Annonaceae substitution rates: a codon model perspective
Autor(a) principal: | |
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Data de Publicação: | 2014 |
Outros Autores: | , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Revista brasileira de fruticultura (Online) |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-29452014000500013 |
Resumo: | The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms. |
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Annonaceae substitution rates: a codon model perspectiveAnnonaceaeBranch lengthsCodon modelsNon-synonymous substitution ratePhylogeneticsSynonymous substitution rateThe Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.Sociedade Brasileira de Fruticultura2014-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-29452014000500013Revista Brasileira de Fruticultura v.36 n.spe1 2014reponame:Revista brasileira de fruticultura (Online)instname:Sociedade Brasileira de Fruticultura (SBF)instacron:SBFRU10.1590/S0100-29452014000500013info:eu-repo/semantics/openAccessChatrou,Lars WillemPirie,Michael DavidVelzen,Robin VanBakker,Freek Theodooreng2014-04-14T00:00:00Zoai:scielo:S0100-29452014000500013Revistahttp://www.scielo.br/rbfhttps://old.scielo.br/oai/scielo-oai.phprbf@fcav.unesp.br||http://rbf.org.br/1806-99670100-2945opendoar:2014-04-14T00:00Revista brasileira de fruticultura (Online) - Sociedade Brasileira de Fruticultura (SBF)false |
dc.title.none.fl_str_mv |
Annonaceae substitution rates: a codon model perspective |
title |
Annonaceae substitution rates: a codon model perspective |
spellingShingle |
Annonaceae substitution rates: a codon model perspective Chatrou,Lars Willem Annonaceae Branch lengths Codon models Non-synonymous substitution rate Phylogenetics Synonymous substitution rate |
title_short |
Annonaceae substitution rates: a codon model perspective |
title_full |
Annonaceae substitution rates: a codon model perspective |
title_fullStr |
Annonaceae substitution rates: a codon model perspective |
title_full_unstemmed |
Annonaceae substitution rates: a codon model perspective |
title_sort |
Annonaceae substitution rates: a codon model perspective |
author |
Chatrou,Lars Willem |
author_facet |
Chatrou,Lars Willem Pirie,Michael David Velzen,Robin Van Bakker,Freek Theodoor |
author_role |
author |
author2 |
Pirie,Michael David Velzen,Robin Van Bakker,Freek Theodoor |
author2_role |
author author author |
dc.contributor.author.fl_str_mv |
Chatrou,Lars Willem Pirie,Michael David Velzen,Robin Van Bakker,Freek Theodoor |
dc.subject.por.fl_str_mv |
Annonaceae Branch lengths Codon models Non-synonymous substitution rate Phylogenetics Synonymous substitution rate |
topic |
Annonaceae Branch lengths Codon models Non-synonymous substitution rate Phylogenetics Synonymous substitution rate |
description |
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms. |
publishDate |
2014 |
dc.date.none.fl_str_mv |
2014-01-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-29452014000500013 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S0100-29452014000500013 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/S0100-29452014000500013 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Sociedade Brasileira de Fruticultura |
publisher.none.fl_str_mv |
Sociedade Brasileira de Fruticultura |
dc.source.none.fl_str_mv |
Revista Brasileira de Fruticultura v.36 n.spe1 2014 reponame:Revista brasileira de fruticultura (Online) instname:Sociedade Brasileira de Fruticultura (SBF) instacron:SBFRU |
instname_str |
Sociedade Brasileira de Fruticultura (SBF) |
instacron_str |
SBFRU |
institution |
SBFRU |
reponame_str |
Revista brasileira de fruticultura (Online) |
collection |
Revista brasileira de fruticultura (Online) |
repository.name.fl_str_mv |
Revista brasileira de fruticultura (Online) - Sociedade Brasileira de Fruticultura (SBF) |
repository.mail.fl_str_mv |
rbf@fcav.unesp.br||http://rbf.org.br/ |
_version_ |
1752122492903751680 |