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I just read about the discovery of the 1.8-million-year-old human skull in Georgia, and how it suggests that early humans were all one species instead of distinct ones. Would an archaeologist unearthing dog bones a million years from now know that a Great Dane and a Chihuahua are the same species?

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It seems as if this article is purely speculative. They didn't mention any DNA testing, but instead discussed physical features.

There are two "types" of archaeologists: clumpers and splitters. Clumpers (like the author of this article) believe that there is wide variety among members of the same species, and so it is often wrong to categorize every new hominid fossil as being a different species. Splitters like to "split" their findings into new species, even though there is no evidence that speciation had ever occurred; they just decide that since the remains look different, they must have speciated.

In the future, I hope that archaeologists will have more sophisticated means of sequencing the DNA of ancient remains, allowing them to construct an accurate phylogeny

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