Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae)
Authors: Moore-Pollard, E. R., Ellestad, P., Mandel, J.
The study examined how polyploidy, hybridization, and incomplete lineage sorting affect phylogenetic reconstructions in the genus Packera, evaluating several published paralog‑processing pipelines. Results showed that the choice of orthology and paralog handling methods markedly altered tree topology, time‑calibrated phylogenies, biogeographic histories, and detection of ancient reticulation, underscoring the need for careful methodological selection alongside comprehensive taxon sampling.
The study examined over six decades of USDA Hard Red Spring Wheat Uniform Regional Nursery data to quantify genetic gains in key agronomic traits. It found a modest positive genetic gain of 0.61% per year for grain yield, with stable grain protein levels despite a negative yield‑protein correlation, and highlighted varying gains among breeding programs, especially a ~1% per annum increase in Minnesota's public program.