Scientists observe real-time evolution of a new chromosome

in an experimental strain of archaea

The accumulation of small heritable changes within populations over time.

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Scientists observe real-time evolution of a new chromosome

#1  Postby Rumraket » May 04, 2018 9:10 am

A major question in evolutionary cell biology has been how the chromosomal architecture evolved where the essential genes of an organism came to be split across multiple chromosomes. Researchers have now observed this process take place naturally for the first time:

Paper is open access:
Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii
Darya Ausiannikava Laura Mitchell Hannah Marriott Victoria Smith Michelle Hawkins Kira S Makarova Eugene V Koonin Conrad A Nieduszynski Thorsten Allers
Abstract
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: (1) mutational diversification of a multi-copy chromosome; (2) capture of a new chromosome by horizontal transfer; (3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly-generated elements are bona fide chromosomes, because each bears ‘chromosomal’ replication origins, rRNA loci and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally-evolved prokaryotic genome to generate two new chromosomes has not been described previously.

Molecular Biology and Evolution, msy075, https://doi.org/10.1093/molbev/msy075 Published: 16 April 2018

The process was fairly straightforward and obvious: One chromosome with multiple Origins-of-replication, splits into two at two loci that doesn't break existing genes. Both fragments retain functional origins-of-replication elements.
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Re: Scientists observe real-time evolution of a new chromosome

#2  Postby Wortfish » Oct 05, 2018 4:24 pm

So a chromosome has split in two. How does this change how the organism functions?
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Re: Scientists observe real-time evolution of a new chromosome

#3  Postby laklak » Oct 05, 2018 5:29 pm

Aaaaand hand waving in 3.....2.....1.....
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Re: Scientists observe real-time evolution of a new chromosome

#4  Postby Thommo » Oct 05, 2018 5:32 pm

Wortfish wrote:So a chromosome has split in two. How does this change how the organism functions?


Incrementally.
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Re: Scientists observe real-time evolution of a new chromosome

#5  Postby Rumraket » Oct 05, 2018 8:07 pm

Wortfish wrote:So a chromosome has split in two. How does this change how the organism functions?

In this particular instance nobody claims that it does. But the question "how does there come to be more chromosomes?" is answered by direct observation.

Got any more irrelevant questions?
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Re: Scientists observe real-time evolution of a new chromosome

#6  Postby InHisImage » Oct 06, 2018 12:18 pm

The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins.


Well, I guesss congratulations are in order for their achievement!
They do however, make some interesting assumptions with their pronouncement of common ancestry being evident. Firstly, they use the word "architecture" which to all intents and purposes imply that someone with intelligence was responsible for the physical layout and functional aspects of the genome. Surely this cannot be right if it all happened by accident or random chemical and physical processes in the beginning?
Secondly, how come there is a chromosome at all? Having the DNA wrapped up in such a highly sophisticated 3-dimensional unit which changes over time and in location smacks of design, so how come it is here due to random chemical and physical processes?
How did the LOGIC arise that specifies how DNA gets wrapped up into chromosomes and how does access get controlled in such a highly secure manner with highly customized logic and machinery required to unlock it?
Here are some illustrations of the sophisticated complexity ( nevermind the chemical instability ) that results:
https://www.nature.com/scitable/topicpa ... omatin-310

So when one begins to ponder the nanoscale of operational sites and the absolute mastery of packaging involved, it does not take long to begin to realize that something is very much amiss in the abiogenesis story.
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Re: Scientists observe real-time evolution of a new chromosome

#7  Postby Keep It Real » Oct 06, 2018 3:03 pm

InHisImage wrote:Having the DNA wrapped up in such a highly sophisticated 3-dimensional unit which changes over time and in location smacks of design, so how come it is here due to random chemical and physical processes?


I'm reminded of this illustration. Made in His image?

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Re: Scientists observe real-time evolution of a new chromosome

#8  Postby Thomas Eshuis » Oct 06, 2018 4:37 pm

InHisImage wrote:
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins.


Well, I guesss congratulations are in order for their achievement!
They do however, make some interesting assumptions with their pronouncement of common ancestry being evident. Firstly, they use the word "architecture" which to all intents and purposes imply that someone with intelligence was responsible for the physical layout and functional aspects of the genome. Surely this cannot be right if it all happened by accident or random chemical and physical processes in the beginning?
Secondly, how come there is a chromosome at all? Having the DNA wrapped up in such a highly sophisticated 3-dimensional unit which changes over time and in location smacks of design, so how come it is here due to random chemical and physical processes?
How did the LOGIC arise that specifies how DNA gets wrapped up into chromosomes and how does access get controlled in such a highly secure manner with highly customized logic and machinery required to unlock it?
Here are some illustrations of the sophisticated complexity ( nevermind the chemical instability ) that results:
https://www.nature.com/scitable/topicpa ... omatin-310

So when one begins to ponder the nanoscale of operational sites and the absolute mastery of packaging involved, it does not take long to begin to realize that something is very much amiss in the abiogenesis story.

Another wall of text that fails to hide it is just one big appeal to personal ignorance and incredulity.
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Re: Scientists observe real-time evolution of a new chromosome

#9  Postby Rumraket » Oct 06, 2018 4:55 pm

Oh look, a new chew toy.

InHisImage wrote:
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins.

Well, I guesss congratulations are in order for their achievement!
They do however, make some interesting assumptions with their pronouncement of common ancestry being evident.

That's not an assumption but an evidentially derived conclusion. If phylogenetic trees inferred from independent sets of data (such as morphology and metabolic enzymes) converge on the same branching topology, then there can be no other rational explanation for that fact, than the species in question from which the data sets are used must share a common genealogical relationship. And they do.

InHisImage wrote:Firstly, they use the word "architecture" which to all intents and purposes imply that someone with intelligence was responsible for the physical layout and functional aspects of the genome.

That's absurd, since countless non-designed phenomena can be said to have an "architecture". Like the architecture of a natural cave system formed by erosion and other geological processes. In the case of "genome architecture" it refers to the presence of particular types of genetic elements within the genomes of the species in question, and their sequence of arrangement in relation to each other. So one could easily well use the word "structure" or "sequence" to refer to the same thing and if you think the use of the word architecture implies there must have been some sort of designing intelligence involved then I recommend you simply ignore the word because your'e letting a particular word confuse you.

InHisImage wrote:Surely this cannot be right if it all happened by accident or random chemical and physical processes in the beginning?

I don't agree that an intelligence cannot also operate on chemical and physical processes. It seems to me that is what your brain does. So there are many intelligent systems that are purely chemical and physical. Your computer is another such entity, operating in a way I would describe as intelligent, by purely physical processes.

And considering how you put "random" in front of "chemical and physical processes" it becomes all the more unclear what you even think the word "random" means.

In any case, evolution isn't really random. It has random mechanisms involved, such as the stochastic nature of mutation, and the unpredictability of how environments will change over time, but then there is the response of natural selection that favors fitter phenotypes.

InHisImage wrote:Secondly, how come there is a chromosome at all?

Well answering that question essentially comes down to the origin of life, and we don't know how life originated. How did there come to be genomes made of ribonucleic acids being replicated? We don't know, it's being investigated.

InHisImage wrote:Having the DNA wrapped up in such a highly sophisticated 3-dimensional unit which changes over time and in location smacks of design

Why does "smack of design" whatever that even means? I don't see why we should think that.

InHisImage wrote:so how come it is here due to random chemical and physical processes?

What is this "random chemical and physical processes"? When water from the tap evaporates leaving calcium carbonate flakes on your kitchenwares, is that "random"? In what way does it make sense to describe that as "random" if it happens every time without exception?

InHisImage wrote:How did the LOGIC arise that specifies how DNA gets wrapped up into chromosomes and how does access get controlled in such a highly secure manner with highly customized logic and machinery required to unlock it?
Here are some illustrations of the sophisticated complexity ( nevermind the chemical instability ) that results:
https://www.nature.com/scitable/topicpa ... omatin-310

Evolution by natural selection.

InHisImage wrote:So when one begins to ponder the nanoscale of operational sites

What is a "nanonscale of operational sites"? That just sounds like mindless technobabble.

InHisImage wrote:it does not take long to begin to realize that something is very much amiss in the abiogenesis story.

Ahh but you're confused. Packaging of DNA into chromatin is not thought to have originated with the first cells, but is a much later evolved process. The last universal common ancestor of all known cellular life did not package it's chromosomes into chromatin.

If God made our genomes in his image, then he is made of at least 50% decaying retroviral elements and ancient defective transposons.
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