title: A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).
abstract: 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.
authors.affiliation: Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, 04510, Coyoacán, Mexico City, Mexico; Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Mexico City, Mexico. Electronic address: i.fragoso@ciencias.unam.mx.
authors.forename: Itzi
authors.initials: I
authors.lastname: Fragoso-Martínez
authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Mexico City, Mexico. Electronic address: gasc@ib.unam.mx.
authors.forename: Gerardo A
authors.initials: GA
authors.lastname: Salazar
authors.affiliation: Herbario de la Facultad de Ciencias (FCME), Universidad Nacional Autónoma de México, Apartado Postal 70-399, 04510 Coyoacán, Mexico City, Mexico. Electronic address: mjmg_unam@yahoo.com.
authors.forename: Martha
authors.initials: M
authors.lastname: Martínez-Gordillo
authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Mexico City, Mexico. Electronic address: s.magallon@ib.unam.mx.
authors.forename: Susana
authors.initials: S
authors.lastname: Magallón
authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Mexico City, Mexico. Electronic address: sanchez.reyes.luna@gmail.com.
authors.forename: Luna
authors.initials: L
authors.lastname: Sánchez-Reyes
authors.affiliation: Department of Biological Science, Florida State University, 319 Stadium Drive, P.O. Box 3064295, Tallahassee, FL 32306-4295, USA. Electronic address: chorusfrog@bio.fsu.edu.
authors.forename: Emily
authors.initials: E
authors.lastname: Moriarty Lemmon
authors.affiliation: Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL 32306-4102, USA. Electronic address: alemmon@fsu.edu.
authors.forename: Alan R
authors.initials: AR
authors.lastname: Lemmon
authors.affiliation: Laboratorio de Ecología Evolutiva - Biología Floral, Instituto Multidisciplinario de Biología Vegetal (IMBIV), Universidad Nacional de Córdoba, CONICET, CC 495, X5000ZAA Córdoba, Argentina. Electronic address: federicosaza@gmail.com.
authors.forename: Federico
authors.initials: F
authors.lastname: Sazatornil
authors.affiliation: Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 70-367, 04510 Coyoacán, Mexico City, Mexico; CONACYT División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica A.C., Camino a la Presa de San José 2055, Lomas 4a. sección, C.P. 78216 San Luis Potosí, San Luis Potosí, Mexico. Electronic address: carolina.granados@ipicyt.edu.mx.
authors.forename: Carolina
authors.initials: C
authors.lastname: Granados Mendoza
mesh_terms: D056426:Genetic Loci / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D010802:Phylogeny; D010865:Pilot Projects; D027544:Salvia / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers
keywords: Anchored phylogenomics; Lamiales; Maximum likelihood; Phylogenetic noise; Target enrichment