Can Evolution Supply What Ecology Demands?

这是Trends in Ecology & Evolution上的一篇新review，这个期刊影响因子超过10，在生态学里还是非常有分量。我的研究生课题是关于进化的，属于分子生态，群体遗传学，蹭着热点做表观遗传。这么简洁的题目，立刻吸引了我，不过我没看懂supply和demand究竟是什么意思？因为摘要里谈到了争议的表观遗传在进化中的地位。我还是决定快速扫一遍这篇总数。

整体上，这边总是很适合做教材，学习进化生态学。

Kokko, H. et al. Can Evolution Supply What Ecology Demands? Trends in Ecology & Evolution 0, (2017).

http://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(16)30238-5

（注释：以前读文献基本不做标记，虽然能读懂，也能知晓实验思路和细节，但自己的写作能力并没有因此提高。现在读文献，觉得有必要做一点标记。）

（注释：默认黑体加粗用于标注专业术语名词等，红色标记重要的形容词和动词等。其他标记，暂无说明。）

摘要：

A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological ‘demands’ change, evolution ‘supplies’ the variation needed for the population to climb to a new peak.

Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves.

Geneticists meanwhile have identified complexities relating to the nature of genetic variation and its architecture, and the importance of epigenetic variation is under debate.

In this review, we highlight how complexity in both ecological ‘demands’ and the evolutionary ‘supply’ influences organisms’ ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards ecologically realistic studies of adaptation.

下面是简版摘要

Adaptation to a changing environment is far from simple.

Ecological demands on populations can vary temporally and spatially.

Likewise, the supply of genetic and epigenetic variation is inherently complex.

Supply and demands can interact and alter evolutionary trajectories.

To track and predict adaptation,we need better integration across disciplines.

目录：

1. Supply and Demand in a Changing World
2. Complex and Changing Demands
3. The Supply Side: When and How Does It Work?
4. Genetic Variation
5. Genetic Architecture
6. Epigenetics, Plasticity, and Parental Effects
7. Concluding Remarks

1、

上图展示了适应的过程，比喻为一个种群爬山的过程，形象展示了蓝色的景观适合度（fitness landscape ，也就是ecology demands，就是环境对生物性状、基因的要求）和性状分布（distribution of the trait，也就是evolution supply）的过程，可以看出：Evolution leads to better adaptation, and organisms evolve to match the demands of their ecology是立不住脚的。左图显示，环境变化过快，可能导致进化跟不上，种群就灭亡了。右图分别展示了最终的适应结果受历史所塑造的性状分布（遗传结构）和遗传突变的影响，并不一定能达到最优。这有点像化学反应里的活化能的图，化学物质也不定能达到最稳定。看来，化学物质的结构多样性和生物多样性是相同的道理，否则总能达到最稳定状态，就只有一种物质，一个物种了，或者压根不会有生命产生。

Adaptation through Time. A two-dimensional fitness landscape (blue curves) is shown as a function of a phenotypic trait. The distribution of the trait in the population is shown as a red peak. The left panel (pale purple) shows how supply can tract demand when the rate of change is slow (A), but when the rate of change is fast, the demand can outpace supply (B). The right panel (green) shows how evolution can be contingent on past experience and the sequence of demands. (C) In the second environment, the fitness landscape is different between the left and right panels; subsequent adaptation to these different environments leads to different evolutionary outcomes in the third (rugged) landscape, such that in the left panel the population moves to a lower fitness peak and in the right it moves to the higher fitness peak. (D) Here the final phenotypes in the population depend on the mutational sequence. All three landscapes are identical, however different mutations arising in the second environment lead to different evolutionary outcomes in the third. env., environment.

Classic population genetic theory is based on predicting responses to a predefined selection pressure . Selection certainly occurs in the wild: general patterns emerging from meta-analyses of selection studies  include (i) directional selection generally favouring increased body size and earlier phenology, (ii) stabilizing selection, which is theoretically predicted to be common, is not often observed, (iii) selection on mating success is typically stronger than selection on viability, and (iv) there is a lot of spatial and temporal variation in strength and direction of selection, though it is often difficult to distinguish such patterns from sampling variation.

下面这一段阐述比较条例，不过翻译出来估计大家都糊涂了。

Interactions between genotype and environment can produce phenotypic, genetic, and epigenetic changes that influence adaptation. These interactions (genotype by environment, or G?×?E) can occur within a generation (i.e., phenotypic plasticity) or between generations (parental effects, transgenerational plasticity). The environment can induce changes to gene expression via epigenetic mechanisms: DNA methylation and histone modification [72, 73], or parental effects, imprinting, and physiological and behavioural manipulation of offspring traits [74, 75, 76, 77, 78]. Epigenetic change is a mechanism that can underlie plasticity and parental effects [73, 79], which could provide faster phenotypic responses to environmental change compared with ‘traditional’ genetic changes.

遗传结构（Genetic Architecture）可以揭示群体的简化潜力。

Constraints on Evolvability. Fitness gradient from low (blue) to high (yellow) is plotted as a function of two phenotypic traits. Red points correspond to the phenotypic values of individuals currently present in the population and white points refer to the phenotypic values that could result from mutation and recombination. (A) Available and potential supply allows for adaptation. (B) Available supply (red points) is restricted, and adaptation relies on generating new individuals with different trait values (white points), which in turn is dependent on population size and structure, mutation, and recombination rate. (C) Available and potential supply is restricted, for example, due to genetic architecture or antagonistic selection acting on traits, and thus adaptation is constrained. (D) Variation in current and potential phenotypes exist, but not in the direction required for adaptation.

附录

词汇表Glossary：

Glossary

• Additive genetic variation: component of trait variation that is the result of the additive effects of genes.
• Bottlenecks: severe reduction in population size.
• Cryptic genetic variation: standing genetic variation that has little or no effect on phenotypic variation under normal conditions, but generates heritable phenotypic variation under changed environmental or genetic conditions.
• Epiallele: a pair (or group) of identical genes that differ in their methylation.
• Epimutation: a heritable change in gene activity not associated with a change in the DNA sequence but with modification of, for example,methylation status or modification of chromatin.
• Evolvability: the ability of a population to undergo adaptive evolution.
• Genetic drift: changes in allele frequencies due to random sampling from one generation to the next.
• Genetic hitchhiking:allele frequency change of probable neutral locus that is genetically linked to a locus under selection.
• Genetic variation: differences in DNA sequence between individuals.
• Hill–Robertson effect:the probability of fixation of a beneficial mutation can be limited because it finds itself in linkage disequilibrium with a deleterious mutation.
• Linkage disequilibrium:nonrandom association of alleles at two or more loci.
• Linked selection:change of the allele frequency of loci genetically linked to a locus under selection. Includes allele frequency change due to any action of selection positive selection or negative/purifying selection (also referred to as background selection).
• Locus/Loci:a position in the genome, could be a single nucleotide position or 1000s of base pairs of DNA sequence, it can correspond to a gene or many 100s of genes.
• Mutation: a permanent change in the DNA sequence of an individual.
• Mutational load: reduction in fitness due to deleterious mutations carried by a population
• Robustness: the ability of a phenotype to resist perturbation by mutations (or the environment).

Additive genetic variationcomponent of trait variation that is the result of the additive effects of genes.Bottleneckssevere reduction in population size.Cryptic genetic variationstanding genetic variation that has little or no effect on phenotypic variation under normal conditions, but generates heritable phenotypic variation under changed environmental or genetic conditions.Epiallelea pair (or group) of identical genes that differ in their methylation.Epimutationa heritable change in gene activity not associated with a change in the DNA sequence but with modification of, for example, methylation status or modification of chromatin.Evolvabilitythe ability of a population to undergo adaptive evolution.Genetic driftchanges in allele frequencies due to random sampling from one generation to the next.Genetic hitchhikingallele frequency change of probable neutral locus that is genetically linked to a locus under selection.Genetic variationdifferences in DNA sequence between individuals.Hill–Robertson effectthe probability of fixation of a beneficial mutation can be limited because it finds itself in linkage disequilibrium with a deleterious mutation.Linkage disequilibriumnonrandom association of alleles at two or more loci.Linked selectionchange of the allele frequency of loci genetically linked to a locus under selection. Includes allele frequency change due to any action of selection − positive selection or negative/purifying selection (also referred to as background selection).Locus/Locia position in the genome, could be a single nucleotide position or 1000 s of base pairs of DNA sequence, it can correspond to a gene or many 100s of genes.Mutationa permanent change in the DNA sequence of an individual.Mutational loadreduction in fitness due to deleterious mutations carried by a population.Robustnessthe ability of a phenotype to resist perturbation by mutations (or the environment).