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

0554661 - BÚ 2023 RIV CH eng J - Článek v odborném periodiku
Kandziora, M. - Sklenář, P. - Kolář, Filip - Schmickl, Roswitha
How to Tackle Phylogenetic Discordance in Recent and Rapidly Radiating Groups? Developing a Workflow Using Loricaria (Asteraceae) as an Example.
Frontiers in Plant Science. Roč. 12, 7 January (2022), č. článku 765719. ISSN 1664-462X. E-ISSN 1664-462X
Grant CEP: GA ČR GA20-10878S
Institucionální podpora: RVO:67985939
Klíčová slova: data sets * gene trees * diversification * gnaphalieae * evolution * concatenation * incongruence * inference * accuracy * dynamics * rapid radiation * hybridization * workflow * incomplete lineage sorting * gene tree discordance * cytonuclear discordance
Obor OECD: Plant sciences, botany
Impakt faktor: 5.6, rok: 2022
Způsob publikování: Open access
https://doi.org/10.3389/fpls.2021.765719

A major challenge in phylogenetics andgenomics 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.
Trvalý link: https://hdl.handle.net/11104/0339166