From the tiny testes of flies, new insight into how genes arise

From the tiny testes of flies, new insight into how genes arise
Developing sperm, in blue, within a fruit fly testis. Credit: Laboratory of Evolutionary Genetics and Genomics at The Rockefeller University

In the battle of the sexes, males appear to have the innovative edge—from a genetic standpoint, at least. Scientists are finding that the testes are more than mere factories for sperm; these organs also serve as hotspots for the emergence of new genes, the raw material for the evolution of species.

Using , a Rockefeller team has gained key insight into how nature's attempts at innovation play out during the development of . In research described August 16 in eLife, they mapped the presence of mutations to DNA at the single-cell level, and the activity of new arising from such changes.

"Our work offers an unprecedented perspective on a process that enables living things to adapt and evolve, and that ultimately contributes to the diversity of life on Earth," says assistant professor Li Zhao, who led the research.

High stakes

In recent years, studies in animals from flies to humans have turned up a number of young genes that originated in the testes. These and other discoveries suggest the testes rank among the most productive sites in the body—male or female—for genetic innovation.

This mass production of genetic novelties comes with significant risks, however. In humans, for example, a father's sperm acquires two to three times more new mutations than do a mother's eggs in the course of normal development, leaving the sperm riddled with genetic mistakes. In some cases, such mistakes may harm his offspring, or even derail the prospect of fatherhood altogether.

In other words, the male stands to lose the one thing that matters in the game of evolution: the opportunity to propagate his into the next generation.

But whatever the potential downside genetic experimentation has for individual males and their offspring, the dynamics of reproduction nevertheless encourage it. Potential fathers face intense pressure to attract females and fend off competitors. Any advantage, such as brighter plumage or hardier sperm, for example, can make all the difference.

At the molecular level, this pressure drives an abundance of new genes within the testes. Scientists think that if these newcomers contribute to males' ability to father healthy offspring, they rapidly acquire a fixed place in the genome and may even go on to contribute elsewhere in the body.

Searching cell by cell

Looking a little closer, however, the picture gets blurry. Scientists haven't yet understood the dynamics by which genetic innovation occurs within the precursor from which sperm develops.

To find out more, Zhao and researchers in her lab tagged individual cells from fly testes, then identified and decoded the RNA sequences each contained. This approach allowed them to see how the activity of specific genes changed throughout the developmental stages. Within the RNA sequences isolated from and five intermediary cell types, the researchers examined innovation from two perspectives: that of mutations and that of genes.

Mutations known as substitutions, in which one letter of DNA's code is swapped for another, are most abundant early on in the development of sperm, then decrease, they found. The sperm cells' DNA-repair machinery follows a similar pattern—it is most active early on, then tapers off—which makes sense, according to Zhao, since the machinery is responsible for fixing errors like these.

Starting from scratch

Within the RNA sequences, Zhao's team hunted for a particular type of young gene—one that arises from scratch rather than through duplication of an existing gene. For Zhao, these so-called de novo genes, which originate from sequences that originally did not code for protein, are the most interesting new genes from an evolutionary perspective. Her team found no less than 184 de novo genes, drawn from a set they had previously identified.

When they examined these de novo genes, the scientists uncovered complex patterns, with certain genes showing up primarily in certain cell types, but not in others. About 15 percent of these genes appeared early on, including in the stem cell stage—which is surprising, Zhao says, because scientists previously thought that new genes rarely show up at the start of development as this phase is tightly controlled. The most active period for de novo genes occurred midstream, however, in the so-called spermatocyte phase of developing sperm.

The scientists are now interested in understanding what purpose, if any, de novo genes serve when they first arise. And although it's possible that some essentially fire at random, making no particular contribution, Zhao suspects that in many cases, these new genes play roles in the maturation of sperm cells.

"Precisely what these de novo genes are doing to move development along is an exciting open question," Zhao says.


Explore further

Female fly genomes also populated with de novo genes derived from ancestral sequences

More information: Evan Witt et al, Testis single-cell RNA-seq reveals the dynamics of de novo gene transcription and germline mutational bias in Drosophila, eLife (2019). DOI: 10.7554/eLife.47138
Journal information: eLife

Citation: From the tiny testes of flies, new insight into how genes arise (2019, August 16) retrieved 20 October 2019 from https://phys.org/news/2019-08-tiny-flies-insight-genes.html
This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.
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Aug 18, 2019
This comment has been removed by a moderator.

Aug 18, 2019
What's up with the intelligent design hypothesis and its math pointing out there isn't enough time in the universe to produce a change in dna that adds more complexity to the lifeform, or is more beneficial for it, through random changes or mutations? The argument seems to be that random changes are far more likely to produce something inferior, or just plain break what already worked fine.

Aug 18, 2019
Life has evolved the ability to evolve.

Aug 18, 2019
What's up with the intelligent design hypothesis


If you deign the idea with the term hypothesis - which is arguable since it is not peer review material - it is rejected from the outset. Evolution does not work that way - and this article demonstrates that, as I think you were aiming at.

No way all those de novo genes would be seen if just random changes was responsible, the religious claims do not fit evidence. Of course, how could they, they are just trolling and/or fantasies.

Aug 18, 2019
Life has evolved the ability to evolve.


Funny, but confusing perhaps. There are ideas that some mutation mechanisms are regulated since too rare or too frequent variation is problematic, but I don't think those are well tested. (If someone finds it confusing, step back and consider life - biological populations - a product of the process of evolution.)

Aug 18, 2019
Evolution does not work that way - and this article demonstrates that, as I think you were aiming at.
Thanks for the helpful answers, i've seen a couple other articles on intelligent design pointing out the math/time issues with evolutionary theory, had to ask about it, not trolling.

Another issue raised, i recall, was finding something biological that has 'irreducible complexity' -- where making even a single change, as with reverse-engineering it in the lab, demonstrates that all the parts of the biological structure are necessary for its functionality. They point out that the existence of such structure necessarily requires an 'intelligent agent' to produce it since it contains high amounts of 'complex and specified information' -- which seems like something that is quantifiable, therefore scientific anyway... am checking one of their sites now...

Aug 18, 2019
How come fly testes are bigger than than Benni and SEU's brains? That takes some doing!

Aug 18, 2019
Perhaps you should examine or have someone like Schneib examine YOUR OWN testes to see why they are shrunken to the size of fly testes. Is that why you and Schneib never had children?

Aug 18, 2019
How come fly testes are bigger than than Benni and SEU's brains? That takes some doing!
Pretty good sense of humor, if by design, in their cases...

Aug 18, 2019
Defining the context of 'specified' and 'complexity' :
For instance, a repetitive sequence is specified without being complex. A random sequence is complex without being specified. A functional sequence, like DNA that codes for proteins, is both complex and specified, and therefore designed.

Aug 18, 2019
Perhaps you should examine or have someone like Schneib examine YOUR OWN testes to see why they are shrunken to the size of fly testes. Is that why you and Schneib never had children?


Hello, dumbo! Still here, sh!tforbrains? Pretty dumb, aren't you (rhetorical)? Get back in your vivarium you uneducated clown.

Aug 18, 2019
Perhaps you should examine or have someone like Schneib examine YOUR OWN testes to see why they are shrunken to the size of fly testes. Is that why you and Schneib never had children?


Hello, dumbo! Still here, sh!tforbrains? Pretty dumb, aren't you (rhetorical)? Get back in your vivarium you uneducated clown.
says CastroVagina

Further proof of shrunken testicles from the mind of Castro the expert on everything. One who reads CastroVagina's rhetoric must be in awe at his ability to show proof of his poor upbringing that is now being exhibited in his old age.

Aug 18, 2019
The intelligent design camp's best example of irreducible complexity:
One such irreducibly complex molecular machine that has become the mascot of the intelligent design movement is the bacterial flagellum. This is a tiny motor-driven propeller on the backs of certain bacteria. It is a marvel of nano-engineering, spinning at tens of thousands of rpm
[note these quotes are from Ten Questions to Ask Your Biology Teacher about Design]

Fairly easy to see why no changes could be made to the flagellum, but at the same time, also easy to see it's an obvious selection for nature to (somehow?) make.

Aug 18, 2019
Defining the context of 'specified' and 'complexity' :
For instance, a repetitive sequence is specified without being complex. A random sequence is complex without being specified. A functional sequence, like DNA that codes for proteins, is both complex and specified, and therefore designed.
says Protoplasmix

By your last sentence you have turned Torbjorn into your enemy. He wants no talk of 'design', intelligent or not. There is such a thing as an insane hatred of any possibility that Life was NOT formed in a random fashion, and did not just happen to BE, without a reason for it. Torbjorn has been indoctrinated into avoiding alternatives to what he believes in. And he is very intolerant of that in which he has no control.

Aug 18, 2019
@Proto
You may find the BACULUM of great interest. Human men are lacking it, but it is found in chimps, gorillas and bonobos.

Aug 18, 2019
By your last sentence you have turned Torbjorn into your enemy. He wants no talk of 'design', intelligent or not.
i highly doubt that, he's intelligent, i think he's blocking your comments SEU.

Aug 18, 2019
Yes he is, which doesn't show as much intelligence as you might think. Intolerance in a science site. Who would've thunk it.
Anyway, you should look up BACULUM BONE. It is very interesting

Aug 18, 2019
@Proto
You may find the BACULUM of great interest. Human men are lacking it, but it is found in chimps, gorillas and bonobos.
As an example of irreducible complexity? Not hardly, pun intended.

Aug 18, 2019
Yes he is, which doesn't show as much intelligence as you might think. Intolerance in a science site. Who would've thunk it.
Low threshold for stupidity, SEU, makes better use of his time, which to you apparently doesn't exist somehow, which is pretty stupid.

Aug 18, 2019
I am far more tolerant of others and their ideas, where such ideas may have merit at a later date. I am also more understanding and self-effacing rather than looking down my nose at others even when I KNOW I'm right. Unlike certain commenters who are know-it-alls (and you KNOW who I mean), I prefer to examine more carefully those things that I am unsure of, lest I miss something.
Torbjorn is less likely to concern himself with possibilities, so he turns those like me off, and I am turned off by that kind of behaviour.

Aug 18, 2019
Torbjorn is less likely to concern himself with possibilities, so he turns those like me off, and I am turned off by that kind of behaviour.

We reap what we sow, don't we SEU?

Aug 18, 2019
As to the said Baculum bone, I am inclined to believe that the human male never had one; never evolved one, whereas animals evolved it and used it with no knowledge of it. But of course, I don't believe it was ever a part of the human male due to "intelligent design". Long story.

Now you're basically quoting a passage in the bible. LOL

Aug 18, 2019
Well, Precious has to go out. Nice talking with you, Proto.

Aug 18, 2019
I am turned off by that kind of behaviour
Good! Maybe you'll leave and go post your bullshit somewhere else soon. Go suck Princess' dick some more. Maybe it will make you feel better, @Scientologist_Sperm_Unit.

Bye now!

Aug 18, 2019
Defining the context of 'specified' and 'complexity' :
For instance, a repetitive sequence is specified without being complex. A random sequence is complex without being specified. A functional sequence, like DNA that codes for proteins, is both complex and specified, and therefore designed.
Note to intelligent designers: the functional sequence has both repetitive and random elements...

Aug 18, 2019
late edit ^^^ i think the above note is properly referred to as "stigmergy" ...

Aug 18, 2019
Schneib's filth has been REPORTED. As usual.

Interesting word, that. From what I have read as to its usage, it seems to be a repetitive action by unrelated groups of fellow travelers at different 'timeframes'. A possible analogy might be a 'mountain trail' or any kind of trail that is frequented by many over a period of years.
Randomness is also subject to conditions.


Aug 19, 2019
Now you're basically quoting a passage in the bible. LOL
i think if you look hard enough you'll find it's a bit of wisdom that predates inclusion in a compendium of Egyptian mythologies ... plus it's one of those self-evident truths that bears repeating to anyone fool enough to expect otherwise from what they sow...

Aug 20, 2019
Now you're basically quoting a passage in the bible. LOL
i think if you look hard enough you'll find it's a bit of wisdom that predates inclusion in a compendium of Egyptian mythologies ... plus it's one of those self-evident truths that bears repeating to anyone fool enough to expect otherwise from what they sow...


It's just another way of saying, "There are consequences."

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