Data_Sheet_1_How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example.pdf

A major challenge in phylogenetics and -genomics is to resolve young rapidly radiating groups. The fast succession of species increases the probability of incomplete lineage sorting (ILS), and different topologies of the gene trees are expected, leading to gene tree discordance, i.e., not all gene trees represent the species tree. Phylogenetic discordance is common in phylogenomic datasets, and apart from ILS, additional sources include hybridization, whole-genome duplication, and methodological artifacts. Despite a high degree of gene tree discordance, species trees are often well supported and the sources of discordance are not further addressed in phylogenomic studies, which can eventually lead to incorrect phylogenetic hypotheses, especially in rapidly radiating groups. We chose the high-Andean Asteraceae genus Loricaria to shed light on the potential sources of phylogenetic discordance and generated a phylogenetic hypothesis. By accounting for paralogy during gene tree inference, we generated a species tree based on hundreds of nuclear loci, using Hyb-Seq, and a plastome phylogeny obtained from off-target reads during target enrichment. We observed a high degree of gene tree discordance, which we found implausible at first sight, because the genus did not show evidence of hybridization in previous studies. We used various phylogenomic analyses (trees and networks) as well as the D-statistics to test for ILS and hybridization, which we developed into a workflow on how to tackle phylogenetic discordance in recent radiations. We found strong evidence for ILS and hybridization within the genus Loricaria. Low genetic differentiation was evident between species located in different Andean cordilleras, which could be indicative of substantial introgression between populations, promoted during Pleistocene glaciations, when alpine habitats shifted creating opportunities for secondary contact and hybridization.</p

MOESM10 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 10. Results: Number of range-expansion dispersal events (mean and standard deviation of all observed “d” dispersals) averaged across 50 biogeographical stochastic mappings under the best inferred model using the best tree

MOESM12 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 12. Results: Number of all dispersal events (mean and standard deviation of all observed anagenetic ‘a’, ‘d’ dispersals, PLUS cladogenetic founder/jump dispersal) averaged from 50 biogeographical stochastic mappings under the best inferred model using the best tree

MOESM7 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 7 Results: Pairwise climate similarity (Schoener’s D) between biogeographic areas for combined PC axes

MOESM8 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 8. Results of the different models under DEC + J and DEC (generally the better models compared to DIVA-like and BAYAREA-like-models)

MOESM3 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 3. Methods: Biogeographic models; example files for BioGeoBEARS analyse

MOESM11 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 11. Results: Number of cladogenetic dispersal events (mean and standard deviation of all observed jump ‘j’ dispersals) averaged from 50 biogeographical stochastic mappings under the best inferred model using the best tree

MOESM1 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 1. Methods: occurrence data

MOESM6 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 6 Results: pairwise climate similarity (Schoener’s D) between biogeographic areas per PC axis

MOESM13 of Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica

Additional file 13. Results: Ancestral area reconstructions inferred using BioGeoBEARS given the best tree under the best fitting model given A: DEC + J; B: DEC; and without range or dispersal constraint: C: DEC + J; D: DEC. For each model the single most probable state is shown first (boxes with areas at nodes) followed by the relative probability of each state represented with pie charts at nodes. Areas are represented by colours: Dark blue for Europe (E); green for Tropical Africa (T); yellow for Madagascar (M); light blue for Drakensberg (D); red for Cape (C); and further colours for widespread distributions as indicated in the legends