Abstract Detail

Phylogenomics

Fragoso-Martínez, Itzi [1], Salazar, Gerardo A. [2], Martí­nez-Gordillo, Martha [3], Magallón, Susana [4], Lemmon, Alan R. [5], Moriarty Lemmon, Emily [5], Moreno-Letelier, Alejandra [6], Granados Mendoza, Carolina [7].

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

Calosphace is the only monophyletic subgenus in Salvia, and it constitutes the most diverse lineage of the genus with ca. 600 species, all of them endemic to the New World. Four diversity centres have been postulated for subgenus Calosphace: Mexico, the Andean Region, Eastern Brazil and the Antilles. The phylogenetic relationships within Calosphace have been assessed based on combinations of three DNA-sequence molecular markers (nuclear ITS, plastid trnL-trnF and trnH-psbA), allowing the discovery of a number of major clades, including a strongly supported group that comprises most of the sampled species of the subgenus (“core” Calosphace). However, the backbone and several internal relationships still lack resolution and support. The Anchored Hybrid Enrichment (AHE) method is a novel strategy originally designed for vertebrates, but has recently been adapted for plants. It uses probes to capture up to 500 low-copy nuclear genes that can be potentially informative at a range of phylogenetic levels. In this study we used a representative set of species belonging to several clades of subgenus Calosphace to test: 1) the effectiveness of gene capture and massive sequencing for this group; 2) the performance of the recovered genes in resolving and supporting internal relationships in the group; and 3) the potential phylogenetic utility of individual loci by means of the phylogenetic informativeness method. We sampled 12 species of subgenus Calosphace and one species of the genus Lepechinia as outgroup. Gene capture yielded 370 loci for most of the species. The maximum likelihood tree resulting from the analysis of the 370 concatenated loci exhibits greater resolution and support as compared with the topology obtained by the combined analysis of ITS, trnL-trnF and trnH-psbA. The phylogenetic informativeness profiles allowed us to detect 133 loci (35.9% of the loci) containing sites with unusually high substitution rates, which might introduce phylogenetic noise (e.g., because of substitution saturation). Exclusion of these problematic sites resulted in an increase of support for many clades compared to the analysis of the complete dataset. This study indicates that AHE is promising for phylogenetic reconstruction in Neotropical sages, as it greatly improves support and resolution of the phylogenetic tree compared to conventional markers. Additionally, it highlights the importance of including a filtering step for potential “outlier” positions before the final AHE data analysis is conducted.

Related Links:
Center for Anchored Phylogenomics

1 - National Autonomous University of Mexico, Botany department, Circuito Exterior s/n, Ciudad Universitaria, Copilco, CoyoacÁn A.P. 70-367, Mexico City, Mexico City, 04510, Mexico
2 - INSTITUTO DE BIOLOGIA, UNAM, INSTITUTO DE BIOLOGIA, UNAM, APARTADO POSTAL 70-367, MEXICO, D.F., N/A, 04510, Mexico
3 - National Autonomous University of Mexico, Herbario de la Facultad de Ciencias (FCME), Circuito Exterior s/n, Ciudad Universitaria, Copilco, CoyoacÁn A.P. 70-367, Mexico City, Mexico City, 04510, Mexico
4 - Instituto De Biologia, Universidad Nacional Autonoma De Mexico, 3er Circuito De Ciudad Universitaria, Del. Coyoacan, A.P. 70-233, Mexico City, Mexico D.F., N/A, 04510, Mexico
5 - Florida State University, Department of Biological Science, 319 Stadium Drive, Tallahassee, FL, FL 32306-4295, USA
6 - National Autonomous University of Mexico, Jardí­n Botánico, Circuito Exterior s/n, Ciudad Universitaria, Copilco, CoyoacÁn A.P. 70-367, Mexico City, Mexico City, 04510, Mexico
7 - Instituto de Biologí­a, National Autonomous University of Mexic, Botany department, Circuito Exterior s/n, Ciudad Universitaria, Copilco, CoyoacÁn A.P. 70-367, Mexico City, Mexico City, 04510, Mexico

Keywords:
anchored phylogenomics
Lamiales
Lamiaceae
Salvia
Calosphace.

Presentation Type: Oral Paper
Session: 1, Phylogenomics I
Location: 101/Savannah International Trade and Convention Center
Date: Monday, August 1st, 2016
Time: 10:30 AM
Number: 1010
Abstract ID:410
Candidate for Awards:None