Preadaptations

[Phronesis]

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:
1
2
3
4
5
6
7

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).

PIC​

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.

Interestingly, the choanoflagellate has nearly as many introns - non-coding regions once referred to as "junk" DNA - in its genes as humans do in their genes, and often in the same spots. Introns have to be snipped out before a gene can be used as a blueprint for a protein and have been associated mostly with higher organisms.

The choanoflagellate genome, like the genomes of many seemingly simple organisms sequenced in recent years, shows a surprising degree of complexity, King said. Many genes involved in the central nervous system of higher organisms, for example, have been found in simple organisms that lack a centralized nervous system.

Likewise, choanoflagellates have five immunoglobulin domains, though they have no immune system; collagen, integrin and cadherin domains, though they have no skeleton or matrix binding cells together; and proteins called tyrosine kinases that are a key part of signaling between cells, even though Monosiga is not known to communicate, or at least does not form colonies.

(Emphasis mine)


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

 

[w1z4rd]

So it is teo. Hi teo.. whats with all the constant nick changing?

Noticed your other post here:

http://richarddawkins.net/forum/viewtopic.php?f=4&p=1437846

 

[Phronesis]

So it is teo. Hi teo.. whats with all the constant nick changing?

Noticed your other post here:

http://richarddawkins.net/forum/viewtopic.php?f=4&p=1437846

Thought I'd exchange one corny moniker for another .

 

[Phronesis]

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

An international team that includes biologists at the University of California, San Diego has determined the complete genetic blueprint of Dictyostelium discoideum, a simple social amoeba long used by researchers as a model genetic system, much like fruit flies and laboratory mice, to gain a better understanding of human diseases.

The scientific details of this seven-year-long genetic sequencing effort, which involved 97 scientists from 22 institutions in five countries, are contained in a paper featured on the cover of the May 5 issue of the journal Nature.

The international team's achievement will have an immediate application for biomedical researchers, who can now mine the Dictyostelium genome for a host of genes that cause human disease, thus gaining a new and efficient way to study those human diseases with a simple organism in their laboratories.

For evolutionary biologists, the genetic blueprint of Dictyostelium, the first amoeba genome to be sequenced, has clarified the place that Dictyostelium occupies in the hierarchy of life.

"It is more closely related to fungi and animals than we had previously thought," says Adam Kuspa, a professor of biochemistry and molecular biology at Baylor College of Medicine in Houston and a senior author of the Nature paper.

The discovery will also improve geneticists' understanding of how the genes from Dictyostelium and other genetic model organisms have been conserved or adapted through evolution in humans and other organisms.

"The cells which gave rise to plants and animals had more types of genes available to them than are presently found in either plants or animals," explains William Loomis, a professor of biology at UCSD and one of the key members of the international sequencing effort. "Specialization appears to lead to loss of genes as well as the modification of copies of old genes. As each new genome is sequenced, we learn more about the history and physiology of the progenitors and gain insight into the function of human genes."

In 1989, Loomis and Kuspa, then a postdoctoral fellow in Loomis' laboratory, initiated a critical portion of the effort when they began the arduous task of constructing a physical map of the genes located on the six chromosomes of Dictyostelium.

The scientists mapped the location of several hundred genes on those chromosomes based on landmarks that had been discovered over the years, then created a set of 5,000 large DNA clones, each about 200,000 nucleotide bases long, that proved useful for other researchers in assembling the genetic sequences of Dictyostelium's genome. Another UCSD biologist involved in the genome effort, Christophe Anjard, an assistant project scientist in Loomis' laboratory, analyzed families of Dictyostelium genes and uncovered relationships with these genes in both animals and plants.

Dictyostelium is used as a model organism for studying cell polarity, how cells move and the differentiation of tissues. It also exhibits many of the properties of white blood cells.

Three years ago, another team of UCSD biologists discovered that two genes that are used by Dictyostelium to guide the organism to food sources are also used to guide human white blood cells to the sites of infections and play a role in the spread of cancer. (see: http://ucsdnews.ucsd.edu/newsrel/science/mcchemo.htm)

Dictyostelium usually exists as a single cell organism that inhabits forest soil, consuming bacteria and yeast. When starved, however, the single cells come together, differentiate into tissues and become a true multicellular organism with a fruiting body composed of a stalk with spores poised on top. This increases its utility in a variety of studies.

"An organism's relationship to humans depends on how related the proteins are that are found in the two cell types," says Kuspa. "You can make direct analogies, or you could learn general principles about how cells regulate their behavior. Both things will apply in the studies we do."

He and the other members of the international sequencing team found that there are more protein coding genes in the organism than they had thought and nearly twice as many as there are in fungi. Their unraveling of the genome also allowed Rolf Olsen, a postdoctoral fellow working in Loomis' laboratory, to generate a tree of life and show that amoebozoa, the group to which Dictyostelium belongs, evolved from the common ancestor of eukaryotes (the group of organisms that contain all animals, plants, algae, protozoa, slime mold and fungi) before fungi. Dictyostelium has about 12,000 genes that produce a greater variety of proteins than the approximately 6,000 found in fungi. And its genes are more closely related to human genes than are the genes from fungi.

"That really speaks to how much we will relate the gene function information we find to humans," Kuspa says. "It makes Dictyostelium a better model for looking for targets against which drugs can act."

Key collaborators in the project at Baylor included Richard Gibbs and George Weinstock, co-directors of Baylor's Human Genome Sequencing Center, and Richard Sucgang, an assistant professor of biochemistry. Baylor performed about one half of the sequencing work.

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? More later.

 

[cyghost]

Thought I'd exchange one corny moniker for another .

And that explains those three posts saying nothing at all except veiled insults you won't even back up with proper discourse.

Its back! Welcome and salutations.

 

[Phronesis]

More interesting preadaptations:
This time sponges (wiki).

Sponges are among the simplest animals. They lack gastrulated embryos, extracellular digestive cavities, nerves, muscles, tissues, and obvious sensory structures, features possessed by all other animals.

Nice site about sponges.
PIC
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

Sponges are very primitive animals. They don't have nerves cells (nor muscles nor eyes nor a lot of other things we commonly associate with animals). So scientists figured sponges split from the tree of life before nerves evolved.

A new study has surprised researchers, however.

"We are pretty confident it was after the sponges split from trunk of the tree of life and sponges went one way and animals developed from the other, that nerves started to form," said Bernie Degnan of the University of Queensland. "What we found in sponges though were the building blocks for nerves, something we never expected to find."

In humans and other animals, nerves deliver messages to and from the brain and all the parts of a body.

Degnan and colleagues studied a sea sponge called Amphimedon queenslandica. "What we have done is try to find the molecular building blocks of nerves, or what may be called the nerve's ancestor the proto-neuron," Degnan said. They found sets of these genes in sponges.

Nice .
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.
"But what was really cool," he said, "is we took some of these genes and expressed them in frogs and flies and the sponge gene became functional — the sponge gene directed the formation of nerves in these more complex animals.

The research, announced this month, was published in the journal Current Biology.

Article with the details:
Article abstract:
Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit

The nerve cell is a eumetazoan (cnidarians and bilaterians) synapomorphy [1]; this cell type is absent in sponges, a more ancient phyletic lineage. Here, we demonstrate that despite lacking neurons, the sponge Amphimedon queenslandica expresses the Notch-Delta signaling system and a proneural basic helix loop helix (bHLH) gene in a manner that resembles the conserved molecular mechanisms of primary neurogenesis in bilaterians. During Amphimedon development, a field of subepithelial cells expresses the Notch receptor, its ligand Delta, and a sponge bHLH gene, AmqbHLH1. Cells that migrate out of this field express AmqDelta1 and give rise to putative sensory cells that populate the larval epithelium. Phylogenetic analysis suggests that AmqbHLH1 is descendent from a single ancestral bHLH gene that later duplicated to produce the atonal/neurogenin-related bHLH gene families, which include most bilaterian proneural genes [2]. By way of functional studies in Xenopus and Drosophila, we demonstrate that AmqbHLH1 has a strong proneural activity in both species with properties displayed by both neurogenin and atonal genes. From these results, we infer that the bilaterian neurogenic circuit, comprising proneural atonal-related bHLH genes coupled with Notch-Delta signaling, was functional in the very first metazoans and was used to generate an ancient sensory cell type.

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.

 

[Geriatrix]

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.

Interesting posts.

Hmmm, I might not really get what your trying to say here but how is it weird that the building blocks of a system is present in a creature with an earlier version of a more built up system?

Don't you need to have to 1's to make 2?

 

[Phronesis]

Hi Geriatrix,

I would argue in the case of a neuronal system it is a bit more complex. You need 1 (developmental genes/Hox genes) +2 (calcium signaling) +3 (tyrosine kinase signaling) +4 (neurotransmitters e.g. epinephrine, acetylcholine and, GABA, and enzymes to process them acetylcholine esterase etc.) +5 (Adherens junctions) +6 (programmed cell death) +7 (Other)= 28 (full blown nervous system).

It is just interesting to find a lot of these toolkits (sometime more elaborate than their descendants) at the base of the tree. Especially some Hox genes and an elaborate tyrosine kinase signaling system as well as elaborate programmed cell death pathways and genes for multicellularity in unicellular, asocial organisms (Monosiga brevicollis). It would be interesting to see what their functions are in these organisms that are at the base of the tree.

For example, Hox genes determine the body shape and body plan layout (where the limbs and head should be etc.) Thus it is interesting to find these genes in organisms with no real body plan, before body plans arrived. Nice article about Hox genes.

 

[Geriatrix]

It is just interesting to find a lot of these toolkits (sometime more elaborate than their descendants) at the base of the tree. Especially Hox genes and an elaborate tyrosine kinase signaling system as well as elaborate programmed cell death pathways and genes for multicellularity in unicellular, asocial organisms (Monosiga brevicollis). It would be interesting to see what their functions are in these organisms that are at the base of the tree.

For example, Hox genes determine the body shape and body plan layout (where the limbs and head should be etc.) Thus it is interesting to find these genes in organisms with no real body plan, before body plans arrived. Nice article about Hox genes.

It is indeed interesting.
Maybe adaption works forwards and backwards depending on what is being adapted to. Maybe a dna sequence needs to develop before the implimintation takes place.
I'm no scientist but this is interesting.

 

[Phronesis]

Maybe adaption works forwards and backwards depending on what is being adapted to.

Adaptation or natural selection? If something adapts towards something (e.g. shifting metabolism from glucose to fatty acids), it implies a pre-existing plan, preparation, "foresight", as in the case of genetic control of metabolomics.

 

[Pooky]

Hey man why are you so clever?

 

[Phronesis]

Hey man why are you so clever?

Hehe, you are most probably incorrect in assuming I am clever . Thanks anyway .

 

[Geriatrix]

Adaptation or natural selection? If something adapts towards something (e.g. shifting metabolism from glucose to fatty acids), it implies a pre-existing plan, preparation, "foresight", as in the case of genetic control of metabolomics.

Uh, no it doesn't. Adaption implies responding to an enviroment.

If you mean that if the organism simply detects(actively or passively) a possible way of reacting to its enviroment as "foresight" or as a pre-existing plan then ok.

Or are you trying to say something else?

 

[pos(t)er]

If something adapts towards something (e.g. shifting metabolism from glucose to fatty acids), it implies a pre-existing plan, preparation, "foresight", as in the case of genetic control of metabolomics.

Pls. elaborate?

Foresight meaning an organism identifies what it will need to survive in the future?Isn't that always the case, where organisms are successful in survivng?

 

[Pooky]

Hehe, you are most probably incorrect in assuming I am clever . Thanks anyway .

When someone posts stuff all the time that i can't even begin to understand, then he is clever in my books.

 

[Phronesis]

Uh, no it doesn't. Adaption implies responding to an enviroment.

If you mean that if the organism simply detects(actively or passively) a possible way of reacting to its enviroment as "foresight" or as a pre-existing plan then ok.

With adaptation, I am referring to an active process controlled by an organism/cell. For example, when a cell is in a glucose-rich environment, it will most likely derive its energy from glycolysis and oxidative phosphorylation of pyruvate. However, when some cell-types are in a fatty-acid rich environment, they are able to switch between metabolic pathways to get its energy from fatty acid oxidation. This is not natural selection, as these are pre-existing processes adapting toward conditions and the direction of the adaptation is controlled.

Did you mean natural selection or adaption in post #9?

 

[Geriatrix]

With adaptation, I am referring to an active process controlled by an organism/cell. For example, when a cell is in a glucose-rich environment, it will most likely derive its energy from glycolysis and oxidative phosphorylation of pyruvate. However, when some cell-types are in a fatty-acid rich environment, they are able to switch between metabolic pathways to get its energy from fatty acid oxidation. This is not natural selection, as these are pre-existing processes adapting toward conditions and the direction of the adaptation is controlled.

Did you mean natural selection or adaption in post #9?

I meant adaption in particular but looking at you example above that may include natural selection.

[hypothetical situation]The organisms ancestors may have been exposed to a fatty-acid rich enviroment previously and through natural selection developed an appropriate response to it.
The enviroment may have later changed to glucose-rich environment, unknown to us, but the original response mechanism is still there. Dormant but there.[/hypothetical situation]

The organism can adapt by switching back to the dormant genes.

What I meant originally was that for an organism to change it self to react with an change in enviroment, it would first need to develop the reaction mechanism.
From one of your posts above;

"We are pretty confident it was after the sponges split from trunk of the tree of life and sponges went one way and animals developed from the other, that nerves started to form," said Bernie Degnan of the University of Queensland. "What we found in sponges though were the building blocks for nerves, something we never expected to find."

That tells me that the intial development may have taken place before a split. It may just be that Mr. Degnan asumed that the groundwork for nerve development took place later than it may have and was surprised to learn otherwise.

Btw, these are just my opinions, I'm no biologist.

 

[Phronesis]

Geriatrix,

In your hypothetical situation, you mentioned the following:

[hypothetical situation]The organisms ancestors may have been exposed to a fatty-acid rich enviroment previously and through natural selection developed an appropriate response to it.
The enviroment may have later changed to glucose-rich environment, unknown to us, but the original response mechanism is still there. Dormant but there.[/hypothetical situation]

The word "developed" again implies a goal of natural selection. For example, an embryo has the necessary pre-existing genetic information to develop say feet, a brain, skin, etc. It still utilizes random variation and selection, but the process of development is controlled and the pre-existing information is laid out during conception and the "plan" is played out during development. I suspect you meant "evolved" rather than "developed", as natural selection only selects for what happens to contribute to fitness and does not have a future goal. Thus, an organism may have previously evolved through happenstance a pathway for fatty acid oxidation and the pathway just happened to enhance fitness, and was thus selected. That is evolution. The constant control of switching back and forth between these pathways under different conditions is adaptation (an active and controlled process).

Also, if genes are dormant and do not contribute to fitness, they are liable to degrade as a result of random variation because selection won't preserve their function. Natural selection only selects for what happens to work and it does not have a goal. Preserving a function or buffering a function from the effects of random variation that does not contribute present fitness implies a goal, a back-up plan for the future when this function might be needed again.

Thus, when you say the following:

The organism can adapt by switching back to the dormant genes.

It again implies that these dormant genes might act as back-up systems for the future. Dormant genes that do not contribute to fitness at present are more liable to degrade as a result of random variation and natural selection are less likely to preserve genes that do not contribute to fitness. Natural selection only selects attributes that contribute to fitness at present, not fitness of future generations. Dormant genes (genes that do not contribute towards fitness) implies that there is some kind of back-up system, and that there is something else besides natural selection that keeps it in tact. Random variation will destroy it.

From one of your posts above;

"We are pretty confident it was after the sponges split from trunk of the tree of life and sponges went one way and animals developed from the other, that nerves started to form," said Bernie Degnan of the University of Queensland. "What we found in sponges though were the building blocks for nerves, something we never expected to find."

That tells me that the intial development may have taken place before a split. It may just be that Mr. Degnan asumed that the groundwork for nerve development took place later than it may have and was surprised to learn otherwise.

That again, is analogous to the development of an embryo. The groundwork for nerve development is laid our during conception and plays out through random variation and selection. Again, I think you meant "evolution", not "development". However, the presence of these toolkits for nervous systems in these organisms that do not have a nervous system, implies that they had to have a function other than nerve development. What the function is should be interesting to find out, but it could not have been for the future development of nerves, as natural selection is myopic and only selects for characteristics that contribute to fitness at present.

Well, that is how I understand it, I may be wrong .

 

[Phronesis]

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

PIC​

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.

 

[Geriatrix]

Phronesis,
Yes I suppose I meant evolution. But I prefer not to use that word as it gets people all upset if you know what I mean.

Regarding the potential random variation of dormant genes, like I said I'm no biologist, but is there not genetic variation on genes to contribute to fitness as well as dormant genes?