[waserwill]

Re: definitions of shared DNA:

Some papers will use different definitions, and it can be confusing.

Between species (e.g. humans and chimps), it's most often considering "non-synonymous mutations," i.e. how many genetic differences there are in protein-coding genes (these are relevant to structure and function of the protein)

For distant relatives (e.g. humans and bananas), it's similar, looking specially at those genes which we can identify across many species (particularly those related to cell upkeep, DNA replication, structure, etc.).

For within-species, there are a few ways of doing it; you could model how much of the genome you expect came from each source (as this study did) (see admixture analysis, coalescence), and you could look for overall differences on the genome (of all existing variation in the species, how much is consistently different between populations) (see F-statistics for example)

[s1artibartfast]

Thank you. This is very helpful!