Unraveling Evolution in the Homoploid Complex of <i>Baccharis</i> L. in Chile

<i>Baccharis × intermedia</i> (Asteraceae), found in central Chile, is a naturally occurring hybrid derived from the parent species <i>B. macraei</i> and <i>B. linearis.</i> It represents an extraordinary example of admixture with additive plant chemistry; however, the genetic structure of the hybrid complex and its evolution are still unclear. Intensive field sampling and Genotyping-by-Sequencing (GBS) were used to clarify the structure of the <i>B. × intermedia</i> hybrid complex. In addition, <i>B. vernalis</i>, another species that resembles the morphology of <i>B. macraei</i>, was subjected to analysis to ascertain its role in the hybridization process. A total of 3724 SNPs and 378 individuals were analyzed using clustering, PCA, Treemix, Patterson's <i>D</i>- and <i>f</i>-statistics. Furthermore, other genetic indicators, such as levels of heterozygosity, Tajima's <i>D</i>, and nucleotide diversity (<i>π</i>) also provided further insight into the hybrid complex. Our results show that <i>B</i>. <i>× intermedia</i> consists mainly of F₁-hybrids with 18% backcrossing to both parental species. <i>B. vernalis</i> was not involved in recent hybridization with <i>B. macraei</i> and <i>B. linearis.</i> Additionally, a recent introgression into the Quintay population of <i>B. macraei</i> from <i>B. linearis</i> was detected during the analysis. There is no indication of hybrid speciation. Altogether, our extensive field sampling combined with genetic analyses has provided deeper insights into the genetic structure and evolution of the <i>B</i>. <i>× intermedia</i> hybrid complex in Chile.