Vitis Phylogenomics: Hybridization Intensities from a SNP Array Outperform Genotype Calls

Abstract

Understanding relationships among species is a fundamental goal of evolutionary biology. Single nucleotide polymorphisms (SNPs) identified through next generation sequencing and related technologies enable phylogeny reconstruction by providing unprecedented numbers of characters for analysis. One approach to SNP-based phylogeny reconstruction is to identify SNPs in a subset of individuals, and then to compile SNPs on an array that can be used to genotype additional samples at hundreds or thousands of sites simultaneously. Although powerful and efficient, this method is subject to ascertainment bias because applying variation discovered in a representative subset to a larger sample favors identification of SNPs with high minor allele frequencies and introduces bias against rare alleles. Here, we demonstrate that the use of hybridization intensity data, rather than genotype calls, reduces the effects of ascertainment bias. Whereas traditional SNP calls assess known variants based on diversity housed in the discovery panel, hybridization intensity data survey variation in the broader sample pool, regardless of whether those variants are present in the initial SNP discovery process. We apply SNP genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape to show the effects of ascertainment bias and to reconstruct evolutionary relationships among Vitis species. We demonstrate that phylogenies constructed using hybridization intensities suffer less from the distorting effects of ascertainment bias, and are thus more accurate than phylogenies based on genotype calls. Moreover, we reconstruct the phylogeny of the genus Vitis using hybridization data, show that North American subgenus Vitis species are monophyletic, and resolve several previously poorly known relationships among North American species. This study builds on earlier work that applied the Vitis9kSNP array to evolutionary questions within Vitis vinifera and has general implications for addressing ascertainment bias in array-enabled phylogeny reconstruction.

Latent developmental and evolutionary shapes embedded within the grapevine leaf

“…Some, but not all, well‐known phylogenetic relationships are reflected in leaf morphology (Fig. 5c) (Zecca et al ., 2012; Miller et al ., 2013). Notably, clustering the averaged shapes from different genotypes reveals that V. vinifera ssp.…”

Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)

“…lincecumii . Miller et al () supported the clade/group of ( V. rupestris , ( V. acerifolia , V. riparia )) using single nucleotide polymorphism (SNP) genotype and hybridization intensity data derived from the Vitis9kSNP array developed for grape (Myles et al, ). Their group of V. riparia ‐ V. acerifolia ‐ V. rupestris is consistent with series Ripariae Munson (Munson, ; Moore, ).…”

Latent developmental and evolutionary shapes embedded within the grapevine leaf

“…Some, but not all, well-known phylogenetic relationships are reflected in leaf morphology (Fig. 5c) (Zecca et al, 2012;Miller et al, 2013). Notably, clustering the averaged shapes from different genotypes reveals that V. vinifera ssp.…”