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The endosymbiont theory proposes that organelles like mitochondria and chloroplasts were once free-living prokaryotic organisms that were engulfed by a host cell and developed a symbiotic relationship. This has implications for phylogeny as it suggests that certain organelles have a different evolutionary history than the rest of the cell, leading to the concept of lateral gene transfer and complicating the interpretation of evolutionary relationships based on traditional phylogenetic methods.
Binomial nomenclature and phylogeny both have to do with organisms. The former refers to the modern scientist's system for naming organisms. The latter is about how an organism evolved over time.
phylogeny.
phylogeny
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