DOI: 10.5061/dryad.mpg4f4r11
title: Taxon-specific or universal? Using target capture to study the evolutionary history of a rapid radiation

description: 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.
description: The bait set was designed using whole-genome sequences and gene
 models from <em>Ananas comosus</em> 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<em> A. comosus</em> or when annotate in other
 species, using BLAST to find the<em> A. comosus</em> 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 <em>A. comosus</em> 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 <em>Ananas comosus</em> v.3 are detailed in
 Supporting information Table S1 and S2.
description: List of bait sequences in fasta format of the
 Bromeliad1776 target capture kit including all 57,445 baits of
 80bp.
description: # Taxon-specific or universal? Using target capture to study the
 evolutionary history of a rapid radiation
 ## Description of the data
 and file structure *
 Baits-80-40-Pass_Client_filtering_GC_Under_70.fas.clust-75-95.fasta -
 FASTA sequences for bait probes. Baits are 80bp with x2 (40bp) overlap and
 designed as described in the manuscript:
 [10.1111/1755-0998.13523](https://doi.org/10.1111%2F1755-0998.13523),
 further information in the github repository:
 *
 supporting_information_Table1.csv - Genes included in the Bromeliad1776
 bait design, with identifiers as annotated in *Ananas comosus* genome v.3
 (Ming et al., 2015). The table includes details about exon composition,
 copy number and putatively associated pathways. See legend in file
 supporting_information_Table1_legend.csv. *
 supporting_information_Table1_legend.csv - Legend for table S1. *
 supporting_information_Table2.csv - Categories of pathways and traits used
 to choose genes of interest for the Bromeliad1776 bait set, including
 literature source and number of genes in each category. *
 supporting_information_Table3.csv - List of accessions used in the study,
 including source and collection details. For samples of *Tillandsia*
 subgenus *Tillandsia* locality codes are also indicated. *
 supporting_information_Table4.csv - Number of reads, numbers and
 percentage of read mapping to target in all samples enriched with the
 Angiosperm353 kir or the Bromelia1776 kit. *
 supporting_information_Table5.csv - Averaged levels of nucleotide
 diversity at synonymous (πS) and non-synonymous (πN) for 5 *Tillandsia*
 subgenus *Tillandsia* species.