A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)

• Published in: Molecular phylogenetics and evolution 2017-12, Vol.117, p.124-134
• Main Authors: Fragoso-Martínez, Itzi, Salazar, Gerardo A., Martínez-Gordillo, Martha, Magallón, Susana, Sánchez-Reyes, Luna, Moriarty Lemmon, Emily, Lemmon, Alan R., Sazatornil, Federico, Granados Mendoza, Carolina
• Format: Article
• Language: English
• Subjects: Anchored phylogenomics; Genetic Loci - genetics; Genetic Markers - genetics; Lamiales; Maximum likelihood; Phylogenetic noise; Phylogeny; Pilot Projects; Salvia - genetics; Sequence Analysis, DNA; Target enrichment
• ISSN: 1055-7903; 1095-9513
• DOI: 10.1016/j.ympev.2017.02.006

[Display omitted] •The Anchored Hybrid Enrichment method was tested in a New World lineage of sages.•Capture and sequencing using the AHE method was successful, yielding 448 loci.•AHE data improved support and resolution compared to conventional markers.•Removal of sites with unusually high substitution rates resulted in increased support. We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia’s s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing “phantom” spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches.