Evolution Y Chromosome in Great Apes Deciphered

Related Articles

Related Articles

New analysis of the DNA sequence of the male-specific Y chromosomes from all living species of the great ape family helps to clarify our understanding of how this enigmatic chromosome evolved.

A clearer picture of the evolution of the Y chromosome is important for studying male fertility in humans as well as our understanding of reproduction patterns and the ability to track male lineages in the great apes, which can help with conservation efforts for these endangered species.

A team of biologists and computer scientists at Penn State sequenced and assembled the Y chromosome from orangutan and bonobo and compared those sequences to the existing human, chimpanzee, and gorilla Y sequences. From the comparison, the team were able to clarify patterns of evolution that seem to fit with behavioral differences between the species and reconstruct a model of what the Y chromosome might have looked like in the ancestor of all great apes.

 

“The Y chromosome is important for male fertility and contains the genes critical for sperm production, but it is often neglected in genomic studies because it is so difficult to sequence and assemble,” said Monika Cechova, a graduate student at Penn State at the time of the research and co-first author of the paper. “The Y chromosome contains a lot of repetitive sequences, which are challenging for DNA sequencing, assembling sequences, and aligning sequences for comparison. There aren’t out-of-the-box software packages to deal with the Y chromosome, so we had to overcome these hurdles and optimize our experimental and computational protocols, which allowed us to address interesting biological questions.”

The Y chromosome is unusual. It contains relatively few genes, many of which are involved in male sex determination and sperm production; large sections of repetitive DNA, short sequences repeated over and over again; and large DNA palindromes, inverted repeats that can be many thousands of letters long and read the same forwards and backwards.

Previous work by the team comparing human, chimpanzee, and gorilla sequences had revealed some unexpected patterns. Humans are more closely related to chimpanzees, but for some characteristics, the human Y was more similar to the gorilla Y.

“If you just compare the sequence identity–comparing the As,Ts, Cs, and Gs of the chromosomes–humans are more similar to chimpanzees, as you would expect,” said Kateryna Makova, Pentz Professor of Biology at Penn State and one of the leaders of the research team. “But if you look at which genes are present, the types of repetitive sequences, and the shared palindromes, humans look more similar to gorillas. We needed the Y chromosome of more great ape species to tease out the details of what was going on.”

The team, therefore, sequenced the Y chromosome of a bonobo, a close relative of the chimpanzee, and an orangutan, a more distantly related great ape. With these new sequences, the researchers could see that the bonobo and chimpanzee shared the unusual pattern of accelerated rates of DNA sequence change and gene loss, suggesting that this pattern emerged prior to the evolutionary split between the two species. The orangutan Y chromosome, on the other hand, which serves as an outgroup to ground the comparisons, looked about like what you expect based on its known relationship to the other great apes.

“Our hypothesis is that the accelerated change that we see in chimpanzees and bonobos could be related to their mating habits,” said Rahulsimham Vegesna, a graduate student at Penn State and co-first author of the paper. “In chimpanzees and bonobos, one female mates with multiple males during a single cycle. This leads to what we call ‘sperm competition,’ the sperm from several males trying to fertilize a single egg. We think that this situation could provide the evolutionary pressure to accelerate change on the chimpanzee and bonobo Y chromosome, compared to other apes with different mating patterns, but this hypothesis, while consistent with our findings, needs to be evaluated in subsequent studies.”

In addition to teasing out some of the details of how the Y chromosome evolved in individual species, the team used the set of great ape sequences to reconstruct what the Y chromosome might have looked like in the ancestor of modern great apes.

“Having the ancestral great ape Y chromosome helps us to understand how the chromosome evolved,” said Vegesna. “For example, we can see that many of the repetitive regions and palindromes on the Y were already present on the ancestral chromosome. This, in turn, argues for the importance of these features for the Y chromosome in all great apes and allows us to explore how they evolved in each of the separate species.”

The Y chromosome is also unusual because unlike most chromosomes it doesn’t have a matching partner. We each get two copies of chromosomes 1 through 22, and then some of us (females) get two X chromosomes and some of us (males) get one X and one Y. Partner chromosomes can exchange sections in a process called ‘recombination,’ which is important to preserve the chromosomes evolutionarily. Because the Y doesn’t have a partner, it had been hypothesized that the long palindromic sequences on the Y might be able to recombine with themselves and thus still be able to preserve their genes, but the mechanism was not known.

“We used the data from a technique called Hi-C, which captures the three-dimensional organization of the chromosome, to try to see how this ‘self-recombination’ is facilitated,” said Cechova. “What we found was that regions of the chromosome that recombine with each other are kept in close proximity to one another spatially by the structure of the chromosome.”

“Working on the Y chromosome presents a lot of challenges,” said Paul Medvedev, associate professor of computer science and engineering and of biochemistry and molecular biology at Penn State and the other leader of the research team. “We had to develop specialized methods and computational analyses to account for the highly repetitive nature of the sequence of the Y. This project is truly cross-disciplinary and could not have happened without the combination of computational and biological scientists that we have on our team.”

PENN STATE

Header Image Credit : Eric Kilby – CC BY-SA 2.0

Download the HeritageDaily mobile application on iOS and Android

More on this topic

LATEST NEWS

Tenochtitlan – The Aztec Capital

Tenochtitlan was the capital of the Aztec civilisation, situated on a raised islet in the western side of the shallow Lake Texcoco, which is now the historic part of present-day Mexico City.

Archipelago in Ancient Doggerland Survived Storegga Tsunami 8,000-Years-Ago

Doggerland, dubbed “Britain’s Atlantis” is a submerged landmass beneath what is now the North Sea, that once connected Britain to continental Europe.

Cereal, Olive & Vine Pollen Reveal Market Integration in Ancient Greece

In the field of economics, the concept of a market economy is largely considered a modern phenomenon.

The Annulment of Henry VIII to Catherine of Aragon at Dunstable Priory

The Priory Church of St Peter (Dunstable Priory) is the remaining nave of a former Augustinian priory church and monastery, that today is part of the Archdeaconry of Bedford, located within the Diocese of St Albans in the town of Dunstable, England.

Teōtīhuacān – Birthplace of the Gods

Teōtīhuacān, named by the Nahuatl-speaking Aztecs, and loosely translated as "birthplace of the gods" is an ancient Mesoamerican city located in the Teotihuacan Valley of the Free and Sovereign State of Mexico, in present-day Mexico.

Chetro Ketl – The Great House

Chetro Ketl is an archaeological site, and the ancient ruins of an Ancestral Puebloan settlement, located in the Chaco Culture National Historical Park, New Mexico, United States of America.

The Gila Cliff Dwellings

The Gila Cliff Dwellings is an archaeological site, and ancient settlement constructed by the pueblos Mimbres branch of the Mogollon, located in southwest New Mexico of the United States of America.

Rare Cretaceous-Age Fossil Opens New Chapter in Story of Bird Evolution

A Cretaceous-age, crow-sized bird from Madagascar would have sliced its way through the air wielding a large, blade-like beak and offers important new insights on the evolution of face and beak shape in the Mesozoic forerunners of modern birds.

Popular stories

Teōtīhuacān – Birthplace of the Gods

Teōtīhuacān, named by the Nahuatl-speaking Aztecs, and loosely translated as "birthplace of the gods" is an ancient Mesoamerican city located in the Teotihuacan Valley of the Free and Sovereign State of Mexico, in present-day Mexico.

Legio IX Hispana – The Lost Roman Legion

One of the most debated mysteries from the Roman period involves the disappearance of the Legio IX Hispana, a legion of the Imperial Roman Army that supposedly vanished sometime after AD 120.

The Secret Hellfire Club and the Hellfire Caves

The Hellfire Club was an exclusive membership-based organisation for high-society rakes, that was first founded in London in 1718, by Philip, Duke of Wharton, and several of society's elites.

Port Royal – The Sodom of the New World

Port Royal, originally named Cagway was an English harbour town and base of operations for buccaneers and privateers (pirates) until the great earthquake of 1692.