So what is the signal in sequence data that provides the evidence for common ancestry? In essence, it is site-specific correlations in the amino acids between different species. These correlations fall off as the coalescence between lineages in a tree becomes deeper in the past, but if there are sufficient data, the correlations' cumulative significance becomes statistically strong. Conversely, if two lineages have completely separate origins, correlations between amino-acid site patterns in the corresponding two extant species vanish.This article basically suggests, if I understand it correctly, that if species were independently created (think: *poof*), they would show smaller correlations in the coalescence results. This indicates that the further back you go, the sequence data shows common descent. As you go back in the fossil record and compare that to the genetic data of different species, certain protein sequences remain in common. Hat tip to Panda's Thumb.
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