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A Ring of Life

  1. Oct 16, 2015 #1

    Ygggdrasil

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    Since the time of Darwin, biologists have looked at the history of life as a tree showing how the common ancestor of all life gave rise to all extant species. However, as we have learned more about biology, we've found that organisms do not inherit genetic information from only their direct ancestors, but many organisms have also obtained genes through horizontal gene transfer, in which distantly related organism can swap genetic information.

    Horizonal gene transfer has been important in many evolutionary events, including the evolution of eukaryotes, the domain of life that includes plants, animals, and all other multicellular life. Eukaryotes evolved from a type of archaea called an eocyte (whose name means "dawn cell") which took up a some bacteria through a process called endosymbiosis. Thus, eukaryotes are not a separate branch of the evolutionary tree, but rather the point at which two branches of the tree of life fuse together.

    In a recent review discussing the evolution of eukaryotes, I found this figure that I'd like to share with you all. Instead of showing the typical evolutionary tree, the author draws the "tree" of life as a series of rings in order to highlight how eukaryotes (along with many other types of species) are the product of both horizontal and vertical gene transfer:
    F2.large.jpg
     
  2. jcsd
  3. Oct 18, 2015 #2

    atyy

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    The diagram still shows only a single root of life. Do you have any thoughts on whether that may become a more nuanced concept, just as the notion of "tree of life"?
     
  4. Oct 18, 2015 #3
    I was unable to find "karyota" searching the internet. Apparently it is an alternate term for "eukaryote". Can anyone confirm this or explain a distinction?
     
  5. Oct 18, 2015 #4

    Ygggdrasil

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    There is fairly strong evidence for a single root of life (i.e. that all extant life on earth shares a common ancestor). There are many lines of evidence pointing to common descent, such as the conservation of ribosome structures, sequence and function between organisms, the universality of the genetic code, and the fact that all life uses primarily L-amino acids and D-sugars. An analysis of current genetic evidence also supports common descent.

    There were very likely many independent origins of life, but only one of these independent lines has survived to the present day. However, it may be the case that the LUCA (last universal common ancestor) retained some elements of extinct lineages through horizontal gene transfer. Of course, there are still plenty of undiscovered species on Earth, so there is always the possibility of finding "alien" life, derived from an independent origin of life, hidden somewhere on Earth.

    Karyota is a term that seems to have been defined by the author of the review article in which I found the figure:
    The reference is to Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. 2005 Decoding the genomic tree of life. Proc. Natl Acad. Sci. USA 102, 6608–6613. (doi:10.1073/pnas.0501996102)
     
  6. Oct 18, 2015 #5
    Hi Ygggdrasil:

    Thanks for your reply to my question. Your cited article looks quite interesting.

    Regards,
    Buzz
     
  7. Oct 18, 2015 #6
    Another important factor is the conservation of neurotransmitters. I think most of the primary neurotransmitters such as the mono-amines (dopamine, serotonin, and norepinephrine) can be traced back and found in even the most ancient prokaryotes:

    http://www.hindawi.com/journals/scientifica/2013/361073/

    "To date, the majority of microbial endocrinology investigations have focused on the interaction of bacteria with stress-associated biochemicals, such as the catecholamine fight and flight hormones adrenaline, noradrenaline, and dopamine ."
     
    Last edited: Oct 18, 2015
  8. Oct 18, 2015 #7

    atyy

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    Thanks, I was wondering whether the many independent origins was still plausible after the Theobald paper. It's interesting that you still think it likely. If there was extensive horizontal gene transfer among the independent origins, then in a way, rather than saying only one origin has survived, presumably one could also say that many independent origins have survived? (For simplicity, let's assume current genetic evidence and no discoveries of still surviving "alien" life.) Of course, that's a continuum of possibilities, but is it still open whether we are "closer" (in some appropriate sense) to one end of the continuum than the other (single origin survived vs all origins survived). Theobald seems to leave both possibilities open, but doesn't indicate their relative likelihoods: "If life began multiple times, UCA requires a ‘bottleneck’ in evolution in which descendants of only one of the independent origins have survived exclusively until the present (and the rest have become extinct), or, multiple populations with independent, separate origins convergently gained the ability to exchange essential genetic material (in effect, to become one species). All of the models examined here are compatible with multiple origins in both the above schemes, and therefore the tests reported here are designed to discriminate specifically between UCA and multiple ancestry, rather than between single and multiple origins of life."
     
  9. Oct 18, 2015 #8

    mfb

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    Independent of the option of multiple origins, LUCA lead to the extinction of everything else (apart from possible horizontal gene transfer) related to it. It is at least plausible that it could have lead to the extinction of different origins of life as well. Something like the genetic code and its current translation to amino acids could have been such a powerful development that other life didn't have a chance.
     
  10. Oct 18, 2015 #9

    atyy

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    I guess one should distinguish two different ideas of "lines". One of these is the idea of the lineage in the "Darwinian" sense (it's a bad term, but let's just use it as convenient name, I borrow it from similar usage in the Woese article below like "Darwinian threshold"), the other is the other of lines that can be traced from "independent origins". It does indeed seem that once the idea of a Darwinian line is possible, then all known life comes from a single Darwinian line.

    But was there a time before the first Darwinian line had formed, but after multiple independent origins, in which eg. that the genetic code had not yet settled down, and was itself evolving? Eg. what is the status of ideas like

    http://www.ncbi.nlm.nih.gov/pubmed/19117371
    Koonin and Novozhilov, Origin and evolution of the genetic code: the universal enigma.


    http://www.pnas.org/content/99/13/8742
    Woese, On the Evolution of Cells
     
  11. Oct 19, 2015 #10

    Ygggdrasil

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    I'd agree that the http://www.nature.com/nature/journal/v465/n7295/full/nature09014.html cannot rule out the possibility that other independent lineages of life arose but have gone extinct. It's unclear whether horizontal gene transfer could occur between independent lineages as they may have had very different ways of encoding genetic information (for example, it's hard to imagine how information could transfer between organisms with different genetic codes). One could imagine a scenario, however, where maybe one form of life led to the abundance of L-amino acids and the current LUCA evolved in such an environment, eventually outcompeting all other forms of life. Here, the preference for L-amino acids originated not with the LUCA, but with other, independent forms of life predating the LUCA.

    It's difficult to estimate the likelihood of whether there were multiple origins of life on Earth. One could argue that for life to have evolved, abiogenesis must not be an extremely improbable event, which would suggest that life could have arisen multiple times. However, it could also be the case that the first "type" of life to arise could have been very successful and filled all the niches on Earth, precluding further abiogenesis events. It is likely a difficult question to answer as evidence would be very difficult to find.

    Given that the genetic code is "one in a million," that is it seems optimized to be robust against mutation and error, it's almost certain that there was a point during which organisms with different genetic codes were competing against each other (these organisms, however, would likely have shared a common ancestor as they would have all been derived from the ancestor of the ribosome).

    With regard to Woese's points about HGT, differences in genetic code would seem to limit the opportunities for HGT prior to the establishment of the genetic code. Indeed, even in today's world with a (very near) universal genetic code, many other factors constrain HGT:
    Simonson AB, Servin JA, Skophammer RG, Herbold CW, Rivera MC, Lake JA. 2005 Decoding the genomic tree of life. Proc. Natl Acad. Sci. USA 102, 6608–6613. (doi:10.1073/pnas.0501996102)
     
    Last edited by a moderator: May 7, 2017
  12. Oct 19, 2015 #11
    That's the tough part I believe. Perhaps multiple rings overlap, each ring containing not only genetic signatures but environmental repercussions which might have effected other rings...

    As the rings of a tree, the core had only mud to grow from and each successive ring has the previous rings machinery and residual environment to evolve from.
     
  13. Oct 20, 2015 #12
    When the average rate of vertical gene transfer is 1/day (say) and the average rate of horizontal gene transfer is 1/4 billion years - at a ratio of 10^-12 - is it really useful to describe the resulting web as a set of "rings"? It is rather a fuzzy tree, as rRNA phylogenies show.

    As an example, the evolution of eukaryotes seems to have involved very little genetic inheritance from the first parasitic, later endosymbiont Rickettsiale. [ http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110685 ] The "eocyta" tree is wrong too, I think, eukaryotes split from within still living archaea, as a sister lineage to Lokiarchaea. [ http://www.nature.com/nature/journal/v521/n7551/abs/nature14447.html ]

    "There were very likely many independent origins of life, but only one of these independent lines has survived to the present day."

    Raup's and Valentine's model is quirky, if one assumes a single origin it gives back a probability of 1 for monophyly (as it should) but the life/death context drops out. It doesn't seem to have anything to say on the UCA lineage.

    Do we also think there were many endosymbiont analogies to the eukaryotes, but only one survivor? I have a feeling we are missing something. Life seems to got started as soon as the conditions allowed (oceans before 4.3 Ga bp http://www.minsocam.org/msa/ammin/toc/2015/open_access/AM100P1355.pdf , first dated lineage splits before 4.2 Ga bp http://www.timetree.org/search/pairwise/2/2157? , first fossils before 4.1 Ga bp http://www.pnas.org/content/early/2015/10/14/1517557112.full.pdf), same for eukaryotes after the GOE. Yet in both cases we don't see any signs of extinct competitors. Ecological lock in effects?
     
  14. Oct 20, 2015 #13
    I read that Neanderthals and Humans interbred in Europe ,so is this another case of two branches fusing together ?although this was due to sexual reproduction and not HGT.
     
  15. Oct 20, 2015 #14

    Ygggdrasil

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    Where do you get these rate estimate? Anyway, while HGT may be more infrequent than vertical transmission, if HGT produces organisms with increased fitness (as in the case of the events that produced eukaryotes), it can have a big impact on evolution. Also, rRNAs are primarily transmitted vertically, so rRNA phylogenies won't show HGT. It's only when you compare the phylogenies from looking at rRNAs with the phylogenies of other genes that you see evidence of HGT.

    If you're talking about the Rickettsiale that eventually became the mitochondrion, there was extensive HGT between that organism and eukaryotes. From the paper you cite, "Starting with 427,186 genes from 30 eukaryotic genomes representing a broad range of phylogenetic diversity, we identified 4,459 genes belonging to 394 families as mitochondria-derived nuclear genes." In other words, they identified >4,000 genes residing in the nucleus of all eukaryotes that were originally derived from alphaproteobacteria. However, other than the genes recieved from the endosymbiotic bacteria that became the chloroplasts and mitochondria, HGT between prokaryotes and eukaryotes is more limited (http://rstb.royalsocietypublishing.org/content/370/1678/20140324d).

    No, the lokiarchaea finding confirms the eocyte hypothesis. From the paper you cite: "[The eukaryotic] lineage might either descend from a common ancestor shared with Archaea (following Woese’s classical three-domains-of-life treehttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref5), or have emerged from within the archaeal domain (so-called archaeal host or eocyte-like scenarioshttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref1, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref14, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref15, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref16, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref17). Recent phylogenetic analyses of universal protein data sets have provided increasing support for models in which eukaryotes emerge as sister to or from within the archaeal ‘TACK’ superphylumhttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref18, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref19, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref20, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref21, http://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref22, a clade originally comprising the archaeal phyla Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeotahttp://www.nature.com/nature/journal/v521/n7551/full/nature14447.html#ref23. [...]Here we describe the discovery of a new archaeal lineage related to the TACK superphylum that represents the nearest relative of eukaryotes in phylogenomic analyses, and intriguingly, its genome encodes many eukaryote-specific features, providing a unique insight in the emergence of cellular complexity in eukaryotes." In other words, Lokiarchaea represent a close relative of the the hypothesized eocyte archaeum that eventually became eukaryotes.
     
    Last edited by a moderator: May 10, 2017
  16. Oct 20, 2015 #15

    Ygggdrasil

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    That's certainly a possibility. Biologists have observed examples of despeciation—species disappearing due to hybridization with related species. A recent example was observed with Darwin's finches in the Gallapagos, where it seems one species of finch may have gone "extinct" though interbreeding with other species:
    http://www.nature.com/nature/journal/v507/n7491/full/507178b.html
    http://www.nature.com/scitable/blog/accumulating-glitches/speciation_in_reverse
     
    Last edited by a moderator: May 7, 2017
  17. Oct 20, 2015 #16
    There is also a recent article I read regarding a much more lucrative mRNA from the father's sperm which can cause immediate genetic benefits in the offspring... There is monstrous amount of genetic information we really don't know much about yet... we certainly need a more dynamic system to get a handle on it all.
     
  18. Oct 20, 2015 #17

    Pythagorean

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    Re: Tobjorn's rate argument.

    There may be times in early evolutionary history when horizontal transfer and endosymbiosis were significant determinants of evolutionary path, does that really have to do with rate or is it more to do with chance and environmental context?

    But I agree with Yggg that it's important to know where those rates come from to really know what you're saying.
     
  19. Oct 25, 2015 #18

    Chronos

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    Viruses are the grand masters of genetic manipulation, so it should come as no suprise they play a significant role in the gene pool. It is a likely explanation for why the plague was so virulent in the middle ages.
     
  20. Oct 25, 2015 #19

    hagar

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    A general term for nucleated cells, as opposed to akaryota, or non-nucleated cells
     
  21. Oct 25, 2015 #20
    Where does fungai fit into this model?
     
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