Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

Target capture emerged as an important tool for phylogenetics and population genetics in non-model taxa. Whereas developing taxon-specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly-developed target capture set for Bromeliaceae, a large and ecologically-diverse plant family with highly variable diversification rates. The set targets 1,776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon-specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon-specific set results in higher enrichment success across the entire family, however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, e.g. the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon-specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.

Methods
The bait set was designed using whole-genome sequences and gene models from Ananas comosus v.3 (Ming et al., 2015). Random protein coding genes were selected based on genetic diversity parameters, total exonic size, individual exon size and copy-number variation. We then added genes associated with key innovative traits in Bromeliaceae, either genes previously annotated in A. comosus or when annotate in other species, using BLAST to find the A. comosus genes with the highest match scores. Genes underpinning innovative traits were included in the bait design, regardless of criteria used for random proteing coding genes, like size and duplication rate. We included markers previously used for phylogenomic inference in Bromeliaceae and genes orthologous to those in the Angiosperms353 bait set. An additional round of filtering was performed by the manufacturer of the final bait set, Arbor Biosciences (Ann Arbor, MI, 167 USA), where multi-copy genes with sequences that are more than 95% identical were collapsed into a single sequence, and baits with more than 70% GC content or containing at least 25% repeated sequences were excluded. In addition, targets including exons smaller than 80 bp were completed with regions flanking the exons according to the A. comosus reference genome. The final kit included 1776 genes and is subsequently referred to as the Bromeliad1776 bait set.

The 1776 selected genes as annonated for Ananas comosus v.3 are detailed in Supporting information Table S1 and S2.