The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations

Supporting Information

Supporting Information

  • Supporting Information - Tables S1-S9, Figures S1-S22, Files S1-S11, and Supporting Information Literature Cited (PDF, 3 MB)
  • Table S2 - The effect of assuming p0 small in the diffusion approximation of the mean absorption time. (PDF, 74 KB)
  • Table S3 - The effect of assuming ρ large in M(p) when deriving the diffusion approximation to the mean absorption time. (PDF, 79 KB)
  • Table S4 - The effect of assuming p0 small in the diffusion approximation to the mean absorption time, given the assumption of ρ large in M(p). (PDF, 81 KB)
  • Table S5 - The mean absorption time under the QLE approximation relative to the one without linkage. (PDF, 75 KB)
  • Table S6 - The error of t̄̃QLE relative to ̅tQLE as in Table S2, but for p0 = 0.005 fixed instead of p0 = 1/(2N). (PDF, 86 KB)
  • Table S7 - The error of t̄̃QLE,ρ>>0 relative to ̅tQLE as in Table S3, but for p0 = 0.005 fixed instead of p0 = 1/(2N). (PDF, 93 KB)
  • Table S8 - The error of t̄̃QLE,ρ>>0 relative to t̄̃QLE,ρ>>0 as in Table S4, but for p0 = 0.005 fixed instead of p0 = 1/(2N). (PDF, 95 KB)
  • Table S9 - The ratio ̅tQLE/̅tOLM as in Table S5, but for p0 = 0.005 instead of p0 = 1/(2N). (PDF, 93 KB)
  • Figure S1 - Critical migration rates and invasion of A1 for a monomorphic continent. (PDF, 133 KB)
  • Figure S2 - Critical recombination rate and invasion of A1 for a polymorphic continent. (PDF, 249 KB)
  • Figure S3 - Invasion probability of A1 as a function of the migration rate for a monomorphic continent. (PDF, 135 KB)
  • Figure S4 - Invasion probability of A1 as a function of the recombination rate and the continental frequency of B1. (PDF, 136 KB)
  • Figure S5 - Invasion probability of A1 as a function of the migration rate. (PDF, 174 KB)
  • Figure S6 - Invasion probability of A1 as a function of the continental frequency of B1. (PDF, 163 KB)
  • Figure S7 - Asymptotic stability of the marginal one-locus migration-selection equilibrium ẼB in continuous time I. (PDF, 178 KB)
  • Figure S8 - Asymptotic stability of the marginal one-locus migration-selection equilibrium ẼB in continuous time II. (PDF, 195 KB)
  • Figure S9 - Asymptotic stability of the marginal one-locus migration-selection equilibrium ẼB in continuous time III. (PDF, 188 KB)
  • Figure S10 - Diffusion approximation to the sojourn-time density of A1 under quasi-linkage equilibrium for a polymorphic continent. (PDF, 166 KB)
  • Figure S11 - Comparison of analytical and simulated sojourn-time densites of A1 for a monomorphic continent. (PDF, 144 KB)
  • Figure S12 - Comparison of analytical and simulated sojourn-time densites of A1 for a polymorphic continent. (PDF, 176 KB)
  • Figure S13 - Comparison of various diffusion approximations of the mean absorption time of A1. (PDF, 315 KB)
  • Figure S14 - Mean absorption time of A1 as a function of the migration rate. (PDF, 661 KB)
  • Figure S15 - Mean absorption time of A1 as a function of its selective advantage. (PDF, 361 KB)
  • Figure S16 - Effect of the continental frequency qc of B1 on the mean absorption time of A1. (PDF, 245 KB)
  • Figure S17 - Mean absorption time of A1 as a function of the continental frequency B1. (PDF, 221 KB)
  • Figure S18 - Effective migration rate at a weakly beneficial mutation arising in linkage to a migration-selection polymorphism. (PDF, 123 KB)
  • Figure S19 - Effect of linkage to two selected sites on the absorption time of a neutral mutation. (PDF, 156 KB)
  • Figure S20 - Effect on neutral coalescence of linkage to two sites at migration-selection balance. (PDF, 170 KB)
  • Figure S21 - Mean invasion probability of A1 with linkage to a background polymorphism compared to no linkage. (PDF, 156 KB)
  • Figure S22 - Comparison of branching-process and 'splicing' approximations to the invasion probability of A1 as a function of the recombination rate. (PDF, 127 KB)
  • File S1 - Additional Methods (PDF, 244 KB)
  • File S2 - Deterministic analysis of a diploid two-locus continent-island model in discrete time. (PDF, 2 MB)
  • File S3 - Branching-process approximation of the invasion probability of a weakly beneficial mutation linked to an established polymorphism at migration-selection balance. (PDF, 1 MB)
  • File S4 - Comparison of the Jacobian of the marginal one-locus migration-selection equilibrium (EB) to the mean matrix of the corresponding branching process. (PDF, 616 KB)
  • File S5 - Analytical approximation of the invasion probability for a slightly supercritical branching process. (PDF, 1 MB)
  • File S6 - Derivative of the weighted mean invasion probability ̅π at recombination rate r = 0. (PDF, 1 MB)
  • File S8 - The effective migration rate experienced by a neutral site linked to two loci at migration-selection balance. (PDF, 1 MB)
  • File S9 - The effect on neutral variation of migration and selection at two linked sites. (PDF, 2 MB)
  • Table S1 - Simulated sojourn and absorption times and comparison to diffusion approximation (.xls, 180 KB)
  • File S7 - Diffusion approximation of sojourn and absorption times assuming quasi-linkage disequilibrium (.zip, 8 MB)
  • File S10 - Archive of Mathematica Notebooks in the NB format (Files S2-S9). (.zip, 39 MB)
  • File S11 - Archive of Java source code, binaries, and JAR files for simulations as described in Methods (.zip, 2 MB)