Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study

Publication date: Available online 17 February 2020Source: Molecular Phylogenetics and EvolutionAuthor(s): Justin C. Bagley, Simon Uribe-Convers, Mónica M. Carlsen, Nathan MuchhalaAbstractTargeted sequence capture is a promising approach for large-scale phylogenomics. However, rapid evolutionary radiations pose significant challenges for phylogenetic inference (e.g. incomplete lineages sorting (ILS), phylogenetic noise), and the ability of targeted nuclear loci to resolve species trees despite such issues remains poorly studied. We test the utility of targeted sequence capture for inferring phylogenetic relationships in rapid, recent angiosperm radiations, focusing on Burmeistera bellflowers (Campanulaceae), which diversified into ∼130 species over less than 3 million years. We compared phylogenies estimated from supercontig (exons plus flanking sequences), exon-only, and flanking-only datasets with 506–546 loci (∼4.7 million bases) for 46 Burmeistera species/lineages and 10 outgroup taxa. Nuclear loci resolved backbone nodes and many congruent internal relationships with high support in concatenation and coalescent-based species tree analyses, and inferences were largely robust to effects of missing taxa and base composition biases. Nevertheless, species trees were incongruent between datasets, and gene trees exhibited remarkably high levels of conflict (∼4–60% congruence, ∼40–99% conflict) not simply driven by poor gene tree resolution. Higher gene tree heter...

Source: Molecular Phylogenetics and Evolution - February 17, 2020 Category: Molecular Biology Source Type: research