Species trees have traditionally been inferred from a few selected markers, andgenome‐wide investigations remain largely restricted to model organisms or smallgroups of species for which sampling of fresh material is available, leaving out mostof the existing and historical species diversity. The genomes of an increasing numberof species, including specimens extracted from natural history collections, are beingsequenced at low depth. While these data sets are widely used to analyse organellegenomes, the nuclear fraction is generally ignored. Here we evaluate different refer-ence‐based methods to infer phylogenies of large taxonomic groups from such datasets. Using the example of the Oleeae tribe, a worldwide‐distributed group, we buildphylogenies based on single nucleotide polymorphisms (SNPs) obtained using tworeference genomes (the olive and ash trees). The inferred phylogenies are overallcongruent, yet present differences that might reflect the effect of distance to thereference on the amount of missing data. To limit this issue, genome complexity wasreduced by using pairs of orthologous coding sequences as the reference, thus allow-ing us to combine SNPs obtained using two distinct references. Concatenated andcoalescence trees based on these combined SNPs suggest events of incomplete line-age sorting and/or hybridization during the diversification of this large phylogeneticgroup. Our results show that genome‐wide phylogenetic trees can be inferred fromlow‐depth sequence data sets for eukaryote groups with complex genomes, and his-tories of reticulate evolution. This opens new avenues for large‐scale phylogenomicsand biogeographical analyses covering both the extant and the historical diversitystored in museum collections.