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This may be better suited for the English language SE, but When discussing evolutionary changes in species is it proper to refer to their phenotypes?

In this context:

"Imagine if a cow did not have to cart around however many gallons of culture nor expend personal time and effort into chewing its cud. It could lose all that anatomy and energy expenditure from its phenotype."

it could just be me, but it sounds strange using it in that context.

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Yes, absolutely. That's what a phenotype is (definition from the biology online dictionary):

noun, plural: phenotypes

(1) The physical appearance or biochemical characteristic of an organism as a result of the interaction of its genotype and the environment.

(2) The expression of a particular trait, for example, skin color, height, behavior, etc., according to the individual’s genetic makeup and environment.

I don't see anything strange in the sentence you quoted. It is phenotypes that are selected for. Genotype differences that don't affect phenotype will have no selective advantage (or disadvantage) and cannot be acted upon by evolutionary forces. What else would you use when discussing evolutionary changes? That's what the word phenotype is for.

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