Genomes of 233 primate species sequenced
New insights into the genetic diversity and evolution of our closest
relatives and the genetic causes of human diseases

Date:
June 2, 2023
Source:
Deutsches Primatenzentrum (DPZ)/German Primate Center
Summary:
Researchers from 24 countries have analyzed the genomes of 809
individuals from 233 primate species, generating the most complete
catalog of genomic information about our closest relatives to
date. The project provides new insights into the evolution of
primates, including humans, and their diversity. In baboons, for
example, hybridization and gene flow between different species
occurred in the past and is still ongoing in several regions of
their range. This makes baboons a good model for the evolution
of early human lineages within and outside Africa. In addition,
using a specially designed AI algorithm, the genomic data enable
new insights into the genetic causes of human diseases.


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==========================================================================
FULL STORY ========================================================================== Researchers from 24 countries have analyzed the genomes of 809 individuals
from 233 primate species, generating the most complete catalog of
genomic information about our closest relatives to date. The project,
which consists of a series of studies in which researchers from the
German Primate Center - - Leibniz Institute for Primate Research (DPZ)
were also involved, provides new insights into the evolution of primates, including humans, and their diversity.

In baboons, for example, hybridization and gene flow between different
species occurred in the past and is still ongoing in several regions of
their range.

This makes baboons a good model for the evolution of early human lineages within and outside Africa. In addition, using a specially designed AI algorithm, the genomic data enable new insights into the genetic causes
of human diseases (Science, Special Issue).

Primates show great genetic diversity that varies between species
and geographic regions. "Studying this diversity is crucial also for understanding human evolution, the causes of human diseases, and for
preserving our closest relatives," says Christian Roos, a scientist in
the Primate Genetics Laboratory at the German Primate Center and one of
the authors. Led by researchers from Universitat Pompeu Fabra, Spain,
Baylor College of Medicine, USA, and Illumina Inc, USA, the genomes of
809 individuals from 233 primate species have been sequenced. This covers nearly half of the extant primate species and increases the number of
available primate genomes fourfold.

New insights into primate evolution and the uniqueness of humans The comparative analyses provide fundamental information on the genetic
diversity and evolutionary history of primates and important insights
into what distinguishes humans from other primates. The genomic data have halved the number of genomic variants thought to occur exclusively in
humans. "This makes it easier to look for mutations that we do not share
with other primates and that could therefore be the basis for the traits
that make us human," says Dietmar Zinner, a scientist in the Cognitive
Ethology Laboratory at the German Primate Center and also one of the
authors. One of the studies looks more closely at baboon evolution
and finds that there have been several, previously unknown episodes
of hybridization and gene flow between baboon species. "We found that
baboons from western Tanzania are the first nonhuman primates to have
received input from three genetic lineages," said Liye Zhang, a doctoral student at the German Primate Center and one of the lead authors of the
baboon study. "These results suggest that the genetic structure of the
baboon population and its history of genetic exchange between species is
more complex than previously thought and show that baboons make a good
model for similar processes in the evolution of early human lineages in
and outside Africa," says Dietmar Zinner.

Species conservation with the help of genome data High genetic diversity enables species to better adapt to changing environmental conditions
and pathogens. Especially in small populations, there is a risk of
inbreeding and thus a reduction in genetic diversity. Already, 63 percent
of all primate species are threatened with extinction, and the analysis
of genetic diversity provides information which species most urgently
need to be protected, at least from a genetic point of view. "We found particularly low genetic diversity in the golden snub-nosed monkey of
China and the aye-aye in Madagascar," says Christian Roos.

Rare mutations can increase disease risk One of the limitations in human
and clinical genetics is that it is currently not possible to identify
among hundreds of thousands of mutations those that cause disease. To
date, the genetic causes of many common diseases, such as diabetes and
heart disease, are unknown, due either to a lack of genetic information or
to the large number of genetic and other factors involved. By comparing
the primate genomes, 4.3 million mutations have now been identified
that may alter protein function and thus lead to disease in humans. Six
percent of the 4.3 million mutations identified are, however, common in primates and are therefore considered to potentially have little impact
on human disease because they are tolerated in these animals. Thanks to
the PrimateAI-3D deep- learning algorithm developed by Illumina Inc, disease-causing mutations can now be better identified. "It's a kind
of ChatGPT for genetics that uses genome sequences instead of human
language," explains Kyle Farh, vice director of the AI group at Illumina
Inc, the global leader in DNA sequencing.

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========================================================================== Story Source: Materials provided by Deutsches_Primatenzentrum_(DPZ)/German_Primate_Center.

Note: Content may be edited for style and length.


========================================================================== Journal Reference:
1. Lukas F. K. Kuderna, Hong Gao, Mareike C. Janiak, Martin Kuhlwilm,
Joseph
D. Orkin, Thomas Bataillon, Shivakumara Manu, Alejandro
Valenzuela, Juraj Bergman, Marjolaine Rousselle, Felipe Ennes
Silva, Lidia Agueda, Julie Blanc, Marta Gut, Dorien de Vries,
Ian Goodhead, R. Alan Harris, Muthuswamy Raveendran, Axel Jensen,
Idrissa S. Chuma, Julie E. Horvath, Christina Hvilsom, David
Juan, Peter Frandsen, Joshua G. Schraiber, Fabiano R. de Melo,
Fabri'cio Bertuol, Hazel Byrne, Iracilda Sampaio, Izeni Farias,
Joa~o Valsecchi, Malu Messias, Maria N. F. da Silva, Mihir Trivedi,
Rogerio Rossi, Tomas Hrbek, Nicole Andriaholinirina, Cle'ment J.

Rabarivola, Alphonse Zaramody, Clifford J. Jolly, Jane
Phillips-Conroy, Gregory Wilkerson, Christian Abee, Joe H. Simmons,
Eduardo Fernandez- Duque, Sree Kanthaswamy, Fekadu Shiferaw,
Dongdong Wu, Long Zhou, Yong Shao, Guojie Zhang, Julius D. Keyyu,
Sascha Knauf, Minh D. Le, Esther Lizano, Stefan Merker, Arcadi
Navarro, Tilo Nadler, Chiea Chuen Khor, Jessica Lee, Patrick Tan,
Weng Khong Lim, Andrew C. Kitchener, Dietmar Zinner, Ivo Gut,
Amanda D. Melin, Katerina Guschanski, Mikkel Heide Schierup, Robin
M. D. Beck, Govindhaswamy Umapathy, Christian Roos, Jean P. Boubli,
Jeffrey Rogers, Kyle Kai-How Farh, Tomas Marques Bonet. A global
catalog of whole-genome diversity from 233 primate species.

Science, 2023; 380 (6648): 906 DOI: 10.1126/science.abn7829 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2023/06/230602115048.htm

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