Phylogenomics reveals widespread ancient hybridization in the evolution of Lychnophorinae (Vernonieae, Asteraceae)

Abstract Hybridization is a prevalent evolutionary process in plants and a potential driver of new species formation. Even though hybridization has been studied in many natural systems, the study of genomic signatures of past events of reticulation and hybridization was accelerated by the wide availability of high‐throughput sequencing methods. Similar to other species‐rich groups of plants, the occurrence of natural hybrids is widely documented in the sunflower family (Asteraceae), yet few studies have focused on ancient hybridization (that occurring between ancestral lineages), mainly due to the lack of comparative genomic data. With the recent increase in phylogenomic studies in Asteraceae made possible by family wide target‐capture probes, it has become clear that gene tree incongruence is widespread across the clade, likely reflective of complex speciation events in the past. One clade where natural hybridization is thought to be especially high is the subtribe Lychnophorinae of tribe Vernonieae, with ca. 145 species mostly endemic to the central Brazilian savannas and campos rupestres . Here, we for the first time propose a phylogenomic hypothesis for this subtribe and study the impacts of hybridization on its diversification. We newly sequenced 49 species (73 in total) with the Compositae1061 probe set and generated six phylogenetic trees based on different data treatments and using both multispecies pseudocoalescence and concatenated maximum likelihood analysis. To test whether a phylogenetic network, indicative of past and current reticulation events, better fits the data, we used a staggered sampling approach with SNaQ to overcome computational limitations. While overall our analyses confirm relationships recovered in previous analyses, we found five main foci of phylogenetic incongruence and hybridization across the tree. We explore how these reticulation events change our interpretation of some lineages in the subtribe, such as the Piptolepis pabstii/P. rosmarinifolia and the Lychnophora penninervia complex, further discussing potential taxonomic changes.