Torreya

Torreya is a classic example of the well‐known EA–NA floristic disjunction with species richness biased toward EA. The genus has seven extant species: two from NA and five from EA. In our study, we used Rad‐seq data in combination with plastome and mitochondrial gene sequences, morphology, and fossil records to reconstruct the phylogenetic and biogeographic histories of the genus and tested hypotheses on anomalies of biodiversity of the eastern Asian‐North American floristic disjunction.

Our results showed that our pipeline recovered many loci missing from the outgroup, and the improved data yielded a more robust phylogeny for Torreya.

Using the fossilized birth–death model and divergence–extinction–cladogenesis method, we resolved a detailed biogeographic history of Torreya that suggested a Jurassic origin spanning Laurasia and differential speciation and extinction among continents accounting for modern diversity, which is biased toward eastern Asia (EA). The biogeographic results also supported a vicariance origin of modern Torreya from a widespread ancestor in EA and North America (NA) in the mid‐Eocene, and cross Beringian exchange in the early Paleogene before the vicariant isolation, in contrast to the “out of NA” pattern common to gymnosperms and to the “out of EA” hypothesis previously proposed for the genus. Furthermore, we observed phylogenetic discordance between the nuclear and plastid phylogenies for Torreya jackii, suggesting differential lineage sorting of plastid genomes among species of Torreya or plastid genome capture in T. jackii.