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.

Accurate taxonomic delimitation in ecological research is absolutely critical as studies that seek to evaluate levels of biodiversity and qualify human effects on the environment are rapidly undertaken. Coloration is a widely used morphological character for species identification through dichotomous keys. However, taxonomic identification based upon coloration is often unreliable because this character can exhibit high degree of intraspecific variation. In this study, we use a DNA barcoding approach to investigate the interpretation of two color morphs (yellow or dark) in the eucerine bee Melissodes nigroaenea. Our hypothesis is that if significant genetic divergence exists between each morphotype of M. nigroaenea, coloration reflects two distinct evolutionary lineages within this species, which may require taxonomic revision. Our alternative hypothesis is that, if genetic divergence is low between each morphotype of M. nigroaenea, we can attribute this variation to color polymorphism. Our Bayesian phylogenetic reconstruction revealed that both yellow and black individuals clustered together in a highly supported phylogenetic group. Additionally, pairwise genetic distances between M. nigroaenea color morphotypes were lower than 3%. These results indicate that both mesosome color morphs correspond to intraspecific variability within the same evolutionary unit. Together, our results indicate that mesosome coloration is not a reliable character for taxonomic differentiation of these Melissodes species, and that the incorporation of DNA barcoding approaches to taxonomic classification can help resolve some of the problems that originate while relying on purely morphological taxonomy.