Increased taxon sampling reveals thousands of hidden orthologs in flatworms

Gene gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is however limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the complement of an organism consists of hidden orthologs, those with no apparent homology with common sequenced animal lineages --mistakenly considered new genes-- but actually representing fast evolving orthologs of presumably lost proteins. Here, we describe 'Leapfrog', an automated pipeline that uses increased taxon sampling to overcome long evolutionary distances and identify