Format: ORAL

Stefanie M. Ickert-Bond1, J. Gordon Burleigh2

1 UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA 2 Department of Biology, University of Florida, PO Box 118525, Gainesville, FL 32611-8525, USA

The gymnosperm genus Ephedra (Gnetales) is widely distributed in New and Old World arid and subtropical regions and has featured prominently in elucidating the phylogenetic interrelationships of seed plants. Reconstructing the evolutionary history of Ephedra has been hampered by fast rates of molecular evolution and extensive polyploidization, with 80% of the c. 54 species known to be polyploids, mostly tetraploids of allopolyploid origin. Recent advances in generating large sequencing datasets and new methodological advances for inferring complex histories from genomic data provide new promise for resolving previously intractable phylogenetic problems. Here we used target sequence capture data, generated using the GoFlag 408 flagellate land plant probe set, to infer the evolutionary history across 139 samples representing nearly all species of Ephedra. We discuss some of the challenges of using target capture data for Ephedra, and explore the value of assembling off-target plastid loci and new methods for phasing polyploid taxa using short read sequences and network inference on our ability to infer the reticulate history of Ephedra and identify putative progenitors of polyploid species. While numerous questions about the evolution of Ephedra remain, our analyses using targeted capture data and comprehensive sampling across the genus present new insights into the complex history of Ephedra as well as the challenges that remain.