Bifurcating trajectories: multidimensional specialization vs multidimensional generalization

Project folder for publication "Bifurcating trajectories: multidimensional specialization vs multidimensional generalization" containing: 1) job scripts and raw data to replicate analyses, 2) intermediate and final files output by scripts, and 3) HTML outputs of RMarkdown files containing results from statistical analyses. Descriptions of files, scripts, and folders in README file. Manuscript Abstract: Habitat specialization underpins biological processes from species distributions to speciation. However, organisms are often described as specialists or generalists based on a single niche axis, despite facing complex, multidimensional environments. Here, we analyzed 236 prokaryotic communities across the United States demonstrating for the first time that 96% of >1,200 prokaryotes followed one of two trajectories: specialization on all niche axes (multidimensional specialization) or generalization on all axes (multidimensional generalization). We then documented that this pervasive multidimensional specialization/generalization had a wide range of ecological and evolutionary consequences, including impacts on (1) species dominance with multidimensional generalists 108-times more abundant than specialists, (2) evolutionary trajectories with generalist-to-specialist transitions occurring ~20% less than expected, and (3) community structure with multidimensional specialists ~45% more connected within microbiome networks. These results indicate that multidimensional generalization supports larger populations and is more evolutionarily stable while multidimensional specialists, which are less common, still play important roles within communities, likely stemming from their overrepresentation among pollutant detoxifiers and nutrient cyclers. Taken together, we demonstrate that virtually all soil prokaryotes are restricted to one of two multidimensional niche trajectories, multidimensional specialization or multidimensional generalization, which then has far-reaching consequences for microbial dominance, evolutionary transitions, and community roles.