How is it known that Homo sapiens and Homo neanderthalensis interbred?

Question

Many recent articles maintain that a small percentages of Neanderthal genes (up to 2%) are found in modern non-African people. (I believe that currently there is insufficient genetic material from older hominids, such as *H. erectus*, to decode a genome). My question is: how is it known the “Neanderthal genes” found in modern humans got there by way of interbreeding? What distinguishes those genes from genes that both species inherited from a common ancestor? After all, Neanderthals and *H. Sapiens* are over 99% genetically identical. How is it determined that gene A is found in both because it was from *H. erectus*, from which both evolved; but gene B was not already present in *H. sapiens*, so it must have arisen through interbreeding?

Answer 1

There are conserved genes across the tree of life, and the closer one thing is related to another thing, the more similar these conserved genes will be. By tracking these differences in conserved genetic sequences (such as mitochondrial DNA in animals, or 16S rRNA in prokaryotes) we can build a phylogenetic tree based on how similar or dissimilar these conserved sequences are. This is one way that we can distinguish neanderthal-derived DNA sequences from sapiens-derived DNA sequences. We can compare a large dataset of DNA and come to a consensus of what the "standard" DNA sequence is for Homo sapiens, but there are a subset of the dataset which have small substitutions, creating a sub-population resulting from interbreeding of closely related species. Another, perhaps more obvious, indicator of neanderthal-sapiens interbreeding is the presence of genes in so-called "genetic deserts." These are locations on the sapiens genome which are normally empty of any coding DNA. But in neanderthal DNA, these locations contain gene coding sequences. The presence of these genetic islands is a strong indication of interbreeding.