Table 3. Distribution of HIV pol sequences used for the phylodynamic and phylogeographic analyses according to subtype and location.

	HIV-1 variant
Location and cohort	Subtype A1	Subtype D	Total
Kampala	125	87	212
FSW	13	7	20
LANLdb	109	72	181
‘Old’ sequences (1986)	3	8	11
Entebbe (LANLdb)	20	13	33
Lake Victoria (FF)	10	16	26
Rural south-west	53	157	210
Masaka district (RCC)	12	30	42
Rakai district (LANLdb)	41	127	168
All	208	273	481

LANLdb, Los Alamos National Laboratory HIV database.

From the original datasets, sequences identified as intra-subtype recombinants by SCUEAL (n = 15, all subtype A1) and sequences with particularly high evolutionary rates according to Path-O-Gen (four subtype A1 and seven subtype D) were excluded to improve the evolutionary analysis in BEAST (see Methods).