And yet we probably don't know why they have so many copies. Maybe it's a crude method of regulating the ratio of activation on genes. If a few genes are either on or off, and you want to have ratios other than 1:0 1:1 or 0:1, maybe independently activating N of the M copies can achieve that. Just speculating as to how multiple copies might be useful.

You can't prove that they are "extra copies" until you understand pretty much everything about them and their interactions with everything else.

While I agree in principle, it does look like in most cases, these 100X large genomes are just due to random events that haven't been selected away. Often, what you see looking at evolutionary processes at a point in time, you want to find a "reason for why it's this way", when the reason is "it was random chance". Compare deinococcus radiodurans, where there's a whole mechanism for exploiting multiple copies of the genome. Plants wiht 10X genomes don't seem to exploit that, afaict.

It’s always random chance. What’s non-random is why it’s kept in the genome. I’m no plant expert, but genome duplications could be linked to increased fitness due to amount of resulting protein product, right?

If it didn't give an advantage it shouldn't have become dominant (that all individuals of that species have that) or not?

that's now how evolution works. evolution tolerates enormous amounts of things that don't 'give advantage', and 'advantage' is a fairly subjective term anyway. Any number of possible events could have occurred to lead to the scenario we see. Population bottlenecks often lead to strange outcomes.

You're conflating the size of a genome with the amount of DNA that is non-functional.

I'm not conflating anything. Those details are scientifically conflated (IE, they are functionally related) in a very interesting way. For exmaple, new genes probably arise from gene or genome duplications.

DNA that doesn't encode proteins is not necessarily non-functional.

Yes, I know that. It's unclear what aspects of those duplications are "functional but not coding for genes, enhancers, promotors, or other well-known and understood coding and regulator elements", and which are "functional because if you remove it the organism dies but we can't explain what the cause is".

Everything in my terminology is entirely correct within the current mainstream understanding and it encapsulates much of the ongoing confusion about what "role" non-coding functional elements play, and how they play it.

See http://cryptogenomicon.org/encode-says-what.html and https://www.cell.com/current-biology/comments/S0960-9822(13)... for the strongest arguments against ENCODE's more wide definition of functional elements, as well as https://www.pnas.org/content/110/14/5294 and https://www.mun.ca/biology/scarr/MGA2_02-10.html

I am of the opinion that nearly everybody in this field is overly dogmatic in their views of how genomes work at the macro scale, and that these squabbles demonstrate that clearly.

For more context, please understand that as a researcher in this field, much of what I say may not make sense to casual readers. I decided it's better to think about minimal organisms, than ones that have 500 copies of the ribosome (http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=...)

Sounds like "non-functional DNA" might in fact have a function, hm?

Probably not in the context of the example I gave; that's more likely to just be a totally random genome duplication which will eventually be functionally selected away.

Non-functional DNA is to all DNA as source code that doesn't call I/O is to all source code.