Given this shows how easily DNA is acquired from an external source; how do we know certain sequences come from common ancestry rather than by other means?
Common ancestry is probably best understood in aggregate. When we look at genetics in aggregate we see a lot of common sequences that are highly conserved across all of nature.
Edit: also shows why most anti-GMO hysteria is nonsense. Everything is "transgenic." Species are fuzzy.
GMO per se are IMO a net good, we're increasing biodiversity.
Also, they are crucial in medicine. Insulin and other peptide-derived treatments are synthesized by GMO bacteria and yeasts (see "recombinant DNA").
Are you sure? Farmers used to have their own subtly different strains of crops at the individual, village, town, and country levels in a kind of expanding concentric ring pattern. Now, at least for cash crops, it's just a few varieties all "manufactured" by one central power.
The current uniformity predates GMOs, it stems from F1 hybrids that are effectively clones, and the legislation that makes it practically illegal to sell or plant non-patented seeds.
Granted.
But in the grand scheme of things, this is as equally an astonishingly new situation as is mechanized agriculture. A hundred years ago, most people lived and worked on farms; now it's like 1% or something like that.
I know that Monsanto's shareholders need to make rivers of dosh, boatloads of cash, money hand over fist, but I don't understand how in practice they've managed to get a vice-grip on everybody's family jewels.
As for glyphosate resistant crops, beyond the currently insufficient science (lots of invalid studies!), I can't see any reason to denounce it or make it illegal).
As a layman, the story I've seen up to now is roughly "these sequences are the same, therefore there is a common ancestry"; but this information shows that argument doesn't work on a wide scale across species in this simplistic form -- so either the basis of common ancestry being inferred from similar DNA is not scientific (or is falsified) or we have results that show whence the particular sequences came from (ie there's a more nuanced result)?
In short that answer is unsatisfyingly vague.
Technologies are just tools. It's all in how they are used.
Also, the reason why a person does or does not do such a thing is rather of less importance than what that thing is that he does or does not do. For example, if pigs carry disease, and your religion proscribes you from eating pigs because "God says so", your life is preserved whether or not you or anyone else have any conception of germ theory whatever.