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Topic: Functional roles of Aves class-specific cis-regulatory elements (Read 395 times) previous topic - next topic

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  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #25
So no explanation as to why the avian situation is so outside the usual.

Pretty sure that the explanation is mentioned in the topic title. It IS the topic title, actually.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #26
This is so far outside the usual that it calls for some kind of explanation.
It's lower than for mammals - according to the paper - but who's to say what is "usual" ?  :dunno:

"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #27
Quote
We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
  • Last Edit: November 29, 2017, 01:17:39 PM by socrates1

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #28
You have - surprise! - misunderstood the paper.
They were surprised that the Aves-specific HCE's were distributed so differently from the NON-Aves-specific HCE's.
Not that that ratio is particularly "unusual" relative any other (unspecified) lineages.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #29
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #30
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #31
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression
Well, forces you to re-examine.   You're only about 30 years behind the times.   Just wait until you get to epigenetics!
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #32
The authors tell you exactly why they were surpised:
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c).
Fig. 1c shows 17.55% of all AVIAN HCE's lying in coding regions, but only 0.31% of all ASHCE's.
No comparison with other classes.
No way to conclude how "usual" or "unusual" that might be.
Quote
We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).

"therefore" = "for the reason just stated"

The reason just stated: the fact that the distribution of ASHCE's appears to be very different from non-AS-HCE's in avian genomes.
Nothing to do with comparison with other classes of animal.

Perhaps you're wondering why the distribution of ASHCE's is "unusual" relative to the distribution of total HCE's - in avian genomes:dunno: 
Probably because regulatory elements controlling genes are more sequence sensitive than the structural contents of the genes themselves. That's what the authors seem to be suggesting.

"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #33
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
If someone knows better than these surprised scientists then give us your explanation. Pretending I do not understand this subject does not cut it.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #34
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
If someone knows better than these surprised scientists then give us your explanation. Pretending I do not understand this subject does not cut it.

Explanation ... for WHAT?
WHAT do you think is "unusual"?
"Unusual" relative to WHAT?



  • Last Edit: November 29, 2017, 02:28:16 PM by VoxRat
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #35
As a sidenote notice that birds have ZERO overlap (on both dimensions) with the other taxa shown in Figure 1a.
https://media.springernature.com/m685/nature-assets/ncomms/2017/170206/ncomms14229/images/ncomms14229-f1.jpg
  • Last Edit: November 29, 2017, 02:26:53 PM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #36
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
  • Last Edit: November 29, 2017, 02:53:14 PM by socrates1

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #37
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
  • Last Edit: November 29, 2017, 03:02:13 PM by socrates1

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #38
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
If someone knows better than these surprised scientists then give us your explanation. Pretending I do not understand this subject does not cut it.

Explanation ... for WHAT?
WHAT do you think is "unusual"?
"Unusual" relative to WHAT?
needs repeating, apparently.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #39
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.

  • VoxRat
  • wtactualf
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #40
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now. I am not wasting time on that.
If this is usual, then why were they surprised? Face it, this is very unusual. But if someone knows better than these surprised scientists then give us your explanation.
Better yet, just admit you have no idea. 
If someone knows better than these surprised scientists then give us your explanation. Pretending I do not understand this subject does not cut it.

Explanation ... for WHAT?
WHAT do you think is "unusual"?
"Unusual" relative to WHAT?
needs repeating, apparently.
You really have no idea, have you?
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #41
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #42
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.
Yes, all the dinosaur genomes we have sequenced clearly show that you are correct.
While you were getting your PhD in virology, I got my PhD in truth detection. :wave:  Dave Hawkins

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #43
For reference:
https://en.wikipedia.org/wiki/Cis-regulatory_element
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
Regulatory genes "have a profound effect on phenotype by altering gene expression". So the regulatory genes for birds "generate phenotypic variance".

And
Quote
very few [protein-coding] lineage-specific genes emerged in the avian genome
Quote
Unlike microevolutionary processes, little is known about the genetic basis of macroevolutionary processes. One of these magnificent examples is the transition from non-avian dinosaurs to birds that has created numerous evolutionary innovations such as self-powered flight and its associated wings with flight feathers.

The (surprising) evidence explains the phenotypes, but does it explain the "numerous evolutionary innovations"?

From the study:
Quote
This result implies that innovation of protein-coding genes might not play a large role in the processes underlying the transitions from dinosaur to the bird lineage.

This result corroborates the above observation that very few lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
Quote
The preferential targets of strong purifying selection are usually on protein-coding regions9, for example, 17.55% of HCEs lie within coding regions, some three-fold higher than the percentage of coding regions in whole genome (Fig. 1c). We were therefore surprised to observe, that the proportion of ASHCEs that lie within coding regions was ca. 50-fold lower (0.31%, Fig. 1c).
Notice that this is not 50% lower but 50 fold lower.
This is so far outside the usual that it calls for some kind of explanation.
Unfortunately, people will not accept your judgement about what is "far outside the usual".
In the past, whenever it became clear what exactly you consider "far outside the usual", and maybe even why you consider it "far outside the usual", it turned out to be something you have misunderstood, and/or based on your ignorance of what "the usual" is.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #44
Notice that there is no input from others.
Insults do not count.
This is not an emotional support site, its purpose is not to stimulate mutual admiration and reciprocal ego building.
Civility has a low priority here.
Opinions are not disqualified simply because they are insulting.
When you say something stupid, or use too many words to say nothing, this will be addressed.
Colorful language is a bonus.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #45
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
Makes perfect sense to me!

No wonder Archaeopteryx was initially confused with Compsognathus.

This confusion seems to survive until today, from time to time:
Quote from: Socrates;1684678
The body of Archaeopteryx is that of a Compsognathus.
Although one could legitimately question she actual scholarship of those confused.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #46
Someone earlier tried to pretend I misunderstood the study. It did not work then and it does not work now.
It did not work for you. That means nothing.
Quote
I am not wasting time on that.
Everything you do here is a waste of your time.
Except for the various flaws in your character and intellect, you have not convinced anybody of anything.
Feel free to prove me wrong about this.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #47
I will be leaving this shortly.

  • Faid
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #48
Wise decision.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Functional roles of Aves class-specific cis-regulatory elements
Reply #49
This study forces us to re-examine what is meant by a phenotype.
Quote
This result corroborates the above observation that very few [protein coding] lineage-specific genes emerged in the avian genome, suggesting changes in non-coding regulatory sequences might play a more important role in the emergence of avian evolutionary innovations than the acquisition of novel protein-coding genes.
AND
Quote
CREs [Cis-regulatory elements] have an important evolutionary role. The coding regions of genes are often well conserved among organisms; yet different organisms display marked phenotypic diversity. It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression

The non-coding regulatory sequences produce the myriad differences (phenotypes) between different types of birds.
And
Quote
very few [protein coding] lineage-specific genes emerged in the avian genome
I suggest that if "very few [protein coding] lineage-specific genes emerged in the avian genome", then very few changes were required in the evolution from bird ancestor to bird.
The non-coding regulatory sequences the study found, produce the myriad differences (phenotypes) between different types of birds.
If very few changes were required in the evolution from bird ancestor to bird then the ancestor must have been quite similar to the first birds.
This is a problem for the dino to bird theory since dinosaurs are completely different than birds.
So we need to look for an ancestor that is similar to the first birds.