DOI: 10.6084/m9.figshare.26096539.v1
title: Bradypodion Microbiome Raw Sequence Data

description: The first descriptions of microbial life presented a microcosm of “animalcula” inhabiting environments similar to those of macroscopic life. Since these early observations, horizons have expanded and the microbial world is now seen as a nuanced and multitudinous system. With the advent of Next-Generation Sequencing (NGS) technologies, the ability to study these microscopic worlds has been expounded, revealing stunning complexity, including the identification and study of the microbiome. Insights gained have also led to the proposal of novel, complex co-evolutionary theories (e.g., the Hologenome Theory of Evolution). The genus Bradypodion is a prime candidate for studying the adaptive ability conferred by symbiotic micro-organisms as, beyond containing a score of comparable species, there is rich ecomorphological variation in the genus allowing many populations to thrive in both natural and transformed environments. Furthermore, microbial descriptions in Bradypodion remain undescribed in the literature, making insights into this aspect novel. This study, therefore, aimed to apply current metagenomic methodologies, in the form of a MiSeq NGS platform (present at SAIAB), a High-Performance Computing facility (Ilifu), and machine learning algorithms (QIIME2), to visualise and apprehend the bacterial microbial communities in Bradypodion. This approach has resulted in the first descriptions of the bacterial communities present in the digestive tracts (both buccal and faecal) for the dwarf chameleon species Bradypodion melanocephalum, Bradypodion thamnobates, and Bradypodion setaroi – endemics to southern Africa. Furthermore, these descriptions were used to inform the potential for phylosymbiosis within the genus based on the divergence times between the three species and the relative diversity of the bacteria present. Here, appreciable microbial diversity was demonstrated across all samples taken using alpha and beta diversity metrics. The comparison of bacterial diversity between the Bradypodion species showed that phylosymbiosis is not clearly defined within the genus, as different sample groupings offer contradictory outcomes to what is expected for phylosymbiosis. Due to the dichotomy, the explanation of partial phylosymbiosis is suggested, whilst further targeted sampling of other species in the genus is recommended and outlined. Furthermore, insights were garnered about the associations between habitation of transformed environments between populations of the three Bradypodion species and their respective microbiome communities, using comparisons against natural populations. This produced a multifaceted result that indicates that differences are not as straightforward as would be hypothesised, as well as demonstrating that microbiome differences between populations are unique to each species in question. Finally, a comparison between the microbiome communities between the sexes was compiled for each of the studied populations. This unveiled no appreciable differences between the composition of male and female microbiomes for all three Bradypodion species. These insights lay the initial groundwork for understanding the microbiome in Bradypodion as a whole. Future research should aim to target the unexplored species in the genus, and can be used to expound and deepen the understanding garnered here.