Iguanian lizards Raw sequence reads

Targeted sequence capture is becoming a widespread tool for generating large phylogenomic datasets to address difficult phylogenetic problems. However, this methodology often generates datasets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolved) question is whether sampling should be designed to maximize sampling of taxa or genes, or minimize the inclusion of missing data cells. Here, we explore this question for an ancient, rapid radiation of lizards, the pleurodont iguanians. Pleurodonts include many well-known clades (e.g. anoles, basilisks, iguanas, spiny lizards) but relationships among pleurodont families have proven difficult to resolve strongly and consistently using traditional sequencing approaches. We generated up to 4,921 ultraconserved elements with sampling strategies including 16, 29, and 44 taxa, from 1,179 to ~2.4 million characters, and ~30% to 60% total missing data.