Data from: Targeted enrichment of large gene families for phylogenetic inference: phylogeny and molecular evolution of photosynthesis genes in the Portullugo clade (Caryophyllales)

Hybrid enrichment is an increasingly popular approach for obtaining
hundreds of loci for phylogenetic analysis across many taxa quickly and
cheaply. The genes targeted for sequencing are typically single-copy loci,
which facilitate a more straightforward sequence assembly and homology
assignment process. However, this approach limits the inclusion of most
genes of functional interest, which often belong to multi-gene families.
Here we demonstrate the feasibility of including large gene families in
hybrid enrichment protocols for phylogeny reconstruction and subsequent
analyses of molecular evolution, using a new set of bait sequences
designed for the “portullugo” (Caryophyllales), a moderately sized lineage
of flowering plants (∼2200 species) that includes the cacti and harbors
many evolutionary transitions to C4 and CAM photosynthesis. Including
multi-gene families allowed us to simultaneously infer a robust phylogeny
and construct a dense sampling of sequences for a major enzyme of C4 and
CAM photosynthesis, which revealed the accumulation of adaptive amino acid
substitutions associated with C4 and CAM origins in particular paralogs.
Our final set of matrices for phylogenetic analyses included 75–218 loci
across 74 taxa, with ∼50% matrix completeness across datasets.
Phylogenetic resolution was greatly improved across the tree, at both
shallow and deep levels. Concatenation and coalescent-based approaches
both resolve the sister lineage of the cacti with strong support:
Anacampserotaceae + Portulacaceae, two lineages of mostly diminutive
succulent herbs of warm, arid regions. In spite of this congruence, BUCKy
concordance analyses demonstrated strong and conflicting signals across
gene trees. Our results add to the growing number of examples illustrating
the complexity of phylogenetic signals in genomic-scale data.