Systematic Botany (2011), 36(1): pp. 209–226 © Copyright 2011 by the American Society of Plant Taxonomists DOI 10.1600/036364411X553289 Nuclear and Chloroplast DNA Suggest a Complex Single Origin for the Threatened Allopolyploid Solidago houghtonii (Asteraceae) Involving Reticulate Evolution and Introgression Pamela J. Laureto 1 and Todd J. Barkman Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan 49008 U. S. A. 1 Current address: Department of Biological Sciences, Grand Rapids Community College, Grand Rapids, Michigan 49503 U. S. A. 1 Author for correspondence (
[email protected]) Communicating Editor: Andrew Hipp Abstract— Solidago houghtonii Torrey & A. Gray ex Gray is a federally threatened polyploid plant species likely of hybrid origin. Several hypothesized combinations of parental species have been suggested but none have been phylogenetically tested. Additionally, it is unclear whether the species is of single or polytopic origin. To study the evolutionary history of S. houghtonii we sequenced four noncoding cpDNA loci ( accD-psaI , psbA-trnH , trnL-trnF , rps16-trnQ ), and the ITS and 3′ETS regions for four accessions of S. houghtonii , which span its geographic range, and 25 other species of Solidago including all sympatric species. Polymorphisms within the direct nrDNA sequences of all S. houghtonii accessions indicated the presence of multiple homoeologue types. These were separated by molecular cloning of the 3055 bp 3′ETS – ITS region, allowing us to positively link the ETS and ITS homoeologue types. Phylogenetic analyses of the nuclear and chloroplast datasets revealed incongruent topologies. Analysis of cloned nrDNA sequence data indicated that S. riddellii, S. ptarmicoides , and S. ohioensis have contributed to the nuclear genome of S.