ED Table 1.
Molecular clock, phylogeographic and recombination estimates for the different data sets
| Data set | TMRCA (subtype B & D) | TMRCA (subtype B) | Location probability (subtype B) | Jump time (CB to US) | TMRCA (US subtype B) | Location probability (US subtype B) | Evolutionary rate | Rate, coefficient of variation | Phi test p-value |
|---|---|---|---|---|---|---|---|---|---|
| “full genome 46”, ED Fig. 2 & ED Fig. 3 | 1953 (1946, 1961) | 1967 (1963, 1970) | CB: > 0.99 | 1970 (1968, 1973) | 1972 (1969, 1973) | US: > 0.99 | 0.0027 (0.0024, 0.0030) | 0.25 (0.20, 0.31) | 0.99 |
| “full genome 38”, Fig. 1 & ED Fig. 2 | 1955 (1946, 1962) | 1967 (1963, 1970) | CB: 0.99 | 1971 (1968. 1973) | 1972 (1970, 1974) | NY: > 0.99 | 0.0024 (0.0021, 0.0027) | 0.26 (0.20, 0.32) | 0.99 |
| “gag”, ED Fig. 3 | 1958 (1950, 1964) | 1969 (1964, 1972) | CB: > 0.99 | 1972 (1969, 1974) | 1974 (1971, 1975) | US: > 0.99 | 0.0023 (0.0020, 0.0026) | 0.23 (0.14, 0.33) | 0.77 |
| “pot”, ED Fig. 3 | 1956 (1947, 1965) | 1967 (1961, 1972) | CB: 0.92 | 1970 (1966, 1973) | 1973 (1969, 1974) | US: > 0.99 | 0.0015 (0.0013, 0.0017) | 0.29 (0.20, 0.37) | 0.21 |
| “env”, ED Fig. 3 | 1953 (1943, 1962) | 1968 (1964, 1972) | CB: > 0.99 | 1970 (1966, 1973) | 1971 (1968, 1974) | US: 0.99 | 0.0037 (0.0032, 0.0043) | 0.25 (0.16, 0.34) | <0.01 |
| “env, recomb. free”* | 1952 (1940, 1961) | 1968 (1964, 1972) | CB: 0.99 | 1970 (1966, 1973) | 1971 (1967, 1973) | US: 0.99 | 0.0039 (0.0031, 0.0047) | 0.26 (0.18, 0.35) | 0.59 |
| “env 105”, ED Fig. 5 | 1954 (1947, 1961) | 1968 (1964, 1971) | CB: > 0.99 | 1970 (1968, 1972) | 1971 (1969, 1973) | US: > 0.99 | 0.0047 (0.0042,0.0052) | 0.23 (0.18,0.28) | 0.01 |
| “env 105, recomb. free”* | 1955 (1947, 1961) | 1968 (1974, 1970) | CB: > 0.99 | 1970 (1968.1972) | 1971 (1969, 1972) | US: > 0.99 | 0.0047 (0.0041,0.0053) | 0.23 (0.18, 0.28) | 0.26 |
| “env 74”, ED Fig. 5 | 1957 (1948, 1963) | 1969 (1963, 1971) | CB: > 0.99 | 1971 (1969, 1973) | 1972 (1969, 1974) | NY: 0.97 | 0.0044 (0.0038, 0.0050) | 0.28 (0.21, 0.36) | <0.01 |
| “env 74, recomb. free”* | 1957 (1948, 1964) | 1969 (1964, 1972) | CB: 0.99 | 1971 (1968, 1973) | 1972 (1970, 1974) | NY: 0.97 | 0.0046 (0.0038, 0.0054) | 0.31 (0.23, 0.39) | 0.91 |
| “env 133”, ED Fig. 6† | 1952 (1944, 1958) | 1966 (1963, 1969) | CB: 0.99 | 1969 (1966, 1971) | 1969 (1967, 1971) | NY: 0.67 | 0.0045 (0.0041, 0.0048) | 0.20 (0.16,0.23) | 0.76 |
*
The recombination free (“recomb. free”) data sets were obtained by deleting the minor recombinant regions from the putative recombinants identified using RDP4.
†
the empirical trees from the “env 133” analysis were used for two different ancestral reconstructions (ED Fig. 6); here we list the location estimates for the analysis that considered different US states for the late samples (ED Fig. 6b).