Research ArticleEVOLUTIONARY BIOLOGY

Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments

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Science Advances  22 May 2020:
Vol. 6, no. 21, eaba3388
DOI: 10.1126/sciadv.aba3388
  • Fig. 1 Reciprocal transplant experiments reveal plastic and genetic differences in gene expression levels between Tibetan and lowland chickens.

    (A) Map showing the locations and altitudes of the two experimental sites in Sichuan Province, China. Adapted with permission from (33). (B) Design of the reciprocal transplant experiment, in which each of the two breeds are phenotyped in its native environment and the other breed’s native environment. Different symbols indicate different breeds, and different colors indicate different environments where chickens are hatched, reared, and phenotyped. The four samples of chickens phenotyped are numbered. The diagram shows the scenario in which the gene expression level is higher in sample 3 than in sample 1, but the same principle applies if the opposite is true. (C) Samples 1, 2, and 3 in (B) respectively represent the original (O), plastic (P), and adapted (A) stages during the forward adaptation from the lowland to highland. (D) Samples 3, 4, and 1 in (B) respectively represent the O, P, and A stages during the reverse adaptation from the highland to the lowland. (E) Venn diagram showing the number (and percentage) of differentially expressed genes (DEGs) in each tissue between samples 1 and 3 in (B). (F) Numbers of DEGs in each tissue that are plastic-change-only (PO) or genetic-change-needed (GN) during the forward (F) or reverse (R) adaptation. (G) Number of DEGs that are PO divided by the number of DEGs that are GN in F or R adaptation in each tissue and all tissues combined. P values are based on a G test of independence.

  • Fig. 2 Reciprocal transplant experiments reveal plastic and genetic differences in egg hatchability between Tibetan and lowland chickens.

    (A) Fraction of fertilized eggs that are hatched. (B) Survival rate of chicken embryos in the first week of hatching, measured by the number of viable embryos on day 7 divided by the corresponding number on day 0. (C) Survival rate of chicken embryos in the second week of hatching, measured by the number of viable embryos on day 14 divided by the corresponding number on day 7. (D) Survival rate of chicken embryos in the third week of hatching, measured by the number of viable embryos on day 21 divided by the corresponding number on day 14. Breeds are indicated by symbols, while environments are indicated by colors. Error bars show one standard error based on the binomial distribution. P values determined by a G test of independence are shown as follows: ns, P > 0.06; o, 0.05 < P < 0.06; *, 0.01 < P < 0.05; ** 0.001 < P < 0.01; and ***, P < 0.001.

  • Fig. 3 Reciprocal transplant experiments reveal plastic and genetic differences in gene expression levels between E. coli strains adapted to a benign environment and those adapted to 1 of 11 harsh environments.

    The experimental design is analogous to that in Fig. 1B. (A) Numbers of DEGs that are GN in the forward adaptation from the benign environment to one of the harsh environments and the reverse adaptation from each harsh environment to the benign environment. Each line represents the result of one pair of forward and reverse adaptations. (B) Number of DEGs that are PO in F and R adaptations. (C) Number of DEGs that are PO divided by the number of DEGs that are GN in F and R adaptations for each harsh environment and all 11 environments combined. P values are based on a G test of independence. The benign environment is the M9 medium with glucose (5 g/liter), whereas the harsh environments numbered 1 to 11 respectively contain cobalt chloride (16 μM), sodium carbonate (32.5 mM), methylglyoxal (350 μM), cetylpyridinium chloride (4.8 μM), crotonate (50 mM), n-butanol (1.25%), methacrylate (8.75 mM), potassium chloride (210 mM), l-lactate (40 mM), sodium chloride (400 mM), and l-malate (30 mM).

  • Fig. 4 A potential mechanism responsible for long-term memories of ancestral environments in the form of phenotypic plasticity by gene expression regulation.

    (A) Lowland expression of a hypothetical gene in lowland-adapted chickens. (B) Highland expression of the gene in lowland-adapted chickens. (C) Highland expression of the gene in highland-adapted chickens. (D) Lowland expression of the gene in highland-adapted chickens. The gray rectangle shows a regulatory motif that binds to a basal transcription factor (gray oval) to allow transcription at the basal level. Green diamonds indicate the mRNA molecules produced. The orange rectangle shows a regulatory motif that binds to a highland-specific transcription factor (orange oval) to increase the transcription level. From (A) to (B), a plastic change is unable to raise the expression level because of the lack of the orange motif, whereas from (C) to (D), a plastic change can lower the gene expression level because of the turnoff of the highland-specific transcription factor in the lowland. A similar model in which the highland-specific transcription factor is a repressor can explain should the optimal gene expression be lower in the highland than in the lowland.

  • Table 1 Numbers of DEGs that are PO or GN in adaptations of guppies from high- to low-predation streams and the potential reverse adaptations.

    Independent evolution occurred in a natural population (natural) and two human-introduced populations (Intro1 and Intro2).

    Intro1Intro2Natural
    Forward
    adaptation
    Reverse
    adaptation
    Forward
    adaptation
    Reverse
    adaptation
    Forward
    adaptation
    Reverse
    adaptation
    PO04130131
    GN20161714554524
    PO/GN*0.000.250.0590.210.000.25
    P0.0140.259.9 × 10−40

    *The number of genes that are PO divided by the number of genes that are GN.

    G test of independence of the numbers of PO and GN genes in forward and reverse adaptations.

    Supplementary Materials

    • Supplementary Materials

      Phenotypic plasticity as a long-term memory easing readaptations to ancestral environments

      Wei-Chin Ho, Diyan Li, Qing Zhu, Jianzhi Zhang

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