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An ab initio based framework for quantitatively assessing the phonon contribution due to magnon-phonon interactions and lattice expansion is developed. The theoretical results for bcc Fe are in very good agreement with high-quality phonon frequency measurements. For some phonon branches, the magnon-phonon interaction is an order of magnitude larger than the phonon shift due to lattice expansion, demonstrating the strong impact of magnetic short-range order even significantly above the Curie temperature. The framework closes the previous simulation gap between the ferro- and paramagnetic limits.