references.bib

@ARTICLE{Ragsdale2020-hv,
  title    = "Unbiased Estimation of Linkage Disequilibrium from Unphased Data",
  author   = "Ragsdale, Aaron P and Gravel, Simon",
  abstract = "Linkage disequilibrium (LD) is used to infer evolutionary
              history, to identify genomic regions under selection, and to
              dissect the relationship between genotype and phenotype. In each
              case, we require accurate estimates of LD statistics from
              sequencing data. Unphased data present a challenge because
              multilocus haplotypes cannot be inferred exactly. Widely used
              estimators for the common statistics r2 and D2 exhibit large and
              variable upward biases that complicate interpretation and
              comparison across cohorts. Here, we show how to find unbiased
              estimators for a wide range of two-locus statistics, including
              D2, for both single and multiple randomly mating populations.
              These unbiased statistics are particularly well suited to
              estimate effective population sizes from unlinked loci in small
              populations. We develop a simple inference pipeline and use it to
              refine estimates of recent effective population sizes of the
              threatened Channel Island Fox populations.",
  journal  = "Mol. Biol. Evol.",
  volume   =  37,
  number   =  3,
  pages    = "923--932",
  month    =  mar,
  year     =  2020,
  keywords = " Ne estimation; demographic inference; linkage disequilibrium;
              sample size",
  language = "en",
  issn     = "0737-4038, 1537-1719",
  pmid     = "31697386",
  doi      = "10.1093/molbev/msz265",
  pmc      = "PMC7038669"
}


@ARTICLE{Thornton2019-nu,
  title    = "Polygenic Adaptation to an Environmental Shift: Temporal Dynamics
              of Variation Under Gaussian Stabilizing Selection and Additive
              Effects on a Single Trait",
  author   = "Thornton, Kevin R",
  abstract = "Predictions about the effect of natural selection on patterns of
              linked neutral variation are largely based on models involving
              the rapid fixation of unconditionally beneficial mutations.
              However, when phenotypes adapt to a new optimum trait value, the
              strength of selection on individual mutations decreases as the
              population adapts. Here, I use explicit forward simulations of a
              single trait with additive-effect mutations adapting to an
              ``optimum shift.'' Detectable ``hitchhiking'' patterns are only
              apparent if (i) the optimum shifts are large with respect to
              equilibrium variation for the trait, (ii) mutation rates to
              large-effect mutations are low, and (iii) large-effect mutations
              rapidly increase in frequency and eventually reach fixation,
              which typically occurs after the population reaches the new
              optimum. For the parameters simulated here, partial sweeps do not
              appreciably affect patterns of linked variation, even when the
              mutations are strongly selected. The contribution of new
              mutations vs. standing variation to fixation depends on the
              mutation rate affecting trait values. Given the fixation of a
              strongly selected variant, patterns of hitchhiking are similar on
              average for the two classes of sweeps because sweeps from
              standing variation involving large-effect mutations are rare when
              the optimum shifts. The distribution of effect sizes of new
              mutations has little effect on the time to reach the new optimum,
              but reducing the mutational variance increases the magnitude of
              hitchhiking patterns. In general, populations reach the new
              optimum prior to the completion of any sweeps, and the times to
              fixation are longer for this model than for standard models of
              directional selection. The long fixation times are due to a
              combination of declining selection pressures during adaptation
              and the possibility of interference among weakly selected sites
              for traits with high mutation rates.",
  journal  = "Genetics",
  volume   =  213,
  number   =  4,
  pages    = "1513--1530",
  month    =  dec,
  year     =  2019,
  keywords = "forward simulation; hitchhiking; linked selection; polygenic
              adaptation",
  language = "en",
  issn     = "0016-6731, 1943-2631",
  pmid     = "31653678",
  doi      = "10.1534/genetics.119.302662",
  pmc      = "PMC6893385"
}