Monotropoideae (Ericaceae) is a wholly leafless and holomycotrophic group of primarily temperate herbs with centers of diversity in western North America and east Asia.   The eleven genera are structurally diverse and also vegetatively reduced, making relationships difficult to assess based on morphology.  Previous molecular analyses have focused primarily on segments of the ribosomal RNA repeat and yielded sometimes conflicting topologies.  We employed a genomic sampling approach to obtain 102 nuclear loci and plastid coding loci for nine of the genera, as well as sampling ITS-26S and plastid rps2 for a broader set of accessions via PCR and Sanger sequencing Data filtering for character completeness had a clear effect on relationships and branch support.  Nuclear and plastid loci agree on a topology that resolves Allotropa and Hemitomes as sisters and Monotropsis sister to Eremotropa+Monotropa+Monotropastrum, relationships that were unclear from previous analyses.  Hypopitys should be recognized as distinct from Monotropa, with previous ambiguity in rps2 relationships here explained by the existence of plastid and mitochondrial paralogs.  Comparison of branch lengths between nuclear and plastid loci reveals increased rates of change in plastid sequences in most cases, especially in Monotropsis and Monotropa, but the reverse situation in Pityopus, with nuclear branches being unusually long, possibly indicating cryptic diversity.  Parallel shifts in plant form to a ground-level floral display correlate with shifts from capsular to berry fruits and reduction in species ranges.  The optimal tree from molecular data requires significant parallelism and/or reversal in morphological features due to the placement of Allotropa and Hemitomes.

Data were collected using Illumina sequencing and a low-coverage genome skimming approach.