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.