Evolution of the Y chromosome in great apes deciphered
Researchers reconstruct the ancestral great ape Y and show its rapid
evolution in bonobo and chimpanzee

Date:
October 6, 2020
Source:
Penn State
Summary:
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.



FULL STORY ==========================================================================
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.

A paper describing the research appears October 5, 2020 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.



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"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."

========================================================================== Story Source: Materials provided by Penn_State. Original written by Sam Sholtis. Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Monika Cechova, Rahulsimham Vegesna, Marta Tomaszkiewicz, Robert S.

Harris, Di Chen, Samarth Rangavittal, Paul Medvedev, Kateryna
D. Makova.

Dynamic evolution of great ape Y chromosomes. Proceedings
of the National Academy of Sciences, 2020; 202001749 DOI:
10.1073/pnas.2001749117 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2020/10/201006153503.htm

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