A) Pairwise relationships | Equal | Grafen | Nee | Pagel |

Equal | 0.969 | 0.976 | 0.983 | |

Grafen | 0.935 | 0.979 | 0.970 | |

Nee | 0.961 | 0.969 | 0.978 | |

Pagel | 0.964 | 0.958 | 0.978 | |

B) Long-term frequency | ||||

Equal | 0.990 | 0.986 | 0.993 | |

Grafen | 0.990 | 0.996 | 0.998 | |

Nee | 0.971 | 0.993 | 0.994 | |

Pagel | 0.990 | 0.996 | 0.990 | |

C) Phylogenetic mean | ||||

Equal | 0.995 | 0.991 | 0.991 | |

Grafen | 0.996 | 0.999 | 0.996 | |

Nee | 0.986 | 0.998 | 0.998 | |

Pagel | 0.990 | 0.997 | 0.998 | |

D) Full vs. indigenous | ||||

Long-term frequency | 0.989 | 0.988 | 0.975 | 0.991 |

Phylogenetic mean | 0.987 | 0.990 | 0.992 | 0.990 |

Conditional | 0.918 | 0.926 | 0.928 | 0.921 |

(A–C) Comparison of results using different branch-length assumptions for A) Pairwise relationship LR values, B) long-term frequency estimates, and C) phylogenetically weighted mean frequency estimates. Upper triangles in italics in A–C represent results using the full sample (

*n*= 304; i.e., including 103 recordings with evidence of horizontal transmission) and the lower triangles represent results using the indigenous subsample (*n*= 201). (D) Comparison of results using full sample vs. indigenous sample. See*SI Methods*for full details and Fig. S2 for visualizations of branch lengths under the assumptions of equal branch length and the transformation methods of Grafen, Nee, and Pagel.