Relative species abundance and population densities of the past: Developing multispecies occupancy models for fossil data

Abstract

The number of individuals of species varies, but estimating abundance, given incomplete and biased sampling in both contemporary and fossilized communities, is challenging. Here, we describe a new occupancy model in a hierarchical Bayesian framework with random effects, in which multispecies occupancy and detection are modeled as a means to estimate relative species abundance and relative population densities. The modeling framework is suited for temporal samples of fossil communities with repeated sampling including multiple species with similar preservation potential. We demonstrate our modeling framework using a fossil community of benthic organisms to estimate relative species abundance dynamics and changing relative population densities of focal species in nine (geological) time intervals over 2.3 Myr. We also explore potential explanatory factors (paleoenvironmental proxies) and temporal autocorrelation that could provide extra information on unsampled time intervals. The modeling framework is applicable across a wide range of questions on species-level dynamics in paleoecological community settings.