Phylogenomics of Liliaceae Subfamily Streptopoideae and a Phylogeographic Study of Rosy Twisted-stalk (Streptopus lanceolatus) Across North America

Wang, Shenyi

ABSTRACT: Liliaceae are a challenging family to classify and the taxonomy of one subfamily, Streptopoideae, has been plagued with controversy. As currently circumscribed, Streptopoideae contain three genera: Prosartes, Scoliopus, and Streptopus with 17 species distributed across the Northern Hemisphere. Phylogenetics among these plants has never been studied adequately. I resolved their relationships, estimated divergence times among clades, and reconstructed historical biogeography within Streptopoideae and several outgroup taxa using de novo assembled and annotated whole chloroplast genomes (15 of 17 ingroup species). The phylogeny is mostly well supported, but some intra-specific relationships are characterized by short branch lengths, especially within Streptopus. Complementary nuclear genomic data derived from Genotyping by Sequencing (GBS) methods were then applied for phylogenetic inferences among 142 accessions, representing 16 of 17 Streptopoideae species. The best supported phylogeny again demonstrated the monophyly of each genus, but now with Prosartes sister to Streptopus, instead of sister to Scoliopus. This result, as well as many of the inter-specific relationships within Prosartes and Streptopus, are not congruent with plastome trees and may be due to hybridization. At least one chloroplast capture event was confirmed. Alternative data and methods may be needed so that hundreds of known orthologues and gene trees can be used to demonstrate events of reticulate evolution within Streptopoideae. Finally, the phylogeography of one North American species, Streptopus lanceolatus, was studied. Analyses of GBS data for 296 individuals from 62 populations strongly supported the presence of three distinct genetic clusters corresponding to NW North America, the Upper Midwest, and E North America. Levels of genetic diversity support a hypothesis that the ancestor of S. lanceolatus colonized far northwestern North America from East Asia, then spread across the continent, eventually being restricted into at least three different glacial refugia. Those areas today are sources from which the species is migrating northward; the eastern and midwestern populations are now hybridizing in the northern Great Lakes of the USA and Canada. One of the suspected refugia, the Driftless Area of SW Wisconsin, is especially interesting and could become important again as a future refugium for plants under threat by climate change