schliessen

Filtern

 

Bibliotheken

Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?

This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from a... Full description

Journal Title: Systematic Biology 2011-12-01, Vol.60 (6), p.782-796
Main Author: Cho, Soowon
Other Authors: Zwick, Andreas , Regier, Jerome C , Mitter, Charles , Cummings, Michael P , Yao, Jianxiu , Du, Zaile , Zhao, Hong , Kawahara, Akito Y , Weller, Susan , Davis, Donald R , Baixeras, Joaquin , Brown, John W , Parr, Cynthia
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/21840842
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_smithsonian_dspace_oai_repository_si_edu_10088_21486
title: Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
format: Article
creator:
  • Cho, Soowon
  • Zwick, Andreas
  • Regier, Jerome C
  • Mitter, Charles
  • Cummings, Michael P
  • Yao, Jianxiu
  • Du, Zaile
  • Zhao, Hong
  • Kawahara, Akito Y
  • Weller, Susan
  • Davis, Donald R
  • Baixeras, Joaquin
  • Brown, John W
  • Parr, Cynthia
subjects:
  • Animals
  • Biological taxonomies
  • Butterflies & moths
  • Classification - methods
  • Datasets
  • Ditrysia
  • gene sampling
  • Genes
  • Genes, Insect - genetics
  • Genetic Heterogeneity
  • Hexapoda
  • Lepidoptera
  • Lepidoptera - classification
  • Lepidoptera - genetics
  • Missing data
  • molecular phylogenetics
  • Molecular structure
  • Moths
  • nuclear genes
  • Nucleotides
  • Nucleotides - genetics
  • Phylogenetics
  • Phylogeny
  • Regular
  • Regular Articles
  • Statistics as Topic
  • Systematic biology
  • Taxa
  • taxon sampling
ispartof: Systematic Biology, 2011-12-01, Vol.60 (6), p.782-796
description: This paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia (> 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa × 26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
language: eng
source: Alma/SFX Local Collection
identifier: ISSN: 1063-5157
fulltext: fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


@attributes
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
RANK2.570762
LOCALfalse
PrimoNMBib
record
control
sourceidjstor_smith
recordidTN_cdi_smithsonian_dspace_oai_repository_si_edu_10088_21486
sourceformatXML
sourcesystemPC
jstor_id41316578
oup_id10.1093/sysbio/syr079
sourcerecordid41316578
originalsourceidFETCH-LOGICAL-1594t-2f9e3897c88b5d24f6af2bd3cb0eb899ecd279e0495f380bb0306f5c093558a3
addsrcrecordideNqFkk9v0zAYxiMEYmNw5AiyuDAOATvOH3tIoFHGWqkIJHbgZjnxm9ZVYgfbqejH4BvjKqVikxAn2_LvefT68ZMkTwl-TTCnb_zO19rGxeGK30tOCa7KlNHy-_39vqRpQYrqJHnk_QZjQsqCPExOMsJyzPLsNPk1kwZ9hE7X4GSAbocWprH90EEAdA0G0De5P6HLcdWDCTJoa9CiH5zdApLo63rX2RWYHbryQffRArXWobCOCrWVpgGFPtuw9kgahT6MIYBrOw0enc_hpxyskhdoCYNWdohX8tX7x8mDVnYenhzWs-Tm09XNbJ4uv1wvZpfLlBQ8D2nWcqCMVw1jdaGyvC1lm9WKNjWGmnEOjcoqDjjnRUsZrmtMcdkWTcysKJikZ8nbydb3Oo5njZZGKD_IBoSVWjgYrNfBup3wWoAaBcGYMZGRnJVR_W5SD2Pdg2piMk52YnAxgqjYG9y-MXotVnYrKOG0KqtoMJ8M7ABGage3tMpAEFaJrKyE5Dklssw4y-pc5Urm8eUM46Jq2gpKGq1eHmZx9scIPohe-wa6ThqwoxeMM0ZZDC2SL-6QGzs6E1MWHGf7SmRFhNIJapz13kF7nIxgsa-cmConpspF_vnfURzpPx2LAL1j2OipRzEZ3f3T9vwQ0Dj8d4JnE7rx8b-OcE5orHvF6G9zVwEb
sourcetypeOpen Access Repository
isCDItrue
recordtypearticle
pqid902840825
display
typearticle
titleCan Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
sourceAlma/SFX Local Collection
creatorCho, Soowon ; Zwick, Andreas ; Regier, Jerome C ; Mitter, Charles ; Cummings, Michael P ; Yao, Jianxiu ; Du, Zaile ; Zhao, Hong ; Kawahara, Akito Y ; Weller, Susan ; Davis, Donald R ; Baixeras, Joaquin ; Brown, John W ; Parr, Cynthia
creatorcontribCho, Soowon ; Zwick, Andreas ; Regier, Jerome C ; Mitter, Charles ; Cummings, Michael P ; Yao, Jianxiu ; Du, Zaile ; Zhao, Hong ; Kawahara, Akito Y ; Weller, Susan ; Davis, Donald R ; Baixeras, Joaquin ; Brown, John W ; Parr, Cynthia
descriptionThis paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia (> 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa × 26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
identifier
0ISSN: 1063-5157
1EISSN: 1076-836X
2DOI: 10.1093/sysbio/syr079
3PMID: 21840842
languageeng
publisherEngland: Oxford University Press
subjectAnimals ; Biological taxonomies ; Butterflies & moths ; Classification - methods ; Datasets ; Ditrysia ; gene sampling ; Genes ; Genes, Insect - genetics ; Genetic Heterogeneity ; Hexapoda ; Lepidoptera ; Lepidoptera - classification ; Lepidoptera - genetics ; Missing data ; molecular phylogenetics ; Molecular structure ; Moths ; nuclear genes ; Nucleotides ; Nucleotides - genetics ; Phylogenetics ; Phylogeny ; Regular ; Regular Articles ; Statistics as Topic ; Systematic biology ; Taxa ; taxon sampling
ispartofSystematic Biology, 2011-12-01, Vol.60 (6), p.782-796
rights
0Copyright © 2011 Society of Systematic Biologists
1The Author(s) 2011. Published by Oxford University Press on behalf of the Society of Systematic Biologists. 2011
lds50peer_reviewed
oafree_for_read
citedbyFETCH-LOGICAL-1594t-2f9e3897c88b5d24f6af2bd3cb0eb899ecd279e0495f380bb0306f5c093558a3
citesFETCH-LOGICAL-1594t-2f9e3897c88b5d24f6af2bd3cb0eb899ecd279e0495f380bb0306f5c093558a3
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/21840842$$D View this record in MEDLINE/PubMed
search
creatorcontrib
0Cho, Soowon
1Zwick, Andreas
2Regier, Jerome C
3Mitter, Charles
4Cummings, Michael P
5Yao, Jianxiu
6Du, Zaile
7Zhao, Hong
8Kawahara, Akito Y
9Weller, Susan
10Davis, Donald R
11Baixeras, Joaquin
12Brown, John W
13Parr, Cynthia
title
0Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
1Systematic Biology
addtitleSyst Biol
descriptionThis paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia (> 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa × 26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
subject
0Animals
1Biological taxonomies
2Butterflies & moths
3Classification - methods
4Datasets
5Ditrysia
6gene sampling
7Genes
8Genes, Insect - genetics
9Genetic Heterogeneity
10Hexapoda
11Lepidoptera
12Lepidoptera - classification
13Lepidoptera - genetics
14Missing data
15molecular phylogenetics
16Molecular structure
17Moths
18nuclear genes
19Nucleotides
20Nucleotides - genetics
21Phylogenetics
22Phylogeny
23Regular
24Regular Articles
25Statistics as Topic
26Systematic biology
27Taxa
28taxon sampling
issn
01063-5157
11076-836X
fulltexttrue
rsrctypearticle
creationdate2011
recordtypearticle
recordideNqFkk9v0zAYxiMEYmNw5AiyuDAOATvOH3tIoFHGWqkIJHbgZjnxm9ZVYgfbqejH4BvjKqVikxAn2_LvefT68ZMkTwl-TTCnb_zO19rGxeGK30tOCa7KlNHy-_39vqRpQYrqJHnk_QZjQsqCPExOMsJyzPLsNPk1kwZ9hE7X4GSAbocWprH90EEAdA0G0De5P6HLcdWDCTJoa9CiH5zdApLo63rX2RWYHbryQffRArXWobCOCrWVpgGFPtuw9kgahT6MIYBrOw0enc_hpxyskhdoCYNWdohX8tX7x8mDVnYenhzWs-Tm09XNbJ4uv1wvZpfLlBQ8D2nWcqCMVw1jdaGyvC1lm9WKNjWGmnEOjcoqDjjnRUsZrmtMcdkWTcysKJikZ8nbydb3Oo5njZZGKD_IBoSVWjgYrNfBup3wWoAaBcGYMZGRnJVR_W5SD2Pdg2piMk52YnAxgqjYG9y-MXotVnYrKOG0KqtoMJ8M7ABGage3tMpAEFaJrKyE5Dklssw4y-pc5Urm8eUM46Jq2gpKGq1eHmZx9scIPohe-wa6ThqwoxeMM0ZZDC2SL-6QGzs6E1MWHGf7SmRFhNIJapz13kF7nIxgsa-cmConpspF_vnfURzpPx2LAL1j2OipRzEZ3f3T9vwQ0Dj8d4JnE7rx8b-OcE5orHvF6G9zVwEb
startdate20111201
enddate20111201
creator
0Cho, Soowon
1Zwick, Andreas
2Regier, Jerome C
3Mitter, Charles
4Cummings, Michael P
5Yao, Jianxiu
6Du, Zaile
7Zhao, Hong
8Kawahara, Akito Y
9Weller, Susan
10Davis, Donald R
11Baixeras, Joaquin
12Brown, John W
13Parr, Cynthia
generalOxford University Press
scope
0TOX
1CGR
2CUY
3CVF
4ECM
5EIF
6NPM
7AAYXX
8CITATION
9K9.
107X8
11BOBZL
12CLFQK
135PM
14K9L
sort
creationdate20111201
titleCan Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
authorCho, Soowon ; Zwick, Andreas ; Regier, Jerome C ; Mitter, Charles ; Cummings, Michael P ; Yao, Jianxiu ; Du, Zaile ; Zhao, Hong ; Kawahara, Akito Y ; Weller, Susan ; Davis, Donald R ; Baixeras, Joaquin ; Brown, John W ; Parr, Cynthia
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-1594t-2f9e3897c88b5d24f6af2bd3cb0eb899ecd279e0495f380bb0306f5c093558a3
rsrctypearticles
prefilterarticles
languageeng
creationdate2011
topic
0Animals
1Biological taxonomies
2Butterflies & moths
3Classification - methods
4Datasets
5Ditrysia
6gene sampling
7Genes
8Genes, Insect - genetics
9Genetic Heterogeneity
10Hexapoda
11Lepidoptera
12Lepidoptera - classification
13Lepidoptera - genetics
14Missing data
15molecular phylogenetics
16Molecular structure
17Moths
18nuclear genes
19Nucleotides
20Nucleotides - genetics
21Phylogenetics
22Phylogeny
23Regular
24Regular Articles
25Statistics as Topic
26Systematic biology
27Taxa
28taxon sampling
toplevel
0peer_reviewed
1online_resources
creatorcontrib
0Cho, Soowon
1Zwick, Andreas
2Regier, Jerome C
3Mitter, Charles
4Cummings, Michael P
5Yao, Jianxiu
6Du, Zaile
7Zhao, Hong
8Kawahara, Akito Y
9Weller, Susan
10Davis, Donald R
11Baixeras, Joaquin
12Brown, John W
13Parr, Cynthia
collection
0Oxford Journals Open Access Collection
1Medline
2MEDLINE
3MEDLINE (Ovid)
4MEDLINE
5MEDLINE
6PubMed
7CrossRef
8ProQuest Health & Medical Complete (Alumni)
9MEDLINE - Academic
10OpenAIRE (Open Access)
11OpenAIRE
12PubMed Central (Full Participant titles)
13Smithsonian Digital Repository
jtitleSystematic Biology
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
au
0Cho, Soowon
1Zwick, Andreas
2Regier, Jerome C
3Mitter, Charles
4Cummings, Michael P
5Yao, Jianxiu
6Du, Zaile
7Zhao, Hong
8Kawahara, Akito Y
9Weller, Susan
10Davis, Donald R
11Baixeras, Joaquin
12Brown, John W
13Parr, Cynthia
formatjournal
genrearticle
ristypeJOUR
atitleCan Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)?
jtitleSystematic Biology
addtitleSyst Biol
date2011-12-01
risdate2011
volume60
issue6
spage782
epage796
pages782-796
issn1063-5157
eissn1076-836X
notes
0Soowon Cho and Andreas Zwick have contributed equally to this work.
1Associate Editor: Karl Kjer
210.1093/sysbio/syr079
31063-5157
4103963
5Cho, Soowon, Zwick, Andreas, Regier, Jerome C., Mitter, Charles, Cummings, Michael P., Yao, Jianxiu, Du, Zaile, Zhao, Hong, Kawahara, Akito Y., Weller, Susan, Davis, Donald R., Baixeras, Joaquin, Brown, John W., and Parr, Cynthia Sims. 2011. " Can Deliberately Incomplete Gene Sample Augmentation Improve a Phylogeny Estimate for the Advanced Moths and Butterflies (Hexapoda: Lepidoptera)? ." Systematic Biology . 60 (6):782-796. https://doi.org/10.1093/sysbio/syr079
6Systematic Biology
7http://hdl.handle.net/10088/21486
abstractThis paper addresses the question of whether one can economically improve the robustness of a molecular phylogeny estimate by increasing gene sampling in only a subset of taxa, without having the analysis invalidated by artifacts arising from large blocks of missing data. Our case study stems from an ongoing effort to resolve poorly understood deeper relationships in the large clade Ditrysia (> 150,000 species) of the insect order Lepidoptera (butterflies and moths). Seeking to remedy the overall weak support for deeper divergences in an initial study based on five nuclear genes (6.6 kb) in 123 exemplars, we nearly tripled the total gene sample (to 26 genes, 18.4 kb) but only in a third (41) of the taxa. The resulting partially augmented data matrix (45% intentionally missing data) consistently increased bootstrap support for groupings previously identified in the five-gene (nearly) complete matrix, while introducing no contradictory groupings of the kind that missing data have been predicted to produce. Our results add to growing evidence that data sets differing substantially in gene and taxon sampling can often be safely and profitably combined. The strongest overall support for nodes above the family level came from including all nucleotide changes, while partitioning sites into sets undergoing mostly nonsynonymous versus mostly synonymous change. In contrast, support for the deepest node for which any persuasive molecular evidence has yet emerged (78-85% bootstrap) was weak or nonexistent unless synonymous change was entirely excluded, a result plausibly attributed to compositional heterogeneity. This node (Gelechioidea + Apoditrysia), tentatively proposed by previous authors on the basis of four morphological synapomorphies, is the first major subset of ditrysian superfamilies to receive strong statistical support in any phylogenetic study. A "more-genes-only" data set (41 taxa × 26 genes) also gave strong signal for a second deep grouping (Macrolepidoptera) that was obscured, but not strongly contradicted, in more taxon-rich analyses.
copEngland
pubOxford University Press
pmid21840842
doi10.1093/sysbio/syr079
oafree_for_read