to water
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ELEV: Elevation
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Slope: slope
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STDAGE: Stand age
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ASPECT: aspect
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COSASP: Cosine of aspect
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SSD: Structural diversity
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FD: Functional diversity
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SLA: Specific leaf area
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LfCN: Leaf C:N ratio
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WD: Wood density
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HT90: 90th percentile tree height
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NumFixer: Number of N-fixed tree number in a plot
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PcntNFixer: Percentage of N-fixed tree number
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BAperha: Basal area per ha
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SSDperha: SSDperha
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SRperha: species richness per ha
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PcntRtDmgTree: percentage of root-damaged trees
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NumDmgTreeperha: Number of damaged trees per ha
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PcntDmgperha: Percentage of damaged trees
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Boms.YrRtperha: Biomass growth rate per ha
tbl.tree.MrgSbPlt.Rdata
- PlotID: PlotID
- StartDate: Measurement Starting date
- EndDate: Measurement Ending date
- SubPlotID: SubplotiD
- TreeID: TreeID
- SPCD: Species code
- Status.StartYr. Tree status status in startYr
- Status.EndYr. Tree status status in EndYr
- DeathCause: cause of deat agent of the trees
- DIA.StartYr: diameter at breast height in start year
- DIA.EndYr: diameter at breast height in end year
- HT.StartYr: Height in start year
- HT.EndYr: Height in end year
- Boms.StartYr: Biomass of trees in start year
- Boms.EndYr: Biomass of trees in end year
- CrownR.StartYr: Crown ratio in start year
- CrownR.EndYr: Crown ratio in end year
- CrownC.StartYr: Crown class code in start year
- CrownC.EndYr: Crown class code in end year
- BomsClass: biomass class: ingrowth; growth; and mortality
- DAMLOC1.StartYr: Damage location in start year
- DAMSEV1.StartYr: Damage severity in start year
- DAMTYPE1.StartYr: Damage types in start year
- DAMLOC2.StartYr: secondary damage location in start year
- DAMSEV2.StartYr: secondary damage severity in start year
- DAMTYPE2.StartYr: secondary damage types in start year
- DAMLOC3.StartYr: Third damage location in start year
- DAMSEV3.StartYr: Third damage severity in start year
- DAMTYPE3.StartYr: Third damage types in start year
- DAMLOC1.EndYr: Damage location in end year
- DAMSEV1.EndYr: Damage severity in end year
- DAMTYPE1.EndYr: Damage types in end year
- DAMLOC2.EndYr: secondary damage location in end year
- DAMSEV2.EndYr: secondary damage severity in end year
- DAMTYPE2.EndYr: secondary damage types in end year
- DAMLOC3.EndYr: Third damage location in end year
- DAMSEV3.EndYr: Third damage severity in end year
- DAMTYPE3.EndYr: Third damage types in end year
- MORTYR: Mortality Year
- SubPlotID.StartYr: Combination of SubplotID and StartYr
- NumSrvys.x: Number of survey of the plot (not really need for the analysis)
- NumSrvys.y: Number of survey of the plot (not really need for the analysis)
- SpcsNm: species scientific names
- Is39Spcs: Yes or no for the 39 species in the dataset
- NumSbplts: Number of subplots in a plot
- YrDiff: Year difference between startdate and enddate
- SHADETOLERANCE: Shade tolerance levels
All the NA values are not measured data.
