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I am a researcher in origins of life, a field that deals with hypotheses about evolutionary processes that took place before LUCA (the last universal common ancestor), and with the chemical processes that gave rise to life and evolution in the first place. This is very hard to study empirically, and as a consequence there are many competing hypotheses. However, I've noticed that many of them have a common form, which I will describe below. My question is about whether hypotheses of this particular form exist (and have been investigated, for example using phylogenetic methods) in post-LUCA evolutionary biology.
My reason for asking is that my colleagues and I were not able to think of a good example. If no example is known in post-LUCA evolutionary biology then it casts doubt on the plausibility of this type of hypothesis in pre-LUCA evolution. I suspect this is the case, and therefore my ideal answer would provide me with bibliographic material to support a claim that there just aren't any good examples of this in evolutionary biology. However, I would also be happy to be proven wrong with a really good example.
Hypotheses regarding the origins of life are difficult to test empirically, because phylogenetic methods can give us little direct evidence about anything before LUCA, and because there are no fossils dating from that time. (The entirety of Earth's surface has since been replaced by plate tectonics.) Consequently there are a number of competing hypotheses that differ from one another in almost every way. However, I've noticed that many of them have a common form: they say that
one or more of the features of a modern (i.e. post-LUCA) cell were originally provided by an external mechanism, in the form of abiotic chemical processes that took place in some very specific microenvironment, and
evolution eventually provided a solution that very closely echoed the one that had originally been provided by the environment.
Point (1) seems relatively easy to satisfy in an evolutionary scenario; it's point (2) that I'm specifically interested in. The two most popular hypotheses in the field both have this form:
Some forms of the The RNA-World hypothesis hold that originally, RNA nucleotides were produced by purely chemical processes in the environment, and that life evolved from self-replicating RNA molecules made up from these abiotically-produced monomers. Later, life evolved a cellular metabolism by which it could construct its own RNA monomers. This satisfies point (2) because it says that the environment provided RNA rather than some other heteropolymer with catalytic properties; the evolutionary solution echoes the environmental one in that it uses the same complex molecule.
Wächterschäuser's Iron-Sulphur World theory, and many of its descendants, including Russel's alkaline vent theory, hold that the reductive tricarbolic acid cycle (rTCA cycle, aka reverse citric acid cycle) was originally catalysed by mineral surfaces. This enabled the formation of the first cells, which eventually evolved enzymes that could be used to catalyse the rTCA cycle without the mineral catalysts. This satisfies point (2) because it says that the first evolved solution used essentially the same chemical pathway as the one provided by the environment, just with different catalysts.
(Not all hypotheses in origins of life have this form. Some versions of the RNA World theory hold that RNA-based life was preceded by life based on some other heteropolymer, for example. But the hypotheses described above are very popular.)
From an evolutionary biology point of view, point (2) seems rather an odd feature for a hypothesis to have. Evolution is great at producing novel solutions to problems, but to my knowledge it isn't good at copying old ones. (Mimicry doesn't provide a counterexample to this, since it's about appearance rather than mechanism, and often the mimic produces the same visual effect through a very different mechanism. For example, although the treehopper Cyphonia clavata mimics the outward appearance of an ant, it does so not by being anatomically similar to an ant but by having a face on its butt.)
Consequently I'm looking for known examples from evolutionary biology that satisfy both point (1) and point (2). That is, I'm looking for examples where a species originally relied on some relatively complex process in its environment, and became less dependent on its environment by evolving a mechanism that closely echoes the one originally provided by the environment.
An example that might fit the bill would be a species that was originally unable to produce a key metabolite (e.g. an amino acid), but then later evolved the ability to produce the metabolite for itself. Evidence for this might be constituted by finding a species that produces the metabolite using a novel set of proteins, indicating that the capability to produce the metabolite was lost and then re-evolved. It would make an even better example if the novel proteins catalyse substantially the same chemical pathway that other species use to produce the same metabolite.
It may be that no good examples of this exist, which is actually better for me than if they do. More than any particular example, the main thing I want to know is whether ideas along these lines have been discussed in evolutionary biology at all (perhaps outside the context of the origins of life), and if so where I can find the literature on it.
It was getting long for a comment:
A species that was originally parasitic, but then evolved to survive independently of its host by independently evolving the same metabolic functions
A predator that originally relied on its prey to synthesise some vital metabolite, but later evolved the ability to produce the
missing metabolite for itself through a similar pathway
A parasite is generally evolved from a free living form. It has a reduced genome and cannot synthesize many vital nutrients. It is unlikely that it would acquire a gene that would enable it to live freely. A parasite, in general does not require to synthesize nutrients; so it is not under any pressure to acquire that function as long as its host is surplus.
Same is in the case of predators.
Basically, in higher organisms it is difficult to conjure a new gene; it is a slow process and happens via gene modification. However, in lower (basically unicellular) organisms lateral gene transfers are much easier and it is possible that they can acquire new metabolic pathways from other organisms. Have a look at this article.
In lower eukaryotes endosymbiosis, is another way by which new metabolic pathways can be acquired relatively fast. A diatom called Rhopalodia gibba, which already had a red alga derived secondary plastid, acquired another cyanobacteria derived green plastid for nitrogen fixation. You can have a look at this post too.
For your question on independent acquisition of traits; almost all metabolic pathways are evolved like that only. Enzymes isoforms that can bind to a slightly different substrate gave rise to another step in the pathway.
It is also possible to engineer a new trait:
Nucleotide analogs have been created to make a 6-letter nucleotide system which can be replicated by PCR[1, 2]. Earlier this year this was demonstrated in-vivo. It has been shown that these new nucleotides can also be transcribed (see cross references in ).
The E. coli long term evolution experiment showed that E. coli had evolved a function (the metabolism of citrate) which was not required in the ancestral environment, but which evolved naturally and was selected for in this new artificial environment. AFAIK, this is the only example of a function that has been observed naturally evolving under controlled conditions.
The reason we are unlikely to see any metazoans evolving new metabolic pathways is due to the fact that they have long lifespans and therefore reproduction times. However, as WYSIWYG has already mentioned, almost all metabolic pathways evolved that way, it is just hard to observe due to the long time spans involved.
See this more as a comment than an answer, since it became too long for a comment. However, I think some of the examples should be relevant to refine your question.
One thing that I find vague in this question is what exactly constitutes a "process"/"function"? To me, this can be almost anything. You seem to be focusing on molecular biology and biological pathways, but I think it is just as reasonable to think in terms of large scale processes. If so, there are lots of processes that seem valid in my mind, relating to e.g. reproduction and dispersal.
For instance, in primitive plants (and other taxa) fertilization is external and dependent on environmental moisture to transport gametes. Organisms with internal fertilization has bypassed this by providing their own mechanism for fertilization, which does not depend on environmental processes (to the same extent). The evolutionary forces behind this was maybe/probably that it was more efficient and allowed colonization of new environments.
Another similar example is seed dispersal in plants, where some are wind dispersed ("primitive" state) and others use active measures to eject seeds (ballochory). By doing this they have bypassed the dependence of wind to disperse their seeds. The same kinds of mechanisms can also be found in groups of mosses.
In both these cases a function that was previously external and environmentally mediated is now provided by the organisms themselves, and they involve quite complicated morphological and anatomical adaptations. Do you find them valid for your question? These are just two examples, but there are lots of similar cases.
More in the line of comments to your question, I think you should provide one or two references to the hypothesis you are referring to (i.e. where it has been used/discussed), which would make it easier to understand exactly what you are after (and also provide an entry into the literature). This could maybe also help explain why the "… evolved solution 'echoes' the one provided by the environment". At the moment I don't understand at all why this should be the case in general. Adaptive evolution happen because of selection that acts on differences in fitness, and it is indifferent to whether the mechanism echoes a previous solution to a similar problem (except for the fact that evolution is constrained by the evolutionary history of organisms).
After considering this question some more, I think a key feature for this hypothesis to work is that the original function must be so integrated and vital for the biology of the organism that it must be mimicked/echoed to some extent. In terms of your RNA-example, it was not enought to evolve the ability to synthesize any complex molecule that could function as an enzyme and information carrier, but had to be RNA since this was already used in the biological pathways of the primitive organism.
With this in mind I think that you should look closely at vitamins (or other essential nutrients) for evidence of similar processes. The key think about vitamins is that they are often large complex molecules that are vital nutrients and the ability to synthesize vitamins differs widely between taxa. In a sense, the nucleotides were essential nutrients for the organisms in the proposed RNA-world, so vitamins/essential nutrients should be a relevant analog to look for similar evolutionary processes. However, keep in mind that molecular biology is not at all my field, and I might be mistaken on some aspects.
Take the example of Vitamin C. This cannot be synthezised by humans, but by most other mammals (vitamin C synthesis is considered ancestral in mammals). It can also be synthesized by plants, yeast and many other animals. However, vitamin C is used in different ways in different organisms. Plants use it e.g. for photosynthesis, photoprotection, cell wall growth and in the synthesis of plant hormones, while humans and other mammals use it as enzyme cofactors and for immune responses. Another key aspect is that plants, yeast and animals all use different pathways to synthezise vitamin C (Drouin et al, 2011), which indicates that the synthesis of vitamin C is not ancestral to all these taxa (i.e. not an ancestral feature of all eukaryotic life). In mammals, the synthesis of vitamin C has also switched between organs multiple times, which also indicates novel adaptations that results in the same molecule.
To me, it seems very likely that vitamin C was initially obtained by animals from plants (which have very high concentrations of vitamin C) as part of their diet (i.e. environmentally provided) and became an essential component in many biological pathways. If this is the case, animals later gained the ability to synthesize vitamin C themselves, using a different biological pathway than plants. This feature has later been secondarily lost (e.g. humans and teleost fish) and regained multiple times in different taxa. However, this is speculation on my part, and I don't know this literature well enought to say if there are studies on the origin of vitamin C synthesis in animals, or if the pathways of vitamin C synthesis in plants and animals are fundamentally related. A review by Smirnoff et al (2001) indicates that there are some similarities between the enzymes involved in the final stages of vitamin C synthesis:
The gene and/or cDNAs encoding GalLDH, GulLO, and AraLO have been isolated and described from several organisms including cauliflower, sweet potato (GalLDH, 54, 121), rat (GulLO, 70), and Saccharomyces cerevisiae (53). In addition, complete nucleotide coding sequences of the A. thaliana and Nicotiana tabacum GalLDH genes (Accession No. AB042279.1, AB024527.1), and the Candida albicans AraLO gene (Accession No. AF031228) have been submitted directly to GenBank and associated databases. The predicted amino acid sequences of these related proteins share substantial amounts of identity. The mature cauliflower GalLDH amino acid sequence shares 28% overall identity with the rat GulLO and 26% identity with the Candida albicans AraLO (using the J Hein method with PAM250 residue weight table).
However, this doesn't necessarily mean that the synthesis of vitamin C is ancestral to both plants and animals. I haven't been able to find any papers on the origin of vitamin C synthesis, and if there is evidence that it is ancestral to all modern life.
In either case, I think it could be useful for you to look closely at vitamins in animals or other organisms for possible examples of the type of processes you are looking for, since they are (by definition) essential nutrients that some animals can and others cannot synthesize. They should therefore be good potential targets to find similar processes as your RNA-example. Vitamin B12 is an extreme to the other end, since it is essential for most animals but can only be synthesized by bacteria (so the main source is through bacterial symbiosis).
It is also possible that I'm mistaken, and that synthesis of all vitamins is ancestral to modern life, and that there has only been subsequent loss of the ability to synthesize certain vitamins/nutrients. Helliwell et al (2013) mentions this as a possibility in relation to the RNA-world, but also points out that the pathways for biosynthesis often differs between taxa, which would suggest that there has indeed been secondary acquisition:
The fundamental nature of vitamins is illustrated by the close structural relation of many vitamins to nucleotides (Figure 1), reflecting the likelihood that they were present in the ancient RNA world. Yet, their biosynthetic pathways appear to have arisen via the patchwork model of pathway evolution , resulting in the recruitment of unrelated proteins in any one pathway. Indeed, many vitamins are synthesized by different routes in different organisms . For example, alternative pathways are found for thiamine biosynthesis in prokaryotes and among different eukaryotes (Figure 2) . Despite this diversity in biosynthetic pathways, there appear to be common trends in the causes and mechanisms underlying pathway loss.