schliessen

Filtern

 

Bibliotheken

Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers

Estimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylog... Full description

Journal Title: Systematic biology 2007, Vol.56 (3), p.400-411
Main Author: Carstens, Bryan C.
Other Authors: Knowles, L. Lacey , Collins, Tim
Format: Electronic Article Electronic Article
Language: English
Subjects:
Quelle: Alma/SFX Local Collection
Publisher: England: Society of Systematic Zoology
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/17520504
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: cdi_proquest_miscellaneous_70521701
title: Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
format: Article
creator:
  • Carstens, Bryan C.
  • Knowles, L. Lacey
  • Collins, Tim
subjects:
  • Accuracy
  • Animals
  • Biological taxonomies
  • Coalescent
  • Computer Simulation
  • Datasets
  • Estimate reliability
  • Evolution
  • gene trees
  • Genetic loci
  • Genetic Speciation
  • Genetic Variation
  • Grasshoppers
  • Grasshoppers - classification
  • Grasshoppers - genetics
  • incomplete lineage sorting
  • Likelihood Functions
  • Models, Genetic
  • Monophyly
  • Phylogenetics
  • Phylogeny
  • Probability
  • Software packages
  • species phylogeny
  • Species Specificity
  • Topology
  • Trees
ispartof: Systematic biology, 2007, Vol.56 (3), p.400-411
description: Estimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated—the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.
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
RANK2.6189938
LOCALfalse
PrimoNMBib
record
control
sourceidjstor_proqu
recordidTN_cdi_proquest_miscellaneous_70521701
sourceformatXML
sourcesystemPC
jstor_id20143046
oup_id10.1080/10635150701405560
sourcerecordid20143046
originalsourceidFETCH-LOGICAL-13853-b42003928df1725e8a29df15f24b73aa7f7b39f57e74bea4afbc2d578aee37623
addsrcrecordideNqNkV9r1EAUxYMo9o9-AB-UwQefGp3_k_Wt1O22umKlFUtfhkn2ZjtrkokzE-h-AL-3E7JUqCA-3Qvndw6Xe7LsBcFvCS7wO4IlE0RghQnHQkj8KNsnWMm8YPL68bhLlidA7WUHIWwwJkQK8jTbI0pQLDDfz37NQ7StibZbo8seKgsBXdxuG7eGbotq71q0gA7yKw-ALrwrTWkbG0fsA4TeRkDnXeXavoG0Lm0HZg3o0vkx8T067tD8zozqlPUZGtO5vhkCWngTwq3re_DhWfakNk2A57t5mH07nV-dnOXLL4vzk-NlTlghWF5yijGb0WJVE0UFFIbO0ipqykvFjFG1KtmsFgoUL8FwU5cVXQlVGACmJGWH2Zspt_fu5wAh6taGCpp0FLghaIUFJembCXz9ANy4wXfpNk1mXBVU8SJBZIIq70LwUOvep1_6rSZYjwXpvwpKnle74KFsYfXHsWskAepBaGVj6sd10Rvb_DP6aHK6of-vS15O-CZE5-8NNAEMc5n0fNJtiHB3rxv_Q0vFlNBn1zeafLyRX8npd_2J_QZhTsIT
sourcetypeAggregation Database
isCDItrue
recordtypearticle
pqid194782748
display
typearticle
titleEstimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
sourceAlma/SFX Local Collection
creatorCarstens, Bryan C. ; Knowles, L. Lacey ; Collins, Tim
contributorCollins, Tim
creatorcontribCarstens, Bryan C. ; Knowles, L. Lacey ; Collins, Tim ; Collins, Tim
descriptionEstimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated—the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.
identifier
0ISSN: 1063-5157
1EISSN: 1076-836X
2DOI: 10.1080/10635150701405560
3PMID: 17520504
languageeng
publisherEngland: Society of Systematic Zoology
subjectAccuracy ; Animals ; Biological taxonomies ; Coalescent ; Computer Simulation ; Datasets ; Estimate reliability ; Evolution ; gene trees ; Genetic loci ; Genetic Speciation ; Genetic Variation ; Grasshoppers ; Grasshoppers - classification ; Grasshoppers - genetics ; incomplete lineage sorting ; Likelihood Functions ; Models, Genetic ; Monophyly ; Phylogenetics ; Phylogeny ; Probability ; Software packages ; species phylogeny ; Species Specificity ; Topology ; Trees
ispartofSystematic biology, 2007, Vol.56 (3), p.400-411
rights
0Copyright 2007 Society of Systematic Biologists
12007 Society of Systematic Biologists 2007
lds50peer_reviewed
citedbyFETCH-LOGICAL-13853-b42003928df1725e8a29df15f24b73aa7f7b39f57e74bea4afbc2d578aee37623
citesFETCH-LOGICAL-13853-b42003928df1725e8a29df15f24b73aa7f7b39f57e74bea4afbc2d578aee37623
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
thumbnail$$Usyndetics_thumb_exl
backlink$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17520504$$D View this record in MEDLINE/PubMed
search
contributorCollins, Tim
creatorcontrib
0Carstens, Bryan C.
1Knowles, L. Lacey
2Collins, Tim
title
0Estimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
1Systematic biology
addtitleSyst Biol
descriptionEstimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated—the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.
subject
0Accuracy
1Animals
2Biological taxonomies
3Coalescent
4Computer Simulation
5Datasets
6Estimate reliability
7Evolution
8gene trees
9Genetic loci
10Genetic Speciation
11Genetic Variation
12Grasshoppers
13Grasshoppers - classification
14Grasshoppers - genetics
15incomplete lineage sorting
16Likelihood Functions
17Models, Genetic
18Monophyly
19Phylogenetics
20Phylogeny
21Probability
22Software packages
23species phylogeny
24Species Specificity
25Topology
26Trees
issn
01063-5157
11076-836X
fulltexttrue
rsrctypearticle
creationdate2007
recordtypearticle
recordideNqNkV9r1EAUxYMo9o9-AB-UwQefGp3_k_Wt1O22umKlFUtfhkn2ZjtrkokzE-h-AL-3E7JUqCA-3Qvndw6Xe7LsBcFvCS7wO4IlE0RghQnHQkj8KNsnWMm8YPL68bhLlidA7WUHIWwwJkQK8jTbI0pQLDDfz37NQ7StibZbo8seKgsBXdxuG7eGbotq71q0gA7yKw-ALrwrTWkbG0fsA4TeRkDnXeXavoG0Lm0HZg3o0vkx8T067tD8zozqlPUZGtO5vhkCWngTwq3re_DhWfakNk2A57t5mH07nV-dnOXLL4vzk-NlTlghWF5yijGb0WJVE0UFFIbO0ipqykvFjFG1KtmsFgoUL8FwU5cVXQlVGACmJGWH2Zspt_fu5wAh6taGCpp0FLghaIUFJembCXz9ANy4wXfpNk1mXBVU8SJBZIIq70LwUOvep1_6rSZYjwXpvwpKnle74KFsYfXHsWskAepBaGVj6sd10Rvb_DP6aHK6of-vS15O-CZE5-8NNAEMc5n0fNJtiHB3rxv_Q0vFlNBn1zeafLyRX8npd_2J_QZhTsIT
startdate200706
enddate200706
creator
0Carstens, Bryan C.
1Knowles, L. Lacey
2Collins, Tim
general
0Society of Systematic Zoology
1Taylor & Francis
2Oxford University Press
scope
0BSCLL
1CGR
2CUY
3CVF
4ECM
5EIF
6NPM
7AAYXX
8CITATION
93V.
107X7
117XB
1288A
1388E
1488I
158AF
168AO
178CJ
188FE
198FH
208FI
218FJ
228FK
238FU
248G5
25ABUWG
26AZQEC
27BBNVY
28BENPR
29BHPHI
30BKSAR
31D1J
32DWQXO
33FYUFA
34GHDGH
35GNUQQ
36GUQSH
37HCIFZ
38K9.
39LK8
40M0L
41M0S
42M1P
43M2O
44M2P
45M7P
46MBDVC
47PADUT
48PCBAR
49PQEST
50PQQKQ
51PQUKI
52PRINS
53Q9U
54S0X
557X8
sort
creationdate200706
titleEstimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
authorCarstens, Bryan C. ; Knowles, L. Lacey ; Collins, Tim
facets
frbrtype5
frbrgroupidcdi_FETCH-LOGICAL-13853-b42003928df1725e8a29df15f24b73aa7f7b39f57e74bea4afbc2d578aee37623
rsrctypearticles
prefilterarticles
languageeng
creationdate2007
topic
0Accuracy
1Animals
2Biological taxonomies
3Coalescent
4Computer Simulation
5Datasets
6Estimate reliability
7Evolution
8gene trees
9Genetic loci
10Genetic Speciation
11Genetic Variation
12Grasshoppers
13Grasshoppers - classification
14Grasshoppers - genetics
15incomplete lineage sorting
16Likelihood Functions
17Models, Genetic
18Monophyly
19Phylogenetics
20Phylogeny
21Probability
22Software packages
23species phylogeny
24Species Specificity
25Topology
26Trees
toplevel
0peer_reviewed
1online_resources
creatorcontrib
0Carstens, Bryan C.
1Knowles, L. Lacey
2Collins, Tim
collection
0Istex
1Medline
2MEDLINE
3MEDLINE (Ovid)
4MEDLINE
5MEDLINE
6PubMed
7CrossRef
8ProQuest Central (Corporate)
9Health & Medical Collection
10ProQuest Central (purchase pre-March 2016)
11Biology Database (Alumni Edition)
12Medical Database (Alumni Edition)
13Science Database (Alumni Edition)
14STEM Database
15ProQuest Pharma Collection
16ProQuest Aquatic Science Journals
17ProQuest SciTech Collection
18ProQuest Natural Science Collection
19Hospital Premium Collection
20Hospital Premium Collection (Alumni Edition)
21ProQuest Central (Alumni) (purchase pre-March 2016)
22ProQuest Discovery
23Research Library (Alumni Edition)
24ProQuest Central (Alumni Edition)
25ProQuest Central Essentials
26Biological Science Collection
27ProQuest Central
28Natural Science Collection
29Earth, Atmospheric & Aquatic Science Collection
30ProQuest Aquatic Science Collection
31ProQuest Central Korea
32Health Research Premium Collection
33Health Research Premium Collection (Alumni)
34ProQuest Central Student
35Research Library Prep
36SciTech Premium Collection
37ProQuest Health & Medical Complete (Alumni)
38ProQuest Biological Science Collection
39Biology Database
40Health & Medical Collection (Alumni Edition)
41Medical Database
42Research Library
43Science Database
44Biological Science Database
45Research Library (Corporate)
46Research Library China
47Earth, Atmospheric & Aquatic Science Database
48ProQuest One Academic Eastern Edition
49ProQuest One Academic
50ProQuest One Academic UKI Edition
51ProQuest Central China
52ProQuest Central Basic
53SIRS Editorial
54MEDLINE - Academic
jtitleSystematic biology
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
au
0Carstens, Bryan C.
1Knowles, L. Lacey
2Collins, Tim
formatjournal
genrearticle
ristypeJOUR
atitleEstimating Species Phylogeny from Gene-Tree Probabilities Despite Incomplete Lineage Sorting: An Example from Melanoplus Grasshoppers
jtitleSystematic biology
addtitleSyst Biol
date2007-06
risdate2007
volume56
issue3
spage400
epage411
pages400-411
issn1063-5157
eissn1076-836X
abstractEstimating phylogenetic relationships among closely related species can be extremely difficult when there is incongruence among gene trees and between the gene trees and the species tree. Here we show that incorporating a model of the stochastic loss of gene lineages by genetic drift into the phylogenetic estimation procedure can provide a robust estimate of species relationships, despite widespread incomplete sorting of ancestral polymorphism. This approach is applied to a group of montane Melanoplus grasshoppers for which genealogical discordance among loci and incomplete lineage sorting obscures any obvious phylogenetic relationships among species. Unlike traditional treatments where gene trees estimated using standard phylogenetic methods are implicitly equated with the species tree, with the coalescent-based approach the species tree is modeled probabilistically from the estimated gene trees. The estimated species phylogeny (the ESP) is calculated for the grasshoppers from multiple gene trees reconstructed for nuclear loci and a mitochondrial gene. This empirical application is coupled with a simulation study to explore the performance of the coalescent-based approach. Specifically, we test the accuracy of the ESP given the data based on analyses of simulated data matching the multilocus data collected in Melanoplus (i.e., data were simulated for each locus with the same number of base pairs and locus-specific mutational models). The results of the study show that ESPs can be computed using the coalescent-based approach long before reciprocal monophyly has been achieved, and that these statistical estimates are accurate. This contrasts with analyses of the empirical data collected in Melanoplus and simulated data based on concatenation of multiple loci, for which the incomplete lineage sorting of recently diverged species posed significant problems. The strengths and potential challenges associated with incorporating an explicit model of gene-lineage coalescence into the phylogenetic procedure to obtain an ESP, as illustrated by application to Melanoplus, versus concatenation and consensus approaches are discussed. This study represents a fundamental shift in how species relationships are estimated—the relationship between the gene trees and the species phylogeny is modeled probabilistically rather than equating gene trees with a species tree.
copEngland
pubSociety of Systematic Zoology
pmid17520504
doi10.1080/10635150701405560