Gut microbiome diversity and divergence among taxa
We sequenced a total of 11,152,147 reads across all samples (Table S2).
We identified 5,174 bacterial taxa in 48 samples. Similar to other
ray-finned fishes (Youngblut et al. 2019), proteobacteria is the
predominate microbial taxon (Figure S3). We did not find any significant
differences among species in Chao1 or Shannon diversity indices
(Kruskal-Wallace [pairwise], P > 0.05; Figure
1). San Salvador Island pupfishes clustered together relative to the
three outgroup generalist species, indicating strong host phylogenetic
signal associated with overall microbiome diversity (Figure 2; Figure
S4). Water and tissue controls were scattered throughout the NMDS plots
but were clearly distinct from Cyprinodon microbiome samples with
the exception of one tissue control that clustered near the outgroup
species, possibly due to contamination during dissections (Figure 2).
Multiple regression analyses of the effects of dietary specialization
(generalist, scale-eater, or molluscivore) and the fixed effect of
population origin (two different lakes on San Salvador Island, Lake
Cunningham, North Carolina, and El PotosÃ) on NMDS axes 1 and 2
confirmed that population origin and scale-eating had a significant
effect on microbiome divergence along both axes (NMDS1: scale-eatersP = 0.001; NMDS2: scale-eaters P = 0.018).