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Let me begin by disclaiming that I am nowhere near a biologist by competence or education and that I am simply interest in some of its fields of study as a matter of general curiosity. So excuse my ignorance.

I've been recently pondering the concepts of genotype and phenotype. This page succinctly summarizes the difference between the two.

I was curious if there are scientific measures, and how accurate they are, for the impact of environment on the phenotype of a specimen. Hypothetically, if the environment had no effect, the phenotype would be 100% determined by the genotype. But, in a simple approximation, phenotype = genotype + environment. Does modern biology have a measuring system for how much the environment affects the ultimate observable features of an organism, on top of what its genotype does?

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In between a long comment and an answer...

For a review of the theory behind the causal variables of phenotype, one might want to have a look at Biology Why is a heritability coefficient not an index of how “genetic” something is?.

One can investigate the impact of a specific environmental variable onto the phenotypic variance but the environmental as a whole is typically computed as whatever is left when other sources of phenotypic variance have been explained. As such you might want to read about estimations methods for heritability and maybe esp. the post How do heredity and regression to the mean work with respect to intelligence?.

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Phenotype is often discussed at a fairly coarse level. In biology classes we ponder simple genotypes from Mendelian genetics, and discern that the pea plant with the YY genotype bears yellow pea seeds.

Consider a suspension of tumor cells being grown in a petri dish, however. A fairly straightforward way to asses the phenotype of the cells is by confocal microscopy

Say you grow the same cells, but some at normal oxygen and some at lower oxygen. Refer to the following figure: enter image description here

In B, the investigators are using fluorescent antibody label, as you'd use in flow cytometry, to perform confocal microscopy. At 1% oxygen for up to 21 days, the phenotype of the same cells profoundly differ (reference). Flow cytometry can also be used to identify difference in phenotype that arise from environmental factors.

Take for example T cells isolated from you blood. I can change the phenotype based on surface receptors detected from flow cytometry, by adding different cytokines to the culture medium. If I add interleukin-12, I'm most likely to differentiate my T cells to discernibly type-1 helper or cytotoxic cells. I can tell due to the presence or absence, or abundance of markers such as CCR5 or CXCR3.

And if you sequence these cells, you get the same material. Epigenetic changes are harder to wrap your head around. In the hypoxia example, the lack of oxygen is thought to change the phenotype by modifying the way the cell machinery can access and express key genes associated with the hypoxia phenotype.

The take home point here, is that in order to discern the techniques that are available to you, it's important to define the system you're researching. For example, I have no idea how they determine the environmental impact on animal species. But, I can sit here and rattle off techniques to analyze single cells or systems of cells.

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