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We evaluated different reference-based methods to infer nuclear DNA phylogenies of large taxonomic groups from low depth sequencing datasets. More...

We evaluated different reference-based methods to infer nuclear DNA phylogenies of large taxonomic groups from low depth sequencing datasets. Using the example of the Olive tribe (Oleeae), we build phylogenies based on single-nucleotide polymorphism (SNP) alignments obtained using two different reference genomes (the olive and ash trees). The inferred phylogenies are highly congruent, but present slight differences in phylogenetic relationships among taxa. Reducing the genome complexity by using pairs of orthologous coding sequences as the reference removes problems of lineage-specific gene duplication events. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence datasets for groups of eukaryotes with complex genomes, and histories of reticulate evolution Less...