Assessment of species abundance from metabarcoding data
To assess the level of variation in the number of reads explained by the
proportion of a certain taxa in the sample, we calculated the proportion
of reads or relative read abundance (RRA), the proportion of biomass and
the proportion of individuals of every family in every plot. We used thebetareg function in the R package “betareg v1.1” (Cribari-Neto
& Zeileis, 2010) to apply beta regression models to each family present
in at least 10 plots. Two models were applied to each family, one for
the RRA as a function of the percentage of mass the family represents in
the sample, and one for the RRA as a function of the percentage of
abundance. We applied the models to each family separately due to the
non-independence of percentages in a sample, and we used 10 as the
minimum presence in plots following the one-in-ten rule tested in other
models (Peduzzi, Concato, Feinstein, & Holford, 1995). Beta regression
models are designed for response variables with proportional data
between 0 and 1. We calculated the adjusted R2 values
and determined the global goodness of fit for each model. Only
significant (p-value < 0.05) models with a
pseudo-R2 > 0.5 and randomly distributed
residuals were considered (Yellareddygari, Pasche, Taylor, Hua, &
Gudmestad, 2015).
RESULTS