Chromosome rearrangements play an important role in partitioning genetic variance, both within and among karyotypically diverse species. Many studies have focused on the role of inversions or reciprocal translocations in protecting population-specific regions of the genome from recombination. Very little work has been done on organisms, such as sedges, that lack localized centromeres. In this study, we evaluate the roles of chromosome rearrangement and geographic distance in the partitioning of genetic variance within Carex scoparia var. scoparia, a sedge that exhibits a great deal of karyotypic diversity (2n = 58 to 70). We collected molecular genetic data (amplified fragment length polymorphisms–AFLP–and microsatellite data) and chromosome counts from 35 populations of Carex scoparia var. scoparia and 2 populations of C. scoparia var. tessellata to test two interrelated hypotheses. First, we tested the hypothesis that the various chromosome ‘races’ within C. scoparia var. scoparia are genetically differentiated from one another to a degree comparable to species or varieties. Second, we used standard and partial Mantel tests to evaluate the effects of geographic distance and chromosome number differences on intraspecific genetic variance.

Results/Conclusions
Although the two varieties of C. scoparia are clearly distinguished from one another, there is no evidence of deep divergence within the karyotypically diverse C. scoparia var. scoparia. Mantel tests indicate no correlation between geographic distance and genetic distance on any permutations of the data set. However, there is a significant positive correlation between chromosome number difference and genetic distance, which is significant even when geographic distance is corrected for using partial Mantel tests. We reanalyzed published data for a second species, Carex pachystachya, which suggest the same relationship between genetic distance and chromosome number difference. Our findings that (1) karyotype difference correlates strongly with genetic distance and (2) gene flow within species is sufficient to prevent the formation of deep phylogeographic breaks constitute the first demonstration that holocentric chromosome rearrangements may play a role in gene flow within species without being sufficient to drive speciation.