Data from: Redefining possible: Combining phylogenomic and supersparse data in frogs

The data available for reconstructing molecular phylogenies have become
wildly disparate. Phylogenomic studies can generate data for thousands of
genetic markers for dozens of species, but for hundreds of other taxa,
data may be available from only a few genes. Can these two types of data
be integrated to combine the advantages of both, addressing the
relationships of hundreds of species with thousands of genes? Here we show
that this is possible, using data from frogs. We generated a phylogenomic
dataset for 138 ingroup species and 3,784 nuclear markers (ultraconserved
elements, UCEs), including new UCE data from 70 species. We also assembled
a supermatrix dataset, including data from 97% of frog genera (441 total),
with 1–307 genes per taxon. We then produced a combined
phylogenomic-supermatrix dataset (a “gigamatrix”) containing 441 ingroup
taxa and 4,091 markers, but with 86% missing data overall. Likelihood
analysis of the gigamatrix yielded a generally well-supported tree among
families, largely consistent with trees from the phylogenomic data alone.
All terminal taxa were placed in the expected families, even though 42.5%
of these taxa each had >99.5% missing data, and 70.2% had
>90% missing data. Our results show that missing data need not be
an impediment to successfully combining very large phylogenomic and
supermatrix datasets, and they open the door to new studies that
simultaneously maximize sampling of genes and taxa.