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.