Contrasting Phylogeographic Patterns of Mitochondrial and Genome-Wide Variation in the Groundwater Amphipod Crangonyx islandicus That Survived the Ice Age in Iceland

• Published in: Diversity
• Main Authors: Eme, David, Westfall, Kristen, Matthíasardóttir, Brynja, Kristjánsson, Bjarni, Pálsson, Snæbjörn
• Other Authors: Riverly (Riverly), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Iceland Reykjavik, Fisheries and Oceans Canada (DFO), National Human Genome Research Institute (NHGRI), Department of Aquaculture and Fish Biology, Holar University College, Hólar University College, Dept of Life and Environmental Sciences
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2023
• Subjects: introgression; incomplete lineage sorting; selection; subglacial refugia; populations; genomics; groundwater; RADseq; [SDV]Life Sciences [q-bio]; Iceland
• Online Access: https://hal.inrae.fr/hal-03946769; https://hal.inrae.fr/hal-03946769/document; https://hal.inrae.fr/hal-03946769/file/Eme_etal_2023_Diversity_ContrastingPhylogeographicPatternsMitoChondrialAndGenomeWideVariationGRoundwaterAmphipodCrangonyxIslandicus.pdf; https://doi.org/10.3390/d15010088

The analysis of phylogeographic patterns has often been based on mitochondrial DNA variation, but recent analyses dealing with nuclear DNA have in some instances revealed mitonuclear 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 also poses additional analytical challenges. Here, we revisited the previously inconclusive phylogeographic history, showing the 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.