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Dinosaur to bird tail transition. Testing the theory. Genetics and the fossil record.

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  • Dinosaur to bird tail transition. Testing the theory. Genetics and the fossil record.

    Hi All,

    


Another essay.



    At this link:-

    From dinosaurs to birds: a tail of evolution

    - is the provisional version of a paper up for publication in the journal EvoDevo.

    It describes how observations in developmental and mutational genetics and the fossil record are being combined to derive plausible routes by which an important evolutionary transition took place. In this case the transition is from dinosaur tails (long, unfused vertebrate, with leg muscle attachments, and no pygostyle) into bird tails (short, fused vertebrate, with no or little leg muscle attachment, and a pygostyle).



    The read is a bit of a task. The transition was complex and the underlying genetics is complex. But within the jumble, some clear patterns have emerged which provide the insights to researchers.

    The following essay over several posts, will be my attempt to describe the paper.

    

A sub theme of these posts is to illustrate one of the ways in which scientists test ideas about evolution. There are many other ways in which researchers test their theories. This is one of those ways and is largely due to:-



    1) a better fossil record. and

    

2) a lot more genetic and mutational data thanks to recent improvements in technology.


    To be continued ...
    Last edited by rwatts; 08-05-2014, 05:03 PM.

  • #2
    Originally posted by rwatts View Post
    Hi All,

    


Another essay.



    At this link:-

    From dinosaurs to birds: a tail of evolution

    - is the provisional version of a paper up for publication in the journal EvoDevo.

    It describes how observations in developmental and mutational genetics and the fossil record are being combined to derive plausible routes by which an important evolutionary transition took place. In this case the transition is from dinosaur tails (long, unfused vertebrate, with leg muscle attachments, and no pygostyle) into bird tails (short, fused vertebrate, with no or little leg muscle attachment, and a pygostyle).



    The read is a bit of a task. The transition was complex and the underlying genetics is complex. But within the jumble, some clear patterns have emerged which provide the insights to researchers.

    The following essay over several posts, will be my attempt to describe the paper.

    

A sub theme of these posts is to illustrate one of the ways in which scientists test ideas about evolution. There are many other ways in which researchers test their theories. This is one of those ways and is largely due to:-



    1) a better fossil record. and

    

2) a lot more genetic and mutational data thanks to recent improvements in technology.


    To be continued ...
    Very good post! The red highlighted text is key. It explains how biological evolution is tested, in spite of the YEC claim that "historical" science is not testable nor falsifiable.

    Now, positing "plausible routes" will surely be attacked by many YECs as "just-so stories."

    They're nothing if not predictable.

    K54

    Comment


    • #3
      INTRODUCTION

      The researchers introduce their paper, pointing out that bird tails are an evolutionary novelty which are used for flight control, mating displays and warning signals.

      Unlike most dinosaur tails which:-


      1. Are long with lots of caudal vertebrae, and
      2. lack any vertebrae fusions, particularly
      3. a pygostyle at the end which supports a “retricial bulb” of muscles and nerves for feather control, and which
      4. have muscle attachments at the tail end closest to the body for a large muscles (caudofermoralis muscles) which are used for hind leg retraction.

      - birds have a short tail consisting of a few caudal vertebrae some of which are fused at the end into the pygostyle with its associated retricial bulb. The bird tail also lacks or has reduced muscle attachments.

      All extant birds have this conventional tail.

      

I say “most dinosaur tails” because close to the evolutionary transition, some non avian (non birdlike) therapod dinosaurs show tails that have some birdlike characteristics.

      However, in a fairly well documented fossil record, the distant relatives of birds generally had the reptilian tail and the more immediate common ancestors to the modern birds display a very sudden transition to the modern bird configuration. This sudden transition could be due to a lack of relevant fossils or the record itself could be revealing actuality - the transition was indeed sudden. The researchers write:-

      


      Originally posted by link at OP
      Given the multiple phenotypes that can arise with single mutations, can the perceived sudden appearance of short-tailed birds be due to a lack of intermediate specimens in the fossil record, or from a very limited number of mutations that caused significant alterations to the primitive bird skeleton in a relatively short period of time?
      The authors deemed that understanding this transition could benefit from current insights into the tail axial developmental mechanisms, that is, insights into how the embryonic tail grows lengthwise, and what happens when mutations occur to the genes underlying the developmental program.

      When it comes to tail shortening, they write:-

      Originally posted by link at OP
      Mutations in key developmental genes and/or their regulation can cause multiple changes in morphology. Indeed, pleiotropic effects are observed in the vertebrate axial skeleton for a number of mutations
      These "pleiotropic effects" where a single mutation can cause several morphological changes, play an important role in defining the evidence as to what may have happened those millions of years ago.


      In the next post I discuss the Background section of their paper.



      To be continued ....

      Last edited by rwatts; 08-02-2014, 09:17 PM.

      Comment


      • #4
        Originally posted by klaus54 View Post
        Very good post! The red highlighted text is key. It explains how biological evolution is tested, in spite of the YEC claim that "historical" science is not testable nor falsifiable.

        Now, positing "plausible routes" will surely be attacked by many YECs as "just-so stories."

        They're nothing if not predictable.

        K54
        You know, you remind me of another guy on Tweb before it crashed. He had an Uncle Sam avatar, is that you?
        Better to illuminate than merely to shine, to deliver to others contemplated truths than merely to contemplate.

        -Thomas Aquinas

        I love to travel, But hate to arrive.

        -Hernando Cortez

        What is the good of experience if you do not reflect?

        -Frederick 2, Holy Roman Emperor

        Comment


        • #5
          Originally posted by TimelessTheist View Post
          You know, you remind me of another guy on Tweb before it crashed. He had an Uncle Sam avatar, is that you?
          That was Tiggy, and yes, there is a resemblance in their style/attitude, only they are not the same person.

          Comment


          • #6
            Originally posted by TimelessTheist View Post
            You know, you remind me of another guy on Tweb before it crashed. He had an Uncle Sam avatar, is that you?
            No, nein, nie, nyet.

            Never had an Uncle Sam avatar anywhere.

            But that's not that I don't like him.

            K54

            Comment


            • #7
              Originally posted by Cerebrum123 View Post
              That was Tiggy, and yes, there is a resemblance in their style/attitude, only they are not the same person.
              This "Tiggy" must've been a cool dude if his style were like mine -- concerned about truth, pointing out logical fallacies, and asking YECs questions they can't or refuse to answer. You know, getting at the core of the issues.

              If you've been paying attention, I've also been trying to get Biblical answers to questions regarding a direct reading of Genesis in an unambiguous manner -- which is the ONLY argument YECs have for Biblical Creation "Science".

              It is a crying shame YECs can't even counter mountains of consilient data with any Biblical physical explanation, yet keep using that there "science" word.

              K54

              Comment


              • #8
                Originally posted by TimelessTheist View Post
                You know, you remind me of another guy on Tweb before it crashed. He had an Uncle Sam avatar, is that you?
                No, he's HMS Beagle now.
                That's what
                - She

                Without a clear-cut definition of sin, morality becomes a mere argument over the best way to train animals
                - Manya the Holy Szin (The Quintara Marathon)

                I may not be as old as dirt, but me and dirt are starting to have an awful lot in common
                Stephen R. Donaldson

                Comment


                • #9
                  Originally posted by TimelessTheist View Post
                  You know, you remind me of another guy on Tweb before it crashed. He had an Uncle Sam avatar, is that you?
                  As pointed out, that "other guy" is now HMS Beagle a.k.a. Beagle Boy a.k.a. Tiggy.

                  Do you know why 'these' people keep changing their names as if changing their underwear? It's because they wish to remain hidden behind a veil of secrecy. Why? Well, if you were tossing out as much nonsense, non-science, irrationality, blind faith, pagan beliefs and other assorted sordidness, you also would be inclined to use a pseudonym and to change it regularly.

                  Bwahahahaha

                  Me? I gave my full name from day one - Jorge A. Fernandez - and have used it (Jorge)
                  from that first day. Nothing to hide ... nothing to keep secret.

                  On the other hand, I've heard of internet wackos using personal information to do harm.
                  Yup - we may have one or two of 'those' kinds of people floating around here ..........
                  So maybe there's a method to their madness.

                  Jorge

                  Comment


                  • #10
                    Originally posted by Jorge View Post
                    As pointed out, that "other guy" is now HMS Beagle a.k.a. Beagle Boy a.k.a. Tiggy.

                    Do you know why 'these' people keep changing their names as if changing their underwear? It's because they wish to remain hidden behind a veil of secrecy. Why? Well, if you were tossing out as much nonsense, non-science, irrationality, blind faith, pagan beliefs and other assorted sordidness, you also would be inclined to use a pseudonym and to change it regularly.

                    Bwahahahaha

                    Me? I gave my full name from day one - Jorge A. Fernandez - and have used it (Jorge)
                    from that first day. Nothing to hide ... nothing to keep secret.

                    On the other hand, I've heard of internet wackos using personal information to do harm.
                    Yup - we may have one or two of 'those' kinds of people floating around here ..........
                    So maybe there's a method to their madness.

                    Jorge
                    If you're so proud of your name, how come the only place you show up on Google is a link to your mendacious TrueOrigins screed?

                    Harping about screen names isn't going to help your cause.

                    Answer questions. Consilience of scientific evidence. Unambiguous Genesis reading to counter science. Your definition of information.

                    ...

                    Keep it up. Your stinking excuse for apologetics and scientific knowledge is amusing at least.



                    K54

                    Comment


                    • #11
                      BACKGROUND

                      In this section, the authors begin by noting that the modern bird tail is an evolutionary novelty, used for flight control, mating displays and warning signals.



                      They introduce the fossil record showing what it currently reveals with respect to dinosaur, transitional, and modern bird tails.

                      

If you go to figure 3 at the link in the OP (the figure is at the back, even though the caption is in the paper. Remember, this is a draft paper), there you will see something of what the record shows. The dark black lines in roughly the middle of the left and right phylogenetic trees show that some non avian (non birdlike) theropod dinosaurs had tails with some birdlike characteristics. These characteristics seem to have been lost for a bit, before returning in the transitionals and remaining with the modern birds we see today. These transitionals and the modern birds form the dark black lines at the bottom of both trees. The temporary loss of these characters is marked by the unfilled lines separating the two sets of dark lines - those in the middle of the diagram, and those on the bottom.


                      Figure 1 at the link in the OP shows this tree, but in another sense. At the time of transition, there were bird like dinosaurs having both the dinosaur/reptilian like tail and the bird like dinosaurs having the bird like tail. To see the difference, go to figure 2. At the top is the dinosaur/reptilian like tail of Archaeopteryx. Below are three transitional tails showing the relatively few vertebrate, with those at the end fused into a pygostyle.

                      

These reptilian tails were relatively long with perhaps 20-30 caudal vertebrae. Those vertebrae closest to the body had attachments for massive muscles which were used for hind leg retraction. The tails lacked any vertebrae fusion. The bird or bird like tails could have a reduced number of vertebrae with only 6 or so near the body being free and the remainder at the end being fused to form the pygostyle, a bony structure to support muscles and nerves used for feather control. And the muscle for hind leg retraction was either absent or much reduced as well. In modern birds, where this muscle does occur, itís attached to the end of the tail at the pygostyle, rather than at the vertebrate nearest the body.

                      The thing is that this transition seems to have been remarkably fast, no matter which way the fossil record is viewed. Even though the fossil record is very incomplete, the transition was fast, and was possibly down to a single mutation or a few mutations at most:-

                      


                      Originally posted by link at OP
                      Despite these variations, there is consensus that short-tailed primitive birds appear in the fossil record relatively suddenly, with fewer caudal vertebrae terminating in a fused distal pygostyle, with abrupt rather than gradual loss of tails [2].
                      

This transtition appears to be associated with the loss of or the reduction of the massive caudofemoralis muscle used for hindlimb retraction. The possibility is that decoupling hind leg retraction from the tail precipitated this tail evolution. With the tail freed from that function, it was able to evolve in new and novel ways:-

                      


                      Originally posted by link at OP
                      CML modifications, and others within the tail, may have facilitated the abrupt transition to short-tailed birds due to function decoupling. Decoupling of locomotor structures from each other is a hallmark of the origin of birds and powered flight and was most focused in the forelimb and tail [30,31].
                      



                      The fossil record also reveals that tail reduction was associated with other changes - a more extensive synsacrum (a fusion of vertebrae bones towards the back of the bird, just before the tail begins), the development of a sternum, and digit fusion.

                      

Some of these fusions are important because the feed into evidence for what may have been the genetic underpinning for the transition.

                      


In the next section, the authors describe how the tail develops.





                      To be continued ....



                      Comment


                      • #12
                        TAIL DEVELOPMENT: Tail structures.

                        The authors spend a lot of time discussing tail development. This is done over several sections as follows:-

                        1) Tail structures.
                        2) Axial extension.
                        3) Regional specification.
                        4) Caudal positional identity.
                        5) Tail termination.
                        6) Skeletal development of the bird synsacrum and tail.

                        The first, tail structures, is a bit hard to describe without repeating word for word what the authors write. They begin by pointing out that the mechanisms governing tail growth are more or less the same across all vertebrates and that these have been the same since well before the dinosaurs. Naturally, this is important for what comes later because it’s the mouse model that the researchers get most of their data from.

                        They continue by noting that vertebrate tail embryos are constructed from the same basic elements, arranged in the same basic pattern. They then go on to describe these elements and the growth pattern. In short, running the length of the embryo are the notochord and, underneath, the neural tube. Around these are the somites, or segments, or units of the same structure that repeat as the tail grows outward from the embryo body. At the end of the tail bud is a pool of undifferentiated cells called the chordoneural hinge which provides the cells for the tail to grow outwards.

                        However, there is more detail to this, which, on describing, means that I essentially repeat the words of the authors.

                        So may I suggest that the reader peruse the short section under “Tail development”, titled “Tail structures”. Figure 4 in the link at the OP is the critical figure here. It’s at the end of the paper while its caption is near the end of the section in the paper.

                        I’ll roughly define some words to help the reader better understand the section.

                        Definitions

                        Caudal = a synonym for posterior, toward the end of the body, in the end of the body.

                        

Chordoneural hinge = cells which are used to grow the tail axially, lengthwise, and which can differentiate into different cell types.

                        Dermis = a layer of tissue below the epidermis, containing blood capillaries, nerve endings etc.

                        Dorsal = upper, top, above.



                        Ectoderm = Outermost layer of cells in a developing embryo. Epidermis and other tissues derive from it.

                        Epidermis = Overlies the dermis. An outer layer of cells.

                        Hindgut = the posterior end of the alimentary canal including latter portions of the colon, the rectum etc.

                        Mesenchyme = loosely organised mesodermic (middle) tissue in an embryo which develop into connective tissue and skeletal tissues.

                        Neural crest cells = transient, undifferentiated cells that migrate during embryonic development and later give rise to all kinds of specialised cells. Initially they reside above (dorsally to) the neural tube.

                        Neural tube = a long tube running the length of the developing embryo from which the brain and the spinal chord develop.

                        Notochord = a long chord under the neutral tube running the length of the developing embryo from which the nucleus pulposis (structure inside of the discs that separate the vertebrate) develops.

                        

Posterior = tail end.

                        Somite = a body segment that gets repeated. Contains the same internal structures. Clearly visible in invertebrates, but also seen in vertebrates during their embryonic stages.

                        Tailgut = the latter part of the hindgut.

                        Ventral = lower, bottom, below.


                        
Next post will be about axial extension - or how the tail grows long.


                        To be continued ...

                        Last edited by rwatts; 08-04-2014, 04:56 PM.

                        Comment


                        • #13
                          TAIL DEVELOPMENT: Axial extension

                          Next the researchers describe how the tail extends during embryonic growth. While a lot remains to be worked out regarding the genetics underpinning body formation, there is much that is known already.

                          Very early in embryonic formation the body plan of the organism is laid down by the release of certain chemicals in the embryo which define all kinds of things such as front and end, top and bottom, arms and legs, head and tail.



                          Just after the formation of a small ball of dividing cells, a process called gastrulation begins, whereby the ball begins to fold into three layers marking out the ectoderm, mesoderm, and endoderm.

 The ectoderm will become the epidermis and nerve tissue. The mesoderm will become muscles and bone. The endoderm will become the gut.

                          The mesoderm at this stage is essentially what is called a presomitic mesoderm (PSM), because it defines where the somites will shortly form.

                          

How does it do this?

                          

Largely by two intersecting chemical gradients, one, a protein gradient produced at the far tail end of the gastrula by what is called the “Wnt/Fgf gradient”, and the other produced by each somite that forms, called the “retinoic acid (RA) gradient”. Because somites begin to form at the head end of the embryo and then extend sequentially tailward, these two gradients are in opposition to each other and where they meet defines what is called a “somite determination front”.

                          

Figure 5 at the link in the OP is the important figure here.

                          Somite formation is periodic, with each somite being laid down in accordance with the “ticking” of a genetic oscillator, a series of interacting genes and proteins which mark out a kind of time. The interactions of the oscillator and the gradients noted above, cause the gradient wavefront to move from the anterior to the posterior of the embryo, marking out somite positions as it traverses the embryo.

                          A presentation showing something of how this works, and the kinds of experiments done to uncover these details can be found here:-

                          Snapshot: The segmentation clock

                          The boundaries of each somite or segment are defined by “Notch pathway” genes. Expression of these genes also define the anterior and posterior ends of each somite, that is, which boundary is front, and which is back.



                          Of course, as a segment is laid down, thereby increasing the length of the embryo, cells are being used up. So new segments are created from cell division which occurs within the PSM as well as in the chordoneural hinge which was mentioned in my last post. Cell division occurs in these areas and, if needed, the new cells migrate to the region of the growing embryo.





                          In short



                          Cell division occurs in the CNH and the PSM and feed cells into a wavefront that travels from the front of the embryo towards its tail. And oscillating genetic clock which interacts with other genes and their associated proteins marks out where the next somite begins and ends.


                          Experiments done with the mouse, chicken and zebrafish during somite extension, has revealed that this method of tail development is highly conserved as are the major genetic pathways which cause it. However which genes oscillate can vary a lot between organisms. Only a few proteins were shown to be consistent oscillators across all three species. Other proteins which also oscillated varied between the species, although they belonged to the Wnt, Fgf and Notch gene families. So there seems to be a lot of evolutionary plasticity in somite (and tail) development, with members of the Fgf, Wnt and Notch gene families being targets for evolution as far as tail axial extension was concerned.


                          Next the paper discusses regional specification. That is, what chemicals informs cells in any particular part of the embryo, what or where they are supposed to be? Naturally, a cell that finds itself in the tail region needs to know that this is what its role will be.


 It has to produce proteins essential for the tail.


                          To be continued ...



                          Last edited by rwatts; 08-05-2014, 05:17 PM.

                          Comment


                          • #14
                            TAIL DEVELOPMENT: Regional specification


                            In the last post we learnt how the embryo is divided into somites or segments which in the case we are dealing with here, concerns itself largely with the vertebrae that form a repeating pattern along the length of the vertebrate body, be the organism a human, a mouse, a bird or a dinosaur.

                            Well an organism’s body is also divided into regions, generally larger identities than the segments mentioned above. In the case of the insect we have the classical head thorax and abdomen and the vertebrate embryo is likewise divided into similar kinds of regions as is shown here. These are named the cervical, thoracic, lumbar, and sacral or caudal.



                            The position and identity of the large regions are determined by what are called Hox genes.

                            Hox genes were first discovered in the fruit fly Drosophila which has 13 of them in one cluster. Other non vertebrates share this arrangement, but with some variation in gene number and base sequence.

                            

Due to a number of duplications, vertebrate Hox genes usually appear in 4 similar clusters, labelled A, B, C and D. And again each cluster can vary in gene count and base sequence.*

                            What this looks like diagramatically can be seen here.



                            Compare the cephalochordates, the tetrapods and the flies. (Ignore the teleosts because if you look closely, you will see that only six clusters are shown. I suspect this is either an error or the seventh one had not yet been discovered.) If you look at the cephalochordate, then from left to right you can count 13 coloured squares. The Hox genes are numbered from left to right, starting at 1 and ending at 13. The fly, supposedly has something like the original primitive cluster which became duplicated several times after lineages to other organisms split off. In the tetrapods, you can see the clusters labelled A, B, C and D.

                            How do these clusters of genes work? Well they get expressed in sequential order from left to right, from head to tail, marking out the embryonic regions seen in the small diagrams on the right. Gene ‘color‘ is associated with embryonic region.

                            What do they do? Well knockout experiments (stoping genes from functioning to see what happens), cause what are called “homeotic transformations”. That is, in the context of the vertebrae, a region where a knocked out gene should express can take on the characteristics of the more anterior or more posterior regional vertebrate. Thus, knock out all three mouse Hox 10 genes (the third column from the right for the tetrapods at the link just above), and the lumbar vertebrate end up looking like thoracic vertebrate with ribs! These kinds of experiments have suggested to researchers that the Hox genes specify broad regional identity, and also later in embryonic development, participate in fine tuning of various tissues. 



                            Generally mutations to these genes retain the same number of vertebrae elements. However sometimes mutations can increase the number, or more often, decrease the number.

                            Where the tail is concerned, even more factors are involved. The paper mentions a gene called Gdf11 which acts to demarcate the beginning of the tail from the end of the trunk. Another gene family called Cdx (related to the Hox gene) is involved in some way. In vertebrates, the family is comprised of three genes and knock out two specific genes (numbers 2 and 4), and the tail does not extend and some trunk and tail features fail to form.

                            What controls the Hox and Cdx genes? The Fgf, Wnt, Notch, and RA singalling pathways mentioned in the previous post do.



                            So while the Fgf, Wnt, RA and Notch pathways are controlling axial extension of the tail and making out the somites, so they are bringing into play the Hox and Cdx genes to mark out the body into its various regions such as the cervical, thoracic, lumbar, and caudal.



                            Next the authors tackle caudal positional identity.


                            To be continued.



 ....




                            * Teleost fish, those with rays of bones in their fins are an exception. They appear to have undergone an additional complete duplication with the possibility of one cluster being deleted - they have 7 clusters. However, lobe finned fish which have fin bones like the bones in tetrapod limbs, retain the classical tetrapod arrangement of Hox genes.
                            Last edited by rwatts; 08-06-2014, 05:47 PM.

                            Comment


                            • #15
                              TAIL DEVELOPMENT: Caudal positional identity


                              
This section is a small one, which is good, given that the next is long and complex. :)



                              Having spent the previous sections describing how somites or segments are marked out along a growing and lengthening embryo, and how body regions are specified while this happens, the authors turn their attention to the tail and deal with the markers that act specifically there.



                              A lot more work needs to be done because to date some of the work is confusing. Thus for both the chicken and the mouse, the Hoxd12 gene marks the transition between the sacral and the tail vertebrae. That gene would be the second from the left on the HOXD cluster as shown here. (This diagram is turned around relative to the one I showed in the previous post). Match the colour coding in the genes with the color coding in the human (mouse, chicken) embryo and you will see what is happening. 



                              Thus, while the Wnt, Fgf and Notch gene families are laying down the vertebrae segments from head to tail, when they get to the end of the trunk they bring in the Hoxd12 gene to mark the transition to the tail region.



                              So far so good for the chicken and the mouse.



                              However, while that gene contributes to caudal specification in the mouse and chicken, knock it out in a mouse, and limb abnormalities also occur. Furthermore, in the mouse, the Hoxd13 gene has been shown to also contribute to tail vertebrae specification. Yet the Hoxb8 gene which marks out a region forward in the body trunk, does get expressed in the mesoderm of the tail. And bones (e.g. vertebrae) arise from the mesoderm. But knock that Hoxb8 gene out, and tail vertebrae are not affected. Adding another twist to this is that when the Cdx2 and Cdx4 genes are knocked out, the mouse tail is shortened (see my previous post), but when Hoxb8 is knocked out in these mice with the Cdx knockout, tail length is recovered, indicating that Hoxb8 may have a role to play in axial extension of the tail.

                              All in all, the detailed picture for the tail itself is somewhat confusing. The authors write:-


                              Originally posted by Link in OP
                              Further genetic analyses will help to determine whether the functions of these Hox genes in the tail are universal in vertebrates.
                              


Having told the reader something of what is known about how bodies (including tails) are formed and grow in vertebrates, in the next section the authors explain what is known about what causes tails to stop growing. This understanding becomes crucial to beginning to fathom out the dinosaur to bird tail transition.







                              To be continued ....


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