Contrasting phylogeographic patterns of mitochondrial and genome-wide variation in the groundwater amphipod (Crangonyx islandicus) that survived the Ice age in Iceland

• Main Authors: David Eme, Kristen M. Westfall, Brynja Matthíasardóttir, Bjarni K. Kristjánsson, Snæbjörn Pálsson
• Format: Dataset
• Language: English
• Published: 2023
• Subjects: introgression; incomplete lineage sorting; selection; subglacial refugia; populations,genomics; groundwater; RADseq; Iceland
• Online Access: https://zenodo.org/record/7506345; https://doi.org/10.5281/zenodo.7506345

In this zip "DataAvailability.zip" all the data and parameter files, as well as R scripts and bash codes used to perform the analyses of the mitochondrial and the RADseq data are provided. A ReadMe file is available at the root describing the content of the different folders and files. Below is the abstract of the associated manuscript: Analysis of phylogeographic patterns have often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mito-nuclear discordances and complex evolutionary histories. These enigmatic scenarios which may involve stochastic lineage sorting, ancestral hybridization, past dispersal, and secondary contacts are increasingly scrutinized with a new generation of genomic tools such as RADseq, which pose also additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing mito-nuclear discordance, of an endemic groundwater amphipod from Iceland, Crangonyx islandicus, which is the only metazoan known to have survived the Pleistocene beneath the glaciers. Previous studies based on three DNA markers documented a mitochondrial scenario with the main divergence occurring between populations in northern Iceland and an ITS scenario with the main divergence between the south and north. We used double digest restriction-site-associated DNA sequencing (ddRADseq) to clarify this mito-nuclear discordance by applying several statistical methods while estimating the sensitivity to different analytical approaches (data-type, differentiation indices and base call uncertainty). A majority of nuclear markers and methods support the ITS divergence. Nevertheless, a more complex scenario emerges, possibly involving introgression led by male-biased dispersal among northern locations or mitochondrial capture which may have been further strengthened by natural selection.