Topology testing of phylogenies using least squares methods

Table 4 Topology testing with a large data set of closely related Hepatitis C Virus sequences.

patient tested	ELW	KH	SH	WLS
none (ML tree)	0.5646	1.0000	1.0000	1 (24612.96)
LC-51	0.0304	0.0830	0.9690	1 (25425.09)
LC-86	0.0232	0.0430	0.6840	1 (25420.40)
LC-26	0.0057	0.0180	0.4890	1 (24920.98)
LC-24	0.0026	0.0090	0.5670	1 (24685.62)
LC-59	0.0051	0.0230	0.6430	1 (25201.22)
LC-53	0.0823	0.1060	0.9790	1 (24663.34)
LC-38	0.1297	0.1640	0.7740	1 (24183.58)
LC-63	0.0131	0.0210	0.5010	1 (25707.20)
EO-79	0.0774	0.0750	0.8960	1 (24590.74)
EO-47	0.0313	0.0840	0.9700	1 (25296.47)
EO-95	0.0009	0.0060	0.3930	1 (26175.50)
EO-12	0.0055	0.0260	0.6230	1 (23654.40)
EO-02	0.0226	0.0620	0.7740	1 (25392.13)
O1–00	0.0000	0.0000	0.0000	1 (39958.46)
O1–69	0.0057	0.0170	0.4890	1 (24920.98)
O2–60	0.0000	0.0000	0.0000	0 (56449.21)
O2–61	0.0000	0.0000	0.0000	1 (37982.68)
O2–29	0.0000	0.0000	0.0000	0 (64100.40)
O3–10	0.0000	0.0000	0.0000	0 (50280.91)
O3–72	0.0000	0.0000	0.0000	0 (57742.44)
O3–62	0.0000	0.0000	0.0010	0 (56689.96)
O3–63	0.0000	0.0000	0.0000	0 (58317.22)
O3–91	0.0000	0.0000	0.0000	0 (54015.96)
O3–12	0.0000	0.0000	0.0000	0 (63679.38)
O3–03	0.0000	0.0000	0.0000	0 (63107.46)
O3–42	0.0000	0.0000	0.0000	0 (62828.41)
O3–50	0.0000	0.0000	0.0000	0 (55717.93)
O3–54	0.0000	0.0000	0.0000	0 (45640.57)
O3–80	0.0000	0.0000	0.0010	0 (63024.57)
O3–79	0.0000	0.0000	0.0000	0 (58853.93)
O3–98	0.0000	0.0000	0.0000	0 (51672.80)

The data set consisted of 295 sequences corresponding to the E1–E2 region of the viral genome taken from 23 patients plus 8 local control (LC) sequences of the same genotype (HCV-1b) taken from individuals unrelated to the outbreak. The results from a more detailed analysis with an expanded data set were used to separate the 23 patients into four groups: EO, excluded from the outbreak; O1, involved in the outbreak, transmission chain 1; O2, involved in transmission chain 2; and O3, involved in transmission chain 3. The test set consisted of 32 trees, the ML tree and 31 trees in which the sequences from each patient where moved to form a monophyletic group with the external controls. For each alternative topology the probability associated to the corresponding test statistic (see abbreviations in Table 1) is shown. Topologies included in the confidence set around the ML tree at the 0.05 level (bold) are indicated. For WLS, the value of the corresponding statistic is shown between parentheses.

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