Generating a phylogenetic hypothesis for Inga using targeted enrichment data

Current systematic hypotheses for the Neotropical tree genus Inga are very poorly resolved. We aim to use targeted enrichment and high-throughput sequencing methods to generate DNA sequence data for 1400 loci. Preliminary analyses indicate these data provide a robustly resolved phylogeny for the genus, even resolving population-level relationships within species. Transcriptomes for one individual from each of three species were generated using Illuminas RNAseq protocol. These transcriptomes were used to design baits for targeted enrichment of subsequent genomic DNA-based libraries. Libraries for each individual were made using Illuminas TruSeq Nano kit, with mean insert sizes of approximately 420 bp. Enrichment was performed using a MyBaits custom kit (manufactured by MYcroarray), with 8 samples pooled per capture reaction. Enriched pools were sequenced on an Illumina MiSeq using 250 base pair paired-end reads.