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Oldest known sex chromosome emerged 248 million years ago in an octopus ancestor

The oldest-known sex chromosome emerged in octopus and squid between 455 million and 248 million years ago — 180 million years earlier than the previous record-holder, scientists have discovered.

Octopus and squid appear to have evolved sex chromosomes at least 248 million years ago.

 (Image credit: Olga Visavi/Shutterstock)


The oldest known sex chromosome in animals has been discovered, pushing back the date for the evolution of sex chromosomes to between 248 million and 455 million years ago.

The ancient chromosome was found in octopus and squid, suggesting that these may have been among the first animals to determine their sex via genetic blueprint, instead of environmental cues.

Sex chromosomes are standard in mammals. In humans, the sex chromosomes are X and Y. Males usually have an X and a Y chromosome, while females have two Xs, although there are some variations, such as XXX or XXY, which can have a wide range of impacts from no effect at all to certain learning disabilities or neurological differences.

For a long time, researchers weren't sure whether cephalopods, the soft-bodied mollusks that include squid and octopuses, determined their sex with chromosomes. Mollusks have a variety of ways to handle reproduction, including hermaphroditism or sequential hermaphroditism, in which individuals swap sexes over time.

Octopuses stick to one sex, but it wasn't clear whether genes or environmental cues determined what sex that would be. In some reptiles and fish, factors like temperature decide the sex of offspring.

Related: Octopuses torture and eat themselves after mating. Science finally knows why.

In 2015, researchers completed the first full gene sequence of a cephalopod, the California two-spot octopus (Octopus bimaculoides). That sequence still included gaps, though, so a team led by Andrew Kern, a biologist at the University of Oregon, set about filling them in with high-fidelity sequencing.


Researchers discovered the chromosome after completing the full gene sequence of the California two-spot octopus. (Image credit: Brent Durand/Getty Images)

They soon noticed that one chromosome, chromosome 17, seemed less filled-out with genes than the other chromosomes in their sequence. Because they had sequenced a female octopus, they compared their results to the earlier individual, a male. In the case of the male, chromosome 17 looked no less populated than other chromosomes in the octopus.

This was a clue that chromosome 17 might have something to do with sex differences. To confirm, the team sequenced four more octopuses, two male and two female, and confirmed that females have just one copy of chromosome 17, while males have two. Thus, they represent the octopus sex chromosomes not as XY and XX as in humans, but as ZZ and Z0.

The researchers then compared their octopus genomes to the genomes of three other octopus species, three species of squid, and the chambered nautilus (Nautilus pompilius).

They found the ZZ/Z0 pattern in the squid and the octopus, but not in the nautilus, a more distantly related species. This showed that the sex chromosomes evolved after the split between the nautilus line and the line leading to modern squid and octopus, which occurred between 455 million and 248 million years ago.

"This is an astoundingly long time for a sex chromosome to be preserved," the researchers wrote in their paper, which is now available pre-peer review on the preprint website BioArxiv.

Prior to this research, the oldest confirmed sex chromosome was in sturgeon fish, according to Nature News, with an age of about 180 million years.

Octopuses Might Have The Oldest Sex Chromosomes in The Animal Kingdom

NATURE09 March 2024

ByCARLY CASSELLA

(Judit Pungor/CC By 4.0)

Cephalopods may have the oldest sex chromosomes of any animal, according to a recent discovery in the octopus genome.

That's a big deal given that scientists didn't know until now that these oddball creatures even had a form of sex determination written into their genes. To determine if an octopus is male or female, biologists have relied purely on observation, differentiating between which individuals lay eggs versus which produce sperm.

Searching the octopus genome had shown no clear sign of a sex chromosome system. Scientists were beginning to wonder if perhaps cephalopods were like some fish and reptiles, with sex determined through environmental factors such as the temperature at which eggs are kept rather than the inheritance of distinct chromosome.

At last, researchers at the University of Oregon claim to have solved the mystery.

Their pre-print study, which is currently under peer review, provides the first evidence of genetic sex determination among octopuses.

Examining the genes of the California two-spot octopus (Octopus bimaculoides) – the first cephalopod to have its whole genome sequenced – researchers have finally found a unique chromosome pair.

They discovered it on chromosome number 17, and it only stood out to researchers when they compared the male octopus genome that had been fully sequenced to a female one. The female octopus seemed to be missing one of their two copies.

Digging further, researchers say they found clear signatures of a ZW sex-determination system, which is seen in birds, crustaceans, and some insects,

We humans rely on an XY system, wherein two X chromosomes create the default female body plan, while the presence of a Y chromosome generally triggers the development of male characteristics.

Octopuses have an opposite system. It is the males that typically have a double-Z pair and females that have only one Z chromosome.

To see if this system was present in other cephalopods, researchers compared the genomes of three octopus species, three squid species, and a nautilus.

They concluded that the Z chromosome is an "evolutionary outlier" that stands apart from similar chromosomes in close relatives.

Only the genomes of the bobtail squid (Euprymna scolopes) and the East Asian common octopus (Octopus sinensis) had similar outlier signatures, but because these creatures are from different lineages, it suggests the Z chromosome originated before their split.

As such, researchers at the University of Oregon argue that the Z chromosome is "of an ancient, unique origin" that probably arose between 455 and 248 million years ago. If the chromosome appeared towards the earlier end of that timeline, the octopus could have the oldest animal chromosome yet found, beating even some insects which are thought to have sex chromosomes that date back 450 million years.

Compared to those of octopuses, however, these arthropod sex chromosomes are poorly conserved across species.

For comparisons, the oldest accepted vertebrate chromosome is that of a sturgeon fish, which is thought to be about 180 million years old. Sturgeon fish females have a ZW sex chromosome set pair as opposed to the female octopus's 'hemizygous' Z chromosome. It's possible the octopus's corresponding W chromosome may have been lost over time in a manner similar to the ill-fated trajectory of the Y chromosome in humans.

The story behind sex chromosomes has changed a lot in recent years. Once, they were thought to be intrinsic features of sex determination in animals. But biological research tends to be biased towards mammals. As it turns out, some fish and reptiles, like crocodiles, don't have sex chromosomes at all. The sex of their offspring is instead determined by other, external factors through epigenetic regulations.

Clearly, there is still much to be learned about how sex chromosome evolved, and why. Octopuses, with their deep evolutionary roots could be fascinating models for future research.

"The data presented in this paper definitely suggests that cephalopods have among the oldest sex chromosomes in both animals and plants," independent evolutionary scientist, Sarah Carey, told Carissa Wong at Nature.

"This is such a cool time to be working on the genetics of sex chromosomes."

The preprint was published in bioRxiv.

Oldest known animal sex chromosome

evolved in octopuses 380 million years ago


Result reveals for the first time how some cephalopods determine sex.

By Carissa Wong
04 March 2024

The California two-spot octopus (Octopus bimaculoides) has one or two copies of chromosome 17, depending on its sex.Credit: Norbert Wu/Minden Pictures via Alamy

Researchers have found the oldest known sex chromosome in animals — the octopus Z chromosome — which first evolved in an ancient ancestor of octopuses around 380 million years ago. The findings1 answer a long-standing question about how sexual development is directed in the group of sea creatures that includes octopuses and squid.

“We stumbled upon probably the oldest animal sex chromosome known to date,” says evolutionary geneticist Andrew Kern at the University of Oregon in Eugene. “Sex determination in cephalopods, such as squids and octopi, was a mystery — we found the first evidence that genes are in any way involved.”

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In many animals, including most mammals and some insects, sex chromosomes determine whether an individual becomes male or female. In humans, females usually have two X sex chromosomes, and males typically have one X and one Y sex chromosome. But for some animal groups, such as cephalopods — which include soft-bodied animals such as squids and octopuses, as well as hard-shelled creatures called nautiluses — researchers have been unsure about how individuals become male or female. Scientists generally thought that environmental factors such as temperature play a part — as they do for some reptiles and fish.

Catching Zs

In 2015, researchers reported2 sequencing a cephalopod genome for the first time — that of a male California two-spot octopus, Octopus bimaculoides. In the latest study1, Kern and his colleagues mapped the genome of a female California two-spot octopus. They discovered 29 pairs of chromosomes and one single chromosome, called chromosome 17. By contrast, the male octopus genome had two copies of chromosome 17. That difference led the researchers to hypothesize that chromosome 17 was a sex chromosome.

Sequencing the DNA of other O. bimaculoides octopuses confirmed the idea. Males always had two copies of chromosome 17, whereas females had one copy. Chromosome 17 also contained several genes similar to those that encode proteins in human reproductive tissues, including a protein found in sperm. In animals including birds and butterflies, males similarly have two Z sex chromosomes, whereas females have one Z and one W sex chromosome.

“It very much looked like we were looking at a Z chromosome in O. bimaculoides,” says Kern. But the researchers failed to find a W chromosome in the female octopuses. That suggested that males have ZZ sex chromosomes, whereas females are ZO, with the O denoting the lack of a W chromosome.

Well conserved

The team also found Z chromosomes in some other octopus and squid species — but not in a nautilus.

“This pattern suggests that the Z chromosome evolved once in the lineage that led to modern squid and octopuses — after this lineage split off from hard-shelled nautiloids,” says Kern. This means the Z chromosome first appeared between 450 million and 250 million years ago and has been retained to the present day, he says. Previously, the oldest known animal sex chromosome was thought to have evolved in sturgeon fish about 180 million years ago3.

This chromosome is profoundly evolutionarily conserved, says Matthias Stöck, an evolutionary geneticist at the Leibniz-Institute of Freshwater Ecology and Inland Fisheries in Berlin.

“The data presented in this paper definitely suggests that cephalopods have among the oldest sex chromosomes in both animals and plants,” says Sarah Carey, who studies the evolution of sex chromosomes at the HudsonAlpha Institute for Biotechnology in Huntsville, Alabama. “This is such a cool time to be working on the genetics of sex chromosomes.”

doi: https://doi.org/10.1038/d41586-024-00637-0

References

1. Coffing., G. C. et al. Preprint at bioRxiv https://doi.org/10.1101/2024.02.21.581452 (2024).

2. Albertin, C. B. et al. Nature 524, 220–224 (2015).

   Article PubMed Google Scholar 

3. Kuhl, H. et al. Phil. Trans. R. Soc. B 376, 20200089 (2021).

When did humans start wearing clothes?

By Ashley Hamer
( lifes-little-mysteries)

published about 22 hours ago


Clothes don't survive the way artifacts made of stone, bone and other hard materials do, so scientists have to get creative to answer this question.

Am illustration of Homo heidelbergensis, a modern human relative, wearing cave bear skins to protect against the cold.

 (Image credit: Benoît Clarys/University of Tübingen)

As early humans evolved from ape-like ancestors, they came down from the trees, began to walk upright and lost their fur. But without fur, our ancestors would have been exposed to the elements. They would have needed clothing for protection.

So when did humans start wearing clothes?

This is a tricky question, because clothes don't survive the way artifacts made of stone, bone and other hard materials do. Instead, scientists have to get creative. The evidence used to answer this question comes from a few main sources, including bones bearing evidence of skinning, sewing needles and awls, and lice.

"We tried to understand what changes have happened in lice evolutionary history that might be correlated with loss of body hair in humans, and then the subsequent acquisition of clothing use in humans," David Reed, a biologist at the University of Florida, told Live Science.

Lice are incredibly specialized to their habitats; a type that evolved to grasp human head hair wouldn't survive among human pubic hair, for example. But before our ancestors lost their fur, those lice probably roamed all over their bodies. So, by looking at DNA to unravel the evolutionary history of lice, scientists have estimated that those two types diverged about 3 million years ago. However a human genetics study indicates that we lost our hair around 1.2 million years ago. Taken together, these studies suggest a range for when our ancestors lost their fur.

Another type of lice evolved to live in human clothing. These lice are generalists that can live on a wide variety of fibers.

"They feed one time a day on average — they kind of engorge themselves, which is gross — and then they retreat back to the clothing, where it's safe," Reed said.

By looking at when head lice separated from clothing lice, Reed and his team estimated that anatomically modern humans started regularly wearing simple clothes around 170,000 years ago, during the second-to-last ice age.

But there's evidence of hominins — the group that includes modern humans and our closely related extinct relatives — wearing clothing much earlier than that. Marks on bear bones found at the Paleolithic site of Schöningen in Germany suggest that hominins, possibly Homo heidelbergensis, wore bear skins to keep warm around 300,000 years ago, according to research published by Ivo Verheijen, a doctoral candidate at the University of Tübingen in Germany, and colleagues in April 2023.

"If you want to take off the skin of an animal, the cut marks you leave behind most are on the ribs, on the skull, and on the hands and feet. And that's exactly what we found in Schöningen," Verheijen told Live Science. "We started comparing that to other sites from more or less the same period, and they also have cut marks on the hands and feet and on the skulls. So it seems to be a pattern around this time period that people were exploiting bears for their skins."

Evidence of skinning isn't necessarily evidence of clothes; hominins could have been using these skins to build shelter, for instance. But because temperatures were about 3.6 degrees Fahrenheit (2 degrees Celsius) colder, on average, at the time, people were likely using these skins to keep warm, Verheijen said.

"People had to be active to collect food around the landscape," Verheijen added. "So some type of clothing must have been necessary to be able to survive here."

But if there's evidence of clothing from 300,000 years ago and clothing lice didn't evolve until 170,000 years ago, what happened in between?

Lice evidence "can only measure when humans were wearing clothes on a very regular basis because the lice have to feed on human skin" regularly, Ian Gilligan, an honorary associate in the School of Humanities at The University of Sydney, told Live Science. "So if someone dons a garment one day and then doesn't use the garment for another week, the lice aren't going to survive," he said.

What's more, the lineage of clothing lice we've studied might not be the only one that's existed. "There are probably other head lice that infested the clothes off and on at many stages over the last, you know, million years," Gilligan said.

Moreover, different human groups probably started and stopped wearing clothes many times throughout history.

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For example, between 32,000 and 12,000 years ago — up to the end of the last ice age — Aboriginal people in Tasmania retreated to caves, probably for protection from the cold. But the archaeological record also shows evidence that they made clothes, including hide-scraper tools used to scrape animal skins and bone awls used to punch holes for sewing.

But then, the weather got warmer and they stopped wearing clothes.

"The hide scraper tools and the bone awls from 12,000 years ago to midway through the Holocene [11,700 years ago to present] — those tools just disappeared from the archaeological record," Gilligan said. He noted that "they elaborately decorated their bodies, they colored their hair, they painted themselves, they had scarification, so they didn't need clothes."

‘Monumental’ experiment suggests how life on Earth may have started


By Mark Johnson

The Washington Post
March 9, 2024 

A much-debated theory holds that 4 billion years ago, give or take, long before the appearance of dinosaurs or even bacteria, the primordial soup contained only the possibility of life. Then a molecule called RNA took a dramatic step into the future: It made a copy of itself.

Then the copy made a copy, and over the course of many millions of years, RNA begot DNA and proteins, all of which came together to form a cell, the smallest unit of life able to survive on its own.

Now, in an important advance supporting this RNA World theory, scientists at the Salk Institute for Biological Studies in La Jolla, Calif., have carried out a small but essential part of the story. In test tubes, they developed an RNA molecule that was able to make accurate copies of a different type of RNA.

The work, published in the journal Proceedings of the National Academy of Sciences, gets them closer to the grand goal of growing an RNA molecule that makes accurate copies of itself.

“Then it would be alive,” said Gerald Joyce, president of Salk and one of the authors of the new paper. “So, this is the road to how life can arise in a laboratory or, in principle, anywhere in the universe.”

The team remains a ways off from showing that this is how life on Earth truly began, but the scenario they tested probably mimics one of the earliest stirrings of evolution, a concept described by the English naturalist Charles Darwin more than 150 years ago.

“This is a steppingstone toward understanding how life evolved,” said Nikolaos Papastavrou, first author of the paper and a Salk postdoctoral fellow.

No more fuzzy copies

To reach this point, the scientists overcame perhaps the greatest barrier to the plausibility of the RNA World theory. Up to now, no RNA molecule in the lab had succeeded in making copies of another RNA that were both sufficiently accurate and functional.

An RNA molecule must make copies very close to the original to achieve the same delicate balance that governs Darwinian evolution in nature. If the copies change too much, the RNA’s abilities degenerate, and things go downhill quickly. Imagine a malfunctioning photocopier that makes a fuzzy or faded copy of an image. When placed in the machine, the fuzzy copy produces a new one that is even worse.

“If the error rate is too high, you can’t maintain the [genetic] information,” Joyce said. “It just blows up.” The errors happen too quickly to allow Darwinian selection to pick the winners, those best equipped to survive, and “round by round of evolution you just see the population dissipate into no man’s land.”

Though the copying has to be very good, it can’t be letter-perfect all the time. Without some room for mistakes, the RNA would be unable to adapt when its environment changed, as living creatures must do in the wild. Imagine, for example, a hairless Sphynx cat trying to survive as temperatures plunge and the world hurtles toward a new ice age. In that unlikely scenario, the cat would need to change its hairless nature in a hurry.

Octopuses and squids can rewrite their RNA. Is that why they’re so smart?

In the new work, the Salk scientists created an RNA that makes copies of something called a hammerhead RNA. Instead of copying other RNA molecules, the hammerhead chops them. When the RNA made copies of the hammerhead, each new generation could still chop; each also grew easier to copy.

John Chaput, a professor of pharmaceutical sciences at the University of California at Irvine who did not participate in the study, called the crossing of that threshold by the Salk team “monumental,” adding that “at first, I looked on it as a little bit jaw-dropping. … It’s super-neat.”


To show that their RNA was getting better at copying, the Salk team tested a 71st-generation version against one of its distant ancestors. The newer generation outperformed its ancestor when it came to making accurate copies.

“In general, I think it’s a great step forward” for the RNA World theory, said Claudia Bonfio, a junior group leader at the University of Strasbourg in France, who did not participate in the study.

Bonfio, who has been researching the origin of life for the last decade, stressed that “the field is becoming a bit more inclusive” by imagining a beginning in which not only RNA existed but also other building blocks of life. The others could include lipids, which form part of a cell’s membrane, and amino acids, organic compounds found in proteins.

A less-accurate version of the RNA making copies created hammerheads that drifted away from their original sequence, top, and lost their ability to chop over time. The new version makes hammerheads that not only retained their function, they evolved fitter sequences, bottom. (Salk Institute)

In this alternative scenario, Bonfio said, the various building blocks inhabit compartments in a kind of primitive version of a cell.

In an emailed response, Joyce said: “I agree with Claudia’s point about there likely being more to the [primordial] soup than just RNA. Maybe RNA-based evolution began within lipid compartments, or on mineral surfaces, or in combination with some other molecules.”

The central point, Joyce said, is that “eventually Darwinian evolution began to operate,” and at some point early in the history of life, RNA fulfilled the crucial roles of holding genetic information and accelerating the chemical reactions needed to make copies of that information.

How to direct evolution

Michael Kay, a professor of biochemistry at University of Utah, called the new paper “a very exciting advance” that has given the RNA World theory “key evidence [to show] it is plausible and reasonable.” He added that the RNA copier developed at Salk will “provide a valuable tool for people wanting to do directed evolution experiments.”

Directed evolution, sometimes called test tube evolution, is a lab process that allows scientists to mimic evolution by guiding molecules from generation to generation, enabling the molecules to acquire improvements that help them survive.

Although the experiments in the new paper took two years, it has taken Joyce and his colleagues closer to 10 years to set the stage, patiently raising generation upon generation of RNA molecules.

Should the scientists succeed in generating an RNA that can copy itself, evolution could then proceed largely on its own.

“All we would need to do is feed it an ongoing supply of the four building blocks,” said Joyce. RNA, like DNA, is made from four chemical bases, three of which are the same for both: adenine, cytosine and guanine. For its fourth component, RNA has the base uracil, while DNA’s fourth is thymine.

The lab version of evolution would allow RNA molecules to adapt as scientists changed the temperature or environment.

“Even more fun,” Joyce said, would be introducing new chemicals beyond the four bases in RNA and seeing what evolution could do with those.

“Once evolution got going on Earth,” he said, “look at all the amazing things it invented.”'



By Mark Johnson  joined The Washington Post in July 2022 after 22 years at The Milwaukee Journal Sentinel, where he covered health and science. He wrote about the first person to survive rabies without vaccine, and reported on the first use of full gene sequencing to diagnose and treat a new disease. Twitter