Format: ORAL

J. Gordon Burleigh1, Lorena Endara2, Stefanie M. Ickert-Bond3

1 Department of Biology, University of Florida, Gainesville, FL 32611-8525, USA 2 Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA 3 UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA

The gymnosperms represent one of the two major lineages of seed plants and are critically important to the biodiversity of many ecosystems. While decades of molecular phylogenetic analyses have resolved many relationships within extant gymnosperms (c. 1080 species), some parts of the tree remain contentious, and there is a need for a comprehensive resource that highlights the complexities of evolution that can be illuminated with genomic data. We generated a phylogenomic dataset using targeted enrichment with the GoFlag 408 flagellate plant probe set, which covers 408 exons from 229 single or low copy nuclear genes, and sampled approximately 1060 taxa, representing all families and genera, and approximately 95% of all extant species. The resulting phylogeny is strongly supported, although some areas of the tree have weaker support and/or high levels of intragenomic conflict. Our analyses also highlight some of the challenges and limitations of targeted enrichment data from a universal probe set. We compare the tree inferred from targeted enrichment data with trees from plastid and transcriptome data. The targeted capture dataset provides new perspectives on some classic questions in gymnosperm phylogenetics and highlights areas where further research is needed, and it provides a resource of comparable and combinable data that can help illuminate future studies of evolutionary processes across the gymnosperms.