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Synapomorphies are important in systematics because they are shared derived characteristics that help scientists infer evolutionary relationships among organisms. By identifying synapomorphies, researchers can determine which species share a common ancestor and group them accordingly in a phylogenetic tree. This information is crucial for understanding the evolutionary history and patterns of biodiversity.
Scientists use the fossil record and structural and molecular comparisons to construct phylogenetic trees. This answer came straight from my freshman Biology book.
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the phylogenetic relationships between species of different phyla