Land-use change threatens global biodiversity and may reshape the tree of life by favoring some lineages over others. Whether phylogenetic diversity loss compromises ecosystem service delivery remains unknown. We address this knowledge gap using extensive genomic, community, and crop datasets to examine relationships among land use, pollinator phylogenetic structure, and crop production. Pollinator communities in highly agricultural landscapes contain 230 million fewer years of evolutionary history; this loss was strongly associated with reduced crop yield and quality. Our study links landscape–mediated changes in the phylogenetic structure of natural communities to the disruption of ecosystem services. Measuring conservation success by species counts alone may fail to protect ecosystem functions and the full diversity of life from which they are derived.
bamm-script
R script for running BAMM analysis to detect rate shifts
control
BAMM configuration file for speciation/extinction analysis
event_data
BAMM event data file for speciation/extinction analysis
mcmc_out
mcmc output file from BAMM speciation/extinction analysis
my_tree
rooted time calibrated tree for BAMM speciation/extinction analysis
myPriors
Prior Block for BAMM speciation/extinction analysis
sample_probs
BAMM speciation/extinction sample probabilities
comm_data_bySiteandYear
community data formatted for path analysis
ExaBayes_topologies.renamed.run-0
Nexus file containing trees from ExaBayes run-1
ExaBayes_topologies.renamed.run-1
Nexus file containing trees from ExaBayes run 2
comm_data
wild bee community data for phylodiversity analysis
comm_data_wHB
community data including both wild bees and honey bees
comm_phylosig
community data for phylogenetic signal analyses
fruit_data
measures of apple fruits including shape, size, and number of seeds
NestednessTurnover_comm_data
community data formatted for analysis of nestedness and turnover
trait_data
species' traits including body size (ITD), average visit duration, proportion of top-working vs. side-working, pollen load purity, and species' response to agricultural gradient.
transect_data
metadata for each sample in the community dataset
PhyDiv_analysis_code
R script for calculating phylogenetic diversity metrics
NestednessTurnover_code
R script for assessing nestedness and turnover in community composition
PhyloSig_analysis_code
R script to calculate phylogenetic signal for traits in trait_data file
path_analysis_code
R script for path analysis of direct and indirect effects of landscape and community on fruit data
chronos.tree
Nexus file containing a rooted time-calibrated phylogeny of the apple pollinator community