Reticulate evolution in Helianthus (Asteraceae)

Many plants have a net-like or reticulate phylogenetic history caused by hybrid speciation or introgression. These more complex histories require additional methods and data for their reconstruction and Helianthus provides an ideal system for which to uncover these past events. Reconstructing the phylogeny of Helianthus is important for two reasons: it contains two economically important crop plants (H. annuus and H. tuberosus) and its annual species have formed an important model system for studying speciation genetics. To reconstruct the reticulate evolution of Helianthus in this study, multiple independent gene phylogenies were collected for the genus: four nuclear regions (rRNA external transcribed spacer (ETS), an actin gene, pistillata and 1548 EST) and four plastid regions (trnY-rpoB spacers, trnL-rpl32 spacer, ndhC-trnV spacer and a portion of ycf1) Each of the five independent datasets were analyzed separately (the four plastid regions were concatenated into one dataset). The resulting ETS phylogeny revealed for the first time a resolved gene tree for Helianthus. Phylogenetic analysis of these data allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliaris, and the monotypic H. sect. Agrestis, all of which are nested within the large perennial and polyphyletic H. sect. Divaricati. Previously collected secondary chemistry characters were mapped onto this phylogeny for examination of their character evolution. Supported incongruences between the five gene-trees were identified as possible reticulation events (hybrid speciation and/or introgression). One of these led to the discovery of a new undescribed species, H. ‘Newhall Ranch’, which our molecular data shows was formed via an allopolyploid reduction event. Two complete chloroplast genomes in the Asteraceae were sequenced, Helianthus annuus (sunflower) and Lactuca sativa (lettuce), which belong to the distantly related subfamilies, Asteroideae and Cichorioideae, respectively. Pair-wise sequence divergence across all both plastid genomes resulted in the discovery of new, fast-evolving DNA sequences for use in species-level phylogenetics in Asteraceae. The complete annotated genome sequences also enabled a novel analysis of repeat patterns (thought to be involved in genome rearrangement) in the genomes and of RNA editing by comparison to available EST sequences.