When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)

Autores
Petersen, Gitte; Aagesen, Lone; Seberg, Ole; Larsen, Ida Hartvig
Año de publicación
2011
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification.
Fil: Petersen, Gitte. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
Fil: Aagesen, Lone. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina
Fil: Seberg, Ole. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
Fil: Larsen, Ida Hartvig. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
Materia
Phylogeny
Hordeum
Direct Optimization
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:11336/68534
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/68534
network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)Petersen, GitteAagesen, LoneSeberg, OleLarsen, Ida HartvigPhylogenyHordeumDirect Optimizationhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification.Fil: Petersen, Gitte. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; DinamarcaFil: Aagesen, Lone. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; ArgentinaFil: Seberg, Ole. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; DinamarcaFil: Larsen, Ida Hartvig. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; DinamarcaWiley Blackwell Publishing, Inc2011-08info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/68534Petersen, Gitte; Aagesen, Lone; Seberg, Ole; Larsen, Ida Hartvig; When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae); Wiley Blackwell Publishing, Inc; Cladistics; 27; 4; 8-2011; 428-4460748-3007CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1111/j.1096-0031.2011.00347.xinfo:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2011.00347.xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:21:01Zoai:ri.conicet.gov.ar:11336/68534instacron: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 10:21:01.626CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
title When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
spellingShingle When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
Petersen, Gitte
Phylogeny
Hordeum
Direct Optimization
title_short When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
title_full When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
title_fullStr When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
title_full_unstemmed When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
title_sort When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
dc.creator.none.fl_str_mv Petersen, Gitte
Aagesen, Lone
Seberg, Ole
Larsen, Ida Hartvig
author Petersen, Gitte
author_facet Petersen, Gitte
Aagesen, Lone
Seberg, Ole
Larsen, Ida Hartvig
author_role author
author2 Aagesen, Lone
Seberg, Ole
Larsen, Ida Hartvig
author2_role author
author
author
dc.subject.none.fl_str_mv Phylogeny
Hordeum
Direct Optimization
topic Phylogeny
Hordeum
Direct Optimization
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification.
Fil: Petersen, Gitte. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
Fil: Aagesen, Lone. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentina
Fil: Seberg, Ole. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
Fil: Larsen, Ida Hartvig. Natural History Museum of Copenhague; Dinamarca. Universidad de Copenhagen; Dinamarca
description Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single-copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re-classification.
publishDate 2011
dc.date.none.fl_str_mv 2011-08
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/11336/68534
Petersen, Gitte; Aagesen, Lone; Seberg, Ole; Larsen, Ida Hartvig; When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae); Wiley Blackwell Publishing, Inc; Cladistics; 27; 4; 8-2011; 428-446
0748-3007
CONICET Digital
CONICET
url http://hdl.handle.net/11336/68534
identifier_str_mv Petersen, Gitte; Aagesen, Lone; Seberg, Ole; Larsen, Ida Hartvig; When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae); Wiley Blackwell Publishing, Inc; Cladistics; 27; 4; 8-2011; 428-446
0748-3007
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/j.1096-0031.2011.00347.x
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1096-0031.2011.00347.x
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
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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score 13.070432

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