(1) Background: Termites are important ecosystem engineers, crucial for the maintenance of tropical biodiversity and ecosystem functioning. But they are also pests which cause billions of dollars in damage annually to humans. Currently, our understanding of the mechanisms influencing species occurrences is limited and we do not know what distinguishes pest from non-pest species. (2) Method: We analyzed how anthropogenic disturbance (agriculture) affects species occurrences. We tested the hypothesis that strong disturbance functions as a habitat filter and selects for a subset of species which are major pests of crop. Using a cross-sectional approach, we studied termite assemblage composition along a disturbance gradient from fields to 12-year-old fallows in a West African savanna. (3) Results: We reliably identified 19 species using genetic markers with a mean of about 10 species—many of them from the same feeding type—co-occurring locally. Supporting our hypothesis, disturbance was associated with environmental filtering of termites from the regional species pool, maybe via its effect on vegetation type. The most heavily disturbed sites were characterized by a subset of termite species which are well-known pests of crop. (4) Conclusion: These results are in line with the idea that strong anthropogenic disturbance selects for termite pest species.
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