Monitoring small mammal abundance using NEON data: Are calibrated indices useful?

Small mammals are important to the functioning of ecological communities
with changes to their abundances used to track impacts of environmental
change. While capture-recapture estimates of absolute abundance are
preferred, indices of abundance continue to be used in cases of limited
sampling, rare species with little data, or unmarked individuals.
Improvement to indices can be achieved by calibrating them to absolute
abundance but their reliability across years, sites, or species is
unclear. To evaluate this, we used the US National Ecological Observatory
Network (NEON) capture-recapture data for 63 small mammal species over 46
sites from 2013–2019. We generated 17,155 absolute abundance estimates
using capture-recapture analyses and compared these to two standard
abundance indices, and three types of calibrated indices. We found that
neither raw abundance indices nor index calibrations were reliable
approximations of absolute abundance, with raw indices less correlated
with absolute abundance than index calibrations (raw indices overall R2
< 0.5, index calibration overall R2 > 0.6). Performance of
indices and index calibrations varied by species, with those having higher
and less variable capture probabilities performing best. We conclude that
indices and index calibration methods should be used with caution with a
count of individuals being the best index to use, especially if it can be
calibrated with capture probability. None of the indices we tested should
be used for comparing different species due to high variation in capture
probabilities.  Hierarchical models that allow for sharing of
capture probabilities over species or plots (i.e., joint likelihood
models) may offer a better solution to mitigate the cost and effort of
large-scale small mammal sampling while still providing robust estimates
of abundance.