Genotyping-by-sequencing resolves relationships in Polygonaceae tribe Eriogoneae

The resolution of cryptic diversity is essential for understanding the evolutionary diversification of lineages and establishing conservation priorities. We examine relationships in Eriogoneae (Polygonaceae), a diverse lineage in western North America. We ask whether Eriogonum umbellatum, a morphologically and ecologically diverse species, is monophyletic and whether its varieties represent evolutionary lineages. We use genotyping-by-sequencing to assemble a SNP dataset for 51 species in the genera Chorizanthe, Eriogonum and Sidotheca. We report a hierarchical phylogenetic analysis using maximum likelihood to estimate the evolutionary history of Eriogoneae. We illustrate admixture components for 21 populations of E. umbellatum, representing four varieties, and test for lineage structure using TreeMix. We identify strongly supported clades within Eriogoneae. Many relationships in the Eucycla + Oregonium and Latifolia clades are supported, while most relationships within the Eriogonum subg. Oligogonum clade and a clade with most Chorizanthe remain unresolved. Eriogonum congdonii resolves within the main E. umbellatum clade, while populations of three varieties of E. umbellatum are closely related to E. ursinum and are associated with serpentine soils. ADmixture and TreeMix analyses suggest E. umbellatum varieties represent evolutionary lineages. These results from SNP data are largely consistent with previous phylogenetic studies of Eriogoneae based on sequence variation. Structure within Oligogonum suggests consistent environmental association and radiation after initial colonization of serpentine. Morphology is unreliable for the infraspecific taxonomy of E. umbellatum. Additional molecular studies are needed to resolve the evolutionary relationships and ecological diversification within this species, in Oligogonum, and in Eriogoneae.We thank SGIker research support services at the University of the Basque Country, Leioa, Spain for DNA extraction and quality control, and acknowledge Centro Nacional de d-Analisi Genomica in Barcelona, Spain for GBS sequencing. We thank J. Andre, N.J. Jensen and J. Steele for contributing samples and D. Marino for collaboration in nucleic acid extractions. We acknowledge the contributions of O. Lao Grueso to the ADmixture and TreeMix analyses. We thank U.S. Forest Service employees D. Austin, J. Fedorchuk, M. Friend, J. Haas, D. Ikeda, L. Janeway, J. Nelson, D. Netz, A. Sanger, and S. Weis among others for facilitating permitting and collecting. This work was supported by funds from the Basque Government in support of the Terrestrial Plant Diversity group of the Department of Plant Biology and Ecology, University of the Basque Country, and an ERC Advanced Grant, FP7-IDEAS-ERC, `ADAPT', project 339941 awarded to T. Brown