Visualizations for genetic assignment analyses using the saddlepoint approximation method

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dc.contributor.author McMillan, Louise en
dc.contributor.author Fewster, Rachel en
dc.date.accessioned 2018-11-04T21:04:23Z en
dc.date.issued 2017-09 en
dc.identifier.citation Biometrics 73(3):1029-1041 Sep 2017 en
dc.identifier.issn 0006-341X en
dc.identifier.uri http://hdl.handle.net/2292/43810 en
dc.description.abstract We propose a method for visualizing genetic assignment data by characterizing the distribution of genetic profiles for each candidate source population. This method enhances the assignment method of Rannala and Mountain (1997) by calculating appropriate graph positions for individuals for which some genetic data are missing. An individual with missing data is positioned in the distributions of genetic profiles for a population according to its estimated quantile based on its available data. The quantiles of the genetic profile distribution for each population are calculated by approximating the cumulative distribution function (CDF) using the saddlepoint method, and then inverting the CDF to get the quantile function. The saddlepoint method also provides a way to visualize assignment results calculated using the leave-one-out procedure. This new method offers an advance upon assignment software such as geneclass2, which provides no visualization method, and is biologically more interpretable than the bar charts provided by the software structure. We show results from simulated data and apply the methods to microsatellite genotype data from ship rats (Rattus rattus) captured on the Great Barrier Island archipelago, New Zealand. The visualization method makes it straightforward to detect features of population structure and to judge the discriminative power of the genetic data for assigning individuals to source populations. en
dc.publisher Wiley en
dc.relation.ispartofseries Biometrics en
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. en
dc.rights This is the peer reviewed version of the article, which has been published in final form at http://dx.doi.org/10.1111/biom.12667. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. en
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm en
dc.rights.uri http://www.biometrics.tibs.org/guidelinesforposting.htm en
dc.title Visualizations for genetic assignment analyses using the saddlepoint approximation method en
dc.type Journal Article en
dc.identifier.doi 10.1111/biom.12667 en
pubs.issue 3 en
pubs.begin-page 1029 en
pubs.volume 73 en
dc.rights.holder Copyright: The International Biometric Society en
dc.identifier.pmid 28182851 en
pubs.author-url http://onlinelibrary.wiley.com/doi/10.1111/biom.12667/full en
pubs.end-page 1041 en
dc.rights.accessrights http://purl.org/eprint/accessRights/OpenAccess en
pubs.subtype Article en
pubs.elements-id 612496 en
pubs.org-id Science en
pubs.org-id Statistics en
pubs.record-created-at-source-date 2017-02-13 en
pubs.online-publication-date 2017-02-09 en
pubs.dimensions-id 28182851 en


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