Ty3/gypsy elements represent one of the most abundant and diverse 
LTR-retrotransposon (LTRr) groups in the Anopheles gambiae genome, but their 
evolutionary dynamics have not been explored in detail. Here, we conduct an in 
silico analysis of the distribution and abundance of the full complement of 1045 
copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy 
elements is inversely related to arm length, with densities being greatest on 
the X, and greater on the short versus long arms of both autosomes. Taking into 
account the different heterochromatic and euchromatic compartments of the 
genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along 
each chromosome arm is determined mainly by the different proportions of 
heterochromatin, particularly pericentric heterochromatin, relative to total arm 
length. Additionally, the breakpoint regions of chromosomal inversion 2La 
appears to be a haven for LTRrs. These elements are underrepresented more than 
7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with 
genes. The euchromatin on chromosome 3R shows a faster turnover rate of 
Ty3/gypsy elements, characterized by a deficit of proviral sequences and the 
lowest average sequence divergence of any autosomal region analyzed in this 
study. This probably reflects a principal role of purifying selection against 
insertion for the preservation of longer conserved syntenyc blocks with adaptive 
importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent 
activity, an important fraction are inactive remnants of relatively ancient 
insertions apparently subject to genetic drift. Consistent with these 
computational predictions, an analysis of the occupancy rate of putatively older 
insertions in natural populations suggested that the degenerate copies have been 
fixed across the species range in this mosquito, and also are shared with the 
sibling species Anopheles arabiensis.