A target capture approach for phylogenomic analyses at multiple evolutionary timescales in rosewoods (Dalbergia spp.) and the legume family (Fabaceae)

Understanding the genetic changes associated with the evolution of
biological diversity is of fundamental interest to molecular ecologists.
The assessment of genetic variation at hundreds or thousands of unlinked
genetic loci forms a sound basis to address questions ranging from micro-
to macro-evolutionary timescales, and is now possible thanks to advances
in sequencing technology. Major difficulties are associated with i) the
lack of genomic resources for many taxa, especially from tropical
biodiversity hotspots, ii) scaling the numbers of individuals analyzed and
loci sequenced, and iii) building tools for reproducible bioinformatic
analyses of such datasets. To address these challenges, we developed a set
of target capture probes for phylogenomic studies of the highly diverse,
pantropically distributed and economically significant rosewoods
(Dalbergia spp.), explored the performance of an overlapping probe set for
target capture across the legume family (Fabaceae), and built a
general-purpose bioinformatics pipeline. Phylogenomic analyses of
Dalbergia species from Madagascar yielded highly resolved and well
supported hypotheses of evolutionary relationships. Population genomic
analyses identified differences between closely related species and
revealed the existence of a potentially new species, suggesting that the
diversity of Malagasy Dalbergia species has been underestimated. Analyses
at the family level corroborated previous findings by the recovery of
monophyletic subfamilies and many well-known clades, as well as high
levels of gene tree discordance, especially near the root of the family.
The new genomic and bioinformatics resources will hopefully advance
systematics and ecological genetics research in legumes, and promote
conservation of the highly diverse and endangered Dalbergia rosewoods.