A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting

Abstract

DNA barcoding has proved difficult in a number of woody plant genera, including the ecologically important oak genus Quercus. In this study, we utilized restrictionsite‐associated DNA sequencing (RAD‐seq) to develop an economical single nucleotide polymorphism (SNP) DNA barcoding system that suffices to distinguish eight common, sympatric eastern North American white oak species. Two de novo clustering pipelines, PyRAD and Stacks, were used in combination with postclustering bioinformatic tools to generate a list of 291 potential SNPs, 80 of which were included in a barcoding toolkit that is easily implemented using MassARRAY mass spectrometry technology. As a proof‐of‐concept, we used the genotyping toolkit to infer potential hybridization between North American white oaks transplanted outside of their native range (Q. michauxii, Q. montana, Q muehlenbergii/Q. prinoides, and Q. stellata) into a horticultural collection surrounded by natural forests of locally native trees (Q. alba and Q. macrocarpa) in the living collection at The Morton Arboretum (Lisle, IL, USA). Phylogenetic and clustering analyses suggested low rates of hybridization between cultivated and native species, with the exception of one Q. michauxii mother tree, the acorns of which exhibited high admixture from either Q. alba or Q. stellata and Q. macrocarpa, and a hybrid between Q. stellata that appears to have backcrossed almost exclusively to Q. alba. Together, RAD‐seq and MassARRAY technologies allow for efficient development and implementation of a multispecies barcode for one of the more challenging forest tree genera.

Conserved DNA polymorphisms distinguish species in the eastern North American white oak syngameon: Insights from an 80-SNP oak DNA genotyping toolkit

“…The two SNPs identified in this RAD-seq were designed to distinguish Quercus stellata from the remaining taxa and should not be considered independent of one another. They are not strongly decisive and do not figure prominently in downstream analyses in this study or in Fitzek et al (2018).…”

“…and Q. prinoides Willd. are separated in name only, as our RAD-seq data failed to distinguish the species (McVay et al , 2017b; Hipp et al , 2018) and SNPs were consequently not designed to separate these two (Fitzek et al , 2018). The species status of these two bears investigation with broader sampling.…”

“…To reduce the opportunity for hybridization with taxa from outside the natural range of each species, samples were preferentially selected from wild populations or from trees grown in gardens from seeds of known wild provenance (as discussed in Fitzek et al , 2018; Hipp et al , 2018); five individuals were analyzed from cultivated material (Table 1). Sample size per species ranges from 7–9 in Quercus montana Willd.…”

“…Additionally, NGS has enabled economical development of genotyping toolkits for smaller applications. In a recent paper, we utilized a large RAD-seq dataset for white oaks (McVay, Hipp, & Manos, 2017b; Hipp et al , 2018) to develop a low-cost SNP genotyping kit for eastern North American white oaks (Fitzek et al , 2018). We demonstrated our 80-marker SNP kit to be effective for identifying 15 species and F 1 hybrids, and validated it in a garden setting, where we found hybridization between non-native species in the collection and the native white oaks of the surrounding woodlands.…”

Genomic landscape of the global oak phylogeny

“…Our hypothesis that there are particular genes or regions of the genome that define the oak phylogeny globally appears to be false: rather, the phylogenetic history of oaks is defined by different genes in different lineages, making evolutionary history of oaks a phylogenetic and genomic mosaic. The effort to find a single best suite of genes for phylogenetic or population genetic inference across the oak genus is thus unlikely to be successful, though markers can clearly be designed for individual clades (Guichoux et al ., 2011; Fitzek et al ., 2018). What is perhaps most remarkable is that this heterogeneity of histories covarying independently along the oak genome yields, in aggregate, an evolutionary history of the complex genus that mirrors the morphological and ecological diversity of living and fossil oak species.…”