Genic and phylogenomic discordances reveal conflicting hybridization episodes in temperate Loliinae grasses

The grass subtribe Loliinae has great ecological and economic importance, as it includes community-dominant species of world mountain grasslands and the most extensively cultivated pasture, fodder and lawn grasses (fescues, ryegrasses). Resolving the phylogeny of recently evolved Loliinae lineages has proven challenging due to frequent introgressions and polyploidizations that occurred throughout their history. Evolutionary reconstruction based on genome-wide data sets is useful for large groups of species, enabling recovering phylogenetic trees, contrasting their topologies, unraveling the origins of the discordances, and testing hypotheses on their reticulate history. Here we present the first target-capture phylogeny of Loliinae using 234 single-copy nuclear coding loci for a large sample of 132 representative taxa, covering all its 29 evolutionary lineages. Additionally, we have completed organelle (plastome) sequences to elucidate the hybridogenic speciation history of the Loliinae from complementary genome sources. Concatenated maximum likelihood and multispecies coalescent trees of single-copy genes showed well-supported relationships for major lineages, which were generally consistent across analyses and genomes, and with previous taxonomic and phylogenetic findings. However, they also revealed high levels of both nuclear and cyto-nuclear discordances. The time-calibrated phylogeny of target-capture data supports an early Miocene origin for Loliinae and Mid-Late Miocene splits for its main broad-leaved and fine-leaved lineages, while current species-rich groups radiated in Plio-Pleistocene times. Hybridization and topological incongruence tests between the nuclear single-copy genes and plastome-based trees using multiple approaches and different sampling subsets confirmed the rampant introgression experienced by Loliinae at deep and shallow nodes. However, hybridization rates differed from lineage to lineage within the major clades and were not correlated with time or ploidy but rather depended on the “hybridogenous” nature of particular lineages. Our analyses detected high hybridization rates in four broad-leaved (Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American and Leucopoa p.p.) and five fine-leaved Loliinae lineages (American II, Aulaxyper, Afroalpine, American-Neozeylandic) containing rogue species that probably originated from trans-clade crosses and are more likely to hybridize greatly. In contrast, they recovered low hybridization rates in four broad-leaved (Schedonorus-Lolium, Subbulbosae, Drymanthele-Pseudoscariosae-Lojaconoa, Leucopoa pp) and six fine-leaved lineages (Festuca, Psilurus-Vulpia, American I, Exaratae-Loretia, American-Vulpia-Pampas, Eskia), with species derived from single ancestors that hybridize only with close congeners. The levels of intragenomic nuclear discordance could have been magnified by the prevalence of allopolyploids in the Loliinae and by methodological bias in the selection of orthologs; however, our nuclear and plastome trees have revealed key hybrid origins in these grasses. [allopolyploidization, lineage-specific hybridization rates, nuclear and cyto-nuclear discordances, Festuca and related genera, phylogenomics, nuclear single-copy genes, plastome].