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 Gala
́
pagos 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

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