Discovering the next-generation of hybrids: evidence from high-throughput SNP assays that three species of Populus lack significant reproductive barriers

Thesis (M.S.) California State University, Los Angeles, 2012Committee members: Stacey L Thompson, Kirsten Fisher, Patrick Krug, Nancy McQueenGenetics, Hybridization, Populus, SNP AssayBy characterizing hybrid zones we can predict the long-term consequences of hybridization. In 1977, eight poplar hybrid zones were studied, comprising two native Californian species,<italic> Populus fremontii</italic> and <italic>P. trichocarpa</italic>, and the European exotic, <italic>Populus nigra</italic>, which is commonly planted as an ornamental. The morphological and phytochemical analyses in this 1977 study identified first generation (F1) hybrids and inferred an F1 block between hybrids and the parental species. To characterize the composition of these poplar hybrid zones in more recent times, eight of the nine hybrid zones from the original 1977 study, plus one newly discovered population, were sampled and genotyped using a 25 single nucleotide polymorphism (SNP) assay. The diagnostic SNPs included 22 species-specific biparental nuclear markers and three chloroplast markers to identify maternal lineage. Hybrid classes were assigned using a molecular hybrid index. In addition to molecular analyses, five leaves from each individual (n= 2260) were digitally scanned and 16 leaf characters were measured and analyzed to determine the accuracy of leaf morphology for hybrid identification. Genotyping results from 468 trees showed an overall frequency of 45.7% of pure species (26.7% <italic>P. fremontii</italic>, 18.6% <italic>P. trichocarpa</italic>, 0.4% <italic>P. nigra</italic>) and 54.3% hybrids/introgressants. F1 hybrids were detected in every population, while advanced-generation hybrids (backcrosses and more complex combinations) were observed at two of the nine sites, with an overall frequency of 3.5%. In the majority of the cases (79.9%), <italic>P. fremontii</italic> was the maternal parent of hybrids of all classes. Hybridization between the native species was more common (59.7% of hybrids), than between <italic>P. fremontii</italic> and <italic>P. nigra</italic>, with a tendency to backcross towards <italic>P. fremontii</italic>. No F1 <italic>P. trichocarpa</italic> x <italic>P. nigra</italic> was found, suggesting the presence of prezygotic or postzygotic reproductive barriers. However, one tri-hybrid was found ((<italic>P. fremontii</italic> x <italic>P. trichocarpa</italic>) x <italic>P. nigra</italic>) at a site that lacked <italic>P. nigra</italic> 30 years ago. Leaf morphological analyses, using the 16 characters, was useful in the identification of pure species and hybrid taxa. The genotypic composition of these hybrid zones suggests increased admixture from the exotic species, while our detection of advanced-generation hybrids implies that there are few reproductive barriers among the species. This rampant hybridization suggests the need for long-term perspective when assessing potential impacts of gene flow on natural resources