Data from: High rate of translocation-based gene birth on the Drosophila Y chromosome

The Y chromosome is a unique genetic environment defined by a lack of
recombination and male-limited inheritance. The Drosophila Y chromosome
has been gradually acquiring genes from the rest of the genome, with only
seven Y-linked genes being gained over the past 63 million years (0.12
gene gains per million years). Using a next-generation sequencing
(NGS)-powered genomic scan, we show that gene transfers to the Y
chromosome are much more common than previously suspected: at least 25
have arisen across three Drosophila species over the past 5.4 million
years (1.67 per million years for each lineage). The gene transfer rate is
significantly lower in Drosophila melanogaster than in the Drosophila
simulans clade, primarily due to Y-linked retrotranspositions being
significantly more common in the latter. Despite all Y-linked gene
transfers being evolutionarily recent (<1 million years old), only
three showed evidence for purifying selection (ω ≤ 0.14). Thus, although
the resulting Y-linked functional gene acquisition rate (0.25 new genes
per million years) is double the longer-term estimate, the fate of most
new Y-linked genes is defined by rapid degeneration and pseudogenization.
Our results show that Y-linked gene traffic, and the molecular mechanisms
governing these transfers, can diverge rapidly between species, revealing
the Drosophila Y chromosome to be more dynamic than previously
appreciated. Our analytical method provides a powerful means to identify
Y-linked gene transfers and will help illuminate the evolutionary dynamics
of the Y chromosome in Drosophila and other species.