Model name | Constraint/optimization of each h^{a} | P-values from LR tests | ||||||||
---|---|---|---|---|---|---|---|---|---|---|

h^{WR}^{C} | h^{G}^{YW} | h^{W}^{A} | h^{T}^{W} | h^{SY}^{C} | h^{G}^{RS} | CH103 | VRC26 | VRC01 | ||

Symmetric WRC/GYW^{a} | ML | h^{WR}^{C} | 0 | 0 | 0 | 0 | 4.6 × 10^{−15} | 6.3 × 10^{−05} | 5.2 × 10^{−03} | |

Asymmetric WRC/GYW | ML | ML | 0 | 0 | 0 | 0 | ||||

Symmetric WA/TW^{a} | 0 | 0 | ML | h^{W}^{A} | 0 | 0 | <1 × 10^{−15} | <1 × 10^{−15} | <1 × 10^{−15} | |

Asymmetric WA/TW | 0 | 0 | ML | ML | 0 | 0 | ||||

Symmetric SYC/GRS^{a} | 0 | 0 | 0 | 0 | ML | h^{SY}^{C} | 0.53 | 2.0 × 10^{−13} | 4.2 × 10^{−03} | |

Asymmetric SYC/GRS | 0 | 0 | 0 | 0 | ML | ML | ||||

Uniform hotspots^{a} | ML | h^{WR}^{C} | h^{WR}^{C} | h^{WR}^{C} | 0 | 0 | 4.2 × 10^{−15} | <1 × 10^{−15} | <1 × 10^{−15} | |

Hierarchical hotspots | ML | h^{WR}^{C} | ML | h^{W}^{A} | 0 | 0 | ||||

SCAH^{a} | ML | ML | ML | ML | ML | h^{SY}^{C} | 0.65 | 1.2 × 10^{−06} | 9.1 × 10^{−04} | |

FCH | ML | ML | ML | ML | ML | ML |

Models of hotspot hierarchy (degree of mutability) and symmetry, specified by placing constraints on how different values of

*h*are optimized. Columns 2–7 show how the parameter*h*is obtained for a particular model. A value of 0 indicates that^{a}*h*is fixed at zero, ML indicates that a parameter is optimized by ML, and*h*indicates that^{a}*h*parameter is equal to another value of*h*. For instance, in*Symmetric WRC/GYW*,*h*^{G}^{YW}is equal to its reverse complement*h*^{WR}^{C}, which is ML optimized. However, in*Asymmetric WRC/GYW*, both are ML optimized. Rows 8–10 show*P*-values obtained from likelihood-ratio tests of each of these nested hotspot models for the bNAb lineage specified in each column. Parameters, log likelihood, and AIC of each fit are shown in Figure S3 in File S1. LR, likelihood ratio; SCAH, symmetric coldspots, asymmetric hotspots; FCH, free coldspots and hotspots.↵a Each of these models is nested with the model immediately below it by one free parameter, allowing hypothesis testing using a likelihood-ratio test.