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An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo

Bootstrapping is a de-facto standard for displaying the validity of a phylogenetic tree. However this may not be the case as bootstrapping assume that the random sequence exist within the genome. In order to examine whether bootstrapping is a valid process, it must be done empirically. Across multi...

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Main Author: So, Wei Huo
Format: Thesis
Published: 2012
Subjects:
QH301 Biology
Online Access:http://studentsrepo.um.edu.my/3716/4/1._Title_page%2C_abstract%2C_content.pdf
http://studentsrepo.um.edu.my/3716/5/2._Chap_1_%E2%80%93_6.pdf
http://studentsrepo.um.edu.my/3716/6/3._Appendices.pdf
http://studentsrepo.um.edu.my/3716/7/4._References.pdf
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spelling my.um.stud.37162013-09-10T04:35:38Z An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo So, Wei Huo QH301 Biology Bootstrapping is a de-facto standard for displaying the validity of a phylogenetic tree. However this may not be the case as bootstrapping assume that the random sequence exist within the genome. In order to examine whether bootstrapping is a valid process, it must be done empirically. Across multiple taxa there are minimal fully curated genomes but there are mitochondrion genomes available to test this. A widely accepted evolutionary tree is chosen with 6 taxa - Pan paniscus (bonobo), Homo sapiens (human), Gorilla gorilla (gorilla), Pongo pygmaeus (orangutan), Hylobates lar (common gibbon) and Gallus gallus (red junglefowl) as the outgroup. A comparison of topology and bootstrap support value is executed between the phylogenetic tree of the whole mitochondrial genome with trees built from all the genes in mitochondrial genome. The result shows that bootstrap support value tend to inflate and larger than the empirical estimate. This suggests that bootstrap support in phylogenetic trees must be interpreted cautiously and not casually accepted at face value. 2012 Thesis NonPeerReviewed application/pdf http://studentsrepo.um.edu.my/3716/4/1._Title_page%2C_abstract%2C_content.pdf application/pdf http://studentsrepo.um.edu.my/3716/5/2._Chap_1_%E2%80%93_6.pdf application/pdf http://studentsrepo.um.edu.my/3716/6/3._Appendices.pdf application/pdf http://studentsrepo.um.edu.my/3716/7/4._References.pdf http://pendeta.um.edu.my/client/default/search/results?qu=An+empirical+assessment+of+the+bootstrap+support+as+an+indicator+of+robustness+in+phylogenetic+trees&te= So, Wei Huo (2012) An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo. Masters thesis, University of Malaya. http://studentsrepo.um.edu.my/3716/
institution Universiti Malaya
building UM Library
collection Institutional Repository
continent Asia
country Malaysia
content_provider Universiti Malaya
content_source UM Student Repository
url_provider http://studentsrepo.um.edu.my/
topic QH301 Biology
spellingShingle QH301 Biology
So, Wei Huo
An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
description Bootstrapping is a de-facto standard for displaying the validity of a phylogenetic tree. However this may not be the case as bootstrapping assume that the random sequence exist within the genome. In order to examine whether bootstrapping is a valid process, it must be done empirically. Across multiple taxa there are minimal fully curated genomes but there are mitochondrion genomes available to test this. A widely accepted evolutionary tree is chosen with 6 taxa - Pan paniscus (bonobo), Homo sapiens (human), Gorilla gorilla (gorilla), Pongo pygmaeus (orangutan), Hylobates lar (common gibbon) and Gallus gallus (red junglefowl) as the outgroup. A comparison of topology and bootstrap support value is executed between the phylogenetic tree of the whole mitochondrial genome with trees built from all the genes in mitochondrial genome. The result shows that bootstrap support value tend to inflate and larger than the empirical estimate. This suggests that bootstrap support in phylogenetic trees must be interpreted cautiously and not casually accepted at face value.
format Thesis
author So, Wei Huo
author_facet So, Wei Huo
author_sort So, Wei Huo
title An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
title_short An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
title_full An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
title_fullStr An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
title_full_unstemmed An empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / So Wei Huo
title_sort empirical assessment of the bootstrap support as an indicator of robustness in phylogenetic trees / so wei huo
publishDate 2012
url http://studentsrepo.um.edu.my/3716/4/1._Title_page%2C_abstract%2C_content.pdf
http://studentsrepo.um.edu.my/3716/5/2._Chap_1_%E2%80%93_6.pdf
http://studentsrepo.um.edu.my/3716/6/3._Appendices.pdf
http://studentsrepo.um.edu.my/3716/7/4._References.pdf
http://pendeta.um.edu.my/client/default/search/results?qu=An+empirical+assessment+of+the+bootstrap+support+as+an+indicator+of+robustness+in+phylogenetic+trees&te=
http://studentsrepo.um.edu.my/3716/
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score 13.211869

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