An Efficient Pipeline to Generate Data for Studies in Plastid Population Genomics and Phylogeography
Published In
Applications in Plant Sciences
Document Type
Article
Publication Date
11-14-2017
Subjects
Plastids -- Phylogeography, Metagenomics, Mitochondrial DNA, Molecular genetics -- Data processing
Abstract
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.
DOI
10.3732/apps.1700053
Persistent Identifier
http://archives.pdx.edu/ds/psu/25351
Citation Details
Kohrn, Brendan F.; Persinger, Jessica M.; and Cruzan, Mitchell B., "An Efficient Pipeline to Generate Data for Studies in Plastid Population Genomics and Phylogeography" (2017). Biology Faculty Publications and Presentations. 208.
http://archives.pdx.edu/ds/psu/25351
Description
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC-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.