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Background  Resolving the short phylogenetic branches that result from rapid evolutionary diversification often requires large numbers of loci. We collected targeted sequence capture data from 585 nuclear loci (541 ultraconserved elements and 44 protein-coding genes) to estimate the phylogenetic relationships among iguanian lizards in the North American genus  Sceloporus . We tested for diversification rate shifts to determine if rapid radiation in the genus is correlated with chromosomal evolution.    Results  The phylogenomic trees that we obtained for  Sceloporus  using concatenation and coalescent-based species tree inference provide strong support for the monophyly and interrelationships among nearly all major groups. The diversification analysis supported one rate shift on the  Sceloporus  phylogeny approximately 20–25 million years ago that is associated with the doubling of the speciation rate from 0.06 species/million years (Ma) to 0.15 species/Ma. The posterior probability for this rate shift occurring on the branch leading to the  Sceloporus  species groups exhibiting increased chromosomal diversity is high (posterior probability = 0.997).    Conclusions  Despite high levels of gene tree discordance, we were able to estimate a phylogenomic tree for  Sceloporus  that solves some of the taxonomic problems caused by previous analyses of fewer loci. The taxonomic changes that we propose using this new phylogenomic tree help clarify the number and composition of the major species groups in the genus. Our study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of  Sceloporus  across North America.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0628-x) contains supplementary material, which is available to authorized users.

Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?