Research ArticleEVOLUTIONARY GENETICS

Evolutionary dynamics of CRISPR gene drives

See allHide authors and affiliations

Science Advances  05 Apr 2017:
Vol. 3, no. 4, e1601964
DOI: 10.1126/sciadv.1601964
  • Fig. 1 CRISPR gene drive inheritance and spread in wild populations.

    (A) Inheritance and spread of a gene drive construct, D, in a population of individuals homozygous for the wild type, W. In the late germ line, the drive construct induces a DSB at its own position on the homologous chromosome, which is repaired either by HR, converting the individual to a DD homozygote, or by NHEJ, producing a small insertion/deletion/substitution mutation at the cut site, which results in a drive-resistant allele. There is also the possibility of no modification, in which case the W allele remains unchanged. This mechanism can lead to rapid spread of the gene drive in a population or spread of resistant alleles, depending on their relative fitness effects. (B) To achieve this mechanism, previously demonstrated drive constructs are inserted at some target sequence (blue) and carry a CRISPR nuclease (for example, Cas9) with a gRNA, as well as a “cargo gene,” which can be chosen arbitrarily for the desired application. Disruption of the target sequence must be nearly neutral for the drive to spread. (C) The construct modeled here, which was proposed by Esvelt et al. (2), reconstitutes the target gene after cutting—so an essential gene can be chosen as the target to select against resistant alleles—and uses multiple (n) gRNAs.

  • Fig. 2 Modeling framework and representative simulations.

    (A) We consider 2n + 2 alleles, where n is the number of drive target sites (prescribed by CRISPR gRNAs): the drive construct (D), the wild type (W), n “neutral” resistant alleles (Si), and n “costly” resistant alleles (Ri). Previous drives (left) used one target site, whereas our proposed drives use multiple target sites (right). (B) Conversion dynamics within DW germline cells during early gametogenesis. Cutting occurs at each susceptible target independently with probability q. Then, repair occurs by HR with probability P or by NHEJ with probability 1 − P. In the case of a single cut (light gray), if there is NHEJ repair, then repair produces a functional target gene with probability γ or a nonfunctional target with probability 1 − γ. Two or more cuts (light red) certainly produce nonfunctional targets after NHEJ repair. (C) Representative simulations using high cutting and HR probabilities (q = P = 0.95), for an initial drive release of 1% in a wild-type population, with γ = 1/3. Fitness parameters are (left) fSS = fSR = 1, fSD = 95%, fRR = 99%, fDD = fDR = (99 × 95%) = 94.1%, where S refers to neutral alleles (either S or W), and (right) fSS = fSR = 1, fSD = fDD = fDR = 95%, fRR = 1%, where S and R refer to alleles W, S1, …, S5 and R1, …, R5, respectively. See section S7.3.2 for details regarding our assignments of the inheritance probabilities.

  • Fig. 3 Quantitative comparison of previously demonstrated and recently proposed drive constructs.

    (A and B) Drive frequency over time for three particular scenarios: a low-cost alteration drive carrying a cargo gene and targeting a neutral site (previous drives) or an essential gene (proposed drives) (red), a low-cost drive whose aim is to disrupt an important target gene (orange), and a high-cost drive (tan). (C) Maximum drive allele frequency (heat) observed in simulations across 200 generations, following an initial release of drive-homozygous organisms comprising 1% of the total population. In white hatched regions, Eq. 1 is not satisfied, so no invasion occurs. (D) Generations to 90% of the maximum frequency. (E) Frequency of the drive constructs after 200 generations, a measure of stability in the population. Parameters used are as follows: (throughout) q = P = 0.95, γ = 1/3; (previous drives) n = 1, fSS = fSR = 1, fSD = 1 − c, fDD = fDR = (1 − c) (1 − s), fRR = 1 − s; (proposed drives) n = 5, fSS = fSR = 1, fSD = fDD = fDR = 1 − c, fRR = 1 − s, where S and R refer to any alleles S0, …, Sn and R1, …, Rn, respectively. Inheritance probabilities are assigned as illustrated in Fig. 2B and described in section S7.3.2.

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/3/4/e1601964/DC1

    section S1. Previous work on homing endonuclease gene drives

    section S2. Model for the evolutionary dynamics of a CRISPR gene drive with n gRNAs

    section S3. Invasion of the drive construct

    section S4. Stability of the drive construct

    section S5. Interior equilibria

    section S6. Numerical examples

    section S7. Neutral resistance

    fig. S1. Numerical simulations of the evolutionary dynamics.

  • Supplementary Materials

    This PDF file includes:

    • section S1. Previous work on homing endonuclease gene drives
    • section S2. Model for the evolutionary dynamics of a CRISPR gene drive with n gRNAs
    • section S3. Invasion of the drive construct
    • section S4. Stability of the drive construct
    • section S5. Interior equilibria
    • section S6. Numerical examples
    • section S7. Neutral resistance
    • fig. S1. Numerical simulations of the evolutionary dynamics.

    Download PDF

    Files in this Data Supplement: