Code for: geoAMBI: A new molluscan biotic index for assessing biological condition of estuaries along the mid-Atlantic coast of the United States

Le résumé fourni par la source

The code included here was used to produce the manuscript: Pruden, M.J., Handley, J.C., Dietl., G.P., 2026. geoAMBI: A new molluscan biotic index for assessing biological condition of estuaries along the mid-Atlantic coast of the United States. Marine Pollution Bulletin. https://doi.org/10.1016/j.marpolbul.2026.119728 Abstract: Biotic indices are used by environmental managers to assess the biological condition of benthic habitats in response to environmental stressors. Successful application depends on availability of reference data characterizing minimally degraded conditions, but long-term monitoring data needed to define such references are often lacking. Mollusks are good surrogates for benthic communities, and their geohistorical record—dead shell remains preserved beneath the seafloor and time-averaged over decades to centuries—can help fill these data gaps. Here, we develop an initial framework for a mollusk-only biotic index applicable to the geohistorical record, using benthic survey data of living mollusks from the mid-Atlantic coastal region of the United States. Machine learning was used to evaluate biotic metrics—taxonomic diversity, pollution tolerance-sensitivity, and biological traits—for their ability to distinguish sites classified a priori as Reference or Degraded. The final model—geoAMBI—is a modified logistic regression version of the AZTI-Marine Biotic Index (AMBI), calculated using reversed rank-order abundance, which is operationally robust to taphonomic biases in the geohistorical record. Before geoAMBI can be applied to the geohistorical record in the mid-Atlantic region or adapted for use elsewhere, the most immediate need is to assess how time averaging and other preservational biases affect its performance.

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