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Converting quadratic entropy to diversity: both animals and alleles are diverse, but some are more diverse than others

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TypeOfResource
Text
TitleInfo
Title
Converting quadratic entropy to diversity: both animals and alleles are diverse, but some are more diverse than others
Name (authority = orcid); (authorityURI = http://id.loc.gov/vocabulary/identifiers/orcid.html); (type = personal); (valueURI = http://orcid.org/0000-0003-4474-3458)
NamePart (type = family)
Smouse
NamePart (type = given)
Peter E.
Affiliation
Ecology, Evolution and Natural Resources, Rutgers University
Role
RoleTerm (authority = marcrt); (type = text)
author
Name (type = personal)
NamePart (type = family)
Banks
NamePart (type = given)
Sam C.
Affiliation
The Australian National University
Role
RoleTerm (authority = marcrt); (type = text)
author
Name (type = personal)
NamePart (type = family)
Peakall
NamePart (type = given)
Rod
Affiliation
The Australian National University
Role
RoleTerm (authority = marcrt); (type = text)
author
Name (authority = RutgersOrg-Department); (type = corporate)
NamePart
Ecology, Evolution and Natural Resources
Name (authority = RutgersOrg-School); (type = corporate)
NamePart
School of Environmental and Biological Sciences (SEBS)
Genre (authority = RULIB-FS)
Article, Refereed
Genre (authority = NISO JAV)
Accepted Manuscript (AM)
Note (type = special display note)
The Antechinus data are archived in Excel workbook form, along with listings of the QDIVER results extracted from GenAlEx6.51 (http://biology.anu.edu.au/GenAlEx/). DC data and analyses are presented in S5 Appendix, and DR data and analyses are presented in S6 Appendix; these latter are ANU's to enable, and will be available with the paper as PLOS ONE access Supplements.
Note (type = peerReview)
Peer reviewed
OriginInfo
DateIssued (encoding = w3cdtf); (keyDate = yes); (qualifier = exact)
2017
Abstract (type = Abstract)
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1] - scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
Language
LanguageTerm (authority = ISO 639-3:2007); (type = text)
English
PhysicalDescription
InternetMediaType
application/pdf
Extent
41 p.
Subject (authority = local)
Topic
Rao’s quadratic entropy
Subject (authority = local)
Topic
Amova
Subject (authority = local)
Topic
Permanova
Subject (authority = local)
Topic
Gamova
Subject (authority = local)
Topic
Hill numbers
Subject (authority = local)
Topic
Phylogenetic diversity
Subject (authority = local)
Topic
Scaled diversity
Subject (authority = local)
Topic
Antechinus
Extension
DescriptiveEvent
Type
Citation
DateTime (encoding = w3cdtf)
2017
AssociatedObject
Name
PLOS ONE
Type
Journal
Relationship
Has part
Identifier (type = volume and issue)
12(10)
Reference (type = url)
https://doi.org/10.1371/journal.pone.0185499
Detail
e0185499
Extension
DescriptiveEvent
Type
Grant award
AssociatedEntity
Role
Funder
Name
U.S. Department of Agriculture
AssociatedEntity
Role
Originator
Name
Peter Smouse
AssociatedObject
Type
Grant number
Name
NJ17160
Extension
DescriptiveEvent
Type
Grant award
AssociatedEntity
Role
Funder
Name
Australian Research Council
AssociatedEntity
Role
Originator
Name
Sam C. Banks
AssociatedObject
Type
Grant number
Name
FT130100043.
RelatedItem (type = host)
TitleInfo
Title
Smouse, Peter E.
Identifier (type = local)
rucore30184700001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T3319ZW1
Genre (authority = ExL-Esploro)
Accepted Manuscript
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Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
RightsEvent
Type
Permission or license
AssociatedObject
Type
License
Name
Multiple author license v. 1
Detail
I hereby grant to Rutgers, The State University of New Jersey (Rutgers) the non-exclusive right to retain, reproduce, and distribute the deposited work (Work) in whole or in part, in and from its electronic format, without fee. This agreement does not represent a transfer of copyright to Rutgers. Rutgers may make and keep more than one copy of the Work for purposes of security, backup, preservation, and access and may migrate the Work to any medium or format for the purpose of preservation and access in the future. Rutgers will not make any alteration, other than as allowed by this agreement, to the Work. I represent and warrant to Rutgers that the Work is my original work. I also represent that the Work does not, to the best of my knowledge, infringe or violate any rights of others. I further represent and warrant that I have obtained all necessary rights to permit Rutgers to reproduce and distribute the Work and that any third-party owned content is clearly identified and acknowledged within the Work. By granting this license, I acknowledge that I have read and agreed to the terms of this agreement and all related RUcore and Rutgers policies.
RightsEvent
Type
Embargo
DateTime (encoding = w3cdtf); (keyDate = no); (point = end); (qualifier = exact)
2018-10-31
DateTime (encoding = w3cdtf); (keyDate = no); (point = start); (qualifier = exact)
2017-10-31
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after October 31, 2018.
RightsDeclaration (AUTHORITY = FS); (ID = rulibRdec0004); (TYPE = [FS] statement #1)
Copyright for scholarly resources published in RUcore is retained by the copyright holder. By virtue of its appearance in this open access medium, you are free to use this resource, with proper attribution, in educational and other non-commercial settings. Other uses, such as reproduction or republication, may require the permission of the copyright holder.
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Document
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1.5
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2017-11-03T09:54:29
DateCreated (point = end); (encoding = w3cdtf); (qualifier = exact)
2017-11-03T09:55:23
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Microsoft® Word 2016
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