Discussion in 'Biology & Genetics' started by Techne, Oct 6, 2008.

  1. Techne Registered Senior Member

    Preadaptations (aka exaptations) are features that perform a function but was not produced by natural selection for its current use. It could be argued that an exaptation forms as a result of co-option from a preadaptation, however Daniel Dennett denies exaptation differs from preadaptation. A simple example of a preadaptation is a feather that evolved (through natural selection) for warmth and was coopted into a new function, flight.

    The genomes of various ancient organisms have been sequenced and it is interesting to view the presence of several preadaptations in the genomes of these creatures. The purpose of this thread is to highlight several of these interesting findings. If anyone come across any interesting findings, post it here .

    Various trees of life exist. For example:

    For the purpose of this thread, tree #2 (Dhushara, trevol.jpg) will be used as it is a nice representation of the evolution of animals (especially vertebrates). Horizontal gene transfer and endosymbiotic events are however not clear and tree #7 (Doolittle) is probably a better way of looking at evolution. Therefore keep #2 and #7 in mind and try and piece them together.

    Preadaptations in the genome of the choanoflagellate, Monosiga brevicollis:

    Choanoflagellates (link) are single-celled organisms thought to be most closely related to animals. The divergence time of this organism was about >600 million years ago (Link) (Blue circle in image).

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    Tyrosine Kinases are crucial for multicellular life to exist and play pivotal roles in diverse cellular activities including growth, differentiation, metabolism, adhesion, motility, death (link). More than 90 Protein Tyrosine Kinases (PTKs) have been found in the human genome. Interestingly Monosiga brevicollis has a tyrosine kinase signaling network more elaborate and diverse than found in any known metazoan.

    Adherens junctions are also crucial components of multicellular life and function to communicate and adhere together in tissues. Even though Monosiga brevicollis are single-celled and do not form colonial assemblages, it is interesting to know they posses about 23 cadherins genes (Cadherins) usually associated with multicellular organisms.

    Calcium signaling toolkits also play a crucial role in multicellular signaling. Calcium signaling plays a crucial part in contraction, metabolism, secretion, neuronal excitability, cell death, differentiation and proliferation. Thus, it is also interesting to note that Monosiga brevicollis has an extensive calcium signaling toolkit and emerged before the evolution of multicellular animals.

    Tyrosine kinases, calcium signaling, and adherens junctions all play a part in neural signaling and other multecellular systems. Monosiga brevicollis does not have a nervous system. Thus it is also interesting to find the presence of the hedgehog gene in the genome of Monosiga brevicollis. Signaling by Sonic hedgehog (Shh) controls important
    developmental processes, including neural stem cell proliferation. (Link).
    Nice article:
    Multigene Phylogeny of Choanozoa and the Origin of Animals
    Compare the hedgehog gene of Monosiga brevicollis to that of humans.

    Another interesting fact about the genome of the Monosiga brevicollis is noted in this article.
    (Emphasis mine)

    Fascinating multicellular preadaptations very early on in the evolution of single-celled organisms.

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  3. Techne Registered Senior Member

    Interesting article about amoebas from 2005 (University of California):
    Biologists determine genetic blueprint of social amoeba

    Phylogenetic analysis suggest Dictyostelium discoideum diverged after plants and before metazoa.

    Any idea how many preadaptations for multi-cellularity existed? E.g.: Unicellular programmed cell death (autophagic, apoptotic metabolic catastrophe and necrotic processes), differentiation, adhesion, calcium toolkits, tyrosine kinase signaling cascades?
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  5. Techne Registered Senior Member

    More interesting preadaptations:
    This time sponges (wiki).
    Nice site about sponges.

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    Evolutionary history of sponges (Sponges = light blue, Divergence time = yellow)​

    Choanoflagellates had a lot of the toolkits necessary to develop a nervous system as well as multi-cellularity, even though they are simple uni-cellular organisms that do not form colonial assemblages.

    Now the Origin of Nerves are Traced to Sponges


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    Free, online peer-reviewed article:
    A Post-Synaptic Scaffold at the Origin of the Animal Kingdom

    There are even more fascinating findings from the genome of the sponge.
    Article with the details:
    Article abstract:
    Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit
    Whole parts of the nervous system were present in animals that do not have a nervous system, yet these parts are interchangeable and function just like they should in animals that do have a nervous system.

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    Last edited: Oct 7, 2008
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  7. Techne Registered Senior Member

    The sea urchin is another interesting creature (Green circle, yellow circle = divergence time):

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    It provides valuable knowledge for cancer, Alzheimer's and infertility research:

    Sea Urchins' Genetics Add To Knowledge Of Cancer, Alzheimer's And Infertility

    What is even more interesting is what lurks in its genome. According to present models, they originated at least 450 million years ago. These organisms have no eyes, ears or a nose, yet they have the genes humans have for vision, hearing and smelling (see above link). They also have a surprisingly complex immune system, which surpasses the human one by far.

    Now the genes in the genetic toolkit (nice video) in animals responsible for assigning specific properties of the various body parts are known as Hox genes. Here is a nice overview of Hox genes. A great deal of Hox genes are found in the sea urchin, the pattern of gene expression just differs, resulting in a different body plan.

    Right at the base of the animal tree, a sundry of genes necessary for sight, smell, hearing as well as the various body plans were present in the genome of the common ancestor.

    The Trichoplax adhaerens genome is equally intriguing.
  8. Techne Registered Senior Member

    A Trichoplax preadaptation:
    The Dlx gene

    What does it do (wiki)?
    A quick BLAST of the sequence reveals it is closely related to human Dlx1, as well as Dlx1 in other vertebrates (including Zebrafish, the mouse, rat opossum, dog etc.)

    More specifically, what does Dlx1 do?
    It is possible to create a homology of this protein to look at its possible structure. The closest match is the human Dlx 5 protein structure. Sequence alignment places the Dlx sequence of Trichoplax closer to human Dlx5 than to human Dlx1 (Figure 1)

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    Figure 1: ClustalW - original settings​
    What does Dlx 5 do?
    The homology model of the protein:
    A good quality protein was generated (Figure 2).

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    Figure 2: Swissmodel of Trichoplax Dlx protein (2djn.pdb as template)​

    So, a Hox gene responsible for a sundry of neurologically associated developmental processes present in an organism with no nerve, sensory or bone cells at the base of the evolutionary tree. Awesome

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  9. iceaura Valued Senior Member

    I'm not following your argument, exactly.

    Did you disagree with Dennett's analysis of these vocabularies? His view, shared by most evolutionary theorists and structurally fundamental to Darwinian theory, seems persuasive.
  10. Techne Registered Senior Member

    I agree, and think that preadaptation does not differ from exaptation.
  11. Techne Registered Senior Member

    More fascinating preadaptations from the Trichoplax:

    The Trichoplax Mnx sequence: ABC86118
    Comparison of this sequence with a few others: Cladogram

    The human Mnx1 gene.

    The fly Mnx gene (exex)
    The Zebrafish Mnx gene

    What does it do?
    It is involved in the development of the pancreas and motor neurons.
    1) Zebrafish mnx genes in endocrine and exocrine pancreas formation.
    2) The Mnx homeobox gene class defined by HB9, MNR2 and amphioxus AmphiMnx.

    Interesting research:​

    Directed Evolution of Motor Neurons from Genetically Engineered Neural Precursors.
    What did these guys do? They enforced the expression of 3 genes associated with neuronal development in order to direct the development of motor neurons. Sonic hedgehog also played a role

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    So four genes played a role:
    1. HB9
    2. Nkx6.1
    3. Ngn2
    4. Sonic hedgehog

    Are similar genes present in the Trichoplax genome?
    1. HB9 (mnx)
    Yes (see above).

    2. Nkx6.1
    Here is the human Nk6 gene
    And here is the Trichoplax version

    3. Ngn2
    Here is the human neurogenin 2 (ngn2) gene
    And here is the Trichoplax version.
    A quick BLAST (blastp) the human genome shows this sequence to be closely related to ngn2 (E-value = 3^-8).

    4. Sonic hedgehog (shh)
    Here is the human shh gene
    This gene seems to absent in from the Trichoplax genome, however, the presence of shh in Monosiga brevicollis (unicellular eukaryote that diverged before Trichoplax) suggest the possibility of gene loss in this lineage.

    Wonder what will happen if shh is co-expressed and together with mnx, Nk6 and ngn2 in Trichoplax, or whether these genes will function like their counterparts in higher animals.

    A complex array of neurologically associated developmental pathways present in this eumetazoan that has no nerves, sensory cells and muscle cells, and there is more

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    Last edited: Oct 22, 2008
  12. Harro Registered Senior Member

    Hi Techne, thanks for the heads up.

    Preadaption sounds very plausable. If you think about it some mutations could change the DNA but not be harmfull to the organism but not advantageous iether. So it remains in the gene pool. This could explain alot of the junk DNA I hear biology articles talk about. Now if there is a shift in the environment where the organism have the preadaption that is actually benificial to the organism that genetic preadaption could become the dominate genes.
  13. Techne Registered Senior Member

    Hi Harro,

    Junk DNA seems like a myth...
    'Junk' DNA proves functional

    On the development of eyes

    Several types of eyes exist and these include the camera-type eye, the compound eye, and the mirror eye (Figure 1). Ernst Mayr proposed that eyes evolved in all animal phyla 40 to 60 times independently.
    A monophyletic program governing the development of the different eye types is proposed and the Pax6 gene is posited to be the master control gene. The Pax6 gene also plays a part in controlling the development of the nose, ears and parts of the brain.

    What is needed for the developmental program of eyes?

    A few core genes include:
    Pax6 (eyeless [eye]) in Drosophila)
    Six-type genes (E.g. Six3)
    Sox-type genes (E.g. Sox2)
    atonal ( E.g. Atoh7)
    Retinoid receptors
    Fox transcription factors (E.g. FoxN4)

    Fascinating experiments have been conducted by shuffling around the genetic program architecture of genes associated with eye development in various animals.
    For example in Drosophila:
    Ectopic eye structures are able to be induced on the antennae, legs, and wings of fruit flies. This is done by targeted expression of the eyeless gene (Pax6 Drosophila homologue) (Figure 2). The Pax6 gene from the mouse is able to do the same job as the Drosophila version (Figure 3). And in Xenopus embryos, ectopic eye structures in can also be induced by the Drosophila eyeless (Pax6) version (Figure 4).

    What about the Trichoplax adhaerens genome? Any genes for eye development?
    It seems quite a chunk of the circuitry needed for eye development is present. (From table 1)
    PaxB (eyeless?)
    Six genes
    Sox gene
    Atonal gene
    Retinoid X Receptor
    Fox transcription factors

    All that is missing seems to be crystalins (plays a part in lens formation). However, Darwin posited that "The simplest organ which can be called an eye consists of an optic nerve, surrounded by pigment-cells and covered by translucent skin, but without any lens or other refractive body." Thus large chunks of the circuitry for eye development in Trichoplax is present but no eyes!

    Now compare the developmental program to evolution.

    Here is an interesting article that shows the parallels between evolution and development.

    For development:
    Primordial germ cells (PGC) are prevented from entering the somatic program and are demethylated (genome-wide erasure of existing epigenetic modifications). Then the gametes are imprinted (targeted DNA methylation) during gametogenesis, only to be demethylated again after fertilization. Then during development, DNA is methylated again, causing totipotential cells to become pluripotent. X-inactivation and reactivation (of the paternal gamete I think) also occurs. The whole process is governed by the genetic (and epigenetic?) program. During the unfolding of this somatic program, random variation and selection occur, ultimately leading to just a few endpoints, every time it is successful. The process is constrained (few end points) as a result of pre-existing information that is set up during the inititiation of the process. All this is controlled by information in the genome.

    For evolution:
    There also seems to be only a few endpoints (small subset, limited variation) out of all the possible endpoints.
    In the article:
    An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution
    It is argued to be as a result of genetic instructions dating earlier in evolutionary time. Preadaptations...

    As already seen in the evolution of eyes, as soon as these sets of genes were formed (E.g. Pax genes), through whatever mechanism), evolution seemed to have been biased to a few end points, and these few endpoints arose 40-60 times, independently, as a result of pre-existing (preadaptations) information in the case of eyes.

    What other "biased" end points can there be? Nervous systems, smell, hearing? And why would evolution be biased, as in development, to only reach a few end points over and over?

    Seeing that evolution is biased towards a few endpoints which is partly due to the massive amounts of preadaptations in organisms at the base of the evolutionary tree. Now evolution seems to learn...

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    Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments
    Biased evolution towards a few endpoints under intrinsic control.

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    And now proteins that control evolution...

    Evolution's new wrinkle: Proteins with cruise control provide new perspective

    Related articles: Number 1
    Mutagenic Evidence for the Optimal Control of Evolutionary Dynamics

    Fitness functions actually guiding evolution?

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    Number 2:
    Optimal control of evolutionary dynamics

    From the conclusion:
    And again from this article:

    Self-regulating systems biasing future evolutionary trajectories towards a few outcomes?
  14. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Very interesting. It would appear that genes now used for specific higher functions were present for lower functions, then slightly modified when circumstances arose to allow the higher functions. It really goes to show the 'plasticity' of genes and their morphological expression. We had a thread about primate/human chromosome number, showing that the Homo lineage has two chromosomes joined into one, which in all other primates remain as two chromosomes. As expected, the chromosomes are joined at the telomeres, and one of the two centromeres is now non-functional. I wonder if perhaps the joining of those two chromosomes somehow activated additional gene functions that might have earlier been suppressed?
  15. Techne Registered Senior Member

    Goes to show you, genomes seem to be prepared/preadapted for evolutionary processes.

    More preadaptations from Trichoplax:
    Its function?
    Critical element in the development of the liver:
    The role of Hex in hemangioblast and hematopoietic development.
    The homeoprotein Hex is required for hemangioblast differentiation.
    The homeobox gene HEX regulates proliferation and differentiation of hemangioblasts and endothelial cells during ES cell differentiation.

    Detoxification of free radicals and damaging molecules play a crucial part in cellular homeostasis as well as systems homeostasis. The liver is mainly responsible for system homeostasis as it contains the highest concentration cells (hepatocytes do the heavy lifting) capable of detoxification, modification and excretion of hazardous molecules. It would be interesting to see what a gene that is associated with the development of the liver is doing in this simple organism at the base of the eumetazoan tree.

    The trend of neurologically associated homeobox genes continues.
    Regulation and function of Dbx genes in the zebrafish spinal cord.

    Pitx: Another neurologically associated Hox gene present in the Trichplax genome.

    The various versions:
    Trichoplax. Function unknown at present. Would be interesting to find out what it is.
    Human Pitx1 Its function:

    Human Pitx2 Its function:
    Human Pitx3 Its function:
    Zebrafish Pitx1
    Zebrafish Pitx2
    Zebrafish Pitx3
    Drosophila Ptx1 (fruitfly)

    More interesting facts about Pitx:
    The Pitx homeobox gene in Bombyx mori: Regulation of DH-PBAN europeptide hormone gene expression

    PITX genes are required for cell survival and Lhx3 activation

    Zebrafish pitx3 is necessary for normal lens and retinal development.

    And the trend of neurologically associated genes present in this basal eumetazoan continues...

    The various versions:
    Trichoplax: Function unknown at present. Interested in its function in a basal eumetazoan.
    Human otp. Its function:
    The role of Otx and Otp genes in brain development.
    The same for mice:
    The murine Otp homeobox gene plays an essential role in the specification of neuronal cell lineages in the developing hypothalamus.
    The Zebrafish version. Its function: More of the same.
    Differential regulation of the zebrafish orthopedia1 gene during fate determination of diencephalic neurons
    In the sea urchin.
    Evolution of OTP-independent larval skeleton patterning in the direct-developing sea urchin, Heliocidaris erythrogramma.
    A clear example of a cooption, whereby the same gene plays a role in neurological development in vertebrates and skeletal development in the sea urchin. Recycling of pre-existing genes for various, distinct, developmental processes.​
  16. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Still even more interesting.

    I read an article yesterday [not at my fingertips - I'll get it this afternoon and provide more detail later] in which a retrovirus gene, inserted in the distant past into the genome as part of the 'junk' DNA, is now used in uterine functions. I'll look for the article [seen on a college hall's wall] and give its cite later.

    As we know, retroviruses simply cause disease of an organism. Those that survive an attack by a retrovirus of the germ cells, survive with the DNA inserted into the germ line, where they can become fixed in the gene pool of that species after the passage of many generations. They are typically inactivated thereafter. The one referenced above later found use in another function. It is not known when it was inserted, and I'm not certain if it is present in non-mammalian vertebrates.

    It's almost like Lincoln Logs. All the pieces are there waiting to make appropriate proteins when activated by a mutation that might have a use when an evolutionary niche arrives.
  17. Techne Registered Senior Member

    Yeah, biomolecular machinery, a reasonably optimal genetic code, optimized for evolution, preadaptation etc. Cells seem prepared for the future

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    Well, it is not a fact that retroviruses are the origin of diseases. They might act as regulatory elements in the immune system and a fault in the system might cause it it to look like erv's are the cause. It would be interesting to learn about the mechanism of how an ERV causes a disease. But, a faulty p53 gene is also the cause of many cancers, yet it is crucial in many functions in normal cells.

    Also, ERVs and LTR elements do play a crucial role in many cellular processes.
    [7] von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res. 2005;110(1-4):108-116.

    [8] Romanish MT, Lock WM, van de Lagemaat LN, Dunn CA, et al. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian evolution. PLoS Genet. 2007 Jan 12;3(1):e10.

    [9] Dunn CA, Medstrand P, Mager DL. An endogenous retroviral long terminal repeat is the dominant promoter for human beta1,3-galactosyltransferase 5 in the colon. Proc Natl Acad Sci U S A. 2003 Oct 28;100(22):12841-12846.

    [10] Wang T, Zeng J, Lowe CB, Sellers RG, Salama SR, Yang M, et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-18618.

    [11] Colmegna I, Garry RF. Abstract Role of endogenous retroviruses in autoimmune diseases. Infect Dis Clin North Am. 2006 Dec;20(4):913-929.
  18. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Sorry for the delay in getting that article.

    It was from David Brown of the Washington Post, reproduced in the Daily Herald on September 2, 2008. He references that a few HERVs [Human Endogenous Retro Viruses] that have been incorporated into the human genome, but then took on new roles [other than viral infection and disease of the host]. "For example, a protein called syncytin, which helps cells fuse together in the placenta, is actually the evelope gene from a HERV." He likely means the HERV gene incorporated into the genome produces a protein called syncytin, and not that the gene is the protein.

    More about this at:

    In another study, 10 versions of HERV-K viruses, incorporated in various parts of the genome but with varying disabling mutations, were examined and the original virus deduced. It was replicated and tested in the laboratory, and found capable of infecting host cells.

    Here's the link to the original newspaper article:
  19. Techne Registered Senior Member

    It is indeed striking how Horizontal Gene Transfer aided in the development of reproduction in eutheria.

    More about Placozoa and predaptations.
    That old tree of life gets uprooted so often it is not even funny. So much for the predictive value of evolutionary science. This time it hits an interesting turn.
    Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern ‘‘Urmetazoon’’ Hypothesis

    This time that interesting little animal with only four cell types but also genetic tool kits for eyes, ears, nerves, bone formation and body plans gets placed at the based of the metazoan tree. See figure:

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    From the article:
    Genetic tool kits present for the development of neurological organs before they evolve...
    Play the tape of life again and it should unfold in a similar fashion.
  20. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Well, that makes sense. If both groupings had the same 'genetic tool kit' already present, then they could both end up relying on that tool kit to engage in parallel evolutionary strategies, independently of each other.

    So what were these 'genetic tool kits' doing in the precursor organisms? For the retrovirus I cited, the one tool-kit that was adapted for helping cells fuse together in the placenta was previously used for the viral envelope of the retrovirus that had invaded a precursor organism.

    Lots more questions every time we look deeper!
  21. Techne Registered Senior Member

    Consider Hox-genes.
    A brief overview of Hox genes

    Basically these genes control the formation of body plans and how they unfold and emerge during development.
    Now consider the following article:
    Homeodomain proteins belong to the ancestral molecular toolkit of Eukaryotes
    So, the findings that genes controlling the emergence of body plans were present waaaay before multicellular organisms were even on the cards. Same can be said for a whole lot of other tool kits for multicellularity.

    The article continues:
    And Figure 1:
    So, the data STRONGLY suggest that the information needed for body plans were present waaaay before body plans were present.

    It continues.

    Natural selection as an evolutionary force is a vacuous concept.
    Will Provine in his book:
    The Origins of Theoretical Population Genetics
    From page 199 (see above link):
    Natural selection DOES NOTHING, it is not an evolutionary force.

    The finding that the Ur-eukaryote was quite complex and had the necessary tool kits to bias evolutionary directions toward multicellularity and organisms with body plans over and over provides a keen insight into the nature of evolutionary processes over deep time.

    Article continues:
    Anyone want to guess what the old view was?

    Preadapted FOR multicellularity. Mmmmmm. Sound familiar?

    So, evolution seems to be biased towards multicellularity. Replay that tape of life and we should get a similar result

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  22. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

    Again, very interesting. And, it makes sense that if the various branches of multicellular eukaryotes [green algae, brown algae, red algae, animals, etc.] already had the genetic kits included in their unicellular ancestors, that they could then all rely on those kits in subsequent evolution to independently obtain multicellularity [as a form of 'convergent evolution'].

    So, what functions did those genetic kits [that later served to allow multicellularity] serve in our common unicellular ancestor to all of our multicellular cousins?
  23. Techne Registered Senior Member

    That is indeed an interesting view of evolution.
    The similarities between evolution and development are striking.

    Interesting question. I am sure we will find out.

    Interesting finding:
    Billions Of Years Ago, Microbes Were Key In Developing Modern Nitrogen Cycle
    Last edited: Mar 16, 2009

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