| Id |
Subject |
Object |
Predicate |
Lexical cue |
| T126 |
0-212 |
Sentence |
denotes |
While there was only limited evidence of diversification at selected sites, we also assessed whether subpopulations among the globally circulating viral population had become genetically differentiated over time. |
| T127 |
213-431 |
Sentence |
denotes |
To do so, we used two measures of population differentiation, the GST and D statistics, which characterize changes in allele frequency across populations and can show fitness differences between subpopulations (30–32). |
| T128 |
432-561 |
Sentence |
denotes |
Genetic distances between two subpopulations can range between 0 and 1, indicating no and complete differentiation, respectively. |
| T129 |
562-733 |
Sentence |
denotes |
We initially compared 30 genomes sampled from the initial outbreak in Wuhan, China, with subsampled alignments of the 18,484 genomes sampled subsequently across the globe. |
| T130 |
734-1013 |
Sentence |
denotes |
Although distances varied across genes, the median genetic distance between these subpopulations was small for both GST (0.0049 ± 0.0047) and D (0.0053 ± 0.0272), indicating little differentiation between the initial outbreak and its global derivatives in the pandemic (Fig. 4A). |
| T131 |
1014-1093 |
Sentence |
denotes |
We then compared subpopulations sampled before and after each consecutive week. |
| T132 |
1094-1280 |
Sentence |
denotes |
Similarly, genetic distances between subpopulations were small for both GST (0.0058 ± 0.0096) and D (0.0098 ± 0.0650) and tended to narrow over time rather than diverge (Fig. 4 B and C). |
| T133 |
1281-1375 |
Sentence |
denotes |
Signatures of host adaptation can also be seen in the branching patterns of viral phylogenies. |
| T134 |
1376-1571 |
Sentence |
denotes |
Bursts in transmissibility are emblematic of increases in relative viral fitness and are reflected in imbalances in the phylogeny, which can be estimated at each internal node (SI Appendix, Figs. |
| T135 |
1572-1592 |
Sentence |
denotes |
S9 and S10) (33–35). |
| T136 |
1593-1882 |
Sentence |
denotes |
We estimated phylogenetic η (36, 37) at each internal node of the SARS-CoV-2 phylogeny reconstructed from subsampled (10%) alignments and compared the distribution of estimates through time to phylogenies simulated under models of neutral and positive time-dependent rates (b(t) = beα(t)). |
| T137 |
1883-1994 |
Sentence |
denotes |
Simulation analyses demonstrated that this metric was robust against sampling fraction (SI Appendix, Fig. S10). |
| T138 |
1995-2245 |
Sentence |
denotes |
The distribution of η in the SARS-CoV-2 phylogenies adhered to expectations of the neutral model and deviated significantly (Student’s t test, P < 0.001) from those of positive time-dependent rates for selection coefficients α ≥ 0.2 (Fig. 4 D and E). |
| T139 |
2246-2405 |
Sentence |
denotes |
Together, the SARS-CoV-2 population and phylogenetic dynamics showed little evidence that the global spread of SARS-CoV-2 was related to viral fitness effects. |
