User blog:Cerne/Vertebrates

This was originally supposed to be one of the sections in my last Update part 2 entry, but as you can see, it kinda outgrew that and had to be placed in its own entry. It is a good example of the opposite to what happens when I drag something on for too long. Sometimes my written/typed material comes along inch by inch for weeks, and sometimes it piles up in a matter of days or even hours. I am not sure whether I will be able to put my next entry in today or not. Maybe right now, or maybe later tonight, or maybe tomorrow.

Just a quick note: I use the six-period page break practically here. There is a long bit on genes further down so if you want to skip that then press ctrl+f and search for six periods. You can then use that to bypass certain parts of this and other entries, if you want to.

Anyway, here we go.

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When I began designing creatures for my conworld, I tended to turn more to the fantastical than the realistic. I wanted something different, but I was biased by my limited experience as to what I could realistically get away with in evolutionary biology, so I would come up with all these familiar-looking creatures with rather far-fetched abilities and physical adaptations. A lot of them got axed through the years but one that remained in my mind was a large chameleon-like creature with six long spindly legs that carried the animal a lot like a spider or mantis. The unrealistic part (in relation to reptiles and amphibians on Earth), of course, was the legs.

In tetrapods, the limbs themselves are quite well-developed already. All that is required to change a fin into an arm or leg is the expression of certain genes and proteins at certain stages in embryonic development. In other words, the tetrapod limb is already there in fish. It merely needs to develop differently to become a tetrapod limb. All four limbs are there, too; fish have two pectoral fins behind their gills and two pelvic fins near the base of their tail. So they do have a pelvis, even though it serves no obvious purpose and we cannot see it from outside the animal. In tetrapods the pelvis connects to the hind limbs and holds the posterior end up. In humans it serves the additional purpose of supporting the anterior part of the body. But there is yet another purpose for the pelvis that I had not thought about until I began researching its origin.

The earliest known vertebrate ancestor to show any signs of limbs was the agnathian fish Ateleaspis. It was a jawless fish, belonging to the Agnatha group of fish that is paraphyletic to Gnathostomata, but it had a pair of pectoral fins and no pelvic fins. This suggests that pectoral fins may have preceded pelvic fins and possibly the pelvic girdle, though I can't seem to find any conclusive evidence that the latter was the case. What I did find were a lot of examples of fish that were more eel-like than fish-like. Much like the hagfish or "slime eels" that are still around today. But hagfish aren't vertebrates; they are primitive chordates with skulls. Regardless, many early vertebrate fish like Ateleaspis did exhibit the same kind of eel-like body morphology. Meaning that limbs themselves may be a vertebrate trait while the pelvic limbs and adjoining pelvic girdle may be linked to the evolution of jaws in some way. Furthermore, I would like to think that this link between jaws and a pelvis may have been causative. Then again, this is all mere supposition: I have made some very specific assumptions that I would like to support or re-examine with more information on the matter but am yet not able to. If someone else can come up with contrary data then that can be just as helpful.

Anyway, what this means for me is that if I were to aim for a tetrapod with more than four limbs (and upon considering that this is all supposed to be loosely based on vertebrate evolution on Earth) then I've got to start with early vertebrates. The reason I pay attention to the pelvis is because it adds a limitation to how long the gut can be and therefore how much room I have to add an additional pair of limbs. Pelvic and pectoral girdles are both adapted for supporting the gut in some way. That is why limbed vertebrates have girdles on both sides of the rib cage, which houses the gut. The pelvic girdle supports the posterior end, but it also restricts the body's digestive system because the girdle itself has such a small circumference in relation to the gut. So the evolution of the pelvic girdle led to a much more compact gut. Might the evolution of jaws have something to do with this? I do not yet know. But with such a compact gut, less appendicular support is required. And I want more appendicular support. So I need a much longer gut. That means no pelvic girdle. Going back to early jawless vertebrates on Earth, if having jaws means you need a more compact gut - maybe the ability to bite and chew means the animal is eating food that requires a different kind of digestion - then no pelvic girdle may mean no jaws. At least not yet.

With no pelvis to limit how much axial support an early vertebrate may need, there becomes a better chance for more than one pectoral girdle. In Earth vertebrates, pectoral girdles are made up of a pair of scapulae - where the forelimbs or pectoral fins are connected to - on the dorsal side of the animal, and a pair of bones that make up the clavicle on the underside or ventral side of the animal. These four bones aren't fused to each other so they can technically form at any point along the vertebrae. What I need to do, then, is to figure out how, when, and why more than one pectoral girdle could have evolved in my giant six-legged chameleon's aquatic ancestor.

I'd already mentioned that pectoral girdles - like pelvic girdles - are for support. They are also for locomotion. One thing I didn't mention is that once a vertebrate-like animal does evolve one pair of pectoral appendages, there is a chance it may not evolve any more of them. One pair is all that is really required for swimming, so other adaptations - like a pelvic girdle - may evolve afterward that make additional pectoral appendages less advantageous for the animal. There could be more pectoral appendages, but for that to happen they may need to appear at around the same time in the animal's evolution as the first set did. That means I need to focus less on actual morphology and more on the genes that make the morphology possible.

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In just about every animal on Earth, there are certain proteins that are encoded by a set of genes known as a homeobox (Hox) and that are responsible for the development of appendages (limbs, wings, antennae in insects).

In vertebrates, the proteins that are responsible for the development of pectoral and pelvic limbs are known as the T-box family of transcription factors and they are controlled by the Tbx series of genes. The protein TBX5 is responsible for the development of the pectoral limbs. It also interacts with NKX2-5 (a.k.a. "Tin man") and GAXA4; the latter being a member of the GAXA family of binding proteins that regulate embryogenesis. All three proteins play a part in normal heart development. TBX5 is also apparently closely linked to the TBX3 protein which may be involved in the anterior and posterior development of the pectoral limb. The TBX4 protein is responsible for pelvic limb development.

The Hox genes seem to have more to do with the arrangement of appendages on the axial plane than to the appendages themselves. They exist in organized linear clusters of four: HoxA, HoxB, HoxC, and HoxD, with the first and last being responsible for the pectoral and pelvic limbs, respectively. The interesting thing about the Hox genes is that they can be replaced or duplicated by affecting the order and timing of their expression. If a gene is disabled, for instance, the preceding gene cluster is replicated. If a gene is made to act prematurely, it is expressed in the preceding anterior cluster. Already, this has a lot of interesting evolutionary ramifications: with no pelvic girdle, I don’t need to think about altering any actual morphology or finding a way to get rid of it because that particular expression in the HoxD gene cluster won’t be there in basal vertebrates. If I want a vertebrate creature with more than one set of pectoral appendages, all I need to do is to make sure the HoxD genes doesn’t interfere with the expression of the HoxA genes.

Now I have two things to think about: 1) how will replicating the HoxA gene cluster affect the subsequent Hox genes, and 2) how do I do it?

Well, the HoxA gene cluster - or its insect counterpart - has been replicated before in Drosophilia flies, and apparently with no terminal consequences. The wings and stomach were replicated, as well as a few other features of the thoracic region. Long-term survival of the organism in question may depend on the genes that are involved with the replicated body segment: in humans and other vertebrates, the HoxA gene cluster is linked to the development of the pectoral limb as well as the heart and lungs. If this part of the animal is replicated, it may bring implications with it that could be beneficial or detrimental. One must also consider what will happen to the subsequent segments; will replicating a heart and lungs mean the loss of a stomache? This is where the Tbx family of genes may come in. Hox proteins don't actually encode for the limbs themselves. As a group of transcription factors, they merely trigger the genes that do. Some anatomical features, like stomachs and other organs, may also be expressed in part by genes in other Hox clusters so it may be possible for those anatomical features to still exist, albeit perhaps in a different form. There is no doubt that if replication occurs in a single Hox gene or an entire Hox cluster the organism may need to adapt somewhat to the change. But I believe that if a Hox gene can be expressed in more than one homeobox then this should be possible. Of course it depends on exactly what the gene does and how extensively it works in the expression of that anatomical feature.

How I go about replicating a cluster of genes naturally is another matter.

I am not sure how much I brought up radioactivity in previous blog entries or how many times I brought it up, but there is a lot of radioactivity on my conworld (relative to Earth, that is). On the planet's surface, most of the radioactivity comes from unstable isotopes of otherwise stable elements like sodium and potassium that get released in volcanic eruptions and from deep-sea trenches. Some of it comes from deposits of the more unstable actinides, some of which I may need to invent. Radiation already has a variety of effects on living organisms; most are negative, but the most common type of radiation is so obvious we take it for granted and don't even notice it for what it is. Ultraviolet-B (UVB) radiation from Earth's sun helps us to synthesize vitamin D3. Its more powerful counterpart, Ultraviolet-C (UVC) is what gives us skin cancers. Organisms on my planet don't need to worry about UVC, so how are they exposed to other types of radiation without killing themselves?

I've mentioned deep-sea trenches and volcanism in the preceding paragraph. Both of which the more "removed" basal vertebrates I have in mind will have access to at some point. Being jawless, primitive vertebrates are pretty much left with eating plankton and detritus, and anything else they can swallow without too much trouble. In order to do this, some of them need to live in extremes like the bottom of the ocean and in subterranean lakes. Keeping in mind what I typed about Chernobyl in a previous entry, there are levels of gamma radiation that can be low enough to not terminally damage wildlife but that can still have some sort of an effect on what grows around it. So, what might happen when a jawless and appendage-less fish swims around low levels of radiation and reproduces in it? Some may die, some may be damaged, some may not be affected at all. And the same will happen to many of their offspring. But some may experience only partial genetic damage which may lead to certain genes being copied. In that same entry where I brought up Chernobyl, I also brought up ways that cells in living organisms could "correct" genetic defects by scanning their own DNA and triggering cell death shortly after fissioning. If done rapidly enough, the organism could effectively use a radioactive isotope without sustaining any permanent cell damage. But that was for my radiosynthetic autotrophs. I don't need to go that far with my vertebrates.

For reference, see Radioresistance.

Going back to where I brought up the issue of how many pectoral girdles would appear in the new vertebrate animal at a given time, I am faced with an additional problem: not only do I need to find a way for two or more appendages to appear at the same time, as opposed to one set of appendages after the other, I now need to figure out how to make the appearance of appendages themselves an externally-conditioned mutation. The problem is pretty easy to solve - simply replicate the segment that will have limbs before the limbs evolve - but it all depends on timing. That is why I am thinking there may be a diversity of new vertebrate groups, each with a different number of paired appendages. Or I could start with four to six pairs (any more will be a stretch) and have the number whittle down in some groups. In any case, this sort of segment replication should be easier for an earlier organism with a simpler physiology and anatomy. In this case, what we are looking at for each segment is relatively simple: all the segments beyond the head and thoracic region are mostly vertebrae, ribs, and digestive tract. There is the swim bladder, the gills, the intestines and rectum, and maybe a few other things. But this isn't something I would suggest for a creature as biologically sophisticated as a mammal or bird. Surely, attempts have been made to tamper with fish genes artificially in such a manner. Giving a lamprey extra fins can't be that complicated. I may not even replicate an entire cluster of Hox genes. I may only replicate a single gene and hope the rest will follow.

So one must then ask: if replicating pectoral fins in a basal vertebrate fish isn't that much of a big deal, then how come the replication needed to happen before the evolution of a pelvic girdle? If a preceding segment is going to be repeated, can't the segment with the pelvis just be lost?

The most obvious answer that I can come up with for the first question is that the pectoral fins most likely evolved first in Earth fish (we can tell that by looking at the fossil record) and pelvic fins become more practical in this regard as an adaptive corollary because it would be rather difficult for a fish - and a long one at that - to swim with pelvic fins alone. Pelvic fins still could evolve on their own but the animal wouldn't be using them as much so there would be no selective pressure for it, and when factoring in population genetics, genetic minorities within a population - in contrast to allopatry - tend to get outnumbered and wiped out rather quickly when they are more-or-less neutral. So there doesn't need to be a teleological argument here.

A less pragmatic answer would be that adding a pelvis - in addition to compacting the gut and limiting the amount of available vertebrae - increases the complexity of the organism by compounding the number of genes that are bound to each cluster. As the animal evolves, more and more genes are tied to a single area. You then risk more unwanted changes by doing something with the genes for the pelvis. Or you can just make the pelvic limbs vestigial and keep the girdle where it is. Which is not what I am looking for. It doesn't appeal to me aesthetically, and it makes no sense; a vertebrate - and especially a terrestrial vertebrate - is not going to lose two well-functioning pelvic limbs so that it can evolve toward using a second or third pair of pectoral limbs when it doesn't really need to. Plus, there are things I want a last pair of pectoral limbs to do that I don't think I can do with a pair pf pelvic limbs.

And as far as the ease of replacing a pelvic girdle, it is actually quite easy to do: keeping in mind the replication process is initiated by damaging or deactivating a gene in a posterior segment, you could very well trigger anterior segment replication by deactivating something like the pelvic girdle. But in addition to the complications involved, I don't really know how well or how extensively it would work. With existing pelvic appendages and girdle, there is the rest of the vertebral column to account for. With no pelvic appendages, you can add just about as many pectoral appendages as you can. So it is less about the ease of the prospect and more about what it takes to get what you are looking for.

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With all that said and done with, what I think I am going to start with is a primitive jawless fish and give it five or six paired appendages at the most. Some I plan to make terrestrial. They will have limbs and several sets of lungs, will evolve jaws independently either shortly before or after becoming terrestrial, and will be blind due to evolving in a subterranean environment. Another group will avoid evolving appendages altogether and increase in size, perhaps becoming the largest creatures in the ocean at more than 50 feet long, and will remain jawless to avoid becoming predatory and devastating the ocean ecosystem, wiping itself out in the process. A third group will evolve multiple ray-shaped fins like Earth's Actinopterygii, and some may even take to the air. The smallest of these will be tiny, capable of true flight, buzzing their "wings" like hummingbirds; the larger species will glide through the air for limited amounts of time before returning to the water. My six-legged chameleon-like creature will not belong to any of these groups, though. Its evolutionary history will be older than that.

Now I want to something clear: the multi-limbed vertebrates I am proposing will not be the only vertebrate group on the planet.

The first terrestrial vertebrates - and the first vertebrates with appendages, for that matter - will be tetrapods. They will have one set of pectoral limbs and one set of pelvic limbs. Many of the terrestrial vertebrates in my conworld will belong to this group, and they will be the first terrestrial vertebrate group. Their aquatic relatives will all go extinct in a mass extinction. So no "fish" on this planet as we think of them.

A second group of vertebrates, these with multiple appendages, will become terrestrial and give rise to the six-legged lizard creature I brought up at the beginning of the entry as well as a number of other species, many of them becoming rather large and dominating their local ecosystem. So, yes, they will have jaws. Their aquatic relatives will mostly go extinct in another mass extinction.

A third group of vertebrates will be the one I brought up previously, a few paragraphs ago. They will currently dominate life in the oceans, and may continue to do so for a while because they do not eat smaller bite-sized creatures (for the most part). Mostly, they eat plankton in much the same way baleen whales on Earth do.

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So vertebrates in my conworld will show up in subsequent waves instead of all at once. I may very well get criticized for abusing one of my favorite evolutionary principles (see: Dollo's Law Of Irreversibility) and I do have a way of explaining all this in regards to that principle but the entry has gone on way too long now. I just wanted to end it explaining what I had done with all of that stuff I did research on and where I had gone with it.

In fact, I am going to end the entry right here. Stay tuned for another long entry after this one. Sorry, I have a lot to cover.

Thanks for reading.