bacterial adaptation. The definition of taxonomically-restricted genes was introduced into the literature to make orphan genes seem less "mysterious." In 2008, a yeast protein of established functionality, BSC4, was found to have evolved de novo from non-coding sequences whose homology was still detectable in sister species. In 2009, an orphan gene was discovered to regulate an internal biological network: the orphan gene, QQS, from Arabidopsis thaliana modifies plant composition. The QQS orphan protein interacts with a conserved transcription factor, these data explain the compositional changes (increased protein) that are induced when QQS is engineered into diverse species. In 2011, a comprehensive genome-wide study of the extent and evolutionary origins of orphan genes in plants was conducted in the model plant Arabidopsis thaliana " Identification Genes can be tentatively classified as orphans if no orthologous proteins can be found in nearby species. One method used to estimate nucleotide or protein sequence similarity indicative of homology (i.e. similarity due to common origin) is the Basic Local Alignment Search Tool (BLAST). BLAST allows query sequences to be rapidly searched against large sequence databases. Simulations suggest that under certain conditions BLAST is suitable for detecting distant relatives of a gene. However, genes that are short and evolve rapidly can easily be missed by BLAST. The systematic detection of homology to annotate orphan genes is called phylostratigraphy. Phylostratigraphy generates a phylogenetic tree in which the homology is calculated between all genes of a focal species and the genes of other species. The earliest common ancestor for a gene determines the age, or phylostratum, of the gene. The term "orphan" is sometimes used only for the youngest phylostratum containing only a single species, but when interpreted broadly as a taxonomically-restricted gene, it can refer to all but the oldest phylostratum, with the gene orphaned within a larger clade. Homology detection failure accounts for a majority of classified orphan genes. Some scientists have attempted to recover some homology by using more sensitive methods, such as remote homology detection. In one study, remote homology detection techniques were used to demonstrate that a sizable fraction of orphan genes (over 15%) still exhibited remote homology despite being missed by conventional homology detection techniques, and that their functions were often related to the functions of nearby genes at genomic loci. Sources Orphan genes arise from multiple sources, predominantly through de novo origination, duplication and rapid divergence, and horizontal gene transfer. De