The genus Packera belongs to the sunflower family and contains an estimated 64 species and varieties endemic to North America. Some Packera are known to hybridize or exhibit polyploidy, making it difficult to reconstruct evolutionary relationships within the group. Previous molecular phylogenetic studies of Packera employing ITS data recovered low resolution trees, providing little information on the evolutionary relationships within this complex genus. Therefore, we used next-generation sequencing data to infer nuclear and plastid phylogenies of Packera and related Senecioneae taxa. The nuclear phylogeny was calibrated to produce a timetree, then used to reconstruct the macroevolutionary history of Packera, including its historical biogeography. We then compared the reconstructed evolutionary history to previously published scenarios based on phylogenetic and geohistorical data. We found that the nuclear and plastid phylogenies were highly incongruent, with the nuclear tree presenting higher resolution than the plastid tree which had an apparent lack of plastid diversity. The nuclear tree indicated that geography may have played a major role in the evolution and taxonomic diversification of Packera. The estimated origin of Packera at approximately 19.2MY - 25.9MY (late Oligocene to early Miocene) is older than in most other studies. Nonetheless, it aligns well with previous geohistorical predictions, which suggest that speciation and diversification events in Packera were driven by changes in geography and climate in North America. Moreover, Packera likely originated in the western United States or Mexico, and subsequently diversified north and east into the rest of North America and Russia, in agreement with other studies.

Premise of the study: Underlying discordance in phylogenomic studies is becoming more common, and the answer is not as simple as adding more data. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are main contributors to these issues and must be considered when generating phylogenies. Otherwise, interpretations of evolutionary relationships could be misleading. Methods: To obtain a better understanding of potential gene flow and its effect on phylogenetic trees, we investigated the causes and consequences of nuclear discordance using the genusPackerato understand how they influence the phylogenetic patterns seen in this complex group. To do this, we compared the topology and support values ofPackeraphylogenies resulting from various paralog selection or pruning methods. We then investigated whether pruning the paralogs instead of performing a selection process affected the topology and support of our phylogeny. To investigate hybridization and its effect on species relationships in our tree, we used likelihood methods to infer phylogenetic networks to find any evidence of gene flow among species lineages in this complicated genus. Key results: We found that performing different paralog selection or pruning methods does impact our understanding of the evolutionary relationships withinPackera, and that addressing these paralogs with more rigorous methods than the typical pipeline increases concordance within the resulting phylogenies. Additionally, investigating reticulation events within highly discordant clades showed that ancestral hybridization and reticulation events are common throughoutPackera. Conclusions: Investigating underlying biological processes by testing various methods can provide further insight into complex species relationships and levels of discordance within phylogenomic studies.

No abstract

Compositae accounts for ca. 10% of all flowering plants, being found in nearly all types of habitats worldwide. The family is particularly diverse in markedly dry and seasonal habitats, raising questions about what processes led to diversification in these challenging environments. The presence of C 4 and CAM metabolism in some Compositae taxa has been known since the 1970s, and although some of these taxa have been extensively studied, such as Flaveria, there has been no systematic effort in gathering and reviewing data about photosynthesis metabolism in the family in the last few decades. In the present paper, we gathered data from more than 50 articles, spanning several different methods, raising information on photosynthesis metabolism for more than 400 Compositae species. We also present newly acquired carbon isotope data for 66 species, mostly from previously unsampled tribes. We analyzed photosynthesis metabolism in the tribe Tageteae using a phylogeny and ancestral character reconstruction. C 4 photosynthesis in Compositae is restricted to two tribes: Tageteae, where it had two independent origins, and Coreopsideae, where it seems to have arisen only once. CAM metabolism is found in succulent members of tribe Senecioneae, and in Astereae and Eupatorieae, with an unknown number of evolutionary origins. We discuss the evolutionary implications of the results and propose future directions for studying photosynthesis metabolism in the family.