Sequence Capture Methods Help Resolve Relationships Among the Arecaceae

Understanding evolutionary relationships among taxa is crucial for the study of trait evolution and comparative biology, both of which can inform genomics and breeding research. A number of processes, including low substitution rates, hybridization, and retention of ancestral polymorphism, can complicate our estimates of species trees. By generating a species tree based on a larger number of genes, these problems may be minimized. Here we describe the use of sequence capture to selectively sequence plastid and low-copy nuclear genes from across populations, species, and tribes in the Arecaceae. Biotinylated RNA baits are designed complementary to exons, and when hybridized to the target DNA, can be pulled from solution with by the biotin label and subsequently sequenced. Additionally, the adjacent intron sequence is captured, resulting in a combination of conserved sites from the exon and phylogenetically informative sites from the intron. A single bait set has been designed for nuclear and chloroplast sequences in the Arecaceae, and has worked at broad taxonomic levels. Future work could utilize the same capture baits or bait design strategy to address a wide variety of questions concerning evolutionary relationships or population structure across a broad diversity of palm lineages.