Supplementary Material for "Automated detection of an insect-infested keystone vegetation phenotype using airborne LiDAR"

Ecologists, foresters and conservation practitioners need "biodiversity scanners" to effectively inventory biodiversity, audit conservation progress and track changes in ecosystem function. Quantifying biological diversity using airborne LiDAR remains challenging, especially for small invertebrates. However, insect aggregations can drastically alter landscapes and vegetation, and these "extended phenotypes" could serve as environmental landmarks of insect presence in LiDAR data. To test the feasibility of this approach, we studied the symbiotic ants that alter canopy shapes of whistling thorn acacia, a keystone tree species of the black cotton soils of east African savannas. We demonstrate a protocol of LiDAR data collection, training data preparation (including a customizable tree-segmentation algorithm) and convolutional neural network-based classification for the detection of ant-infested, within-species acacia tree phenotypic variations. Surveying ant occupancy of 402 hectares of 9,680 acacia trees took 1,000 work hours, while surveyed patterns of ant distribution was replicated by trained classifier based on an hour-long airborne LiDAR collection. We suggest that large scale surveys of insect occupancy (or insect-vectored disease) can be automated through a combination of airborne LiDAR and machine learning.