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An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)

PREMISE OF THE STUDY: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Wh...

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Detalles Bibliográficos
Autores principales: Kohrn, Brendan F., Persinger, Jessica M., Cruzan, Mitchell B.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Botanical Society of America 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703179/
https://www.ncbi.nlm.nih.gov/pubmed/29188144
http://dx.doi.org/10.3732/apps.1700053
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author Kohrn, Brendan F.
Persinger, Jessica M.
Cruzan, Mitchell B.
author_facet Kohrn, Brendan F.
Persinger, Jessica M.
Cruzan, Mitchell B.
author_sort Kohrn, Brendan F.
collection PubMed
description PREMISE OF THE STUDY: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure. METHODS: We developed sampling methodologies and an application, CallHap, that uses a least-squares algorithm to evaluate the fit between observed and predicted SNP allele frequencies from pooled samples based on haplotype network phylogeny structure, thus enabling pooling for chloroplast sequencing for large-scale studies of chloroplast genomic variation. This method was tested using artificially constructed test networks and pools, and pooled samples of Lasthenia californica (California goldfields) from southern Oregon, USA. RESULTS: CallHap reliably recovered network topologies and haplotype frequencies from pooled samples. DISCUSSION: The CallHap pipeline allows for the efficient use of resources for estimation of genetic structure for studies using nonrecombining haplotypes such as intraspecific variation in chloroplast, mitochondrial, bacterial, or viral DNA.
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spelling pubmed-57031792017-11-29 An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1) Kohrn, Brendan F. Persinger, Jessica M. Cruzan, Mitchell B. Appl Plant Sci Application Article PREMISE OF THE STUDY: Seed dispersal contributes to gene flow and is responsible for colonization of new sites and range expansion. Sequencing chloroplast haplotypes offers a way to estimate contributions of seed dispersal to population genetic structure and enables studies of population history. Whole-genome sequencing is expensive, but resources can be conserved by pooling samples. Unfortunately, haplotype associations among single-nucleotide polymorphisms (SNPs) are lost in pooled samples, and treating SNP allele frequencies as independent markers provides biased estimates of genetic structure. METHODS: We developed sampling methodologies and an application, CallHap, that uses a least-squares algorithm to evaluate the fit between observed and predicted SNP allele frequencies from pooled samples based on haplotype network phylogeny structure, thus enabling pooling for chloroplast sequencing for large-scale studies of chloroplast genomic variation. This method was tested using artificially constructed test networks and pools, and pooled samples of Lasthenia californica (California goldfields) from southern Oregon, USA. RESULTS: CallHap reliably recovered network topologies and haplotype frequencies from pooled samples. DISCUSSION: The CallHap pipeline allows for the efficient use of resources for estimation of genetic structure for studies using nonrecombining haplotypes such as intraspecific variation in chloroplast, mitochondrial, bacterial, or viral DNA. Botanical Society of America 2017-11-14 /pmc/articles/PMC5703179/ /pubmed/29188144 http://dx.doi.org/10.3732/apps.1700053 Text en © 2017 Kohrn et al. Published by the Botanical Society of America https://creativecommons.org/licenses/by-nc-sa/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/) ), which permits unrestricted noncommercial use and redistribution provided that the original author and source are credited and the new work is distributed under the same license as the original.
spellingShingle Application Article
Kohrn, Brendan F.
Persinger, Jessica M.
Cruzan, Mitchell B.
An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title_full An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title_fullStr An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title_full_unstemmed An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title_short An efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
title_sort efficient pipeline to generate data for studies in plastid population genomics and phylogeography(1)
topic Application Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5703179/
https://www.ncbi.nlm.nih.gov/pubmed/29188144
http://dx.doi.org/10.3732/apps.1700053
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