| Allele frequency in generation/timepoint *t* |

| Allele frequency change between generations and *t*, |

| Frequency change due to nonheritable variation in fitness, (1), (2) |

| Frequency change due to Mendelian segregation, (1), (2) |

| Frequency change due to heritable differences, (1), (2) |

*N* | Census population size of breeding individuals |

| Effect population size |

| Fitness (expected number of offspring) of individual *i*, (28) |

| Effect size in generation *t* and locus *l*, (5), (36) |

*L* | Total number of loci impacting fitness, (5) |

| Individual *i*’s gene count at locus *l*, (37) |

| Individual *i*’s neutral gene count at the tracked neutral site, (5), (37), (38) |

or | Gametic linkage disequilibrium between the tracked neutral site and selected locus *l* at time *t*, Supplementary Figure SA.2, (5), (37), (38) |

| Nongametic disequilibrium between the tracked neutral site and selected locus *l* at time *t*, Supplementary Figure SA.2, (5), (37), (38) |

| The squared correlation coefficient of linkage disequilibrium between the tracked neutral site and selected site *l* at time *t*, (7), (44) |

| The recombination fraction between the tracked neutral site and selected site *l* |

| The additive genic variance, (8) |

| The additive genetic variance, (17) |

*R* | The total level of recombination in the region, in morgans, (9) and Figure 1 |

| A mapping function (*i.e.*, Haldane’s), which maps a position *g* to a recombination fraction. |

*ρ* | The population recombination rate, , *Temporal autocovariance for an average neutral polymorphism* |

| The average linkage disequilibrium in a region of *R* M, that persisted from generation *t* to generation *s*, (10) |

| The nonheritable variance in offspring number, (11) |

| The sum of site heterozygosity at selected sites time *t*, (13) |

| The sum of site heterozygosity at neutral sites at time *t*, (13) |

| The proportion of sum of site heterozygosity at neutral sites at time *t* relative to , (15) |

| The breeding value of the trait that determines fitness, , see Temporal Variance and Autocovariance Under Multilocus Selection in Appendix |

| The fitness of individual *i* with fitness function , see Temporal Variance and Autocovariance Under Multilocus Selection in Appendix |

**Q** | The sample standardized variance–covariance matrix, (16) |

| The elements of the observed sample matrix **Q**, (16) |

**Σ** | The standardized variance–covariance matrix, based on our theoretical expressions |

| The elements of the standardized variance–covariance matrix, (10), (11) |

| The allele frequency change at site *n* between times time and *t*, (16) |

*τ* | The number of allele frequency changes observed, *e.g.*, after sampling for timepoints |

| The additive genic variation at time *s* as approximated by the observed decay in the sum of site heterozygosity at neutral sites, (15) |

| The variance in trait values taken over individuals, (17) |

| The method-of-moments estimate of the additive genetic variance in the first generation, (19), (18) |

| The method-of-moments estimate of Wright’s standardized variance, , (19), (18) |

| The method-of-moments estimate of drift-effective population size, |

| The sampling noise around each element of the sample variance–covariance matrix. |

*B* | The total number of windows after partitioning the genome, (22) |

| Width of windows (in base pairs), (22) |

| The average additive genetic variance per base pair |

| Number of coding base pairs in a window, (22) |

| Total number of coding base pairs in the genome, (23) |

*G* | A conservative measure of the total variance in allele frequency change due to linked selection, (24) |

| An alternate, less conservative measure of the total variance in allele frequency change due to linked selection, (25) |

| A variant of *G* using the absolute value of covariances, (27) |