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dc.contributor.author
Fragoso Martínez, Itzi
dc.contributor.author
Salazar, Gerardo A.
dc.contributor.author
Martínez Gordillo, Martha
dc.contributor.author
Magallón, Susana
dc.contributor.author
Sánchez-Reyes, Luna
dc.contributor.author
Moriarty Lemmon, Emily
dc.contributor.author
Lemmon, Alan R.
dc.contributor.author
Sazatornil, Federico David
dc.contributor.author
Granados Mendoza, Carolina
dc.date.available
2017-07-19T15:43:58Z
dc.date.issued
2017-02-09
dc.identifier.citation
Fragoso Martínez, Itzi; Salazar, Gerardo A.; Martínez Gordillo, Martha; Magallón, Susana; Sánchez-Reyes, Luna; et al.; A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae); Academic Press Inc Elsevier Science; Molecular Phylogenetics and Evolution; 9-2-2017; 1-39
dc.identifier.issn
1055-7903
dc.identifier.uri
http://hdl.handle.net/11336/20926
dc.description.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 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.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Academic Press Inc Elsevier Science
dc.rights
info:eu-repo/semantics/embargoedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
Anchored Phylogenomics
dc.subject
Lamiales
dc.subject
Maximum Likelihood
dc.subject
Phylogenetic Noise
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Target Enrichment
dc.subject.classification
Ciencias de las Plantas, Botánica
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Ciencias Biológicas
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CIENCIAS NATURALES Y EXACTAS
dc.title
A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2017-07-13T18:26:37Z
dc.identifier.eissn
1095-9513
dc.journal.pagination
1-39
dc.journal.pais
Estados Unidos
dc.description.fil
Fil: Fragoso Martínez, Itzi. Universidad Nacional Autónoma de México; México. Institute Of Biology Of Unam;
dc.description.fil
Fil: Salazar, Gerardo A.. Universidad Nacional Autónoma de México; México
dc.description.fil
Fil: Martínez Gordillo, Martha. Universidad Nacional Autónoma de México; México
dc.description.fil
Fil: Magallón, Susana. Universidad Nacional Autónoma de México; México
dc.description.fil
Fil: Sánchez-Reyes, Luna. Universidad Nacional Autónoma de México; México
dc.description.fil
Fil: Moriarty Lemmon, Emily. Florida State University; Estados Unidos
dc.description.fil
Fil: Lemmon, Alan R.. Florida State University; Estados Unidos
dc.description.fil
Fil: Sazatornil, Federico David. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto Multidisciplinario de Biología Vegetal. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas Físicas y Naturales. Instituto Multidisciplinario de Biología Vegetal; Argentina
dc.description.fil
Fil: Granados Mendoza, Carolina. Instituto Potosino de Investigación Científica y Tecnológica; México. Universidad Nacional Autónoma de México; México
dc.journal.title
Molecular Phylogenetics and Evolution
dc.rights.embargoDate
2018-03-01
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/http://dx.doi.org/10.1016/j.ympev.2017.02.006
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1055790316303256
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