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\begin{document}

\title{Estimating relative species abundance using fossil data identified to
different taxonomic levels}



\author[1]{Trond Reitan}%
\author[1]{Emanuela Di Martino}%
\author[1]{Lee Hsiang Liow}%
\affil[1]{University of Oslo}%


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  \date{May 21, 2024}


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\begin{abstract}
Site-occupancy modeling is widely used in ecology but its application is
still limited in paleoecology, where incomplete detection is routine.
Here, we make extensive expansions to an earlier multispecies occupancy
model used to estimate the dynamics of relative species abundance in
fossil communities. These expansions include incorporating counts of
individuals at sites, explicitly allowing for the inclusion of specimens
assignable to genus- but not species-level, a situation common in
paleontology, and modelling regional presence/absence. We provide
simulations to check the performance of this new model, as well as
simulations to quantify the benefits of using individual count data
versus subsample occupancy data and model estimates versus face-value
(raw) estimates, respectively. We also provide an empirical case study
using occupancy data from a community of marine benthic colonial animals
preserved in the Pleistocene of New Zealand. We find that the new model
performs well, especially when it comes to recovering relative abundance
dynamics and that it is well worth the effort to both collect individual
count data and to include individuals unidentified to species-level in
the site-occupancy modelling framework. This extended model can be
widely applied in paleoecological settings and is necessary when both
the average and uncertainty values of relative abundance dynamics need
to be robustly estimated.%
\end{abstract}%



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