Cloacal microbiomes of sympatric and allopatric Sceloporus lizards vary with environment and host relatedness

Animals and their microbiomes exert reciprocal influence; the host’s environment, physiology, and phylogeny can impact the composition of the microbiome, while the microbes present can affect host behavior, health, and fitness. While some microbiomes are highly malleable, specialized microbiomes that provide important functions can be more robust to environmental perturbations. Recent evidence suggests Sceloporus virgatus has one such specialized microbiome, which functions to protect eggs from fungal pathogens during incubation. Here, we examine the cloacal microbiome of three different Sceloporus species (spiny lizards; Family Phrynosomatidae) – Sceloporus virgatus, Sceloporus jarrovii, and Sceloporus occidentalis. We compare two species with different reproductive modes (oviparous vs. viviparous) living in sympatry: S. virgatus and S. jarrovii. We compare sister species living in similar habitats (riparian oak-pine woodlands) but different latitudes: S. virgatus and S. occidentalis. ..., Cloacal swabs were collected from Sceloporus lizards species in Washington and Arizona, between 2017 and 2021. Microbial DNA was extracted and amplified from these samples, and sequences of the 16s V4 regions were generated at IBest Genomics Core (University of Idaho) on the Illumina MiSeq platform. More detailed methodology can be found in Bunker and Weiss, \"Effect of habitat variation and host relatedness on Sceloporus cloacal microbiomes,\" or in the attached README file.,