Data from: Using targeted enrichment of nuclear genes to increase phylogenetic resolution in the neotropical rain forest genus Inga (Leguminosae: Mimosoideae)

Evolutionary radiations are prominent and pervasive across many plant
lineages in diverse geographical and ecological settings; in neotropical
rainforests there is growing evidence suggesting that a significant
fraction of species richness is the result of recent radiations.
Understanding the evolutionary trajectories and mechanisms underlying
these radiations demands much greater phylogenetic resolution than is
currently available for these groups. The neotropical tree genus Inga
(Leguminosae) is a good example, with ~300 extant species and a crown age
of 2-10 MY, yet over 6kb of plastid and nuclear DNA sequence data gives
only poor phylogenetic resolution among species. Here we explore the use
of larger-scale nuclear gene data obtained though targeted enrichment to
increase phylogenetic resolution within Inga. Transcriptome data from
three Inga species were used to select 264 nuclear loci for targeted
enrichment and sequencing. Following quality control to remove probable
paralogs from these sequence data, the final dataset comprised 259,313
bases from 194 loci for 24 accessions representing 22 Inga species and an
outgroup (Zygia). Bayesian phylogenies reconstructed using either all loci
concatenated or a subset of 60 loci in a gene-tree/species-tree approach
yielded highly resolved phylogenies. We used coalescent approaches to show
that the same targeted enrichment data also have significant power to
discriminate among alternative within-species population histories in the
widespread species I. umbellifera. In either application, targeted
enrichment simplifies the informatics challenge of identifying orthologous
loci associated with de novo genome sequencing. We conclude that targeted
enrichment provides the large volumes of phylogenetically-informative
sequence data required to resolve relationships within recent plant
species radiations, both at the species level and for within-species
phylogeographic studies.