Genetic Analysis Reveals Evolution of the Enigmatic Y Chromosome in Great Apes

Great Ape Y Chromosome Evolution

Researchers have reconstructed the ancestral sequence of the great ape Y chromosome by comparing three existing (gorilla, human, and chimpanzee) and two newly generated (orangutan and bonobo) Y chromosome assemblies. The new research shows that many gene families and multi-copy sequences were already present in the great ape Y common ancestor and that the chimpanzee and bonobo lineages experienced accelerated gene death and nucleotide substitution rates after their divergence from the human lineage. Credit: Dani Zemba and Monika Cechova, Penn State

Researchers reconstruct the ancestral great ape Y and show its rapid evolution in bonobo and chimpanzee.

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 was 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.

A paper describing the research was published in the journal Proceedings of the National Academy of Sciences.

“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.”

Reference: “Dynamic evolution of great ape Y chromosomes” by Monika Cechova, Rahulsimham Vegesna, Marta Tomaszkiewicz, Robert S. Harris, Di Chen, Samarth Rangavittal, Paul Medvedev and Kateryna D. Makova, 5 October 2020, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.2001749117

In addition to Cechova, Makova, Vegesna, and Medvedev, the research team at Penn State included Marta Tomaszkiewicz, Robert S. Harris, Di Chen, and Samarth Rangavittal. The research was supported by the U.S. National Institutes of Health, the U.S. National Science Foundation, the Clinical and Translational Sciences Institute, the Institute of Computational and Data Sciences, the Huck Institutes of the Life Sciences, and the Eberly College of Science of the Pennsylvania State University, and by the CBIOS Predoctoral Training Program awarded to Penn State by the National Institutes of Health.

12 Comments on "Genetic Analysis Reveals Evolution of the Enigmatic Y Chromosome in Great Apes"

  1. A question still does remain, why are males even needed? Just let all be self-fertilizing females, who just have an “Immaculate Conception” around the age 25. Who ever invented this dynamics of the sexes, is devious.

    • Shamar Whitestone | February 5, 2021 at 1:44 pm | Reply

      Joe, your post is a perfect example of why abortions take place. Not all idiots should be granted breath.

  2. The majority of scientist do not believe that humans evolved from apes. The scientists represented here don’t understand the fact that correlation is not always causation. When I see repots like this it reminds me that scientists only get paid for progress in their research. This driver forces them to release their research regardless of how ridiculous or invalid they might be.

  3. This is idiocy…

    Chromosome count is evidence for common ancestry?


    Anyone think otherwise?

  4. Robert A Burkhart | February 6, 2021 at 1:27 am | Reply

    The evidence for rapid evolution of the bonobo and chimpanzee y chromosomes post the human divergence is the extent of the differences. There is an implicit assumption that the divergence occurred, yet the differences could also be taken as evidence that humans and those great apes do not share a common ancestor.

  5. Tyrone Ellington | February 6, 2021 at 5:31 am | Reply


    I wrote an article about the creation of humanity using information from the Sumerians from ancient Mesopotamia cuneiform tablets, the Bible, the Quran, and many other books.  I also used data from Charles Darwin, his theory on human evolution.

    My article has fascinating sources such as “Lucy.”

    If we all share our knowledge, there is no telling what we could learn from each other. 

    Knowledge is Power

    If you like the article, please join the Facebook
    page to stay updated on future articles.

  6. Babu G. Ranganathan | February 6, 2021 at 8:27 am | Reply

    Babu G. Ranganathan*
    (B.A. Bible/Biology)


    ONLY LIMITED EVOLUTION (micro-evolution or evolution within biological “kinds”) is genetically possible (such as the varieties of dogs, cats, horses, cows, etc.), but not macro-evolution, or evolution across biological “kinds,” (such as from sea sponge to human). All real evolution in nature is simply the expression, over time, of already existing genes or variations of already existing genes. For example, we have breeds of dogs today that we didn’t have a few hundred years ago. The genes for these breeds had always existed in the dog population but never had opportunity before to be expressed. Only limited evolution, variations of already existing genes and traits, is possible.

    The genes (chemical instructions or code) for a trait must first exist or otherwise the trait cannot come into existence. Genes instruct the body to build our tissues and organs. Nature is mindless and has no ability to design and program entirely new genes for entirely new traits.

    Evolutionists believe that, if given millions of years, accidents in the genetic code of species caused by the environment will generate entirely new code making evolution possible from one type of life to another. It’s much like believing that by randomly changing the sequence of letters in a romance novel, over millions of years, can turn the novel into a book on astronomy! Not to worry. We’ll address the issue of “Junk DNA” in a moment.

    WHAT ABOUT NATURAL SELECTION? Natural selection doesn’t produce biological traits or variations. It can only “select” from biological variations that are possible and which have survival value.

    HOW COULD SPECIES HAVE SURVIVED if their vital tissues, organs, reproductive systems, etc. were still evolving? A partially evolved trait or organ that is not complete and fully integrated and functioning from the start would be a liability to a species, not a survival asset. Plants and animals in the process of macro-evolution would be unfit for survival. For example, “if a leg of a reptile were to evolve (over supposedly millions of years) into a wing of a bird, it would become a bad leg long before it became a good wing” (Dr. Walt Brown, scientist and creationist). Survival of the fittest actually would have prevented evolution across biological kinds!

    NEW SPECIES BUT NOT NEW DNA: Although it’s been observed that new species have come into existence, they don’t carry any new genes. They’ve become new species only because they can’t be crossed back with the original parent stock for various biological reasons. A biological “kind” allows for new species but not new genes. Nature has no ability to invent new genes for new traits. Only limited variations and adaptations are possible in nature, and all strictly within a biological “kind” (i.e. varieties of dogs, cats, etc.).

    Dr. Randy J. Guliuzza’s extensive research points to a better explanation than natural selection for variation and adaptation in nature. Dr. Guliuzza explains that species have pre-engineered mechanisms that enable organisms to continuously track and respond to environmental changes with system elements that correspond to human-designed tracking systems. This model is called CET (continuous environmental tracking). His research strongly indicates that living things have been pre-engineered to produce the right adaptations and changes required to live in changing environments. It’s much like a car that’s been pre-engineered so that the head lights turn on automatically when day changes to night.

    What about genetic and biological similarities between species? Genetic information, like other forms of information, cannot happen by chance, so it is more logical to believe that genetic and biological similarities between all forms of life are due to a common Designer who designed similar functions for similar purposes. It doesn’t mean all forms of life are biologically related! Only genetic similarities within a natural species proves relationship because it’s only within a natural species that members can interbreed and reproduce.

    Many people have wrong ideas of how evolution is supposed to work. Physical traits and characteristics are determined and passed on by genes – not by what happens to our body parts. For example, if a woman were to lose her finger this wouldn’t affect how many fingers her baby will have. Changing the color and texture of your hair will not affect the color and texture of your children’s hair. So, even if an ape or ape-like creature’s muscles and bones changed so that it could walk upright it still would not be able to pass on this trait to its offspring. Only changes or mutations that occur in the genetic code of reproductive cells (i.e. sperm and egg) can be passed on to offspring.

    What about the new science of epigenetics? Epigenetics involves inheritable factors which can turn already-existing genes on, but epigenetics doesn’t create new genes.

    Most biological variations are from new combinations of already existing genes, not mutations. Mutations are accidents in the genetic code caused by nature (i.e. environmental radiation), are mostly harmful, and have no capability of producing greater complexity in the code. Even if a good accident occurred, for every good one there would be hundreds of harmful ones with the net result, over time, being harmful, even lethal, to the species. Even if a single mutation is not immediately harmful, the accumulation of mutations over time will be harmful to the species resulting in extinction. At very best, mutations only produce further variations within a natural species.

    All species of plants and animals in the fossil record are found complete, fully formed, and fully functional. This is powerful evidence that all species came into existence as complete and fully formed from the beginning. This is only possible by creation.

    God began with a perfect and harmonious creation. Even all the animals were vegetarian (Genesis 1:30) in the beginning and did not struggle for survival nor kill and devour each other. Macro-evolutionary theory does not begin with a perfect and harmonious creation as the Bible states. The Bible and macro-evolutionary theory cannot both be true.

    All the fossils that have been used to support human evolution have been found to be either hoaxes, non-human, or human, but not non-human and human (i.e. Neanderthal Man was discovered later to be fully human).

    There has never been unanimous agreement among evolutionary scientists on ANY fossil evidence that has been used to support human evolution over the many years, Including LUCY.

    The actual similarity between ape and human DNA is between 70-87% not 99.8% as commonly believed. The original research stating 99.8% similarity was based on ignoring contradicting evidence. Only a certain segment of DNA between apes and humans was compared, not the entire DNA genome.

    Also, so-called “Junk DNA” isn’t junk. Although these “non-coding” segments of DNA don’t code for proteins, they have recently been found to be vital in regulating gene expression (i.e. when, where, and how genes are expressed, so they’re not “junk”). Also, there is evidence that, in certain situations, they can code for protein.

    ARE FOSSILS REALLY MILLIONS OF YEARS OLD? (Internet article by author)

    Visit my latest Internet site: THE SCIENCE SUPPORTING CREATION (This site answers many arguments, both old and new, that have been used by evolutionists to support their theory)


    *I have given successful lectures (with question and answer period afterwards) defending creation before evolutionist science faculty and students at various colleges and universities. I’ve been privileged to be recognized in the 24th edition of Marquis “Who’s Who in The East” for my writings on religion and science.

  7. Just one comment…
    It is actually the arm that became a wing, not the leg…

    As should be obvious to humans, it is possible to stand and walk on your two legs and use your two arms for other purposes. So arms and hands could be used to pick up things, to fight, etc. Grow some feathers along the arms as well, and you can glide between trees. This is a multipurpose arm, not a bad one! Then, specialising with feathers made powered flight possible. The subsequent loss of the hand manipulation function wasn’t ‘bad’ either, because beaks and feet could be used for this.

    In short, this is not a good argument. I understand you will not accept this, I’m posting for the benefit of others. The rest of your post is equally open to challenge.

  8. How close are other species? Rather than evolution, the fact that all species need DNA to live and procreate is a simile, so why cannot humans have sex with an ape and produce offspring? Because the code is different from each species. Shakespeare used the same 26 letters of the alphabet as does my granddaughter but the results are not the same.

  9. … what I find interesting in evolution is that no other species has developed intelligence at the level humans did…
    … So, strange, indeed. Interesting trade, was not so likely to happen! It just puts a question mark on real need for the brain if you need to watch for you self all of the time..
    … I guess, the savages will never tunnel to another level..

  10. Wagner’s Continental Drift Theory supported with platetectonics poses this hypothesis of the model of isolationism with Felis genus of African cats as the leopard chetah etc. DNA as compared to jaguars n ocelots etc. of the Americas. This proposes our comparative indigenous Homo sapiens populations and distictions as originations are offered with rather obvious migrations of various varieties and hypotheses intermixed – not too different from Eurasian “old world” distinctions n proposed patterns.

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