Resolving evolutionary relationships in the groundsels: phylogenomics, divergence time estimates, and biogeography ofPackera(Asteraceae: Senecioneae)

Abstract

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.

Compositae-ParaLoss-1272: Complementary sunflower specific probe-set reduces issues with paralogs in complex systems

“…When comparing the 1061 and 1272 tree topologies to the larger Packera phylogeny (Moore-Pollard and Mandel, 2023), the 1272 tree's evolutionary relationships was in higher agreement with the whole-genus phylogeny (RFadj = 0.6) as compared to 1061 (RFadj = 0.667), Jones,Mandel 15 potentially indicating this new probe set is more robust to species sampling compared to 1061.…”

“…An Illumina sequence run was performed using the new probe set on a selection of 19 total taxa, 16 Packera and three outgroup taxa, that were previously sequenced with the 1061 probe set. Packera taxa were selected to be representative across the entire Packera phylogenetic tree from Moore-Pollard and Mandel (2023). One outgroup taxon, Packera loratifolia (Greenm.)…”

“…One outgroup taxon, Packera loratifolia (Greenm.) W.A.Weber & Á.Löve, was included in this analysis as an outgroup instead of an ingroup since previous studies have shown it is likely misclassified in Packera and instead should be in Senecio (Barkley, 1985;Bain and Jansen, 1995;Bain and Golden, 2000;Pelser et al, 2007;Moore-Pollard and Mandel, 2023). Illumina sequencing was performed on the 19 taxa utilizing the 1272 probe set following the steps below.…”

“…DNA extraction and sequencing methods followed steps outlined by Moore-Pollard and Mandel (2023). Briefly, dried leaf tissue collected from herbarium specimens was used to extract DNA.…”

“…To estimate similarity scores between the 1061 and 1272 tree topologies, we calculated the adjusted Robinson-Foulds (RFadj) distance as outlined by Moore-Pollard and Mandel (2023) between the two trees using the RF.dist function in package phangorn (Schliep, 2011) in R.…”