Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds

Autores
Lavinia Oblanca, Pablo Damián; Kerr, Kevin C. R.; Tubaro, Pablo Luis; Hebert, Paul David Neil; Lijtmaer, Dario Alejandro
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Estimating the age of species or their component lineages based on sequence data is crucial for many studies in avian evolutionary biology. Although calibrations of the molecular clock in birds have been performed almost exclusively using cytochrome b (cyt b), they are commonly extrapolated to other mitochondrial genes. The existence of a large, standardized cytochrome c oxidase subunit I (COI) library generated as a result of the DNA barcoding initiative provides the opportunity to obtain a calibration for this mitochondrial gene in birds. In this study we compare the evolutionary rate of COI relative to cyt b across ten different avian orders. We obtained divergence estimates for both genes from nearly 300 phylogenetically independent pairs of species through the analysis of almost 5000 public sequences. For each pair of species we calculated the difference in divergence between COI and cyt b. Our results indicate that COI evolves on average 14% slower than cyt b, but also reveal considerable variation both among and within avian orders, precluding the use of this value as a standard adjustment for the COI molecular clock for birds. Our findings suggest that this variation is partially explained by a clear negative relationship between the difference in divergence in these genes and the age of species. Distances for cyt b are higher than those for COI for closely related species, but the values become similar as the divergence between the species increases. This appears to be the result of a stronger pattern of negative time‐dependency in the rate of cyt b than in that of COI, a difference that could be related to lower functional constraints on a small number of sites in cyt b that allow it to initially accumulate mutations more rapidly than COI.
Fil: Lavinia Oblanca, Pablo Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Kerr, Kevin C. R.. Toronto Zoo; Canadá
Fil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Hebert, Paul David Neil. University of Guelph; Canadá
Fil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Materia
Molecular Clock
Coi
Cyt B
Birds
Nivel de accesibilidad
acceso abierto
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:11336/46588

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network_name_str CONICET Digital (CONICET)
spelling Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birdsLavinia Oblanca, Pablo DamiánKerr, Kevin C. R.Tubaro, Pablo LuisHebert, Paul David NeilLijtmaer, Dario AlejandroMolecular ClockCoiCyt BBirdshttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Estimating the age of species or their component lineages based on sequence data is crucial for many studies in avian evolutionary biology. Although calibrations of the molecular clock in birds have been performed almost exclusively using cytochrome b (cyt b), they are commonly extrapolated to other mitochondrial genes. The existence of a large, standardized cytochrome c oxidase subunit I (COI) library generated as a result of the DNA barcoding initiative provides the opportunity to obtain a calibration for this mitochondrial gene in birds. In this study we compare the evolutionary rate of COI relative to cyt b across ten different avian orders. We obtained divergence estimates for both genes from nearly 300 phylogenetically independent pairs of species through the analysis of almost 5000 public sequences. For each pair of species we calculated the difference in divergence between COI and cyt b. Our results indicate that COI evolves on average 14% slower than cyt b, but also reveal considerable variation both among and within avian orders, precluding the use of this value as a standard adjustment for the COI molecular clock for birds. Our findings suggest that this variation is partially explained by a clear negative relationship between the difference in divergence in these genes and the age of species. Distances for cyt b are higher than those for COI for closely related species, but the values become similar as the divergence between the species increases. This appears to be the result of a stronger pattern of negative time‐dependency in the rate of cyt b than in that of COI, a difference that could be related to lower functional constraints on a small number of sites in cyt b that allow it to initially accumulate mutations more rapidly than COI.Fil: Lavinia Oblanca, Pablo Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Kerr, Kevin C. R.. Toronto Zoo; CanadáFil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaFil: Hebert, Paul David Neil. University of Guelph; CanadáFil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; ArgentinaWiley Blackwell Publishing, Inc2016-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/46588Lavinia Oblanca, Pablo Damián; Kerr, Kevin C. R.; Tubaro, Pablo Luis; Hebert, Paul David Neil; Lijtmaer, Dario Alejandro; Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds; Wiley Blackwell Publishing, Inc; Journal Of Avian Biology; 47; 1; 1-2016; 84-910908-8857CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/jav.00766info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/jav.00766info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:46:09Zoai:ri.conicet.gov.ar:11336/46588instacron: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 09:46:10.2CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
title Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
spellingShingle Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
Lavinia Oblanca, Pablo Damián
Molecular Clock
Coi
Cyt B
Birds
title_short Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
title_full Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
title_fullStr Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
title_full_unstemmed Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
title_sort Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds
dc.creator.none.fl_str_mv Lavinia Oblanca, Pablo Damián
Kerr, Kevin C. R.
Tubaro, Pablo Luis
Hebert, Paul David Neil
Lijtmaer, Dario Alejandro
author Lavinia Oblanca, Pablo Damián
author_facet Lavinia Oblanca, Pablo Damián
Kerr, Kevin C. R.
Tubaro, Pablo Luis
Hebert, Paul David Neil
Lijtmaer, Dario Alejandro
author_role author
author2 Kerr, Kevin C. R.
Tubaro, Pablo Luis
Hebert, Paul David Neil
Lijtmaer, Dario Alejandro
author2_role author
author
author
author
dc.subject.none.fl_str_mv Molecular Clock
Coi
Cyt B
Birds
topic Molecular Clock
Coi
Cyt B
Birds
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Estimating the age of species or their component lineages based on sequence data is crucial for many studies in avian evolutionary biology. Although calibrations of the molecular clock in birds have been performed almost exclusively using cytochrome b (cyt b), they are commonly extrapolated to other mitochondrial genes. The existence of a large, standardized cytochrome c oxidase subunit I (COI) library generated as a result of the DNA barcoding initiative provides the opportunity to obtain a calibration for this mitochondrial gene in birds. In this study we compare the evolutionary rate of COI relative to cyt b across ten different avian orders. We obtained divergence estimates for both genes from nearly 300 phylogenetically independent pairs of species through the analysis of almost 5000 public sequences. For each pair of species we calculated the difference in divergence between COI and cyt b. Our results indicate that COI evolves on average 14% slower than cyt b, but also reveal considerable variation both among and within avian orders, precluding the use of this value as a standard adjustment for the COI molecular clock for birds. Our findings suggest that this variation is partially explained by a clear negative relationship between the difference in divergence in these genes and the age of species. Distances for cyt b are higher than those for COI for closely related species, but the values become similar as the divergence between the species increases. This appears to be the result of a stronger pattern of negative time‐dependency in the rate of cyt b than in that of COI, a difference that could be related to lower functional constraints on a small number of sites in cyt b that allow it to initially accumulate mutations more rapidly than COI.
Fil: Lavinia Oblanca, Pablo Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Kerr, Kevin C. R.. Toronto Zoo; Canadá
Fil: Tubaro, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
Fil: Hebert, Paul David Neil. University of Guelph; Canadá
Fil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina
description Estimating the age of species or their component lineages based on sequence data is crucial for many studies in avian evolutionary biology. Although calibrations of the molecular clock in birds have been performed almost exclusively using cytochrome b (cyt b), they are commonly extrapolated to other mitochondrial genes. The existence of a large, standardized cytochrome c oxidase subunit I (COI) library generated as a result of the DNA barcoding initiative provides the opportunity to obtain a calibration for this mitochondrial gene in birds. In this study we compare the evolutionary rate of COI relative to cyt b across ten different avian orders. We obtained divergence estimates for both genes from nearly 300 phylogenetically independent pairs of species through the analysis of almost 5000 public sequences. For each pair of species we calculated the difference in divergence between COI and cyt b. Our results indicate that COI evolves on average 14% slower than cyt b, but also reveal considerable variation both among and within avian orders, precluding the use of this value as a standard adjustment for the COI molecular clock for birds. Our findings suggest that this variation is partially explained by a clear negative relationship between the difference in divergence in these genes and the age of species. Distances for cyt b are higher than those for COI for closely related species, but the values become similar as the divergence between the species increases. This appears to be the result of a stronger pattern of negative time‐dependency in the rate of cyt b than in that of COI, a difference that could be related to lower functional constraints on a small number of sites in cyt b that allow it to initially accumulate mutations more rapidly than COI.
publishDate 2016
dc.date.none.fl_str_mv 2016-01
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/11336/46588
Lavinia Oblanca, Pablo Damián; Kerr, Kevin C. R.; Tubaro, Pablo Luis; Hebert, Paul David Neil; Lijtmaer, Dario Alejandro; Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds; Wiley Blackwell Publishing, Inc; Journal Of Avian Biology; 47; 1; 1-2016; 84-91
0908-8857
CONICET Digital
CONICET
url http://hdl.handle.net/11336/46588
identifier_str_mv Lavinia Oblanca, Pablo Damián; Kerr, Kevin C. R.; Tubaro, Pablo Luis; Hebert, Paul David Neil; Lijtmaer, Dario Alejandro; Calibrating the molecular clock beyond cytochrome b : assessing the evolutionary rate of COI in birds; Wiley Blackwell Publishing, Inc; Journal Of Avian Biology; 47; 1; 1-2016; 84-91
0908-8857
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1111/jav.00766
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/jav.00766
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
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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