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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/46588
Ver los metadatos del registro completo
id |
CONICETDig_2d0d589be13c4ddc912a3495ab0baddd |
---|---|
oai_identifier_str |
oai:ri.conicet.gov.ar:11336/46588 |
network_acronym_str |
CONICETDig |
repository_id_str |
3498 |
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 |
_version_ |
1844613442151907328 |
score |
13.070432 |