Primate Genomic Study Offers Key Insights into Human Biology and Disease

Primate Genomic Study: In a groundbreaking scientific endeavor, a team of dedicated scientists has successfully sequenced the genomes of an astounding 233 primate species, marking the most extensive study of its kind ever conducted. Published in the prestigious journal Nature, the study's findings have illuminated new insights into the evolutionary trajectory of primates and carry significant implications for conservation efforts.

Among the study's most unexpected revelations is the revelation that the level of genetic diversity within a species does not necessarily correspond to its risk of extinction. This intriguing discovery challenges conventional assumptions by demonstrating that certain endangered species, like the Sumatran orangutan, exhibit high levels of genetic diversity, while others, such as the northern white rhinoceros, possess considerably lower levels.

The researchers attribute this phenomenon to the diverse array of factors that endanger different species. For instance, the Sumatran orangutan faces imminent threats from habitat loss and poaching, while the northern white rhinoceros grapples with the perils of poaching and a deficiency in genetic diversity.

Furthermore, the study has shed light on how climate changes occurring over six million years ago instigated a notable shift in the social structure of monkeys. Formerly characterized by small groups comprising a single male and a few females, these primates transitioned to complex societies encompassing multiple males and females. This transformative shift suggests that environmental influences can exert significant influence over the evolution of social behavior.

With the intention of enhancing conservation efforts for primates, the researchers express their hope that the study's findings will enable conservationists to target their initiatives with greater precision. By comprehending the genetic underpinnings of extinction risk, conservationists can optimize their strategies and maximize their effectiveness.

Undoubtedly, the largest study ever conducted on primates has yielded astonishing discoveries that transcend the boundaries of primate biology and extend to humanity itself, unraveling the intricate genetic factors that set us apart from our closest relatives. This ambitious international study has generated a wealth of new data applicable to an extensive range of scientific disciplines, including human health, conservation biology, and behavioral science.

Presently, our planet is home to over 500 primate species, encompassing humans, monkeys, apes, lemurs, tarsiers, and lorises. Unfortunately, many of these remarkable creatures face grave threats from climate change, habitat destruction, and illegal hunting. To tackle this pressing issue, the researchers sequenced genomes from nearly half of all known primate species, diligently analyzing over 800 genomes derived from 233 species spanning the globe, representing all 16 primate families. The comprehensive findings of this study have been published across a series of papers in esteemed scientific journals such as Science and Science Advances.

Alison Behie, a prominent primatologist from the Australian National University in Canberra, emphasizes the profound implications of primate genomics on our understanding of human genomics. “The more we understand about primate genomics, the more we’ll understand about human genomics”, she also adds, “There’s a potential there to do a lot more really interesting work as they grow that sample size to bring in more species.”

Reflecting on the immense progress made, Dong-Dong Wu, an evolutionary biologist from the Chinese Academy of Sciences in Kunming, reveals that just five years ago, genomes from less than 10% of primate species had been sequenced.

However, an instrumental breakthrough occurred when Kyle Farh and his team at Illumina, a renowned sequencing company based in San Diego, devised a method to determine whether mutations in the human genome could cause disease by examining similar mutations in great apes. This groundbreaking work, built upon ape genomes sequenced by Tomàs Marquès Bonet and his colleagues from the University of Pompeu Fabra in Barcelona, Spain, paved the way for investigating human diseases through the lens of primate genomes, underscoring the potential for unraveling the mysteries of conservation, evolution, and human genomics.

Marquès Bonet recalls, “Kyle called me one day, and essentially, he was asking if I had more genomes in the queue for sequencing,” Marques also adds, “There was an opportunity for conservation, evolution and understanding the human genome.”

 This pivotal conversation sparked a worldwide collaborative effort involving researchers from 24 countries, all eager to contribute samples and participate in the sequencing endeavor. Marquès Bonet commends the dedication of primatologists in Brazil and India, applauding their instrumental contributions to a project of Herculean proportions.

“I am particularly proud of primatologists in Brazil and in India,” he says, because these hotspots for primate biodiversity were previously under-represented in genetic studies. “This is really a Herculean effort” he says.

While sequencing efforts continue to forge ahead, Wu emphasizes that this project marks only the beginning of an ongoing exploration. Nevertheless, Marquès Bonet acknowledges the growing challenge of sourcing samples from unsequenced species, as the project encounters an inevitable plateau. Although the path forward to expand the study from 233 to 300 species appears increasingly arduous, the researchers remain undeterred in their pursuit of knowledge.

Insights

With regard to human biology and disease, the primate resource promises invaluable insights to enhance our understanding. In a study led by Marquès Bonet and fellow researchers, the genomes of the 233 primate species were harnessed to classify 4.3 million common gene variants found in the human genome. By examining the prevalence of these variants across species, the researchers inferred that approximately 98.7% of the tested variants likely pose no harm to humans. This knowledge can be leveraged to identify disease-causing mutations in individuals whose entire genome or protein-coding region (exome) has been sequenced.

Another study conducted by Wu and colleagues involved comparing the genomes of 50 species to trace the evolutionary history of the primate family tree. Through this comprehensive analysis, they identified thousands of genetic sequences that emerged as dominant throughout various branches of the tree. Notably, genes associated with brain development arose in the common ancestors of humans, apes, and new world monkeys, laying the foundation for the rapid evolution of large brains in humans. Wu emphasizes that the expansion of brain capacity commenced long ago, offering insight into this remarkable evolutionary journey.

An extensive collection of gene variants previously presumed to be exclusive to humans, as they were absent in archaic human relatives such as Neanderthals and Denisovans, has been discovered across various primate species. Astonishingly, almost two-thirds of the variants initially deemed solely human were found in at least one other primate species, with over half detected in two or more species.

Behaviour

In the realm of behavioral sciences, a key aspiration is to identify genetic mechanisms underlying specific behaviors. One of the studies successfully establishes this connection. Led by Xiao-Guang Qi, a behavioral ecologist from Northwest University in Xi'an, China, the research focused on the five species of snub-nosed monkeys, including humans, that form complex multilevel societies consisting of large troops composed of smaller family units.

By comparing the genomes of these socially intricate snub-nosed monkeys with those of less-social related monkeys, known as odd-nosed monkeys, as well as more distant primate relatives, Qi and his colleagues identified genes potentially associated with the formation of expansive multilevel societies.

The study reveals that climatic changes over six million years ago catalyzed the monkeys' transition from small groups with a single male and a few females to complex societies featuring multiple males and females.

Co-author Cyril Grueter, an evolutionary anthropologist from the University of Western Australia in Perth, underscores the significance of past environmental factors in shaping the present social organization of these primates. According to Grueter, the brain hormones dopamine and oxytocin played a pivotal role. “It’s not the present environment that neatly explains their social organization, it’s what happened in the past that’s probably equally important or even more important”.

Moreover, the comprehensive analysis of genomes from all 233 primate species carries profound implications for conservation efforts. Notably, it challenges the widely accepted notion that lower genetic diversity, resulting from inbreeding during population decline, indicates a species at the brink of extinction. Surprisingly, the study reveals that for certain threatened species, population decline has occurred so rapidly that inbreeding has not had sufficient time to manifest. Consequently, factors other than inbreeding, such as habitat destruction, emerge as the primary threats to a species' resilience.

The largest ever study of primate genomes has unveiled surprises about humanity and our closest relatives https://t.co/vwwcZxjArT

— nature (@Nature) June 2, 2023

This groundbreaking study, encompassing the largest primate genome sequencing endeavor to date, has yielded unparalleled discoveries that extend beyond the confines of primate biology. Its transformative impact permeates multiple scientific disciplines, and the researchers express unwavering optimism that these findings will fuel enhanced conservation efforts, illuminate the intricacies of human biology, and foster a deeper understanding of our place within the primate lineage.