Joining forces in Ochnaceae phylogenomics: A tale of two targeted sequencing probe kits

Premise: Both universal and family-specific targeted sequencing probe kits
are becoming widely used for the reconstruction of phylogenetic
relationships in angiosperms. Within the pantropical Ochnaceae, we show
that with careful data filtering, universal kits are equally as capable in
resolving intergeneric relationships as custom probe kits. Furthermore, we
show the strength in combining data from both kits to mitigate bias and
provide a more robust result to resolve evolutionary relationships.
Methods: We sampled 23 Ochnaceae genera and used targeted sequencing with
two probe kits, the universal Angiosperms353 kit, and a family-specific
kit. We used maximum likelihood inference with a concatenated matrix of
loci and multispecies-coalescence approaches to infer relationships in the
family. We explored phylogenetic informativeness and the impact of missing
data on resolution and tree support. Results: For the Angiosperms353 data
set, the concatenation approach provided results more congruent with those
of the Ochnaceae-specific data set. Filtering missing data was most
impactful on the Angiosperms353 data set, with a relaxed threshold being
the optimum scenario. The Ochnaceae-specific data set resolved consistent
topologies using both inference methods, and no major improvements were
obtained after data filtering. The merging of data obtained with the two
kits resulted in a well-supported phylogenetic tree. Conclusions: The
Angiosperms353 data set improved upon data filtering, and missing data
played an important role in phylogenetic reconstruction. The
Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as
equally well as the family-specific data set. All analyses indicated that
both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed
are polyphyletic and require revised delimitation.