Brief Study Abstract: Targeted 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, as a case study. Our findings suggest that targeted sequence capture is feasible for resolving rapid, recent angiosperm radiations, and that results based on supercontig alignments containing nuclear exons and flanking sequences have higher phylogenetic utility and accuracy than either alone.
Brief Data Overview: Accessioned in this project are the raw data from 46 Burmeistera species, plus 10 Centropogon and Siphocampylus species (closely related genera within Lobelioideae) used as outgroups in our phylogenomics study (Bagley et al. 2020). As described in the corresponding manuscript, these raw data were obtained through one round of 100-bp single-end sequencing followed by 150-bp paired-end sequencing (with a minimum sequencing depth of coverage of 40x per sample) on an Illumina HiSeq 3000 sequencer. The PE and SE data were combined, and then they were cleaned and filtered, and then additional quality control, assembly, and extraction of target sequences and flanking sequences were conducted in the HybPiper v1.3.1 pipeline (Johnson et al. 2016). Final datasets were analyzed using standard approaches in phylogenomics (gene tree and species tree analyses), as well as in-depth analyses of phylogenetic informativeness of the loci as well as gene tree congruence/incongruence with the species tree. See additional information in Bagley et al. (2020) and the Mendeley Data accession for that paper (http://dx.doi.org/10.17632/wsbjwr3p42.1).
REFERENCES
Bagley, J.C., Uribe-Convers, S., Carlsen, M., Muchhala, N., 2020. Utility of targeted sequence capture for phylogenomics in rapid, recent angiosperm radiations: Neotropical Burmeistera bellflowers as a case study. Mol. Phylogenet. Evol. Available online at: .
Johnson, M.G., Gardner, E.M., Liu, Y., Medina, R., Goffinet, B., Shaw, A.J., Zerega, N.J.C., Wickett, N.J., 2016. HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Appl. Plant Sci. 4, 1600016. Less...