By selecting co-distributed, closely related montane sedges from the Rocky Mountains that are similar in virtually all respects but one – their microhabitat affinities – we test predictions about how patterns of genetic variation are expected to differ between Carex nova, an inhabitant of wetlands, and Carex chalciolepis, an inhabitant of drier meadows, slopes, and ridges. Although contemporary populations of the taxa are similarly isolated, the distribution of glacial moraines suggests thattheirpast population connectedness would have differed. Sampling of co-distributed population pairs from different mountain ranges combined with the resolution provided by over 24,000 SNP loci supportsmicrohabitat-mediated differences in the sedges’ patterns of genetic variation that are consistent with their predicted differences in the degree of isolation of ancestral source populations.Our results highlight how microhabitat preferences may interact with glaciations to produce fundamental differences in the past distributions of presently co-distributed species. We discuss the implications of these findings for generalizing the impacts of climate-induced distributional shifts for communities, as well as for the prospects of gaining insights about species-specific deterministic processes, not just deterministic community level responses, from comparative phylogeographic study.

Carex chalciolepis distribution pointsThis file contains the latitude and longitude for populations from throughout this species' range. The data are gathered from verified voucher specimens at the Rocky Mountain Herbarium and personal field work. This information was used for Maxent distribution modeling.chal.txtCarex nova distribution pointsThis file contains the latitude and longitude for populations from throughout this species' range. The data are gathered from verified voucher specimens at the Rocky Mountain Herbarium and personal field work. This information was used for Maxent distribution modeling.nova.txtQC script for cleaning raw Illumina dataThis script was used to filter low quality reads from the raw Illumina data.thin_illumina_fastq_based_on_quality_singleEnd.pyQC script for removing adaptorsThis script was used for removing portions of the Illumina reads that were not needed.remove_adaptors_illumina_reads.pychal_structureThis file contains the data for Carex chalciolepis that was used for Structure and PCA analyses.nova_structureThis file contains the data for Carex nova that was used for Structure and PCA analyses.