. "6 Effects of Passage History and Sampling Bias on Phylogenetic Reconstruction of Human Influenza A Evolution." Variation and Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years after Stebbins. Washington, DC: The National Academies Press, 2000.
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Variation and Evolution in Plants and Microorganisms: TOWARD A NEW SYNTHESIS 50 YEARS AFTER STEBBINS
TABLE 3. The distribution of nonsilent (NS) substitutions across internal and terminal branches
Branch type
Number of branches
Exp NS
Obs NS
χ2
Terminal
357
373.6
510
49.8
Internal
355
371.4
235
50.1
Sum
712
745.0
745
99.9
The tree in Fig. 1 has significantly more nonsilent substitutions assigned to its terminalbranches than expected based on the relative numbers of internaland terminal branches, (P < 0.05, df = 1). Exp, expected; Obs, observed.
First, we looked for evidence that mutations were occurring at the 22 known HM codons. Second, we determined whether there were any additional codons, besides the 22 in the HM set, that showed evidence for undergoing HM mutations.
HM Mutations in the Egg and Cell Branches
If HM mutations were occurring in the 22 HM codons, then we should see excess mutations in the HM codons on the egg branches, or the terminal branches attaching sequences from egg-cultured isolates to the tree (Fig. 1). The expectations for this test are based on the distribution of mutations in the non-HM codons across the egg and cell branches. As would be expected if HM mutations were occurring, the set of 22 HM codons underwent a significantly greater number of nonsilent substitutions on the egg branches than expected based on the distribution of mutations at the non-HM codons (Table 4). The number of excess nonsilent substitutions caused by HM change can be estimated as follows. We first assume that the distribution of nonsilent substitutions in the non-HM codons to the egg and cell branches (49.6% and 50.4%, respectively) is
TABLE 4. The distribution of nonsilent (NS) substitutions in HM and non-HM codons across egg and cell branches
Branch type
Obs NS non-HM
Exp NS HM
Obs NS HM
χ2
Egg branches
138
75.45
105
11.57
Cell branches
140
76.55
47
11.40
Sum
278
152.00
152
22.98
The HM codons had significantly more nonsilent substitutions on theterminal branches attaching sequences from egg-cultured isolatesto the tree in Fig. 1 than on branches attaching sequences from cell-cultured isolates(P < 0.05, df = 1). Expectations are based on the distribution of nonsilentsubstitutions in non-HM codons. Obs, observed; Exp, expected.
