Genomic and ecological insights into phylogeography: the complex history of the widespread herb Carex nigra (Cyperaceae) revisited

Carex nigra is a widespread sedge in the northern hemisphere. Some subspecies have been proposed within C. nigra s.l., reflecting the complex morphological and biogeographical variability within the group. Given this variability and its widespread distribution, we aim to (i) study the phylogeography of C. nigra s.l. by reconstructing the evolutionary relationship of its populations across the entire range, (ii) study its genetic structure and demographic history, and (iii) model the species and main lineages niche and infer their potential distributions. We sequenced RADseq markers for 75 populations representatively covering the entire range of the species and addressed phylogenetic, genetic, and demographic analyses using the software IQTREE, Structure and G-PhoCS, respectively. We modelled species and main lineages potential distributions, including projections to the Pliocene and the Last Glacial Maximum (LGM) using different algorithms (Maximum Entropy algorithm (Maxent), generalized additive models (GAM), Random Forest and generalized linear models (GLM)). The phylogeny was retrieved with high support, confirming the monophyly of the species. We identified three main lineages that could be associated to three monophyletic subspecies: subsp. nigra, subsp. intricata and subsp. transcaucasica. The genetic analyses showed two and four optimal genetic clusters lacking any specific pattern, while the demographic analyses showed genomic migration events among the three subspecies. The species distribution models retrieved the potential distribution of C. nigra complex for the Pliocene and of the three subspecies for the present and the LGM. Additionally, we also recognize climatic refugia during the Quaternary glaciations which could have favored the diversification of the subspecies.