Observations of F region electron density, electron and ion temperatures and ion drift velocity over the latitude interval 40¿<&Lgr;70¿ have been made from Millstone Hill by means of incoherent scatter radar. We conclude that the F region density through that forms on the nightside of the earth may have more than one cause. Current computer models indicate that it can be produced as a consequence of the competing effects of convection and corotation that cause some flux tubes to remain for long periods in darkness in the premidnight sector, thereby allowing the ionisation in them to decay. Our observations show that troughs often are first seen in the late afternoon sector in regions of fast sunward convective flow and can move in latitude in association with substorms. We suggest that these troughs are produced by convection of low density regions from the nightside into daylight and the increased recombination rate that occurs in regions where the O+ ions are forced through the neutral air at high speed (~1 km/s). Troughs created in the dusk sector by this mechanism during substorms can be left as the ionospheric signature of the substorm or ''fossil'' when the region of fast convective flow moves poleward following the substorm. These extended E-W troughs then are carried across the nightside of the earth by corotation. Relative to the surrounding regions, the trough changes little with time and finally is destroyed only when it is carried into sunlight on the dawnside.