Researchers reconstruct the genome of the ‘first animal’

Humans and mice share approximately 98% of genes, and have similar physiology and anatomy. This is because we share a relatively recent common ancestor, around 80 million-years-ago. In contrast, the ancestor of all animals lived over 500 million-years-ago. As genomic data becomes available for more animal species a detailed family tree can be created, allowing novel insight into the genomes of long extinct species. In the guest post below Jordi Paps summarises recent research that attempts to reconstruct the genome of the ‘first animal’ by using the genomic data available on living animals.

The first animals emerged on Earth at least 541m years ago, according to the fossil record. What they looked like is the subject of an ongoing debate, but they’re traditionally thought to have been similar to sponges.

Like today’s animals, they were made up of many, many different cells doing different jobs, programmed by thousands of different genes. But where did all these genes come from? Was the emergence of animals a small step in evolution, or did it represent a big leap in the DNA that carries the instructions for life?

To answer these questions and more, my colleague and I have reconstructed the set of genetic instructions (a minimal genome) present in the last common ancestor of all animals. By comparing this ancestral animal genome to those of other ancient lifeforms, we’ve shown that the emergence of animals involved a lot of very novel changes in DNA. What’s more, some of these changes were so essential to the biology of animals that they are still found in most modern animals after more than 500m years of independent evolution. In fact, most of our own genes are descended from this “first animal”.

Previous research on lifeforms that are closely related to animals – single-celled organisms such as choanoflagellates, filastereans and ichthyosporeans – has shown they share many genes with their animal cousins. This means that these genes are older than animals themselves and date back to some common ancestor of all these creatures. So the recycling of old genes into new functions, a kind of genome tinkering, must have been an important force in the origin of animals.

But Professor Peter Holland and I wanted to find out which new genes emerged when animals evolved. We used sophisticated computer programs to compare 1.5m proteins (the molecules that genes contain the instructions for) across 62 living genomes, making a total of 2.25 trillion comparisons to find out which genes are shared between different organisms today.

We then created a computer program that could combine this information with the evolutionary relationships of the animals to reconstruct which genes were present in the last common ancestor of all animals. The results don’t represent the ancestor’s full genome, as many genes and other genetic information will no longer exist in today’s animals. But using evolutionary trees to infer what happened in the past in this way is one of the most powerful applications of evolutionary biology, as close as we can come to travelling back in time.

Our results suggest the genomes of the first animals were surprisingly similar to those of modern ones, containing the same proportions of biological functions. Around 55% of modern human genes descend from genes found in the last common ancestor of all animals, meaning the other 45% evolved later.

By applying the same techniques to the genomes of modern relatives of animals, we also reconstructed the genome of even older ancestral organisms. We found that the first animal genome was in many ways very similar to the genomes of these unicellular ancestors.

But then we looked at the novel genes in the first animal genome that weren’t found in older lifeforms. We discovered the first animal had an exceptional number of novel genes, four times more than other ancestors. This means the evolution of animals was driven by a burst of new genes not seen in the evolution of their unicellular ancestors.

Finally, we looked at those novel genes from the first animal that are still found in most of the modern animals we studied. Natural selection should mean that animals keep genes with essential biological functions as the species evolve. We found 25 groups of such genes that had been kept in this way, five times more genes than in other, older, ancestors. Most of them have never been associated with the origin of animals before.

These novel genes that are still widely found today control essential functions that are specifically related to lifeforms with multiple cells. Three groups of these genes are involved in transmitting different nervous system signals. But our analyses show that these genes are also found in animals that do not have a nervous system, such as sponges. That means the genetic basis of the nervous system may have evolved before the nervous system itself did.

Our research shows that both new genes and the recycling of old genes were important in the evolution of animals. But these results raise even more questions. Were novel genes also important in the rise of other types of large multicellular lifeforms such as plants or fungi? What was behind the explosion of novel genes that drove the evolution of animals? Did it happen faster than in other groups or did animal ancestors take a long time to accumulate all the new genes? Answering those questions will require more and better genome data (or improved time-travelling capabilities).

>>Sounds like you got the false Creo teaching down pat. Now get the to your lab for enlightenent.

See, it always comes down to that here on FR and in Progressive classrooms. I do not agree that evolution/uniformitarianism as it is currently believed is Truth, but I do not disagree with it either. It is an unobservable and unrepeatable theory that is more philosophy than biology. I simply question the method and then get attacked by people who claim to be open but still have a worldview that requires adherence to a certain humanist orthodoxy.

It is interesting that you repeatedly use the word “enlightenment”, a word associated closely with Humanist thought (that leads into Existentialist thought, then Post-Modernist thought, and then Progressive thought).

Like the Deep State Republicans, the philosophies of Post-Modernism are deeply ingrained in our side of the political divide just as the exact same philosophies are ingrained in the other side.

I don’t believe in Young Earth Creationism one bit, but I do like to use it to explore the worldview phenomenon to better understand why our nation as an actual Free Republic is doomed.

Thank you for participating.

Indeed. The periodic table is an ingenious method of laying out a whole set of chemical properties in one easy to consult format. It’s invention is worthy of a Nobel prize, although I think it predates Nobel.

In some of my advanced chemistry classes, we were supposed to have the table memorized, at least for the top part where the common elements are.

But it had the same hip structure as an extinct clade of mainly herbivorous dinosaurs. Sometimes similarity of structure is not the immediate obvious!

Also birds have scales the scales of birds are composed of the same keratin as beaks, claws, and spurs. They are found mainly on the toes and metatarsus, but may be found further up on the ankle in some birds. Most bird scales do not overlap significantly, except in the cases of kingfishers and woodpeckers.

However you’re right no shell, of course neither did T-Rex or the Geico Gecko!

Yes I will. Natural selection is micro-evolution, not macro-evolution. The Galapagos Finch had a different beak than a regular finch. It did not have scales or vestiges of a shell. People often confuse natural selection for evolution because that’s what the humanist agenda in schools teaches.

Those movies that show mutants that have special powers and do not look like normal humans are fictional. That is not how mutation or evolution works in real life. In real life, few mutations have any discernable effect alone, and the effects of mutation are only going to be seen after the accumulation of many mutations. Thus, your claim that evolution did not occur because the Galapagos finches did not have scales or vestiges of shells is nonsensical. No scientist would expect to see anything resembling a shell on a bird, because no bird has a shell. The Galapagos finches differentiated from mainland finches as a result of many mutations occurring over many thousands of years in both populations, which eventually resulted in them being different species. Oh, and birds actually do have scales, look at their feet. They are feathery little dinosaurs, and the fossil record suggests that scales were common in all dinosaurs.

The claim that evolution does not exist because we have never seen an animal have offspring that are a new species is a wonderful example of a straw man. No scientist ever has claimed that new species suddenly appear because of an event equivalent to a cow spontaneously birthing a lamb. But Creationists attempt to debunk evolution on that claim all the time.

FYI, the practice of sequencing genomes is a biochemical procedure practiced in many labs, taking advantage of the well-known characteristics of nuclei acids. Analyzing the results using informatics is, again, a completely scientific discipline. The fact that I, personally, have sequenced DNA and used DNA sequence data to conduct analyses of evolutionary relationships on the basis of phylogeny means that you have an uphill battle to prove that these are not valid, objective, repeatable techniques which yield valid data.

exDemMom: "Is there an ultimate creator who created a universe in which life could arise, evolve, and exist?
That is not a question that is easily answered by scientific inquiry.
Personally, I think that the existence of physical laws that allow for life to exist is worthy of a great deal of wonder and awe."

Actually, it is easily answered, but not by scientific inquiry.
Rather, it's answered by basic scientific assumption and definition.
Science, by definition, only concerns natural explanations for natural processes.
Everything else, including the role of a supernatural Creator is outside the realm of natural science and therefore cannot be considered, even if clear & obvious.

So we can't learn our Creator's role in all this from science because science by definition refuses to see it.
To find God in nature we must look elsewhere for guidance, which, fortunately is readily available in any house, community and book dedicated to such purposes. ;-)

Bryanw92: "Observation of theoretical knowledge that is assumed to be true is not observational science.
What it is though, is the circular logic where one theory is presented as fact to prove another and then the second is used as proof for the first."

There's nothing "circular" or even "theoretical" about DNA testing & profiling -- it's used in law to establish paternity, prove innocence of crimes or association, etc.
But DNA analysis comparing various species to each other is based on theoretical assumptions of evolution, that for example, the better the match-ups of alleles, the more closely related are the species.
A recent surprising example was learning that Neanderthals, far from being a distantly related genus (like Indian & African elephants) were instead our own more closely related "kissing cousins".

Bryanw92: "This is 'Settled Science' or 'Consensus Science'. "

Strictly defined no science is ever 100% "settled" since every observation and theory can be overturned by better observations and better explanations.
Only in politics does science become a club to be used by one partisan side against any others.
Scientists themselves are never (or at least should never be) confused about the distinctions between actual observations (aka "facts"), hypothetical explanations (falsifiable but not confirmed) and seriously confirmed theories.
For examples:

Ideas known as "Panspermia" can be theoretically falsifiable hypotheses.
Basic Darwinian evolution is a strongly confirmed theory built on many observed facts.

Bryanw92: "See Climate Change for more on that form of dishonesty."

"Anthropogenic climate change" is just one example of science corrupted by politics, there are others, all unfortunate.
Evolution theory is not one of them.

>>Basic Darwinian evolution is a strongly confirmed theory built on many observed facts.

Why did it stop? Where is a lizard-bird or a ape-man? Because there are no transition fossils to observe. You cal it an observed fact to point to a scapula or something to prove common ancestry, but it can also just be form following function. Basic evolution is just natural selection of mutations within a species, so a function could become unnecessary or necessary for a species, which adds or subtracts a particular form from the species.

But, a finch is still a finch, regardless of beak size. A finch with a large beak is not an alligator, or vice-versa.

exDemMom: "The claim that evolution does not exist because we have never seen an animal have offspring that are a new species is a wonderful example of a straw man.
No scientist ever has claimed that new species suddenly appear because of an event equivalent to a cow spontaneously birthing a lamb.
But Creationists attempt to debunk evolution on that claim all the time."

Well said!
The anti-evolution argument against "macro-evolution" as opposed to "adaption" or "micro-evolution" is a straw man that very few have argued directly against.
My argument is that in fact there's no scientific difference between so-called "adaption" or "micro-evolution" and alleged "macro-evolution".
They are all the same things, only their timescales differ.
The only distinctions are those we ourselves arbitrarily draw between, for examples, breeds, sub-species, species, genera, etc.

Bryanw92: "It is interesting that you repeatedly use the word “enlightenment”, a word associated closely with Humanist thought (that leads into Existentialist thought, then Post-Modernist thought, and then Progressive thought)."

Here's an idea you need to fix firmly in your own mind: we Americans especially are children of the Enlightenment.
Our Founding Fathers were the Enlightenment's finest expression and accomplishment.
Thinkers like Thomas Jefferson and Benjamin Franklin were among the best of their age.
Our adherence to both the Constitution and Bible (not necessarily in that order) reflect their outlook on life.

Oh, no, some people claim, our Founders were atheists or deists.
Nonsense, they all understood, without exception, the importance of traditional (Judeo) Christian teachings and the impossibility of making their Constitutional Free Republic work without them.

Sure, the Enlightenment Age was followed by Romanticism, Existentialism, modernism, post-modernism, etc-ism, etc-ism, all unfortunate.

But the idea of conservatism is that we anchor our views of these more recent effervescences in traditional understandings of the Bible and our Founders' Enlightenment intentions.

"Enlightenment" is a good word.

Bryanw92 post #41: "I do not agree that evolution/uniformitarianism as it is currently believed is Truth, but I do not disagree with it either.
It is an unobservable and unrepeatable theory that is more philosophy than biology.
I simply question the method and then get attacked by people who claim to be open but still have a worldview that requires adherence to a certain humanist orthodoxy."

Bryanw92 post #52: "Where is a lizard-bird or a ape-man?
Because there are no transition fossils to observe.
You cal it an observed fact to point to a scapula or something to prove common ancestry, but it can also just be form following function.
Basic evolution is just natural selection of mutations within a species..."

I think your post #52 puts the lie to your claims in post #41.
In #41 you pose as almost agnostic, simply "question the method", etc., but in #52 you reveal your true self as a committed anti-evolution ideologue, nothing agnostic or reasonable about it.

Specifically, repeated claims of "no transition fossils" from anti-evolutionists are only possible to maintain by denying obvious evidence from billions of collected fossils in hundreds of thousands of extinct species in many well represented transitional sequences.
Faced with literal mountains of evidence you tightly close your eyes, loudly proclaiming: I see nothing!

Bryanw92: "But, a finch is still a finch, regardless of beak size.
A finch with a large beak is not an alligator, or vice-versa."

Sure, by definition, all finches are finches, until they're not.
All told there are hundreds of species of finch in 50 different genera, representing maybe 15 million years of speciation.
But there are also dozens of other species which have recently been reclassified as "not-finch" (including Darwin's finches!) because of more careful morphological and DNA analyses.
So, yes, "a finch is a finch is a finch" except when it's not really and that is determined by scientific analysis rooted in evolution theory.

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