Table 2.

Summary of intra-animal amino acid and nucleotide diversity and sequence length in V1V2 env. Pairwise distances were calculated using the Gamma distance method with gamma shape parameter of 0.3 in the program Mega 2.0 b. Shown are the mean, standard deviation, maximum, and minimum pairwise amino acid and nucleotide diversity and mean, maximum and minimum amino acid sequence length for each animal, at each time point.

Animal	Date	Diversity (aa) (Min, Max)	St Dev (aa)	Diversity (nt) (Min, Max)	St Dev (nt)	Length (aa) (Min, Max)	# N-glyc sites (Min, Max)
FQi	3-99	0.097 (0, 0.21)	0.047	0.051 (0, 0.115)	0.024	142.11 (140, 145)	6.6 (5, 9)
	5-99	0.067 (0, 0.13)	0.037	0.033 (0, 0.065)	0.018	141.41 (140, 144)	7.1 (5, 9)
	5-01	0.087 (0, 0.18)	0.037	0.047 (0, 0.107)	0.017	142.64 (140, 144)	7.9 (6, 9)
FDo	3-99	0.041 (0.01, 0.09)	0.018	0.021 (0.006, 0.042)	0.009	143.77 (142, 145)	8.4 (8, 9)
	5-99	0.033 (0, 0.07)	0.014	0.020 (0.003, 0.042)	0.008	143.53 (141, 145)	8.5 (7, 9)
	5-01	0.059 (0, 0.11)	0.024	0.029 (0.003, 0.059)	0.011	144.89 (141.149)	7.5 (4, 9)
FJo	3-99	0.123 (0.02, 0.26)	0.052	0.063 (0.006, 0.128)	0.026	156.83 (148, 163)	7.9 (6, 10)
	5-99	0.076 (0, 0.18)	0.050	0.045 (0, 0.113)	0.028	148.43 (145, 153)	6.1 (6, 7)
	5-01	0.160 (0, 0.38)	0.082	0.088 (0, 0.177)	0.041	150.26 (144, 152)	6.1 (3, 7)
FBo	3-99	0.086 (0, 0.2)	0.041	0.045 (0, 0.101)	0.020	147.16 (137, 156)	6.6 (5, 8)
	5-99	0.118 (0.01, 0.31)	0.047	0.058 (0.003, 0.136)	0.022	146.64 (137, 151)	6.9 (6, 8)
	5-01	0.110 (0, 0.21)	0.047	0.053 (0, 0.102)	0.022	147.61 (142, 153)	6.6 (6, 8)
FFj	3-99	0.029 (0, 0.08)	0.015	0.017 (0, 0.035)	0.007	141.39 (140, 145)	7.8 (7, 8)
	5-99	0.051 (0, 0.11)	0.023	0.024 (0, 0.046)	0.010	141.42 (133, 145)	7.8 (7, 8)
	5-01	0.032 (0, 0.07)	0.018	0.016 (0.006, 0.031)	0.006	144.83 (141, 149)	7.6 (6, 8)