Phylogenomics reveals extreme gene tree discordance in a lineage of dominant trees: hybridization, introgression, and incomplete lineage sorting blur deep evolutionary relationships despite clear species groupings in Eucalyptus subgenus Eudesmia

Incomplete lineage sorting and hybridization as drivers of tree discordance in Petunia and related genera (Petunieae, Solanaceae)

“…The discordance in tree topologies within the short corolla tube Petunia clade and Calibrachoa subgenus Stimomphis arises from a combination of ILS due to their rapid diversification and past and ongoing hybridization events. Instances of high ILS and extensive hybridization are not uncommon in the evolutionary history of plants (e.g., Kleinkopf et al 2019;Morales-Briones et al 2021;McLay et al 2023), but pinpointing the specific taxa involved in the hybridization events is still a daunting task, and one of the reasons why different methods often yield conflicting results (Gates et al 2023). These introgression events likely contributed to the species' genetic diversity, aiding their adaptation during their radiation.…”

Navigating phylogenetic conflict and evolutionary inference in plants with target capture data

“…Perhaps the best-known Australian example where phylogenetic inference has been confounded by frequent chloroplast capture is in the eucalypts (McKinnon et al 1999;Nevill et al 2014). Organelle capture can sometimes be inferred from conflict in the topology of species trees generated with plastid, morphological and nuclear data, in combination with tests for introgression in the nuclear dataset (McLay et al 2023).…”

“…Bloesch et al 2022;Bradican et al 2023); however the method requires careful selection of the presence of diploid references for putative parental clades, and is often unsuitable for groups with complex or ancient reticulation (e.g. McLay et al 2023). The need for a diploid reference is overcome through the Bayesian implementation of phasing in homologizer (Freyman et al 2023), but may require subsampling of target-capture datasets to reduce computational demands.…”

“…For the Australian flora, this means answering long-standing questions that have been hampered by the 'lack of resolution' intractable from previously available technologies. To date, target capture studies have greatly enhanced our understanding of the timing and tempo of radiations (Joyce et al 2023;Nge et al 2024), the role of hybridisation and introgression in evolution (Bloesch et al 2022;McLay et al 2023;Nge et al 2021 -Adenanthos), polyploidy and WGD events (Nge, Kellermann, et al 2021;, and the evolution of diverse and important ecological groups in Australia (Crisp et al 2024;McLay et al 2023;Peakall et al 2021;Schmidt-Lebuhn and Bovill 2021). They have also shed light on biogeography within Australia (Nge et al 2021a;2021b -Calytrix and Pomaderris), as well as Australia's biotic connection with other land-masses (Joyce et al 2023;Nge et al 2021 -Pomaderris), demonstrating Australia's role as both a source and sink of global plant diversity (Pillon et al 2021;Van Dijk et al 2023).…”

“…In the Australian flora, conflict has been attributed to likely WGD events in target capture datasets of Adenanthos , Pomaderris (Nge, Kellermann, et al 2021), Calytrix (Nge et al 2022), Cryptandra (Nge et al 2024), Senecio , Celmisiinae (Nicol et al 2024) and many lineages in Sapindales (Joyce et al 2023). Conflict due to reticulation has been detected in Adansonia (Karimi et al 2020) and Thelypteridaceae (Bloesch et al 2022), and reticulation in concert with deep coalescence in Adenanthos and Eucalyptus (McLay et al 2023). As illustrated by these examples, conflict in target capture data, if handled carefully, can actually give novel insight into key biological processes in the evolutionary history of plants.…”