A Harvester Sub-Queen is the leader and matriarch of the smaller but still immense Colony ships, and are likely a different Harvester species. The Sub-Queens' apparent purpose is to seek out planets with useful resources and prepare them for greater extraction by the swarms' Harvester Mothership.
For thousands of years, the Harvesters and their Sub-Queens have been destroying civilizations and homeworlds, including the Sphere's, under the command of Harvester Queens.
War of 1996
A Sub-Queen and her Colony ship was sent by a hive queen to Earth to extract it's resources. The Sub-Queen was eventually killed on the third day of the invasion when Steven Hiller and David Levinson destroy her ship with a nuclear warhead from the inside out.
With the Sub-Queen's death, the survivors of her swarm were cut off from the hive mind. 20 years later, upon receiving a distress call from a surviving City destroyer, the IDR Harvester Queen brought her Harvester Mothership to Earth to eradicate the humans herself as revenge. This led to the War of 2016.
During the War of 2016, David Levinson would speculate about the Sub-Queen's presence on the Colony ship and the fact that her death was what truly ended the War of 1996.