Supplementary material: Ultraconserved elements improve the resolution of difficult nodes within the rapid radiation of neotropical sigmodontine rodents (Cricetidae: Sigmodontinae)

Sigmodontine rodents (Cricetidae, Sigmodontinae) represent the second
largest muroid subfamily and the most species-rich group of New World
mammals, encompassing above 410 living species and ca. 87 genera. Even
with advances on the clarification of sigmodontine phylogenetic
relationships that have been made recently, the phylogenetic relationships
among the 11 main group of genera (i.e., tribes) remain poorly resolved,
in particular among those forming the large clade Oryzomyalia. This
pattern has been interpreted as consequence of a rapid radiation upon the
group entrance into South America. Here, we attempted to resolve
phylogenetic relationships within Sigmodontinae using target capture and
high-throughput sequencing of ultraconserved elements (UCEs). We enriched
and sequenced UCEs for 56 individuals and collected data from four already
available genomes. Analyses of distinct data sets, based on the capture of
4,634 loci, resulted in a highly resolved phylogeny consistent across
different methods. Coalescent species-tree based approaches, concatenated
matrices, and Bayesian analyses recovered similar topologies that were
congruent at the resolution of difficult nodes. We recovered good support
for the intertribal relationships within Oryzomyalia; for instance, the
tribe Oryzomyini appears as the sister taxa of the remaining oryzomyalid
tribes. The estimates of divergence times agree with results of previous
studies. We inferred the crown age of the sigmodontine rodents at the end
of Middle Miocene, while the main lineages of Oryzomyalia appear to have
radiated in a short interval during the Late Miocene. Thus, the collection
of a genomic scale data set with a wide taxonomic sampling, provided
resolution for the first time of the relationships among the main lineages
of Sigmodontinae. We expect the phylogeny presented here will become the
backbone for future systematic and evolutionary studies of the group.