Abstract
Regime shifts are often used to describe sharp changes between two or more ecological states, each characterized by their own dynamics, stochastic fluctuations, or cycles. Ecological theory indicates they can occur either as a result of an abrupt environmental forcing (extrinsic regime shift), or be indicative of complex responses to local‐scale dynamics and thresholds (intrinsic regime shift). One important area of ecological research is to develop quantitative tools to analyze regime shifts, but there are few studies that have applied these methods to the long‐term ecological record. In this study, we introduce a framework to investigate regime shifts in diatom assemblages and mangrove ecosystem dynamics in a coastal lagoon from the Galápagos Islands over the past 2600 years. The framework integrates a set of established statistical methodologies for investigating regime shift dynamics in long‐term ecological records. We use these methods to (1) identify the presence of regime shifts; (2) test for a series of hypothetical relationships (i.e., linear through to threshold) between ecological response and environment using nonlinear regression; and (3) investigate the relative importance of intrinsic and extrinsic dynamics in response to environmental perturbations. The transitions in the diatoms closely track the sequence of disturbance, recovery, and habitat shifts that have occurred in the lagoon over the past 2600 years, demonstrating extrinsic responses to environmental forcing. In contrast, the shift from a mangrove‐ to a microbial mat‐dominated system ∼945 cal yr BP provides potential evidence of an intrinsic regime shift. Our framework enables robust interpretations into the underlying dynamics of regime shifts in the paleoecological record and is widely applicable for investigating abrupt ecological changes in a range of systems.