Título

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

Autor

ITZI FRAGOSO MARTINEZ

GERARDO ADOLFO SALAZAR CHAVEZ

MARTHA JUANA MARTINEZ GORDILLO

Susana Magallón

LUNA LUISA SANCHEZ REYES

Emily Moriarty Lemmon

Alan R. Lemmon

Federico D Sazatornil

CAROLINA GRANADOS MENDOZA

Nivel de Acceso

Acceso Abierto

Identificador alterno

doi: https://doi.org/10.1016/j.ympev.2017.02.006

Resumen o descripción

"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 704 bp. 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."

Editor

Elsevier

Fecha de publicación

2017

Tipo de publicación

Artículo

Versión de la publicación

Versión aceptada

Formato

application/pdf

Sugerencia de citación

Itzi Fragoso-Martínez, Gerardo A. Salazar, Martha Martínez-Gordillo, Susana Magallón, Luna Sánchez-Reyes, Emily Moriarty Lemmon, Alan R. Lemmon, Federico Sazatornil, Carolina Granados Mendoza, A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae), Molecular Phylogenetics and Evolution, Volume 117, 2017, Pages 124-134.

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