Monotropoid Ericaceae 102-locus nuclear sequences matrices and plastid locus sequence matrix

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.