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.