Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization
Autor(a) principal: | |
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Data de Publicação: | 2008 |
Outros Autores: | , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Genetics and Molecular Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000500027 |
Resumo: | We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO), named Ant-Based Phylogenetic Reconstruction (ABPR). ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences). The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets. |
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Genetics and Molecular Biology |
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Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimizationphylogenetic estimationdistance algorithmsant colony optimizationWe propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO), named Ant-Based Phylogenetic Reconstruction (ABPR). ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences). The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets.Sociedade Brasileira de Genética2008-12-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000500027Genetics and Molecular Biology v.31 n.4 2008reponame:Genetics and Molecular Biologyinstname:Sociedade Brasileira de Genética (SBG)instacron:SBG10.1590/S1415-47572008000500027info:eu-repo/semantics/openAccessVittori,KarlaDelbem,Alexandre C.B.Pereira,Sérgio L.eng2008-12-18T00:00:00Zoai:scielo:S1415-47572008000500027Revistahttp://www.gmb.org.br/ONGhttps://old.scielo.br/oai/scielo-oai.php||editor@gmb.org.br1678-46851415-4757opendoar:2008-12-18T00:00Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG)false |
dc.title.none.fl_str_mv |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
title |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
spellingShingle |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization Vittori,Karla phylogenetic estimation distance algorithms ant colony optimization |
title_short |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
title_full |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
title_fullStr |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
title_full_unstemmed |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
title_sort |
Ant-Based Phylogenetic Reconstruction (ABPR): A new distance algorithm for phylogenetic estimation based on ant colony optimization |
author |
Vittori,Karla |
author_facet |
Vittori,Karla Delbem,Alexandre C.B. Pereira,Sérgio L. |
author_role |
author |
author2 |
Delbem,Alexandre C.B. Pereira,Sérgio L. |
author2_role |
author author |
dc.contributor.author.fl_str_mv |
Vittori,Karla Delbem,Alexandre C.B. Pereira,Sérgio L. |
dc.subject.por.fl_str_mv |
phylogenetic estimation distance algorithms ant colony optimization |
topic |
phylogenetic estimation distance algorithms ant colony optimization |
description |
We propose a new distance algorithm for phylogenetic estimation based on Ant Colony Optimization (ACO), named Ant-Based Phylogenetic Reconstruction (ABPR). ABPR joins two taxa iteratively based on evolutionary distance among sequences, while also accounting for the quality of the phylogenetic tree built according to the total length of the tree. Similar to optimization algorithms for phylogenetic estimation, the algorithm allows exploration of a larger set of nearly optimal solutions. We applied the algorithm to four empirical data sets of mitochondrial DNA ranging from 12 to 186 sequences, and from 898 to 16,608 base pairs, and covering taxonomic levels from populations to orders. We show that ABPR performs better than the commonly used Neighbor-Joining algorithm, except when sequences are too closely related (e.g., population-level sequences). The phylogenetic relationships recovered at and above species level by ABPR agree with conventional views. However, like other algorithms of phylogenetic estimation, the proposed algorithm failed to recover expected relationships when distances are too similar or when rates of evolution are very variable, leading to the problem of long-branch attraction. ABPR, as well as other ACO-based algorithms, is emerging as a fast and accurate alternative method of phylogenetic estimation for large data sets. |
publishDate |
2008 |
dc.date.none.fl_str_mv |
2008-12-01 |
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=S1415-47572008000500027 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000500027 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/S1415-47572008000500027 |
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 Genética |
publisher.none.fl_str_mv |
Sociedade Brasileira de Genética |
dc.source.none.fl_str_mv |
Genetics and Molecular Biology v.31 n.4 2008 reponame:Genetics and Molecular Biology instname:Sociedade Brasileira de Genética (SBG) instacron:SBG |
instname_str |
Sociedade Brasileira de Genética (SBG) |
instacron_str |
SBG |
institution |
SBG |
reponame_str |
Genetics and Molecular Biology |
collection |
Genetics and Molecular Biology |
repository.name.fl_str_mv |
Genetics and Molecular Biology - Sociedade Brasileira de Genética (SBG) |
repository.mail.fl_str_mv |
||editor@gmb.org.br |
_version_ |
1752122381514571776 |