Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls.

Area of Science:

• Evolutionary biology
• Genomics
• Bioinformatics

Background:

• Understanding species relationships is key in evolutionary biology.
• Single nucleotide polymorphisms (SNPs) from next-generation sequencing aid phylogeny reconstruction.
• SNP arrays offer efficient genotyping but can suffer from ascertainment bias.

Purpose of the Study:

• To investigate the impact of ascertainment bias on SNP-based phylogeny reconstruction.
• To evaluate the effectiveness of hybridization intensity data versus genotype calls in mitigating this bias.
• To reconstruct the evolutionary relationships within the Vitis genus using an improved method.

Main Methods:

• Utilized SNP genotype and hybridization intensity data from the Vitis9kSNP array.
• Compared phylogenies constructed using traditional genotype calls versus hybridization intensity data.
• Applied data to reconstruct evolutionary relationships among Vitis species.

Main Results:

• Hybridization intensity data significantly reduce ascertainment bias compared to genotype calls.
• Phylogenies built with hybridization intensities are more accurate.
• Reconstructed Vitis phylogeny confirms North American subgenus Vitis species are monophyletic and resolves relationships among them.

Conclusions:

• Hybridization intensity data offer a more accurate approach for array-enabled phylogeny reconstruction by minimizing ascertainment bias.
• This method provides a robust tool for resolving evolutionary relationships, particularly in the Vitis genus.
• The findings have broad implications for phylogenetic studies using SNP array data.