Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions
Mitochondrial genomes are becoming more available thanks to recent technological advances in molecular biology. Its popularity as the tool of choice for phylogenetic analyses in a variety of taxa is increasing, and has resulted in improvement of overall results, as compared to traditional use of sin...
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ftunivlosandes:oai:repositorio.uniandes.edu.co:1992/11417 2023-11-12T04:24:12+01:00 Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions Duchene Garzón, Sebastián Caballero Gaitán, Susana 2011 37 hojas application/pdf http://hdl.handle.net/1992/11417 eng eng Uniandes Maestría en Ciencias Biológicas Facultad de Ciencias Departamento de Biología http://hdl.handle.net/1992/11417 u468995.pdf instname:Universidad de los Andes reponame:Repositorio Institucional Séneca repourl:https://repositorio.uniandes.edu.co/ Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores. http://creativecommons.org/licenses/by-nc-sa/4.0/ info:eu-repo/semantics/openAccess http://purl.org/coar/access_right/c_abf2 instname:Universidad de los Andes reponame:Repositorio Institucional Séneca Filogenia - Investigaciones Genomas - Investigaciones Biología Trabajo de grado - Maestría info:eu-repo/semantics/masterThesis info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_bdcc http://purl.org/coar/version/c_ab4af688f83e57aa Text http://purl.org/redcol/resource_type/TM 2011 ftunivlosandes 2023-10-28T17:03:55Z Mitochondrial genomes are becoming more available thanks to recent technological advances in molecular biology. Its popularity as the tool of choice for phylogenetic analyses in a variety of taxa is increasing, and has resulted in improvement of overall results, as compared to traditional use of single mitochondrial markers such as the control region and CYTB. These differences in phylogenetic robustness provide incongruent conclusions among studies based on single mitochondrial markers and complete mitogenomes. Through detailed analysis of phylogenetic estimates from different genes we detected the most informative regions and the minimum amount of data necessary to reproduce mitogenomic-type results. We made use of two recently published complete mitogenome datasets of delphinids (Family Delphinidae) and killer whales (Orcinus orca) to compare phylogenetic estimation among individual genes and the mitogenome. Statistical comparative phylogenetics were employed to address differences in topologies, divergence dates and clock-like behavior among genes for both taxonomic groups. In both cases informative regions were coding genes and corresponded to less than a quarter of the complete mitogenome, yet these were not the same across both taxonomic groups, suggesting gene information content can depend on divergence time and taxonomy of the group studied. Although our results indicate that complete mitogenomes provide the most robust results, a minimum amount of data can be used when the complete sequence is unavailable, and previous studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates closer to those obtained using the entire mitogenome. Magíster en Ciencias Biológicas Maestría Master Thesis Orca Orcinus orca Repositorio institucional Séneca |
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Repositorio institucional Séneca |
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ftunivlosandes |
language |
English |
topic |
Filogenia - Investigaciones Genomas - Investigaciones Biología |
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Filogenia - Investigaciones Genomas - Investigaciones Biología Duchene Garzón, Sebastián Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
topic_facet |
Filogenia - Investigaciones Genomas - Investigaciones Biología |
description |
Mitochondrial genomes are becoming more available thanks to recent technological advances in molecular biology. Its popularity as the tool of choice for phylogenetic analyses in a variety of taxa is increasing, and has resulted in improvement of overall results, as compared to traditional use of single mitochondrial markers such as the control region and CYTB. These differences in phylogenetic robustness provide incongruent conclusions among studies based on single mitochondrial markers and complete mitogenomes. Through detailed analysis of phylogenetic estimates from different genes we detected the most informative regions and the minimum amount of data necessary to reproduce mitogenomic-type results. We made use of two recently published complete mitogenome datasets of delphinids (Family Delphinidae) and killer whales (Orcinus orca) to compare phylogenetic estimation among individual genes and the mitogenome. Statistical comparative phylogenetics were employed to address differences in topologies, divergence dates and clock-like behavior among genes for both taxonomic groups. In both cases informative regions were coding genes and corresponded to less than a quarter of the complete mitogenome, yet these were not the same across both taxonomic groups, suggesting gene information content can depend on divergence time and taxonomy of the group studied. Although our results indicate that complete mitogenomes provide the most robust results, a minimum amount of data can be used when the complete sequence is unavailable, and previous studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates closer to those obtained using the entire mitogenome. Magíster en Ciencias Biológicas Maestría |
author2 |
Caballero Gaitán, Susana |
format |
Master Thesis |
author |
Duchene Garzón, Sebastián |
author_facet |
Duchene Garzón, Sebastián |
author_sort |
Duchene Garzón, Sebastián |
title |
Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
title_short |
Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
title_full |
Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
title_fullStr |
Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
title_full_unstemmed |
Mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
title_sort |
mitogenome phylogenetics: variation in topologies, divergence dates,and mutation rates among analysis partitions |
publisher |
Uniandes |
publishDate |
2011 |
url |
http://hdl.handle.net/1992/11417 |
genre |
Orca Orcinus orca |
genre_facet |
Orca Orcinus orca |
op_source |
instname:Universidad de los Andes reponame:Repositorio Institucional Séneca |
op_relation |
http://hdl.handle.net/1992/11417 u468995.pdf instname:Universidad de los Andes reponame:Repositorio Institucional Séneca repourl:https://repositorio.uniandes.edu.co/ |
op_rights |
Al consultar y hacer uso de este recurso, está aceptando las condiciones de uso establecidas por los autores. http://creativecommons.org/licenses/by-nc-sa/4.0/ info:eu-repo/semantics/openAccess http://purl.org/coar/access_right/c_abf2 |
_version_ |
1782338733071138816 |