Data from: Phylogenomic discordances reveal conflicting hybridization episodes and widespread lineage-sorting events in temperate Loliinae grasses

The grass subtribe Loliinae has great ecological and economic importance,
as it includes community-dominant species of mountain grasslands and the
most extensively cultivated pasture, fodder, and turf 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. Here we present
the first target-capture phylogeny of Loliinae using 270 orthologous
single-copy nuclear coding loci for a large sample of 132 representative
taxa, covering all its 29 evolutionary lineages. Additionally, we
assembled plastome sequences to complement the inferred hybrid speciation
history of the Loliinae. Concatenated maximum likelihood and multispecies
coalescent trees of ortho-homeolog 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
cytonuclear discordances estimated to be caused by hybridization and
incomplete lineage sorting. We complemented this with a phylogenetic
network analysis with representative samples from the main clades to infer
reticulation events in the evolution of these grasses.
 Furthermore, we performed gene tree – species tree
reconciliation methods using gene duplication and loss models and
multi-labeled trees for polyploidy analysis to estimate the proportion of
duplicated genes and the nature of polyploidy of the major Loliinae
lineages. These analyses agreed that the Fine-Leaved (FL) Loliinae clade
could have evolved from hybridization between more ancestral Broad-Leaved
(BL) Loliinae lineages and that both groups underwent ancestral and recent
hybridizations. The time-calibrated phylogeny of for the main Loliinae
clades supports an early Miocene origin for Loliinae and Mid-Late Miocene
splits for its main BL and FL lineages, while current species-rich groups
radiated in the Late Miocene. Hybridization tests of nuclear data and
topological incongruence assays between the nuclear single-copy genes and
plastome-based trees using various approaches and different sampling
subsets confirmed the rampant hybridization 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 level, but rather depended on their different propensities to
hybridize with species within and/or outside their own clade. Our analyses
detected high hybridization rates in four broad-leaved
(Subulatae-Hawaiian, Tropical-South African, Mexico-Central-South American
(MCSA I-II), and Leucopoa p. p.) and five fine-leaved Loliinae lineages
(American II, Aulaxyper, Afroalpine, American-Neozeylandic,
Australia-Tasmania) 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 p. p.) 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.
Inferences from gene duplications and allopolyploidizations, along with
inheritance probabilities from the phylogenetic network, point to the BL
Loliinae lineages as ancient hybrids or paleo-allopolyploids, while the FL
lineages, especially those of the core FL clade, correspond to more recent
meso- or neo-allopolyploids.