The rise of the Isthmus of Panama ~3.5 mya separated populations of many marine organisms, which then diverged into new geminate sister species currently living in the Eastern Pacific Ocean and Caribbean Sea. However, we know very little about how such evolutionary divergences of host species have shaped their microbiomes. Here, we compared the microbiomes of whole-body and shell-surface samples of geminate species of marine gastropods in the genera Cerithiumand Cerithideopsis to those of congeneric outgroups. Our results show that the effects of the Isthmus on microbiome composition varied among host genera and between sample types within the same hosts. In the whole-body samples, microbiome compositions of geminate species pairs in the focal genera tended to be similar, likely due to host filtering, although the strength of this relationship varied among the two groups and across similarity metrics. Shell-surface communities showed contrasting patterns, with co-divergence between the host taxa and a small number of microbial clades evident in Cerithideopsis, but not Cerithium. These results suggest that (i) the rise of the Isthmus of Panama affected microbiomes of geminate hosts in a complex and clade-specific manner and (ii) host-associated microbial taxa respond differently to vicariance events than the hosts themselves. 

These data were collected by sequencing the V4 region of the 16S rRNA gene from seven species of intertidal gastropods collected from four sites across the Isthmus of Panama, as well as environmental samples. Three of these hosts are from the genus Cerithium, the others are from the genus Cerithideopsis. Whole-body tissues and shell-surface swabs from each sample were processed using the Qiagen DNeasy Blood and Tissue kit, the 16S rRNA gene region was amplified using the 515f-806rb primer pair and amplicons were barcoded using the NexTeraXT barcode kit. Sequencing was conducted on an Illumina MiSeq (2x250bp, paired end). Sequences were processed via DADA2 and assigned taxonomy using the Silva 138 database.

The associated mapfile should provide all necessary metadata for the usage of the ASV table. Raw sequences are available from the NCBI SRA under BioProject accession #PRJNA74415.