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

Autores
Fragoso Martínez, Itzi; Salazar, Gerardo A.; Martínez Gordillo, Martha; Magallón, Susana; Sánchez-Reyes, Luna; Moriarty Lemmon, Emily; Lemmon, Alan R.; Sazatornil, Federico David; Granados Mendoza, Carolina
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
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.
Fil: Fragoso Martínez, Itzi. Universidad Nacional Autónoma de México; México. Institute Of Biology Of Unam;
Fil: Salazar, Gerardo A.. Universidad Nacional Autónoma de México; México
Fil: Martínez Gordillo, Martha. Universidad Nacional Autónoma de México; México
Fil: Magallón, Susana. Universidad Nacional Autónoma de México; México
Fil: Sánchez-Reyes, Luna. Universidad Nacional Autónoma de México; México
Fil: Moriarty Lemmon, Emily. Florida State University; Estados Unidos
Fil: Lemmon, Alan R.. Florida State University; Estados Unidos
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
Fil: Granados Mendoza, Carolina. Instituto Potosino de Investigación Científica y Tecnológica; México. Universidad Nacional Autónoma de México; México
Materia
ANCHORED PHYLOGENOMICS
LAMIALES
MAXIMUM LIKELIHOOD
PHYLOGENETIC NOISE
TARGET ENRICHMENT
Nivel de accesibilidad
acceso embargado
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/20926
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/20926
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)Fragoso Martínez, ItziSalazar, Gerardo A.Martínez Gordillo, MarthaMagallón, SusanaSánchez-Reyes, LunaMoriarty Lemmon, EmilyLemmon, Alan R.Sazatornil, Federico DavidGranados Mendoza, CarolinaANCHORED PHYLOGENOMICSLAMIALESMAXIMUM LIKELIHOODPHYLOGENETIC NOISETARGET ENRICHMENThttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1We 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.Fil: Fragoso Martínez, Itzi. Universidad Nacional Autónoma de México; México. Institute Of Biology Of Unam;Fil: Salazar, Gerardo A.. Universidad Nacional Autónoma de México; MéxicoFil: Martínez Gordillo, Martha. Universidad Nacional Autónoma de México; MéxicoFil: Magallón, Susana. Universidad Nacional Autónoma de México; MéxicoFil: Sánchez-Reyes, Luna. Universidad Nacional Autónoma de México; MéxicoFil: Moriarty Lemmon, Emily. Florida State University; Estados UnidosFil: Lemmon, Alan R.. Florida State University; Estados UnidosFil: 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; ArgentinaFil: Granados Mendoza, Carolina. Instituto Potosino de Investigación Científica y Tecnológica; México. Universidad Nacional Autónoma de México; MéxicoAcademic Press Inc Elsevier Science2017-02-09info:eu-repo/date/embargoEnd/2018-03-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/20926Fragoso 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; 1-391055-79031095-9513CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.ympev.2017.02.006info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1055790316303256info:eu-repo/semantics/embargoedAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:56:42Zoai:ri.conicet.gov.ar:11336/20926instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:56:42.51CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
title A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
spellingShingle A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
Fragoso Martínez, Itzi
ANCHORED PHYLOGENOMICS
LAMIALES
MAXIMUM LIKELIHOOD
PHYLOGENETIC NOISE
TARGET ENRICHMENT
title_short A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
title_full A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
title_fullStr A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
title_full_unstemmed A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
title_sort A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae)
dc.creator.none.fl_str_mv Fragoso Martínez, Itzi
Salazar, Gerardo A.
Martínez Gordillo, Martha
Magallón, Susana
Sánchez-Reyes, Luna
Moriarty Lemmon, Emily
Lemmon, Alan R.
Sazatornil, Federico David
Granados Mendoza, Carolina
author Fragoso Martínez, Itzi
author_facet Fragoso Martínez, Itzi
Salazar, Gerardo A.
Martínez Gordillo, Martha
Magallón, Susana
Sánchez-Reyes, Luna
Moriarty Lemmon, Emily
Lemmon, Alan R.
Sazatornil, Federico David
Granados Mendoza, Carolina
author_role author
author2 Salazar, Gerardo A.
Martínez Gordillo, Martha
Magallón, Susana
Sánchez-Reyes, Luna
Moriarty Lemmon, Emily
Lemmon, Alan R.
Sazatornil, Federico David
Granados Mendoza, Carolina
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv ANCHORED PHYLOGENOMICS
LAMIALES
MAXIMUM LIKELIHOOD
PHYLOGENETIC NOISE
TARGET ENRICHMENT
topic ANCHORED PHYLOGENOMICS
LAMIALES
MAXIMUM LIKELIHOOD
PHYLOGENETIC NOISE
TARGET ENRICHMENT
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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.
Fil: Fragoso Martínez, Itzi. Universidad Nacional Autónoma de México; México. Institute Of Biology Of Unam;
Fil: Salazar, Gerardo A.. Universidad Nacional Autónoma de México; México
Fil: Martínez Gordillo, Martha. Universidad Nacional Autónoma de México; México
Fil: Magallón, Susana. Universidad Nacional Autónoma de México; México
Fil: Sánchez-Reyes, Luna. Universidad Nacional Autónoma de México; México
Fil: Moriarty Lemmon, Emily. Florida State University; Estados Unidos
Fil: Lemmon, Alan R.. Florida State University; Estados Unidos
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
Fil: Granados Mendoza, Carolina. Instituto Potosino de Investigación Científica y Tecnológica; México. Universidad Nacional Autónoma de México; México
description 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.
publishDate 2017
dc.date.none.fl_str_mv 2017-02-09
info:eu-repo/date/embargoEnd/2018-03-01
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/20926
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
1055-7903
1095-9513
CONICET Digital
CONICET
url http://hdl.handle.net/11336/20926
identifier_str_mv 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
1055-7903
1095-9513
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.ympev.2017.02.006
info:eu-repo/semantics/altIdentifier/url/http://www.sciencedirect.com/science/article/pii/S1055790316303256
dc.rights.none.fl_str_mv info:eu-repo/semantics/embargoedAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv embargoedAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Academic Press Inc Elsevier Science
publisher.none.fl_str_mv Academic Press Inc Elsevier Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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