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Suppose a species possessed different sets of DNA for different parts of its anatomy. I'm not suggesting one set for every function in the body; that would result in hundreds of thousands of unique sets of DNA.

Instead, suppose there was one set (core DNA) that determined how the body was laid out, such as the position of arms and legs, skin color, eye shape, number of teeth, etc.; one set (functional DNA) that controlled the transfer of energy through the body, be it through the cardiovascular system, nervous system, or another transfer plan laid out by the core DNA; and a third set (translational DNA) that ensures the various DNA sets can communicate with each other.

This is certainly a complex system, but how reasonable is it to believe that it could exist, whether by nature progression (preferred) or engineering?

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    $\begingroup$ It sort of does exist, see Mitochondrial DNA $\endgroup$
    – Scott Downey
    Commented Jan 11, 2016 at 15:23
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    $\begingroup$ I don't really understand what you mean. DNA is the support of genes. Genes are more or less independent and fulfil a specific task. My thinking is that if we parse a single DNA into genes, there would be no differences with the parsing of multiple DNA into genes. More or less like a multidimensional array can be casted into a single-dimensional array. $\endgroup$
    – Kii
    Commented Jan 11, 2016 at 15:32
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    $\begingroup$ This is a recent case that you may be interested in : independent.co.uk/news/science/… $\endgroup$
    – Kii
    Commented Jan 11, 2016 at 15:49
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    $\begingroup$ @Frostfyre: AT the scales you're talking about the distinction between 'the same' and 'different' gets a little blurry. Viral DNA strands replicate using human cellular structures, but they aren't human. Mitochondrial DNA is noticeably different from other DNA used elsewhere, to the point where it's posited that mitochondria were actually consumed by other single celled organisms before undergoing a (now very, very, long term) symbiotic partnering. $\endgroup$
    – Joe Bloggs
    Commented Jan 11, 2016 at 16:03
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    $\begingroup$ There needs to be some way for all the different sets of DNA to make it into the offspring. Otherwise, no problem, as the answers demonstrate. But do think about what reproduction would look like. Also, there are probably hundreds to low thousands of independent genetic regulatory networks in humans, which is pretty much a complex version of what you're suggesting. There just isn't any good reason to keep the DNA segregated (especially since the networks partially overlap), so it's all run off the same DNA. Chromosome condensation is used, in part, to control which subset is used in each cell. $\endgroup$
    – Rex Kerr
    Commented Jan 11, 2016 at 22:58

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As Scott Downey noted in his comment, this already happens in humans.

If you're looking for something a little more macroscopic in nature: The Portugese Man-O-War seems to fit the bill pretty effectively. It's several different creatures (Edit thanks to Mike Nichols that all share the same DNA, so maybe not exactly what you're after) that are so reliant on each other they cannot function independently.

EDIT: I feel compelled to point to QuadmasterXLII's answer on Lichen. I think what you're after is something on the scale of the Man-O-War, but with the lichen's level of symbiosis (which stops short of the full mitochondrial integration we've got).

So yes is the answer to your question. Can happen, has happened, feel free to make it happen again.

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    $\begingroup$ Can you give a reference for the claim that Portuguese Man-O-Wars' zooids having genetic differences? I'm not an expert on the subject, but I believe since every zooid in the colony arises from the same embryo they are all genetically identical. Ref1 Ref2 Ref3 $\endgroup$
    – Mike Nichols
    Commented Jan 12, 2016 at 7:28
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    $\begingroup$ @MikeNichols: You are in fact completely correct. I hang my head in shame and blame a misremembered biology lecture. I was under the impression that the zooids were first identified as separate animals because of their different genetic patterns, but it appears I remembered wrong! Edited. $\endgroup$
    – Joe Bloggs
    Commented Jan 12, 2016 at 9:35
  • $\begingroup$ Also, women. See barr body - roughly half of woman's cells contains one set of active DNA and other half - other set. Other DNA is there, but deactivated. $\endgroup$
    – Mołot
    Commented Jan 12, 2016 at 15:44
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    $\begingroup$ @Mołot: This can be seen clearly in cats, where fur color is determined on the X chromosome. When a cat gets two different fur pattern X genes, you end up with an odd mix of colors known as "calico," which is why calico cats are always female. $\endgroup$
    – Mason Wheeler
    Commented Jan 12, 2016 at 20:37
  • $\begingroup$ @masonwheeler: that is an exceptionally good factoid that I'll remember whenever I see a multicoloured moggy! $\endgroup$
    – Joe Bloggs
    Commented Jan 12, 2016 at 21:23
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Lichen is an excellent example that exactly matches what you describe. The fungus DNA determines the structure of the organism, and the algae DNA is responsible for producing energy.

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  • $\begingroup$ Ooh! I'd forgotten Lichen! Well done sir! $\endgroup$
    – Joe Bloggs
    Commented Jan 11, 2016 at 16:15
  • $\begingroup$ Interestingly it now looks likely that Lichen are actually a union not of two species (fungus and algae) but three (two different forms of fungi and an algae) $\endgroup$
    – Jack Aidley
    Commented Mar 21, 2018 at 13:22
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This exists in the real world: Chimeras

There actually are creatures (including humans) who have multiple cellular DNA streams flowing through their body. These folks (or beasts, as the case may be) are called Chimeras.

Tetragametic chimerism (or monstrous chimerism) is usually congenital and is the result of merging of non-identical twin zygotes. Such chimeras may sometimes have multiple sets of sex organs, for instance, with different genetic makeup. These usually result in a non-standard body plan.

Most cases are far more subtle and result in a normal body plan, often going undetected. There have been cases of women giving birth to what are genetically their own sisters or nieces (because genetic material from their own mothers or twins made it into the embryo).

The most famous case along these lines is that of Lydia Fairchild, who had birthed children that did not seem to be genetically hers, which landed her in hot water with the courts when she asked for child support. She was later shown to be a chimera.

None of these examples are quite as specialized as what you describe, but from reality to your example isn't as great a leap as one might expect

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Chimeras are only half the answer (not heritable)

Although chimeras have cells in different parts of the body containing different genomes, this condition will not be passed to offspring since human reproduction generally only involves combining one cell from each parent. So a human child may be a chimera if two or more fertilised ova fuse, but the distribution of cells of each genome within the human body will not correlate with the distribution of different genomes in either parent. So this fits your request for "multiple DNA, one creature", but does not have the specialisation of different genomes for specific aspects of the body. The distribution will be largely random, and not consistent from one chimera to the next.

Heritable divergent genomes are in principle possible

It is possible to have a multicellular animal that does not reproduce using only a single cell, but instead allows all of its cells to divide until the entire animal can divide into two. This means that a specialised type of cell in the offspring is descended from the same specialised type of cell in the parent. The existence of this type of animal means that in principle it would be possible for the genome of a specialised type of cell to drift and become significantly different from other types of cell within the same organism.

The known example we have on Earth of a multicellular organism with specialised cells that reproduce independently is called the Trichoplax.

The specialised cell types can only diverge over time if reproduction is solely through dividing. This may be possible with trichoplax as they appear to have lost the ability to reproduce sexually (which would otherwise cause all cells to share the same genome again).

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You may find the line you draw is more artificial than you think. The idea of "multiple DNAs" is a construct to make it easy for humans to observe the behaviors they see. When it comes to the actual function of cells, the cells care not for this artificial line: DNA is DNA.

Consider viral DNA, which is clearly from an foreign species, by our observations. And yet, the cells treat it no different. Consider they are so similar that, in fact, every now and then a bit of viral DNA accidentally gets spliced into our own DNA by the repair mechanisms.

Consider we have 46 unique separate chromosomes, but they come in pairs that are sufficiently similar that we often think of it as 23 pairs. And yet we think of it as one genome.

Consider that we "upregulate" different genes in different areas. While all cells have roughly the same genetic content, what makes teeth teeth is that they have upregulated the production of proteins essential to being teeth.

It may turn out that you can actually roughly divide up our genome as your multiple DNA, with some dna handling body structure, some handling teeth, etc. However, the body has to solve an interesting problem: how does a cell know if it is a tooth? Part of that result is clever management as the early stem cells divide, but part of it is that the body is resilient to errors. Instead of being "I'm a tooth DNA" you have "I'm a body of DNA that is useful for teeth." If it gets upregulated in the wrong place, it might be okay for a bit. In fact, a tooth gene in the liver might upregulate by accident for a bit, and then be shut down when the cell realizes that gene isn't being very helpful.

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While the other answers have responded to the title of your question, I don't think anyone has really addressed the specific question you asked. Can an organism use different sets of DNA in different organs or organ systems? The answer is almost certainly yes, with a couple of caveats.

Caveat 1: The reproductive cells of the organism, the ones that give rise to all the other cells, will need a complete copy of every organ's genome, otherwise that organ's genome, since it doesn't reproduce itself, will be lost. This means that your embryo is going to have all the DNA needed to create every organ in the body, and as the cells differentiate they will discard the DNA they no longer use. The germ line cells however will retain all of the DNA for the next generation.

Caveat 2: Many of the genes in a multicellular organisms are actually used by every cell. These are called housekeeping genes and they handle things like basic upkeep of the cell. Genes like RNA Polymerase II, Ribosomal RNAs, and the Nuclear Pore Complex are going to need to be in every cell, so your different DNA sets are going to have a large amount of overlap.

That said, I see no reason why a multicellular organism couldn't handle differentiation via loss of DNA. Currently, all organisms I've ever heard of create different cell types and organs by differential regulation of the genes in their DNA. They have a million ways of modulating the output of genes and create incredibly complex regulatory networks full of feedback loops and bistable switches. By comparison just deleting the genes necessary for being a neuron when you decide to become a glial cell seems pretty straightforward.

The only trick is that the DNA for different functions needs to be spatially segregated in the genome for easy deletion. The simplest way would perhaps be by chromosome. For instance, say chromosomes 1, 2 and 3 contain all of the ubiquitous housekeeping genes, 4, 5, and 6 contain ectoderm specific genes, 7, 8 and 9, contain mesoderm factors, and 10, 11, and 12 are necessary for endoderm. When a cell decides to become ectoderm it simply degrades chromosomes 7-12.

Obviously its sort of tricky for this sort of spatial organization to have evolved. Multicellular organisms would have had to originally start off with this method of differentiation. If that's the case however, regulation of what cells do what actually gets a whole lot simpler since the cells really have no choice in the matter. On the upside, you've always cured cancer!

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Consider the humble butterfly. It has but one genome, which it shares with the even humbler caterpillar.

The butterfly has six skinny legs, wings, a loooong rolled proboscis, a diet of nectar... the caterpillar has sixteen stumpy legs (six of them "real", ten "prolegs"), web spinerettes, hairs, mandibles, and a diet of leaves... completely different creature. From the same genes.

The two forms are switched between by activating one part of the genome and deactivating another. Thus, genes to create and operate two essentially completely different creatures can work from a single genome.

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    $\begingroup$ "most likely, originally a fly and a parasite" - I'm just curious, is it a figure of speech, or was it actually found that different parts of butterfly DNA resemble those of a fly and a "parasite"? $\endgroup$
    – user8808
    Commented Jan 12, 2016 at 11:50
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    $\begingroup$ It is very definitely NOT a parasite. Fly has just a bit complicated life cycle, as many (most) insects do. But very likely there is a parasite wasp specializing on laying eggs in exact this species of caterpillar. $\endgroup$
    – Peter M. - stands for Monica
    Commented Jan 12, 2016 at 22:22
  • $\begingroup$ Awr crudcheese. Thanks, @PeterMasiar - not sure where I picked that up from, I thought I remembered reading it in New Scientist some years back, but can't find a trace of it now. It's probably me misremembering reading some net nonsense. Deleted, so's not to spread the nonsense further. $\endgroup$
    – Dewi Morgan
    Commented Jan 13, 2016 at 2:39
  • $\begingroup$ @Roux Likely I was misremembering - edited to remove that. $\endgroup$
    – Dewi Morgan
    Commented Jan 13, 2016 at 2:42
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It already happens. At least, something similar to what you have in mind.
Humans have a whole microbiome of many different organisms living inside of us doing various things for us. A surprisingly small percentage of the cells in your body are actually "your" DNA. Mothers especially will also pass on a lot of helpful "non-human" genetic material to their offspring.

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There are many good answers here but I want to attack the root of the question. I think the OP's fundamental concept of DNA is wrong. DNA is the blueprint of an organism that contains the instructions of how to construct and operate each cell that makes that organism. DNA by itself does not perform any biological function. Therefore an organism can only have one set of DNA. NOTE: that DNA can differ slightly from cell to cell due to various biological processes like teleometric decay, selective retention, etc but the DNA is still the same just potentially missing parts that were contained in the original DNA.

I think what the OP is really looking for is hyper symbiosis to the point of mutual dependence. Symbiosis is where different organisms share the same physical body and distribute different biological processes resulting in greater prosperity for the body (my butchered definition of it anyways). One possible example of this is our digestive system, where we rely on a multitude of different organisms to break down the food we consume into nutrition that is absorb able by our actual body. Our body gets the nutrition it needs and the organisms get a safe habitat with a higher promise of nutrition they need. If you were to kill off all of these organisms I'm pretty sure you would die.

Going back to the OP's intended level of complexity, it is possible. It would require several organisms to enter into a symbiotic relationship and then evolve that relationship. This is highly unlikely because of how much evolutional cooperation it would require but I believe with all the potential life in our galaxy, somewhere some group of organisms won the cosmic lottery.

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It is very reasonable to believe in the existence of such systems. Fungal and algae symbiosis as described in answers above can serve as an instant example.

On a theoretical basis we can have endosymbiosis as an example where certain cell organelles have a dna that is different from that of the cell.

And from recent technological advances I do not see why it is impossible for the same to be applied in bioengineering or related disciplines.

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  • $\begingroup$ Welcome to the site Often. Could you elaborate a little bit on why you believe this is reasonable by supporting it with your own content. We try to not only answer the yes/no but also explain why and provide support for assertions made in answers. If you have questions just ask. $\endgroup$
    – James
    Commented Jan 13, 2016 at 19:21
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It is hard to say, since we've only sequenced a small number of species in comparison to all in existence. But a straightforward answer is try it for yourself via the field of Synthetic Biology. Ask more questions on the Google Group DIYbio if you want to know more about how and where to get started, and if school or a hackerspace or a home-lab is more your style.

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A species with multiple bodies will at the same time have multiple DNA

The Man o' War is a type of creature that is not one, but instead multiple creatures, all of which come together to form a single species. Each of the four species have their own DNA. An advanced version of this multi-bodied concept is the anthill. While the creature does have multiple strands of DNA, one could argue that a multiple bodied creature is even its own creature.

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