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Data for Context-dependent biotic interactions control plant abundance across altitudinal environmental gradients, 2014, 2016, Colorado, USA

General Information
Data Package:
Local Identifier:edi.391.2
Title:Data for Context-dependent biotic interactions control plant abundance across altitudinal environmental gradients, 2014, 2016, Colorado, USA
Abstract:

Many biotic interactions influence community structure, yet most distribution models for plants have focused on plant competition or used only abiotic variables to predict plant abundance. Furthermore, biotic interactions are commonly context-dependent across abiotic gradients. For example, plant-plant interactions can grade from competition to facilitation over temperature gradients. We used a hierarchical Bayesian framework to predict the abundances of 12 plant species across a mountain landscape and test hypotheses on the context-dependency of biotic interactions over abiotic gradients. We combined field-based estimates of six biotic interactions (foliar herbivory and pathogen damage, fungal root colonization, fossorial mammal disturbance, plant cover, and plant diversity) with abiotic data on climate and soil depth, nutrients, and moisture. All biotic interactions were significantly context-dependent along temperature gradients. Results supported the stress gradient hypothesis: As abiotic stress increased, the strength or direction of the relationship between biotic variables and plant abundance generally switched from negative (suggesting suppressed plant abundance) to positive (suggesting facilitation/mutualism). For half of the species, plant cover was the best predictor of abundance, suggesting that the prior focus on plant-plant interactions is well-justified. Explicitly incorporating the context-dependency of biotic interactions generated novel hypotheses about drivers of plant abundance across abiotic gradients and may improve the accuracy of niche models.

Publication Date:2019-06-06

Time Period
Begin:
2014-06-01
End:
2016-07-31

People and Organizations
Contact:Lynn, Joshua S (University of New Mexico; Rocky Mountain Biological Laboratory) [  email ]
Contact:Rudgers, Jennifer A (University of New Mexico; Rocky Mountain Biological Laboratory) [  email ]
Creator:Lynn, Joshua S (University of New Mexico; Rocky Mountain Biological Laboratory)
Creator:Kazenel, Melanie R (University of New Mexico; Rocky Mountain Biological Laboratory)
Creator:Kivlin, Stephanie N (University of New Mexico; Rocky Mountain Biological Laboratory; The University of Tennessee, Knoxville)
Creator:Rudgers, Jennifer A (University of New Mexico; Rocky Mountain Biological Laboratory)
Associate:Brown, Wendy (Rocky Mountain Biological Laboratory, Assisted In Data Collection)
Associate:Canfield, Samuel (Rocky Mountain Biological Laboratory, Assisted In Data Collection)
Associate:Forrester, Chiara (Rocky Mountain Biological Laboratory, Assisted In Data Collection)
Associate:Spellman, Ian (Rocky Mountain Biological Laboratory, Assisted In Data Collection)

Data Entities
Data Table Name:
LynnETAL2019_Ecography_ContDep
Description:
Grass abundance was estimated along three parallel 20 m transects placed perpendicular to the mountain slope.
Detailed Metadata

Data Entities


Data Table

Data:https://pasta-s.lternet.edu/package/data/eml/edi/391/2/d2c61bf3e2d71503a9f68bf0d8281d37
Name:LynnETAL2019_Ecography_ContDep
Description:Grass abundance was estimated along three parallel 20 m transects placed perpendicular to the mountain slope.
Number of Records:840
Number of Columns:26

Table Structure
Object Name:LynnETAL2019_Ecography_ContDep.csv
Size:141336 byte
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Text Format:
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Record Delimiter:\r\n
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Field Delimiter:,
Quote Character:"

Table Column Descriptions
 
Column Name:peak  
site  
spp  
year  
abund  
Latitude  
Longitude  
Elevation_m  
Avg_VWC1  
Avg_VWC2  
Avg_Soil_Depth  
pH  
p1MAT  
tot_N  
nitrate  
ammon  
phos  
goph  
cov  
Hdiv  
richness  
SimpDiv  
InvSimpDiv  
w_herb  
w_fung  
AVG_amf  
Definition:Name of the peak associated with a mountain transectNumber designation for a unique site within a transect that is loosely based on 100m elevation bands. Sites with x refer to extra sites sampled in 2016.Species codeYear that the site was sampledAbundance of a given species at a site expressed as counts over 60m of transectsLatitude of the site in WGS 84Longitude of the site in WGS 84Elevation of the site above sea levelAverage soil volumetric water content for a site at first sample between 12-24 July 2014 (Water L/Soil L)*100Average soil volumetric water content for a site at first sample between 23 Sept-8 Oct 2014 (Water L/Soil L)*100Average soil depth for a siteSoil pH of the siteMean annual temperature (MAT) of the site measuredTotal nitrogen ion exchange rate for a site determined by the addition of ammonium (ammon) and nitrateNitrate exchange rate for a siteAmmonium exchange rate for a sitePhosphate exchange rate for a siteAverage gopher disturbance counts across three 40m transects at a site (Lynn et al. 2018 for details)Total vegetative % cover for a site summed across 33 20x20cm plots (maximum 3300)Shannon diversity for plants at a site based on vegetation surveys. Calculated in R with the vegan package.Species richness of plants for a site calculated by summing the number of unique species found at a site in the vegetation surveys.Simpsons diversity for plants at a site based on vegetation surveys. Calculated in R with the vegan package.Inverse Simpsons diversity for plants at a site based on vegetation surveys. Calculated in R with the vegan package.Percent leaf area damaged by herbivory. Measure is for a site by weighted averaging (by abundance) across the grass species present at a sitePercent leaf area damaged by leaf pathogens. Measure is for a site by weighted averaging (by abundance) across the grass species present at a sitePercent microscope views of roots that contained aseptate fungi (candidate arbuscular mycorrhizal fungi). Measure is for a site by weighted averaging (by abundance) across the grass species present at a site
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Measurement Type:nominalnominalnominalratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratioratio
Measurement Values Domain:
Allowed Values and Definitions
Enumerated Domain 
Code Definition
CodeA
DefinitionAvery
Source
Code Definition
CodeC
DefinitionCinnamon
Source
Code Definition
CodeHH
DefinitionHunters Hill
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Code Definition
CodeR
DefinitionRuby
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Code Definition
CodeTeo
DefinitionTeocalli
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CodeTR
DefinitionTreasury
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DefinitionNumber designation for a unique site within a transect that is loosely based on 100m elevation bands. Sites with x refer to extra sites sampled in 2016.
Allowed Values and Definitions
Enumerated Domain 
Code Definition
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DefinitionAchnatherum lettermanii (Vasey) Barkworth
Source
Code Definition
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DefinitionAchnatherum nelsonii (Scribn.) Barkworth
Source
Code Definition
CodeELSC
DefinitionElymus scribneri (Vasey) M.E. Jones
Source
Code Definition
CodeELTR
DefinitionElymus trachycaulus (Link) Gould ex Shinners
Source
Code Definition
CodeFEBR
DefinitionFestuca brachyphylla Schult. ex Schult. & Schult. f.
Source
Code Definition
CodeFERU
DefinitionFestuca rubra L.
Source
Code Definition
CodeFESA
DefinitionFestuca saximontana Rydb.
Source
Code Definition
CodeFETH
DefinitionFestuca thurberi Vasey
Source
Code Definition
CodePOAL
DefinitionPoa alpina L.
Source
Code Definition
CodePOPR
DefinitionPoa pratensis L.
Source
Code Definition
CodePOST
DefinitionPoa stenantha Trin.
Source
Code Definition
CodeTRSP
DefinitionTrisetum spicatum (L.) K. Richt.
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Typenatural
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Unitnumber
Typewhole
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Max173 
Unitdegree
Typereal
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Unitdegree
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Max4023.25 
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Max26.02 
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Max31.01 
Unitmillimeter
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Min83.2 
Max1362.7 
Unitdimensionless
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Min4.6 
Max7.7 
Unitcelsius
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Min-1.59 
Max3.32 
UnitmicroGramsNitrogenPerTenCentimeterSquareExchangeResinPerTenWeeks
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Max316 
UnitmicroGramsNitratePerTenCentimeterSquareExchangeResinPerTenWeeks
Typereal
Min
Max309 
UnitmicroGramsAmmoniumPerTenCentimeterSquareExchangeResinPerTenWeeks
Typereal
Min
Max
UnitmicroGramsPhosphorusPerTenCentimeterSquareExchangeResinPerTenWeeks
Typereal
Min
Max24 
Unitnumber
Typereal
Min
Max63 
Unitdimensionless
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Min405 
Max3222 
Unitdimensionless
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Max3.01 
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Max38 
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Max0.93 
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Max14.79 
Unitdimensionless
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Max26.68 
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Max11.36 
Unitdimensionless
Typereal
Min34 
Max85 
Missing Value Code:      
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Accuracy Report:                                                    
Accuracy Assessment:                                                    
Coverage:                                                    
Methods:                                                    

Data Package Usage Rights

This information is released under the Creative Commons license - Attribution - CC BY (https://creativecommons.org/licenses/by/4.0/). The consumer of these data ("Data User" herein) is required to cite it appropriately in any publication that results from its use. The Data User should realize that these data may be actively used by others for ongoing research and that coordination may be necessary to prevent duplicate publication. The Data User is urged to contact the authors of these data if any questions about methodology or results occur. Where appropriate, the Data User is encouraged to consider collaboration or co-authorship with the authors. The Data User should realize that misinterpretation of data may occur if used out of context of the original study. While substantial efforts are made to ensure the accuracy of data and associated documentation, complete accuracy of data sets cannot be guaranteed. All data are made available "as is." The Data User should be aware, however, that data are updated periodically and it is the responsibility of the Data User to check for new versions of the data. The data authors and the repository where these data were obtained shall not be liable for damages resulting from any use or misinterpretation of the data. Thank you.

Keywords

By Thesaurus:
(No thesaurus)Ecological niche model, species distribution model, stress-gradient hypothesis, Dobzhansky-MacArthur hypothesis, mountain ecosystems, biotic interactions
LTER Controlled Vocabularyplants, abundance, soil nutrients, climate

Methods and Protocols

These methods, instrumentation and/or protocols apply to all data in this dataset:

Methods and protocols used in the collection of this data package
Description:

Methods copied from-

Lynn, J.S., M.R. Kazenel, S.N. Kivlin, and J.A. Rudgers. In press. Context-dependent biotic interactions control plant abundance across altitudinal environmental gradients. Ecography. doi: 10.1111/ecog.04421

Study site selection, focal species, and abundance estimates

We collected data in the Upper Gunnison Basin of the Colorado Rocky Mountains, USA (Figure 1). In 2014, we surveyed six independent peak-to-valley gradients spanning about 1300 m (2700 m to 4000 m a.s.l.; Figure 1). Sites were established every 100 m in elevation from peak-to-valley. This method produced 67 grassland sites, about 11 sites per gradient. To bolster data for alpine species, in 2016, we surveyed an additional 2-3 sites on five gradients (3462-3960 m a.s.l.), resulting in 79 total sites (Figure 1).

We focused on native perennial grasses. Grass abundance was estimated along three parallel 20 m transects placed perpendicular to the mountain slope and spaced 10 m apart. The focal taxa were bunch grasses (with the exception of Poa pratensis) with a maximum diameter of about 0.5 m at the ground; therefore, 20 m sufficiently captured species abundance. We estimated abundance by counting the number of individuals/species that intersected transects. This process resulted in abundance estimates for 16 species, but four were insufficiently represented (4 occurrences).

The ability to detect context-dependency may depend on spatial scale. For example, sampling the whole stress gradient occupied by a species may indicate that plant-plant interactions range from facilitation to competition, but this pattern may be obscured when only part of the species range is sampled. Therefore, we grouped species by the spatial extent of sampling effort: the whole elevation range (Elymus trachycaulus, Festuca rubra, F. saximontana, Poa stenantha, Trisetum spicatum), only the high-elevation range portion/limit (Achnatherum lettermanii, A. nelsonii, F. thurberi, P. pratensis), or only the low-elevation range portion/limit (E. scribneri, F. brachyphylla, P. alpina; summary statistics in Supplementary material Appendix 1).

Abiotic environment predictors

Abiotic variables were chosen to assess hypotheses in Table 1. At each site, two 20 m transects were placed perpendicularly, with one transect horizontal to the prevailing slope. We estimated soil volumetric water content (VWC) every 5 m along transects (10 estimates per site) using a Fieldscout TDR (10 cm probes; Spectrum Technologies, Aurora, IL, USA) at two time points over the growing season (12-24 July, 23 Sept-8 Oct, 2014), then averaged VWC within a site and sampling date. We estimated soil depth at the same points with a 1.5 m tile probe (AMS, inc., American Falls, ID, USA) inserted until it met bedrock (about 10 estimates per site). We deployed Plant Root Simulator probes (Western Ag Innovations, Saskatoon, SK, Canada) at the ends of each transect for about 10 weeks (12 July - 30 Sept, 2014). The probes were analyzed together to produce a single measure of total soil N (nitrate and ammonium) and phosphorus availability per site. We also collected and pooled soil from the four transect ends to measure soil pH (Hanna Instruments HI 9813-6 Portable; Woonsocket, RI, USA). We used regional meteorological stations to interpolate climate data for each study site based on its elevation, slope, and aspect (methods in Lynn et al. 2018). Only mean annual temperature (MAT) was used in analyses due to high collinearity among climate variables. Supplementary material Appendix 2 contains a schematic diagram of site measurements.

Biotic interaction predictors

We briefly describe methods for measuring biotic predictors but provide detail in Supplementary material Appendix 2. Estimates of plant cover and Shannon diversity were assessed with vegetation surveys. Herbivory and pathogen damage were visually estimated as percentage leaf area damaged on 10 individuals per focal species per site. To model consumptive interactions when a species was not present, we calculated grass community weighted means of herbivory and pathogen damage to represent the site-level herbivory and pathogen "pressure". Similar community weighted means were applied to arbuscular mycorrhizal fungi (AMF) colonization of roots, following Ranelli et al. (2015). Gopher disturbance was assessed using methods of Lynn et al. (2018).

Supplementary Material Appendix 2 methods

Biotic interaction predictors

Competition/facilitation.

We assessed plant community composition using visual cover estimates. We placed a 0.2 m x 0.2 m quadrat every 2.5 m along four 20 m transects per site. In each quadrat, we visually estimated percentage cover of every plant species or bare ground to total 100% (33 plant cover estimates per site). Specimens were collected and identified using Shaw (2008) for grasses and Weber and Wittmann (2012) for non-grasses. We corrected for current taxonomy using the USDA PLANTS Database (USDA and NRCS 2017). Unidentified species (e.g., non-flowering sedges) were morphotyped, assigned unique species codes, and matched to unknowns at other sites. Plant cover for a site was represented by the summed percentage cover estimate across the 33 quadrats (maximum of 3300 if site was 100% vegetated). We used the vegan package in R to calculate plant species diversity indices (Oksanen et al. 2017). Because diversity metrics were highly colinear, we used Shannon diversity (hereafter diversity) in all subsequent analyses, as it had the highest correlation with other diversity metrics.

Potential antagonisms.

We assessed insect herbivory and leaf pathogens via calibrated visual estimates of percentage leaf damage for 10 randomly selected individuals per focal grass species per site, with a minimum distance of two m between individuals. Insect herbivory and pathogen damage present a dilemma for niche modeling: how can one estimate a biotic interaction when a species is not present at a site? Therefore, we created a site-level metric of herbivore/pathogen pressure by calculating community weighted mean damage over all grass species present at a site. This metric estimated the expected damage that a grass individual would experience if it were present at the site.

We measured pocket gopher (Thomomys talpoides) disturbance to soil at each site along three 40 m long belt transects (methods in Lynn et al. 2018). Briefly, each belt transect was 1 m wide and each characteristic sign of gopher disturbance (e.g., mounds, eskers) were summed across the transects.

Potential mutualisms.

We assessed percentage fungal colonization of roots by pooling equal amounts of root tissue by volume from six plant individuals per species per site (methods in Ranelli et al. 2015). We scored colonization of roots by arbuscular mycorrhizal fungi (AMF; aseptate hyphae with vesicles and/or arbuscules; Glomeromycotina). We estimated site-level root colonization with community weighted means over all grass species present at a site.

QA/QC Procedures:

We performed QA/QC checks with data entry checking (entry and rechecking the entries), outlier analysis, scatterplots, and internal consistency checks.

People and Organizations

Creators:
Individual: Joshua S Lynn
Organization:University of New Mexico; Rocky Mountain Biological Laboratory
Email Address:
jslynn@unm.edu
Individual: Melanie R Kazenel
Organization:University of New Mexico; Rocky Mountain Biological Laboratory
Email Address:
mkazenel@unm.edu
Individual: Stephanie N Kivlin
Organization:University of New Mexico; Rocky Mountain Biological Laboratory; The University of Tennessee, Knoxville
Email Address:
skivlin@utk.edu
Individual: Jennifer A Rudgers
Organization:University of New Mexico; Rocky Mountain Biological Laboratory
Email Address:
jrudgers@unm.edu
Contacts:
Individual: Joshua S Lynn
Organization:University of New Mexico; Rocky Mountain Biological Laboratory
Email Address:
jslynn@unm.edu
Individual: Jennifer A Rudgers
Organization:University of New Mexico; Rocky Mountain Biological Laboratory
Email Address:
jrudgers@unm.edu
Associated Parties:
Individual: Wendy Brown
Organization:Rocky Mountain Biological Laboratory
Role:Assisted In Data Collection
Individual: Samuel Canfield
Organization:Rocky Mountain Biological Laboratory
Role:Assisted In Data Collection
Individual: Chiara Forrester
Organization:Rocky Mountain Biological Laboratory
Role:Assisted In Data Collection
Individual: Ian Spellman
Organization:Rocky Mountain Biological Laboratory
Role:Assisted In Data Collection

Temporal, Geographic and Taxonomic Coverage

Temporal, Geographic and/or Taxonomic information that applies to all data in this dataset:

Time Period
Begin:
2014-06-01
End:
2016-07-31
Geographic Region:
Description:A
Bounding Coordinates:
Northern:  38.98512406Southern:  38.86523
Western:  -106.9885206Eastern:  -106.9123563
Geographic Region:
Description:C
Bounding Coordinates:
Northern:  38.99665621Southern:  38.88163
Western:  -107.0704268Eastern:  -106.96172
Geographic Region:
Description:HH
Bounding Coordinates:
Northern:  38.94594843Southern:  38.84758708
Western:  -106.819641Eastern:  -106.7777649
Geographic Region:
Description:R
Bounding Coordinates:
Northern:  38.90226451Southern:  38.856165
Western:  -107.1283646Eastern:  -107.031725
Geographic Region:
Description:Teo
Bounding Coordinates:
Northern:  38.96006224Southern:  38.89571492
Western:  -106.8912166Eastern:  -106.8761911
Geographic Region:
Description:TR
Bounding Coordinates:
Northern:  39.0113075Southern:  38.9186175
Western:  -107.095645Eastern:  -107.0362825

Project

Parent Project Information:

Title:Graduate Student Research Award
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: Western Ag Innovations
Related Project:
Title:King of the Hill? Potential for novel biotic interactions
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: Botanical Society of America Graduate Student Research Award
Related Project:
Title:Harry Wayne Springfield and Grove Scholarships
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: University of New Mexico Biology Department
Related Project:
Title:King of the hill? Climate change effects on biotic interactions in alpine plant communities
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: Rocky Mountain Biological Laboratory Jean Langenheim Graduate Student Fellowship
Related Project:
Title:King of the Hill? Predicting the population consequences of climate change altered species interactions
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: American Philosophical Society Lewis and Clark Fund
Related Project:
Title:DISSERTATION RESEARCH: King of the hill? How competitive interactions affect biogeographical pattern and species responses to environmental variability
Personnel:
Individual: Joshua Lynn
Role:Principal Investigator
Funding: NSF-DEB: 1701221
Related Project:
Title:The potential for climate-induced disruption of plant-microbe symbioses along altitudinal gradients
Personnel:
Individual: Jennifer Rudgers
Role:Principal Investigator
Funding: NSF-DEB: 1354972

Maintenance

Maintenance:
Description:completed
Frequency:
Other Metadata

Additional Metadata

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EDI is a collaboration between the University of New Mexico and the University of Wisconsin – Madison, Center for Limnology:

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