# So-called 'junk' DNA plays a key role in speciation
**URL:** https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194
**Category:** Conversation
**Tags:** Science
**Created:** [September 1, 2021, 4:22pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194 "2021-09-01T16:22:59Z")
**Posts on this page:** 20
**Page:** 1
### Author:  [@swamidass](https://discourse.peacefulscience.org/u/swamidass)
#### Post date: [September 1, 2021, 4:22pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/1 "2021-09-01T16:22:59Z")
> **[So-called 'junk' DNA plays a key role in speciation](https://phys.org/news/2021-08-so-called-junk-dna-key-role.html)**
>
> More than 10 percent of our genome is made up of repetitive, seemingly nonsensical stretches of genetic material called satellite DNA that do not code for any proteins. In the past, some scientists have referred to this DNA as "genomic junk."
> Now, in the latest installment of their work, published online July 24 in the journal _Molecular Biology and Evolution_ , Yamashita and former postdoctoral fellow Madhav Jagannathan, currently an assistant professor at ETH Zurich, Switzerland, take these studies a step further, proposing that the system of chromosomal organization made possible by satellite DNA is one reason that organisms from different species cannot produce viable offspring.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [September 1, 2021, 4:58pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/2 "2021-09-01T16:58:23Z")
So much wrong with that brief excerpt. Calling Larry Moran.
1. “do not code for proteins” used as synonym for “junk”.
2. “organisms from different species cannot produce viable offspring”
3. “key role in speciation”
Some of this is probably not the fault of Yamashita and Jagannathan but of whoever wrote that article/press release.
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### Author:  [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)
#### Post date: [September 1, 2021, 5:45pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/3 "2021-09-01T17:45:47Z")
> [@John\_Harshman](#):
>
> Some of this is probably not the fault of Yamashita and Jagannathan but of whoever wrote that article/press release.
From their actual paper:
> [@](#):
>
> The divergence of satellite DNA repeats between species has been long postulated to mediate hybrid incompatibility (HI) and reproductive isolation. However, poor conservation of these noncoding repeats across species is also one of the main reasons why satellite DNA is typically considered to be “junk DNA,” making it difficult to speculate on the “incompatibility of (useless) junk.”
> **[Defective Satellite DNA Clustering into Chromocenters Underlies Hybrid...](https://academic.oup.com/mbe/article/38/11/4977/6327694)**
>
> Abstract. Although rapid evolution of pericentromeric satellite DNA repeats is theorized to promote hybrid incompatibility (HI) (Yunis and Yasmineh 1971; Heniko
Little or no sequence conservation is not a criterion for a genome segment to be regarded as junk. This is probably what contributed to the misunderstanding of popular press article writer.
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### Author:  [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)
#### Post date: [September 1, 2021, 5:45pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/4 "2021-09-01T17:45:49Z")
> “Well, these are junk sequences, who cares if your junk is different from mine?'” said Jagannathan.
You mean other than Susumu Ohno in the paper that coined the term?
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### Author:  [@RonSewell](https://discourse.peacefulscience.org/u/RonSewell)
#### Post date: [September 1, 2021, 5:45pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/5 "2021-09-01T17:45:53Z")
Link to source paper:
[Defective Satellite DNA Clustering into Chromocenters Underlies Hybrid Incompatibility in Drosophila](https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab221/6327694)
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [September 1, 2021, 6:16pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/6 "2021-09-01T18:16:57Z")
> [@Michael\_Okoko](#):
>
> Little or no sequence conservation is not a criterion for a genome segment to be regarded as junk.
Lack of conversation is definitely a significant indication of whether some given stretch of DNA is likely to be actual junk or not. If something is not functional, it’s going to be under relaxed selection (probably only weak purifying selection will be affecting the locus), and hence it won’t be conserved as mutations can almost indiscriminately accumulate. That means generally expect junk to be show lack of conservation, and hence lack of conservation is evidence favoring the junk hypothesis.
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### Author:  [@Tim](https://discourse.peacefulscience.org/u/Tim)
#### Post date: [September 1, 2021, 6:22pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/7 "2021-09-01T18:22:17Z")
> [@Rumraket](#):
>
> Lack of conversation is definitely a significant indication of whether some given stretch of DNA is likely to be actual junk or not.
The rise of inarticulate DNA – what is the world coming to. 😉
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### Author:  [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)
#### Post date: [September 1, 2021, 6:38pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/8 "2021-09-01T18:38:41Z")
> [@Rumraket](#):
>
> Lack of conversation is definitely a significant indication of whether some given stretch of DNA is likely to be actual junk or not
I’m surprised more people don’t talk about this.
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [September 1, 2021, 6:38pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/9 "2021-09-01T18:38:44Z")
Not even gonna edit that.
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### Author:  [@RonSewell](https://discourse.peacefulscience.org/u/RonSewell)
#### Post date: [September 1, 2021, 7:17pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/10 "2021-09-01T19:17:51Z")
> [@Rumraket](#):
>
> If something is not functional, it’s going to be under relaxed selection (probably only weak purifying selection will be affecting the locus), and hence it won’t be conserved as mutations can almost indiscriminately accumulate. That means generally expect junk to be show lack of conservation, and hence lack of conservation is evidence favoring the junk hypothesis.
So if I have this right (and I’m not sure I do), just because increasing divergence of junk DNA might play a role in genetic isolation of descendent species, does not mean that the DNA is any less “junky”; in fact the opposite, its non-essential character may allow the accumulation of hybrid incompatibility while passing without notice within each isolated population.
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [September 1, 2021, 7:17pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/11 "2021-09-01T19:17:52Z")
> [@CrisprCAS9](#):
>
> I’m surprised more people don’t talk about this.
I frequently run into the misapprehension that lack of conservation is meant to _conclusively prove_ junk, and the reverse that conservation is meant to conclusively prove function. But we do of course know of examples of both genes that were relatively well conserved, only to no longer become necessary and turn into junk, and where a useful gene with a significant effect on fitness recently evolved from junk DNA that had, up to that point, been accumulating mutations under almost no purifying selection.
Conservation is nevertheless evidence. A very good indicator of whether you are dealing with junk or not. But exceptions, minor(though important) deviations from that main pattern are of course known.
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### Author:  [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)
#### Post date: [September 1, 2021, 7:42pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/12 "2021-09-01T19:42:42Z")
Thoughtful response, but…
> [@Tim](#):
>
> > [@Rumraket](#):
> >
> > Lack of **conversation** is definitely a significant indication of whether some given stretch of DNA is likely to be actual junk or not.
>
> The rise of **inarticulate** DNA – what is the world coming to.
> [@CrisprCAS9](#):
>
> I’m surprised more people don’t **talk** about this.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [September 1, 2021, 8:52pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/13 "2021-09-01T20:52:55Z")
> [@Michael\_Okoko](#):
>
> Little or no sequence conservation is not a criterion for a genome segment to be regarded as junk.
I’d have to disagree. It’s one of the main diagnostic criteria. That doesn’t mean it always works, though. Further, junk DNA could easily cause reproductive incompatibility and remain junk. Reproductive incompatibility is not a function.
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### Author:  [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)
#### Post date: [September 1, 2021, 9:20pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/14 "2021-09-01T21:20:32Z")
> [@Rumraket](#):
>
> > [@Michael\_Okoko](#):
> >
> > Little or no sequence conservation is not a criterion for a genome segment to be regarded as junk.
>
> Lack of conversation is definitely a significant indication of whether some given stretch of DNA is likely to be actual junk or not.
> [@John\_Harshman](#):
>
> I’d have to disagree. It’s one of the main diagnostic criteria. That doesn’t mean it always works, though
Oops! I forgot to insert “sure” before “criterion”. Don’t blame me, blame my exam-study-fatigued brain at the time when that comment was written (is my brain me?).
To me, the authors seemed to saying that if there is poor sequence conservation then biologists would **definitely** proclaim junk DNA. I was kicking against the seeming absoluteness in that excerpt.
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### Author:  [@Roy](https://discourse.peacefulscience.org/u/Roy)
#### Post date: [September 2, 2021, 10:08am UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/16 "2021-09-02T10:08:46Z")
> [@John\_Harshman](#):
>
> Reproductive incompatibility is not a function.
Surely reproductive compatibility is a function and incompatibility is hence a lack of function?
(I’m imagining junk DNA preventing chromosomes lining up properly or some such).
P.S. Serious question for a change, in case it’s not obvious.
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### Author:  [@swamidass](https://discourse.peacefulscience.org/u/swamidass)
#### Post date: [September 2, 2021, 10:11am UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/17 "2021-09-02T10:11:31Z")
> [@John\_Harshman](#):
>
> Reproductive incompatibility is not a function.
Function is in the eye of the beholder.
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### Author:  [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)
#### Post date: [September 2, 2021, 2:05pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/18 "2021-09-02T14:05:59Z")
> [@Roy](#):
>
> Surely reproductive compatibility is a function and incompatibility is hence a lack of function?
Yes. Though there is such a thing as reinforcement. If there is strong selection against hybrid individuals, selection may favor increased prezygotic isolation.
> [@swamidass](#):
>
> Function is in the eye of the beholder.
Careful. That way lies ENCODE. Words do have meanings.
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### Author:  [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)
#### Post date: [September 2, 2021, 2:40pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/19 "2021-09-02T14:40:44Z")
> [@Roy](#):
>
> Surely reproductive compatibility is a function and incompatibility is hence a lack of function?
>
> (I’m imagining junk DNA preventing chromosomes lining up properly or some such).
>
> P.S. Serious question for a change, in case it’s not obvious.
Yes reproductive compatibility is a function, and of course critical to the continued existence of the species, so any locus that is strictly required for reproduction I would say isn’t actually junk, even if the sequence in question is evolving under very little sequence constraint. We could imagine that despite the locus evolving near to the neutral rate, this is nevertheless still so slowly that any two members of the population are unlikely to be so different from each other that they are incompatible.
But reproductive compatibility between members of ostensibly different species is not a function that is critical to the continued existence of either of two such populations, so the inability of sufficiently diverged members of two populations to reproduce with each other doesn’t mean the locus has become nonfunctional, it just means they’ve diverged too much from each other. Within each population(which we could define due to their reproductive compatibility) they might very well still be similar enough that they can reproduce.
The question is, has anyone ever pinpointed the specific DNA analyzed in the OP paper and declared this to be junk, or is that just a more general inference about most fast-evolving microsattelite repeats? I’ve seen too many papers declaring that they’ve found a new function for “something previously thought to be junk”, only to not actually cite anyone declaring the DNA being studied junk. For the most part I think these geneticists don’t understand the rationale behind the junk inference, nor it’s non-absolutism.
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### Author:  [@system](https://discourse.peacefulscience.org/u/system)
#### Post date: [September 9, 2021, 2:41pm UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/20 "2021-09-09T14:41:11Z")
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### Author:  [@thoughtful](https://discourse.peacefulscience.org/u/thoughtful)
#### Post date: [September 26, 2021, 12:34am UTC](https://discourse.peacefulscience.org/t/so-called-junk-dna-plays-a-key-role-in-speciation/14194/21 "2021-09-26T00:34:39Z")
This was interesting to me. Interested also in comments from the forum.
> **[So-called “junk” DNA plays a key role in speciation](https://wi.mit.edu/news/so-called-junk-dna-plays-key-role-speciation)**
>
> Researchers propose a new framework for how satellite DNA, sometimes called “genomic junk,” is essential in the organization of chromosomes in cells. They suggest this quickly-evolving DNA is one reason different species are unable to successfully...
> Furthermore, the researchers could create a healthy hybrid fly by mutating certain genes in the parent flies called “hybrid incompatibility genes,” which have been shown to localize to satellite DNA in the cells of pure species. Via these experiments, the researchers were able to demonstrate how these genes affect chromosomal packaging in hybrids, and pinpoint the cellular phenotypes associated with them for the first time. “I think for me, that is probably the most critical part of this paper,” Jagannathan said.
> Taken together, these findings suggest that because satellite DNA mutates relatively frequently, the proteins that bind the satellite DNA and keep chromosomes together must evolve to keep up, leading each species to develop their own “strategy” for working with the satellite DNA. When two organisms with different strategies interbreed, a clash occurs, leading the chromosomes to scatter outside of the nucleus.
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