Chromosome evolution at the origin of the ancestral vertebrate genome

[Witchdoc]

Many creationists deny that primates and humans have a common ancestor, or that humans were and are lobe finned fish (and many deny that duplication can provide material for evolution to work with via duplication and subsequent neofunctionalisation/subfunctionalisation).

Chromosomal studies have shown good evidence that the original prevertebrate common ancestor had 17 chromosomes, which duplicated to form 34, after which there were seven chromosomal fusions to 27, and another round of chromosomal duplications to 54, fusions to the bony vertebrate ancestor at 50, to 48 for apes, then 46 for humans.

Chromosome evolution at the origin of the ancestral vertebrate genome

@colewd any thoughts? Is this evidence? Is the existence of chromosomal tetrads good evidence for two rounds of chromosomal duplications, and that you and I have a common ancestor with all vertebrates?

Or do you think God wanted to trick us, so just made it look like we had two rounds of duplication when in fact there never was?

We reconstruct the evolution of chromosomes at the beginning of vertebrate evolution. We first compare 61 extant animal genomes to reconstruct the highly contiguous order of genes in a 326-million-year-old ancestral Amniota genome. In this genome, we establish a well-supported list of duplicated genes originating from the two whole genome duplications to identify tetrads of duplicated chromosomes. From this, we reconstruct a chronology in which a pre-vertebrate genome composed of 17 chromosomes duplicated to 34 chromosomes and was subject to seven chromosome fusions before duplicating again into 54 chromosomes. After the separation of the lineage of Gnathostomata (jawed vertebrates) from Cyclostomata (extant jawless fish), four more fusions took place to form the ancestral Euteleostomi (bony vertebrates) genome of 50 chromosomes.

[colewd (Bill Cole)]

@Witchdoc

@colewd any thoughts? Is this evidence? Is the existence of chromosomal tetrads good evidence for two rounds of chromosomal duplications, and that you and I have a common ancestor with all vertebrates?

Hi WD
Let me read the paper and think about your question. I am busy the next couple of days and will try to get back to you this weekend.

[John_Harshman]

Let’s not forget that teleosts have an extra, third round of whole-genome duplication. Even more fun. And plants do this sort of thing as a matter of course.

[davecarlson]

@John_Harshman

plants do this sort of thing as a matter of course.

Indeed. There are many, many plant species where genome copy number is a trait that varies among different populations or individuals within a population.

[evograd (Blogging Graduate Student)]

@Witchdoc

the original amniota common ancestor had 17 chromosomes…

I think you mean the pre-vertebrate ancestor here.

[Witchdoc]

Fixed.

@colewd whenever you’re ready.

[colewd (Bill Cole)]

@Witchdoc

@colewd any thoughts? Is this evidence? Is the existence of chromosomal tetrads good evidence for two rounds of chromosomal duplications, and that you and I have a common ancestor with all vertebrates?

Or do you think God wanted to trick us, so just made it look like we had two rounds of duplication when in fact there never was?

I think that the paper is interesting. Like common pseudo genes this is evidence of common ancestry. The question is if it is conclusive given all the other differences. The fact that you can hypothesize gene duplication from the historic gene counts is interesting but not conclusive IMO. Is your thought that the ancestral relationship was through reproduction and associated variation alone? Are you including directed evolution as a possibility?

[Rumraket (Mikkel R.)]

@colewd

The question is if it is conclusive given all the other differences.

Nothing in science is ever really conclusive. All conclusions are tentative and can in principle be changed in light of new evidence.

@colewd

Is your thought that the ancestral relationship was through reproduction and associated variation alone? Are you including directed evolution as a possibility?

What does that even mean in the context of reproduction and variation? Is God intervening at the quantum level and causing particular mutations to occur, or does he reach into organism’s brains and make them pick particular mates they otherwise wouldn’t, or cause the lion to ignore the smell in the wind and instead go 3 kilometers east because He needs it to kill a particular Gazelle carrier of some mutation? Or do lightning bolts appear out of thin air to kill that Gazelle? Let me ask you your favorite question right back: Can you model it?

[John_Harshman]

@colewd

Are you including directed evolution as a possibility?

Are you? If we allow for directed evolution, are you willing to accept that the evidence of common descent is conclusive?

[Witchdoc]

@colewd

I think that the paper is interesting. Like common pseudo genes this is evidence of common ancestry. The question is if it is conclusive given all the other differences. The fact that you can hypothesize gene duplication from the historic gene counts is interesting but not conclusive IMO. Is your thought that the ancestral relationship was through reproduction and associated variation alone? Are you including directed evolution as a possibility?

So you’ve read the paper.

Mere “gene duplication” isn’t just it.

It’s wholesale large volume gene duplication via 2 rounds of whole genome duplication.

Anyway. Time for us to try putting on our scientist hats and think about the different predictions of evolution + common descent vs design/ID/creationism regarding gene ohnologs.

How many gene ohnologs does design/ID/creationism predict?

How many gene ohnologs do humans have?

Does the pattern of gene ohnologs match that of common descent, and does this provide strong evidence for us having a common ancestor with all vertebrates?

You mentioned “directed evolution”. How does one distinguish “directed evolution” vs “undirected evolution”?

[colewd (Bill Cole)]

@Witchdoc

It’s wholesale large volume gene duplication via 2 rounds of whole genome duplication.

Hi WD
This is clear from the paper. Thanks for the correction as I should have said genome vs gene.

The problem I see is it is very hard to differentiate common design from common descent when you are comparing similarities as they could be the result of either.

How do you eliminate design as the cause? You may eliminate it in this case for the different chromosome configurations yet you have not eliminated design as part of the overall process.

The paper makes a claim that the different gene configurations in non vertebrates and vertebrates can be caused by whole genome duplications. This can be possible yet design may have been required to develop the new genes that are observed in the transition. While common descent is a possible explanation for the similarities it is problematic in explaining many of the differences.

Combining common descent with design intervention is a viable overall hypothesis IMO. The challenge is then to parse out the events where design was not necessary and we can assign the result to reproduction/variation and other associated mechanisms.

[wallischris10 (Christopher Wallis)]

Common descent is a constrained, observable mechanism, common design isn’t, i.e ANYTHING is compatible with common design, it makes no predictions and can never be ruled out. You can only really infer common design if you happen to know the intentions of the designer.

[RonSewell (RonS)]

@colewd

The challenge is then to parse out the events where design was not necessary and we can assign the result to reproduction/variation and other associated mechanisms.

I thought the ID methodology was about parsing out the events where design was necessary. Do you now hold that everything is to be regarded as directly created until proven otherwise?

[John_Harshman]

@colewd

Combining common descent with design intervention is a viable overall hypothesis IMO. The challenge is then to parse out the events where design was not necessary and we can assign the result to reproduction/variation and other associated mechanisms.

And there’s Bill, still confusing common descent with the origin of variation. No matter how many times he’s told.

[colewd (Bill Cole)]

@RonSewell

I thought the ID methodology was about parsing out the events where design was necessary. Do you now hold that everything is to be regarded as directly created until proven otherwise?

ID is about inferring design. If you show a solution that is part of nature then inference of ID in that instance is rejected.

[Timothy_Horton]

@colewd

ID is about inferring design. If you show a solution that is part of nature then inference of ID in that instance is rejected.

The problem is every last “inference” by the ID crowd is completely subjective and doesn’t stand up to the slightest scientific scrutiny. There’s also the fact the DI is on record as saying ID’s purpose is religious/political in nature and involves overthrowing “materialism” and reintroducing the Christian God into everyday life including science classes.

[Mercer (John Mercer)]

@Witchdoc

ohnologs

Freudian slip?

[Witchdoc]

Well. Apparently its the technical term!

Vertebrate Ohnologs.

[Mercer (John Mercer)]

I learned something new there!