  Orphans are genes restricted to a single phylogenetic lineage and emerge at
high rates. While this predicts an accumulation of genes, the gene number has
remained remarkably constant through evolution. This paradox has not yet been
resolved. Because orphan genes have been mainly analyzed over long evolutionary
time scales, orphan loss has remained unexplored. Here we study the patterns of
orphan turnover among close relatives in the Drosophila obscura group. We show
that orphans are not only emerging at a high rate, but that they are also
rapidly lost. Interestingly, recently emerged orphans are more likely to be
lost than older ones. Furthermore, highly expressed orphans with a strong
male-bias are more likely to be retained. Since both lost and retained orphans
show similar evolutionary signatures of functional conservation, we propose
that orphan loss is not driven by high rates of sequence evolution, but
reflects lineage specific functional requirements.
