Reconstructing a robust species phylogeny and disentangling the evolutionary and biogeographic history of the gymnosperm genus Ephedra,which has a large genome and rich polyploids,re-main a big challenge.Here we reconstructed a transcriptome-based phylogeny of 19 diploid Ephedra species,and explored evolutionary retic-ulations in this genus represented by 50 diploid and polyploid species,using four low-copy nuclear and nine plastid genes.The diploid species phylogeny indicates that the Mediterranean species diverged first,and the remaining species split into three clades,including the American species(Clade A),E.rhytidosperma,and all other Asian species(Clade B).The single-gene trees placed E.rhytido-sperma sister to Clade A,Clade B,or Clades A+B in similar proportions,suggesting that radiation and gene flow likely occurred in the early evolution of Ephedra.In addition,reticulate evolution occurred not only among the deep nodes,but also in the recently evolved South American species,which further caused difficulty in phylogenetic re-construction.Moreover,we found that allopolyploid speciation was pervasive in Ephedra.Our study also suggests that Ephedra very likely originated in the Tethys coast during the late Cretaceous,and the South American Ephedra species have a single origin by dispersal from Mexico or North America.

The advances accelerated by next-generation se-quencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study. In the past decade, a large number of phylo-genetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era. In the meantime, a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent. This review focuses on the utility of genomic data (from organelle genomes, to both reduced representation sequencing and whole-genome se-quencing) in phylogenetic and evolutionary inves-tigations, describes the baseline methodology of experimental and analytical procedures, and sum-marizes recent progress in flowering plant phyloge-nomics at the ordinal, familial, tribal, and lower levels. We also discuss the challenges, such as the adverse impact on orthology inference and phylogenetic re-construction raised from systematic errors, and un-derlying biological factors, such as whole-genome duplication, hybridization/introgression, and in-complete lineage sorting, together suggesting that a bifurcating tree may not be the best model for the tree of life. Finally, we discuss promising avenues for future plant phylogenomic studies.