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Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments

Citation

Luiken, Jon; Gamble, Tony; Berendzen, Peter (2022), Comparative riverscape genomics of the rainbow darter (Etheostoma caeruleum) in glaciated and unglaciated environments, Dryad, Dataset, https://doi.org/10.5061/dryad.6m905qg17

Abstract

Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.

Methods

This is a dataset generated through the use of Restriction Site-Assocated DNA Sequencing (RADseq) with the Illumina HiSeq 4000 and NovaSeq 6000 platforms. Raw read data was processed for the appropriate barcode sequences for individual organisms and assembled de novo using Stacks (v.2.59). This data was processed further with the populations function within Stacks to generate three separate data groupings for the Volga River of NE Iowa, the Meramec River of Missouri, as well as a combined set.

Usage Notes

To use this data, one would need a familiarity with the following software packages; fastStructure, R (adegenet, ade4, hierfstat), Arlequin, PGDSpider. A spreadsheet with the sample IDs, locality IDs, MID sequences used, as well as geographic locations is included, as well as a text ReadMe file describing archive contents.