SRA

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historic species diversity. The genomes of an increasing number of species, including specimen extracted from natural history collections, are being sequenced at low depth. While these datasets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored because the low coverage prevents assembly. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such datasets. Using the example of the Oleeae tribe, a worldwide-distributed group including the olive tree, we build phylogenies based on single-nucleotide polymorphism (SNP) alignments obtained with two different reference genomes (from the olive and ash trees). The inferred phylogenies are highly congruent, but present slight differences. Reducing the genome complexity by using pairs of orthologous coding sequences as the reference removes problems of lineage-specific gene duplication and recent polyploidy events. Concatenated and coalescence trees based on these conserved markers reconcile multiple whole genome datasets and can reveal events of incomplete lineage sorting and/or hybridization during the diversification of large phylogenetic groups. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence datasets for groups of eukaryotes with complex and variable genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographic analyses covering both the extant and historic diversity stored in museum collections.