Phylogenomics of polyploid Fothergilla (Hamamelidaceae) by RAD‐tag based GBS—insights into species origin and effects of software pipelines

Abstract

Fothergilla (Hamamelidaceae) consists of Fothergilla gardenii (4x) from the coastal plains of the southeastern USA, F. major (6x) from the piedmont and mountains of the same region, and a few allopatric diploid populations of unknown taxonomic status. The objective of this study was to explore the relationships of the polyploid species with the diploid plants. Genotyping by sequencing (GBS) was applied to generate genome-wide molecular markers for phylogenetic and genetic structure analyses of 36 accessions of Fothergilla. Sanger sequencing of three plastid and one nuclear regions provided data for comparison with GBS-based results. Phylogenetic outcomes were compared using data from different sequencing runs and different software workflows. The different data sets showed substantial differences in inferred phylogenies, but all supported a genetically distinct 6x F. major and two lineages of the diploid populations closely associated with the 4x F. gardenii. We hypothesize that the 4x F. gardenii originated through hybridization between the Gulf coastal 2x and an extinct (or undiscovered) 2x lineage, followed by backcrosses to the Atlantic coastal 2x before chromosome doubling, and the 6x F. major also originated from the "extinct" 2x lineage. Alternative scenarios are possible but are not as well supported. The origins and divergence of the polyploid species likely occurred during the Pleistocene cycles of glaciation, although fossil evidence indicates the genus might have existed for a much longer time with a wider past distribution. Our study demonstrates the power of combining GBS data with Sanger sequencing in reconstructing the evolutionary network of polyploid lineages.

Characterizing the allopolyploid species among the wild relatives of soybean: Utility of reduced representation genotyping methodologies

“…Research into the origin of polyploid species and their subsequent adaptation will continue to benefit from the advent of short read and other sequencing technologies (Burrell et al, 2015;Qi et al, 2015;Rothfels et al, 2017;Stetter & Schmid, 2017). Newly developed data analysis methods will make the identification of allopolyploids and studies of their evolution tractable (Jones et al, 2013;McKinney et al, 2017;Gompert & Mock, 2017).…”

Congruent species delimitation of two controversial gold‐thread nanmu tree species based on morphological and restriction site‐associated DNA sequencing data

“…This technique can produce a vast number of short sequences from various genomic DNA loci and was designed originally as a tool for finding single-nucleotide polymorphisms (SNPs) for population genetic structural inference, linkage mapping, association study, and other intraspecific genomic analyses (Miller et al, 2007;Baird et al, 2008). Recently, RAD-seq has also been used to resolve phylogenetic relationships of diverse lineages including polyploids (e.g., Rubin et al, 2012;Eaton & Ree, 2013;Wagner et al, 2013;Wang et al, 2013;Escudero et al, 2014;Hipp et al, 2014;Takahashi et al, 2014;Qi et al, 2015;Ree & Hipp, 2015;Takahashi & Moreno, 2015;Boucher et al, 2016;Takahashi & Sota, 2016;Fitz-Gibbon et al, 2017;Tripp et al, 2017).…”

Breaking RAD: an evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation

“…; Combosch & Vollmer ; Qi et al . ). Markers generated by RADseq have also been quite useful for constructing linkage maps and identifying quantitative trait loci (QTL; Pfender et al .…”

“…RADseq markers come in the form of RAD-tags, which are shortread sequences adjacent to restriction enzyme cut sites. Because many polymorphic markers are produced by RADseq, it has frequently been used successfully for population genetic analyses, including assessment of population structure, hybridization, demographic history, phylogeography and migration (Catchen et al 2013;Cavender-Bares et al 2015;Combosch & Vollmer 2015;Qi et al 2015). Markers generated by RADseq have also been quite useful for constructing linkage maps and identifying quantitative trait loci (QTL; Pfender et al 2011;Houston et al 2012;Weber et al 2013;Laporte et al 2015;Lowry et al 2015).…”