Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of sp...

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Autores principales:	Monika Zavodna, Catherine E Grueber, Neil J Gemmell
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7ba4c10e3c1e4e38a4710d33bae1b5d8
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spelling	oai:doaj.org-article:7ba4c10e3c1e4e38a4710d33bae1b5d82021-11-18T07:48:53ZParallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.1932-620310.1371/journal.pone.0061471https://doaj.org/article/7ba4c10e3c1e4e38a4710d33bae1b5d82013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23637841/?tool=EBIhttps://doaj.org/toc/1932-6203Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.Monika ZavodnaCatherine E GrueberNeil J GemmellPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e61471 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Monika Zavodna Catherine E Grueber Neil J Gemmell Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
description	Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches - parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.
format	article
author	Monika Zavodna Catherine E Grueber Neil J Gemmell
author_facet	Monika Zavodna Catherine E Grueber Neil J Gemmell
author_sort	Monika Zavodna
title	Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
title_short	Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
title_full	Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
title_fullStr	Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
title_full_unstemmed	Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
title_sort	parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7ba4c10e3c1e4e38a4710d33bae1b5d8
work_keys_str_mv	AT monikazavodna paralleltaggednextgenerationsequencingonpooledsamplesanewapproachforpopulationgeneticsinecologyandconservation AT catherineegrueber paralleltaggednextgenerationsequencingonpooledsamplesanewapproachforpopulationgeneticsinecologyandconservation AT neiljgemmell paralleltaggednextgenerationsequencingonpooledsamplesanewapproachforpopulationgeneticsinecologyandconservation
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Parallel tagged next-generation sequencing on pooled samples - a new approach for population genetics in ecology and conservation.

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