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On why this is not evidence for common ancestry:

Finally, a piece of evidence Dr. Miller commonly cites as demonstrating human/chimp common ancestry is the fusion of chromosome 2 in humans, which he argues has a structure similar to what one would expect if chimp chromosomes 2a and 2b were fused together, end to end. Without belaboring the details (which are covered elsewhere23), the evidence for human chromosomal fusion simply indicates that our ancestors once had 48 chromosomes. But it tells us nothing definitive about whether our lineage leads back to a common ancestor shared with with apes. Human chromosomal fusion merely shows that at some point within our human lineage, two chromosomes became fused. That’s it.

http://www.evolutionnews.org/2009/11/confusing_evidence_for_...
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