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Large datasets and trichoptera phylogenetics

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TitleInfo
Title
Large datasets and trichoptera phylogenetics
SubTitle
dna barcodes, partitioned phylogenetic models, and the evolution of phryganeidae
Name (type = personal)
NamePart (type = family)
Frandsen
NamePart (type = given)
Paul Bryan
NamePart (type = date)
1986-
DisplayForm
Paul Bryan Frandsen
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Kjer
NamePart (type = given)
Karl M
DisplayForm
Karl M Kjer
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
May
NamePart (type = given)
Michael
DisplayForm
Michael May
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Fonseca
NamePart (type = given)
Dina
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Dina Fonseca
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Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Holzenthal
NamePart (type = given)
Ralph
DisplayForm
Ralph Holzenthal
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (encoding = w3cdtf); (qualifier = exact)
2015
DateOther (qualifier = exact); (type = degree)
2015-10
CopyrightDate (encoding = w3cdtf); (qualifier = exact)
2015
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Large datasets in phylogenetics—those with a large number of taxa, e.g. DNA barcode data sets, and those with a large amount of sequence data per taxon, e.g. data sets generated from high throughput sequencing—pose both exciting possibilities and interesting analytical problems. The analysis of both types of large datasets is explored in this dissertation. First, the use of DNA barcodes in phylogenetics is investigated via the generation of phylogenetic trees for known monophyletic clades. Barcodes are found to be useful in shallow scale phylogenetic analyses when given a well-supported scaffold on which to place them. One of the analytical challenges posed by large phylogenetic datasets is the selection of appropriate partitioned models of molecular evolution. The most commonly used model partitioning strategies can fail to characterize the true variation of the evolutionary process and this effect can be exacerbated when applied to large datasets. A new, scalable algorithm for the automatic selection of partitioned models of molecular evolution is proposed with an eye toward reducing systematic error in phylogenomics. The new algorithm is tested on a range of empirical datasets and found to provide a better fit of the model to the data as measured by information theoretic metrics like AICc. Indeed, the algorithm is found to perform particularly well when applied to a phylogenomic dataset consisting of ultra-conserved elements (UCEs). Finally, the phylogeny of Phryganeidae is estimated using a large dataset generated using targeted enrichment and high throughput sequencing. Trees generated from different modeling strategies give incongruent, but strongly supported results. The differences between the trees are examined and a new hypothesis for the relationships among the genera within Phryganeidae is posited.
Subject (authority = RUETD)
Topic
Entomology
Subject (authority = ETD-LCSH)
Topic
Phylogeny
Subject (authority = ETD-LCSH)
Topic
Data mining
Subject (authority = ETD-LCSH)
Topic
DNA
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_6665
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (viii, 103 p. : ill.)
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = statement of responsibility)
by Paul Bryan Frandsen
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T3251M5H
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Frandsen
GivenName
Paul
MiddleName
Bryan
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2015-08-21 15:25:30
AssociatedEntity
Name
Paul Frandsen
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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Technical

RULTechMD (ID = TECHNICAL1)
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ETD
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windows xp
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