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Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment


Almeida, Ryan et al. (2020), Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment, Dryad, Dataset,


Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially-clustered, to those derived from a commonly-used extinction estimation method, the Species-Area Relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.


The master dataset (GoldenrodData_Master.xlsx) contains abundance and occupancy data of arthropod communities for each sampling period of the experiment described in the associated manuscript. Taxa are identified to morphospecies or the lowest taxonomic unit possible. Each of the available R scripts corresponds to a different analysis outlined in the associated manuscript (for more information, see README_AlmeidaEtAlGCB.docx).

Usage Notes

To reproduce the analyses from the associated manuscript, follow the workflow outlined in the provided ReadMe file (README_AlmeidaEtAlGCB.docx).


National Science Foundation, Award: DEB-1650554