‘Representative Genes’, is it OK to use a small amount of data to obtain a phylogeny that is at least close to the true tree?

Despite the problems associated with the one‐gene‐constructed phylogenetic relationships, recently it has been shown that merely adding more sequences to the analyses is not enough to resolve all the inconsistencies present in these relationships. In this work, the existence of ‘representative’ genes for groups of species is evaluated in terms of efficiency (costs/benefits), employing the cytochrome c oxidase subunit I (COI) and the penguins' phylogeny as a case study. ‘Representative’ genes are very useful and they could produce good results for first approaches or humble laboratories, especially if the gene is chosen depending on the time scale and objectives of our work.