Detection of differentially abundant microbial ASVs and genera
between captive and wild populations
ANCOM2 (Mandal et al. 2015) was employed in R
(github.com/FrederickHuangLin/ANCOM) to test whether any individual
microbial ASVs or genera were differentially abundant between the
captive and wild individuals for every captive NHP population. Each
analysis focused on ASVs or genera present in >10% of
samples from the pair of captive and wild populations. Volcano plots
displaying differentially abundant ASVs and genera were created in R
with ggplot2. For these analyses, captive chimpanzees retired from the
New Iberia Research Center (USA2) were paired with wild chimpanzees from
Tanzania (TZA) and zoo captive chimpanzees (USA1) were paired with wild
chimpanzees from the DRC (DRC). Pairings were chosen such that samples
from wild and captive conspecific populations were processed and
sequenced by the same laboratories, minimizing any potential study
effects that could confound downstream analyses.
In addition, we tested whether microbial ASVs and genera differed
repeatedly in relative abundance between the wild and captivity in
multiple captive NHP populations. Specifically, we employed
hypergeometric tests to assess the significance of the overlap between
the sets of microbial taxa (i.e., ASVs and genera) whose abundances
differ from the wild in pairs of captive NHP populations. These analyses
tested whether the number of microbial taxa that shifted in relative
abundance in the two captive NHP populations relative to wild
conspecific NHP populations was significantly greater than the number
expected by chance, given the observed number of microbial taxa shared
between the multiple replicate captive NHP populations. In addition, we
employed regression analyses to test for significant associations of W
statistics between pairs of captive NHP populations.