A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data

Abstract

Previous phylogenetic studies in oaks (Quercus, Fagaceae) have failed to resolve the backbone topology of the genus with strong support. Here, we utilize next-generation sequencing of restriction-site associated DNA (RAD-Seq) to resolve a framework phylogeny of a predominantly American clade of oaks whose crown age is estimated at 23–33 million years old. Using a recently developed analytical pipeline for RAD-Seq phylogenetics, we created a concatenated matrix of 1.40 E06 aligned nucleotides, constituting 27,727 sequence clusters. RAD-Seq data were readily combined across runs, with no difference in phylogenetic placement between technical replicates, which overlapped by only 43–64% in locus coverage. 17% (4,715) of the loci we analyzed could be mapped with high confidence to one or more expressed sequence tags in NCBI Genbank. A concatenated matrix of the loci that BLAST to at least one EST sequence provides approximately half as many variable or parsimony-informative characters as equal-sized datasets from the non-EST loci. The EST-associated matrix is more complete (fewer missing loci) and has slightly lower homoplasy than non-EST subsampled matrices of the same size, but there is no difference in phylogenetic support or relative attribution of base substitutions to internal versus terminal branches of the phylogeny. We introduce a partitioned RAD visualization method (implemented in the R package RADami; http://cran.r-project.org/web/packages/RADami) to investigate the possibility that suboptimal topologies supported by large numbers of loci—due, for example, to reticulate evolution or lineage sorting—are masked by the globally optimal tree. We find no evidence for strongly-supported alternative topologies in our study, suggesting that the phylogeny we recover is a robust estimate of large-scale phylogenetic patterns in the American oak clade. Our study is one of the first to demonstrate the utility of RAD-Seq data for inferring phylogeny in a 23–33 million year-old clade.

RAD-seq derived genome-wide nuclear markers resolve the phylogeny of tunas

“…thynnus branch is supported by 3 analyses only when lowering the BV to 80% (Table 1). As reported by other studies (Cruaud et al, 2014;Hipp et al, 2014;Hou et al, 2015;Jones et al, 2013;Leaché et al, 2015;Rubin et al, 2012;Wagner et al, 2013), the use of IUPAC encoded sites and allowing higher missing data percentages not only produces larger matrices, but also results in better resolved trees (Table 1). Yet, although high bootstrap alone is not evidence of tree accuracy (Rodríguez-Ezpeleta et al, 2007), the congruence obtained among our different analyses is considered a good indicator of true evolutionary signal in the data (Hillis, 1995;Rubin et al, 2012).…”

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

“…The sample set consisted of 228 acorns, 37 adult trees not previously genotyped (including nine mother trees), and 59 learning samples drawn from the 63 samples originally sequenced using RAD‐seq and used to identify SNPs. Maximum‐likelihood analysis of the SNP dataset from parent trees and learning samples recovers a topology comparable to that described in previous studies (Hipp et al., 2014, 2018; McVay, Hipp et al., 2017) (Figure 4). UPGMA analyses provide no additional insights over maximum‐likelihood analyses and are excluded from further discussion.…”

“…RAD‐seq DNA extraction, library preparation, and sequencing were conducted as presented previously in oaks (Cavender‐Bares et al., 2015; Hipp et al., 2014, 2018; McVay, Hauser et al., 2017, McVay, Hipp et al., 2017). Briefly, DNA for all RAD‐seq samples was extracted from fresh or frozen material using the DNeasy plant extraction protocol (DNeasy, Qiagen, Valencia, CA, USA).…”

“…In the past few years, restrictionsite‐associated DNA sequencing (RAD‐seq) and related methods (e.g., genotyping by sequencing, double‐digest RAD) have emerged as particularly efficient approaches to genotype as well as to identify SNPs for further study (Baird et al., 2008; Barchi et al., 2011; Davey & Blaxter, 2010; Pegadaraju, Nipper, Hulke, Qi, & Schultz, 2013; Scaglione et al., 2012). These methods have been applied with great success to understanding phylogeny, species circumscription, and hybridization patterns in oaks (Cavender‐Bares et al., 2015; Eaton, Hipp, González‐Rodríguez, & Cavender‐Bares, 2015; Fitz‐Gibbon, Hipp, Pham, Manos, & Sork, 2017; Hipp et al., 2014; McVay, Hauser, Hipp, & Manos, 2017). However, the costs are often relatively high per individual and require a library of identified individuals for comparison, making RAD‐seq and related methods impractical for identification of individual trees outside of the context of tree diversity research programs.…”

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“…67 Recent molecular phylogenetic studies at and below the genus level focussed on the nucleome of 68 oaks (Oh and Manos, 2008;Denk and Grimm, 2010;Hipp et al, 2014;Hubert et al, 2014 (Bouchal et al, 2014;Hubert et al, 2014;Grímsson et al, 2015). This early radiation of the 76 Quercus/Protobalanus lineage left its imprints in the molecular signatures of the few modern 77 species of Group Protobalanus and two narrow endemic white oak species, Quercus pontica 78 (north-eastern Turkey, south-western Georgia; Denk and Grimm, 2010) and Q. sadleriana 79 (California;Hubert et al, 2014).…”