It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Artist's reconstruction of the two species described in the paper—Mytonius williamsae (L) and Diablomomys dalquesti (R)—in Big Bend country in West Texas 44 million years ago in the middle Eocene. The volcano on the skyline is a reminder of the active volcanism that was occurring in this part of Texas during the Eocene and Oligocene epochs. Image: Randwulph. Credit: University of Texas at Austin
Fossil evidence from the Tornillo Basin in West Texas and the Uinta Basin in Utah reveals two new species of omomyids—a family of small-bodied early primates from the Eocene epoch. The findings also clarify previously disputed taxonomic distinctions among these primates, according to researchers from The University of Texas at Austin, Des Moines University in Iowa and Midwestern University in Arizona.
The study, published in the Journal of Human Evolution, significantly expands the fossil record of primates from these regions and also allowed the researchers to confirm the existence of three distinct genera of omomyids.
"Since fossil primates were first discovered in North America in the 1860s, only a handful of specimens from the late middle Eocene of Texas and Utah have been described," said Chris Kirk, professor of anthropology at UT and first author on the paper. "For the larger members of the extinct primate family Omomyidae, these small sample sizes have led to some confusion, with past authors unable to agree whether there are one, two or three genera represented."
Omomyids initially had body masses below 500 grams, but some evolved to double that size during the late middle Eocene. The two new species identified—from the genera Ourayia and Mytonius—are on the larger end of the spectrum. They probably resembled present-day small to medium-size lemurs and consumed a diet of fruit and leaves.
Both new species appear to be endemic to the Tornillo Basin and differ from fossil primates found in other parts of North America.
"This distinctiveness of the West Texas primate community suggests that they were evolving at least partly in isolation, with perhaps relatively few opportunities for migration or gene flow with communities of primates living in other parts of North America at the same time," Kirk said. "Eocene primates in the Big Bend may also have been adapting to the local environmental conditions."
The study also expanded the fossil evidence of three previously discovered species—Diablomomys dalquesti, Mytonius hopsoni and Ourayia uintensis—painting a clearer picture of these primates' anatomies and diets.
Previous studies on the evolution of Eocene primates focused on earlier periods and regions with more abundant fossil samples, such as Bighorn and Bridger basins in Wyoming. Increasing the sample of fossil primates from different regions may offer insights into the changing environmental factors that shaped these divergent populations.
"The fact that more than 150 years after the first Eocene primates from North America were first described, I can travel eight hours from my home in Austin and find new species of fossil primates in the Big Bend country is still astonishing to me," Kirk said.
"There is so much interesting research that remains to be done on these Texas primates. It's a reminder of how many gaps still exist in the fossil record, and how many important paleontological discoveries are waiting to be made, sometimes even more or less in our own back yards."
More information: E. Christopher Kirk et al, New specimens of middle Eocene omomyines (Primates, Omomyoidea) from the Uinta Basin of Utah and the Tornillo Basin of Texas, with clarification of the generic status of Ourayia, Mytonius, and Diablomomys, Journal of Human Evolution (2023). DOI: 10.1016/j.jhevol.2023.103425
More research labs are retiring monkeys when studies finish
By CARRIE ANTLFINGER
1 of 6 In this May 13, 2019, photo, Bella the vervet monkey looks at the camera at Primates Inc., in Westfield, Wis. Besides Bella, previously a pet, the sanctuary has five rhesus macaque monkeys that were previously used in medical research. More research labs are retiring primates to sanctuaries like Primates Inc., a 17-acre rural compound in central Wisconsin, where they can live their remaining years after research studies are done, according to sanctuaries and researchers. (AP Photo/Carrie Antlfinger)
WESTFIELD, Wis. (AP) — Izzle, Timon, Batman, River and Mars spent years confined inside a lab, their lives devoted to being tested for the benefit of human health.
But these rhesus macaques have paid their dues and are now living in retirement — in larger enclosures that let them venture outside, eat lettuce and carrots, dip their fingers in colorful plastic pools, paint, and hang from pipes and tires — in relative quiet.
More research labs are retiring primates to sanctuaries like Primates Inc., a 17-acre (7-hectare) rural compound in central Wisconsin, where they can live their remaining years, according to the sanctuaries and researchers. For some monkeys, it’s their first time hanging out in the fresh air.
“Just to see them look around in amazement. You know it was all very calm and peaceful,” said Amy Kerwin, who worked for 15 years to get the Westfield, Wisconsin, sanctuary off the ground after being employed in a University of Wisconsin research lab.
There were approximately 110,000 primates in research facilities in 2017, according to the most recent data available from the U.S. Department of Agriculture.
While most research facilities need primates to be euthanized to examine their tissues, technological advances, such as brain scans, mean fewer monkeys need to be put down. Plus, researchers who become close with the animals are making more efforts to give the ones who can survive a retirement, rather than euthanization.
In 2015, a group of researchers, graduate students and an ethicist created the Research Animal Retirement Foundation. It raises funds for labs to pay the sanctuaries to retire them. So far they have given $33,000 in funding for three monkeys who went to the Wisconsin sanctuary.
A visit to the Peaceable Primate Sanctuary in Indiana helped convince Rep. Jackie Walorski, R-Ind., to author a bill introduced last month, along with Rep. Brendan Boyle, D-Penn., that requires federal agencies to develop a policy allowing animals no longer needed for research to be adopted out or put in sanctuaries. Currently, no federal regulations dictate what happens to them. Some are sold to other studies when one study is done.
The bill doesn’t address funding, one of the main hurdles to get primates into retirement sanctuaries.
Currently, grants through the National Institutes of Health, which is the largest public funder of biomedical research in the world, don’t include money for retirement. That leaves the labs and sanctuaries to find the tens of thousands of dollars per monkey, per year needed to care for them.
Monkeys are finished with studies at different ages and some can live for decades. Some can also leave with lingering issues, like compulsive behaviors caused by boredom.
That’s why many sanctuaries require the labs to send some funding, often between $10,000 and $20,000, to help care and create space for monkeys. Since many of the primates have only lived in labs, they don’t have the skills needed to live in the wild.
Most primates in accredited sanctuaries are chimpanzees, capuchins, and squirrel monkeys, according to Erika Fleury, program director for the North American Primate Sanctuary Alliance, or NAPSA, an advocacy group for captive primates. They come from research, the entertainment industry or private homes.
Chimpanzees are no longer used in most research. The NIH announced in 2013 it would stop supporting them in research and that they should be moved to sanctuaries, with funding. It pointed to a report from the Institute of Medicine in 2011 that concluded the use of chimpanzees in biomedical research was unnecessary.
Cindy Buckmaster, chair of the Americans for Medical Progress, which represents research universities and medical research companies, said that besides funding, researchers are concerned about sanctuaries standards, their financial viability and whether some sanctuaries’ ties to animal rights groups will cause them to badmouth the institution.
“We really feel very grateful to them and we want them to have wonderful lives after,” Buckmaster said. “They certainly deserve it. But it has to be done well and it has to be done properly because we’re not going to put our animals in harm’s way.”
Some animal rights groups, including People for the Ethical Treatment of Animals, don’t support research but do agree with retiring monkeys to sanctuaries rather than having them euthanized.
Sanctuaries have been around for decades but, in 2010, more than a half-dozen came together to create NAPSA.
Currently, there are eight member sanctuaries, with about 775 primates. Membership requires the sanctuaries be USDA licensed, accredited by the Global Federation of Animal Sanctuaries or certified by the Association of Zoos & Aquariums, among many guidelines. There are 31 other, nonmember sanctuaries in the U.S. and Canada that have primates but have a variety of standards, according to NAPSA.
Besides requiring high standards for sanctuaries, NAPSA is also upping efforts with researchers to encourage them to ask for retirement funding upfront.
An NIH spokeswoman wouldn’t respond to whether the agency would consider adding money to grants for monkey retirement care, only saying in a statement that the animals’ owners are responsible for ongoing care.
Kerwin, who started the Wisconsin sanctuary, said she’s seen monkeys become calmer in retirement. Her goal is to have 100 monkeys over the next 20 years.
“Just knowing that these little individual personalities are in the thousands and largely no one knows about them and even the need to help them. That’s why I feel it’s important,” she said.
In this May 13, 2019, photo, Amy Kerwin holds a mirror up to Izzle, a rhesus macaque at Primates Inc., in Westfield, Wis. Izzle loves to watch people in mirrors, according to Kerwin. The sanctuary now has five rhesus macaque monkeys that were previously used in medical research and one vervet monkey that used to be a pet. (AP Photo/Carrie Antlfinger)
In this May 13, 2019, photo, River, left, and Timon, both rhesus macaques, sit in an outdoor enclosure at Primates Inc., in Westfield, Wis. It's a sanctuary that so far has five rhesus macaque monkeys that were previously used in medical research and one vervet monkey that used to be a pet. More research labs are retiring primates to sanctuaries like Primates Inc., a 17-acre rural compound in central Wisconsin, where they can live their remaining years when their studies are done, according to sanctuaries and researchers. (AP Photo/Carrie Antlfinger)
Monday, February 14, 2022
Do chimpanzees have the right to life?
YES
Non-human primates are self-aware. And they plan for the future. So should they get basic rights like humans? The Swiss canton of Basel, home to drug research, has voted. Apes like the chimpanzee are close relatives of humans. Should they have similar rights to us? In a referendum on Sunday, people in the Swiss canton of Basel voted against giving non-human primates the right to life and physical and mental integrity.
Almost 75% rejected a plan to give non-human primates similar rights to humans. It was a contentious referendum, as referendums often are. But in this specific case the question of whether non-human primates should be given or deserve basic rights, such as human rights, was contentious because of where it took place.
Basel is the third-most populous city in Switzerland. It is also home to two large, international pharmaceutical companies, Roche and Novartis. Both have used animals in their research to develop drugs.
Neither company current works with primates, and as private companies, Roche and Novartis would have been exempt from any local law on basic rights for primates. It would only have applied to public institutions, such as hospitals and the university in town.
A world first
"It's the first time, globally, that an electorate got to vote on whether non-human primates should have basic rights," said Tamina Graber, head of the campaign for primates' rights at Sentience, the group that initiated the Basel referendum.
Speaking before the vote, Graber told DW they hoped that other cantons in Switzerland and indeed other countries would also "consider whether we humans are the only ones who can have rights."
Switzerland's animal welfare law aims to "protect the dignity and welfare of animals." But Graber said it does not offer sufficient protection to animals.
The law, Graber said, places the interest of humans, no matter how small, over the interests of non-human primates, no matter how big.
MONKEY ISLAND: HOME OF THE LIBERIAN LAB CHIMPS
Medical tests on chimpanzees
In 1974, researchers from the US nonprofit blood bank, the New York Blood Center (NYBC), opened an experimental laboratory on the west coast of Liberia. Working with the Liberia Biomedical Research Institute, they trapped wild chimpanzees and used them to conduct research and drug trials.
That's why they are campaigning for more fundamental rights — specifically for non-human primates, apes, such as chimpanzees, gorillas and orangutans.
"They are our closest relatives. We know the most about what they want," said Graber. "Science has taught us that they want to live, that they plan for the future and that they want to remain physically and mentally unharmed." 'Animals experience feelings'
Switzerland is not the only country where animal rights have been in the news lately.
The UK government introduced an Animal Welfare (Sentience) Bill in 2021, which is still passing through Parliament. But with it, the UK would formally recognize animals as sentient beings.
That means that "any new legislation [would] have to take into account the fact that animals can experience feelings such as pain or joy," the government wrote in a press release last year.
The measures would stop most live animal exports and stop people from keeping primates as pets. But it would not ban animal testing.
A ban on animal testing would have disastrous consequences, said Understanding Animal Research, a British nongovernmental organization that says it advocates for the humane use of animals in research.
"A ban on using animals in research would remove the only way of deriving information that's vital for medical, veterinary and environmental science," said Chris Magee, the organization's head of policy and media. It's not just about avoiding suffering
As for the situation in Germany, some say there's a problem with implementing the law.
Karsten Brensing, a biologist and behavioral scientist, said Germany's animal welfare laws are good.
"Biologically, adequate husbandry isn't just about avoiding pain and suffering for the animals," said Brensing. "It's about actively ensuring that the animals have joy in their lives.
Brensing said the initiative for primates' basic rights in Switzerland is "fully reasonable, scientifically speaking."
Primates have a sense of self, he said — they exhibit cognitive abilities, such as logical thinking, and they display empathy. Other animals, such as rodents, have also demonstrated care for one another.
For example, in one study, rats were given the choice of either freeing other rats from a cage or getting a chocolate treat. And the results seemed to suggest that the rats preferred helping others than treating themselves. They were even observed cuddling each other after the caged rats were freed.
"They do experience empathy," said Brensing. "And if rats have that, primates definitely have it, too." Rats are willing to give up sweet treats in order to free other rats
Human vs. animal experiences
Some researchers question whether animals truly experience empathy or whether our observations are a case of researchers transferring their own human experiences and emotional needs onto non-human animals.
Peter Kunzmann, a professor of ethics in veterinary medicine, said it's dangerous to ascribe rights to animals based on human attributes.
Kunzmann, who teaches at the University of Veterinary Medicine in Hannover, is against initiatives like the one started by Sentience in Basel.
"I am a big defender of the principle of human dignity and of the concept that there are certain things humans deserve by sheer virtue of being human," said Kunzmann. "And I get very, very concerned when there are attempts to dilute this. Humans have rights and dignity simply because they are human."
Sentience said it's not calling for human rights as they apply to people, "but fundamental rights adjusted for non-human primates."
But he remains concerned.
"If you're consistent with this, a number of people would lose the status that grants them rights," said Kunzmann. "Newborns would have different rights from adults because they [lack] intelligence and don't have plans for the future yet. Mentally ill people could lose their rights, dementia patients would lose them, people in a coma would, too."
Kunzmann does, however, believe that animals deserve to be treated in a respectful way.
HOW ANIMALS HEAL THEMSELVES ― AND GET HIGH
Magic of zoopharmacognosy
Being sick is a drag. Animals think so, too. Many different species use remedies found in nature to take care of their wounds or get rid of parasites (or, in some cases, to get high). The process of animals healing themselves is called zoopharmacognosy. Recently, researchers observed how chimpanzees in Gabon treat their wounds.
Climate change and deforestation may drive tree-dwelling primates to the ground, large-scale study shows
by San Diego Zoo Wildlife Alliance
Propithecus Verreauxi. Credit: San Diego Zoo Wildlife Alliance
A large-scale study of 47 species of monkeys and lemurs has found that climate change and deforestation are driving these tree-dwelling animals to the ground, where they are at higher risk due to lack of preferred food and shelter, and may experience more negative interaction with humans and domestic animals.
The study, slated to publish Oct. 10 in the journal Proceedings of the National Academy of Sciences (PNAS), was led by Timothy Eppley, Ph.D., a postdoctoral associate at San Diego Zoo Wildlife Alliance (SDZWA), and examined more than 150,000 hours of observation data on 15 lemur species and 32 monkey species at 68 sites in the Americas and Madagascar. This study was a remarkable worldwide collaboration, including 118 co-authors from 124 unique institutions.
"This study began with a discussion among colleagues about how we'd noticed certain populations of arboreal primates spending more time on the ground," said Dr. Eppley, "yet at sites with relatively less disturbance, members of the same species may never descend to the ground."
The authors estimated the influence of ecological drivers, including potential human-induced pressures and/or species-specific traits, on the level of terrestriality (time spent on the ground) in arboreal primates. The study found that primates that consume less fruit and live in large social groups were more likely to descend to the ground. The authors suggest that these traits act as a potential "pre-adaptation" to terrestriality. Furthermore, primates living in hotter environments, and with less canopy cover, were more likely to adapt to these changes by shifting toward more extensive ground use.
Many of these species are already burdened with living in warmer, fragmented and heavily disturbed environments that often have fewer available dietary resources. As climate change worsens and arboreal habitats diminish, the study suggests primates consuming a more generalized diet and living in larger groups may more easily adapt to a terrestrial lifestyle.
"It's possible that spending more time on the ground may cushion some primates from the effects of forest degradation and climate change; however, for the less-adaptable species, fast and effective conservation strategies will be necessary to ensure their survival," Eppley said.
The study also found that primate populations closer to human infrastructures are less likely to descend to the ground. Luca Santini, Ph.D., from Sapienza University of Rome, one of the two senior authors of the study, said, "This finding may suggest that human presence, which is often a threat to primates, may interfere with the natural adaptability of the species to global change."
The transition from an arboreal to terrestrial lifestyle has occurred previously in primate evolution, but today's rapid changes are a serious threat.
"Though similar ecological conditions and species traits may have influenced previous evolutionary shifts of arboreal primates, including hominins, to ground living, it is clear that the current pace of deforestation and climate change puts most primate species in peril," said Giuseppe Donati, Ph. D., of Oxford Brookes University, one of the senior authors of the study.
Nadine Lamberski, SDZWA Chief Conservation and Wildlife Health Officer, who was not involved in the study, remarked on the impressive scale of this collaborative scientific initiative.
"This is an extraordinary effort to convene 118 authors and review data of this magnitude. It is also a tremendous example of the insights that can be gleaned and strides that can be made when conservation is examined on a global scale," Lamberski said.Primates' ancestors may have left trees to survive asteroid
HOUSTON – (June 1, 2023) – A new investigation led by researchers at Baylor College of Medicine’s Human Genome Sequencing Center, the Institute of Evolutionary Biology and Pompeu Fabra University in Barcelona, Spain, and Illumina, Inc. analyzed the genomes of 233 nonhuman primate species and revealed key features of primate evolution, human disease and biodiversity conservation. The findings are published in a series of studies in a special issue of the journal Science.
The Primate Genome Project generated the most complete catalog of genomic information for primates to date, covering nearly half of all existing primate species on Earth. Researchers from 24 countries compared the genomes of 809 individual primates from 233 species and identified 4.3 million common missense mutations. The resulting studies uncovered DNA sequence variants and developed phylogenies for primate species that will provide new data on primate and human evolution, as well as primate biodiversity. In addition, researchers used primate genomic data to identify new insights into the genetic causes of human disease and developed an algorithm that will help predict pathogenic variants in humans.
“The simultaneous publication of this broad array of papers on primate genomics demonstrates the value and the power of comparative genetics,” said Dr. Jeffrey Rogers, lead investigator and associate professor at the Human Genome Sequencing Center at Baylor. “When we investigate the genomics of nonhuman primates, we not only learn about these species, which is important and timely, but we can also place human genetics into its proper comparative context, which provides new insights into human health and human evolution.”
“Primates have a great genetic diversity that increases between the different geographical regions and taxonomies,” said Dr. Tomà s Marquès-Bonet, lead investigator from Pompeu Fabra. “The study of this diversity is crucial for human evolutionary studies, human disease and for their future conservation.”
“Our studies show which species are in most dire need of conservation efforts and can help identify the most effective strategies for preserving these species,” said Dr. Lukas Kuderna, lead investigator from the Institute of Evolutionary Biology.
Interspecies gene flow in baboons may shed light on human evolution
One of the consortium studies focused on hybridization of genetically distinct lineages in baboons. Researchers used whole genome sequence data from 225 baboons representing multiple populations to identify several new geographic sites of gene flow between populations. They found that yellow baboons (P. cynocephalus) from western Tanzania are the first nonhuman primate shown to have received genetic input from three distinct lineages. The evolutionary dynamics of baboon populations suggest that other early hominins may display similar complexity.
“These results suggest that the population genetic structure and history of introgression among baboon lineages is more complex than was previously thought, and that shows that the baboons are a good model for the evolution of humans, Neanderthals and Denisovans,” Rogers said.
Using primate mutations to predict risk of human disease
One of the consortium studies with key implications for human disease focused on determining clinical relevance of genetic variants. Out of the 4.3 million missense mutations identified in primates in this study, researchers found that 6% can be considered likely benign in human disease because their abundant frequency in primate populations does not appear to have a negative effect. Meanwhile, in the other 94%, researchers used the PrimateAI-3D deep learning algorithm, an artificial intelligence algorithm developed by the team at Illumina, to predict variant pathogenicity in human disease.
“We discovered that if a ‘rare’ mutation cannot be found in the primate genome, it is very likely to cause a human disease,” said Dr. Kyle Farh, lead investigator from Illumina. “In addition, some of these rare mutations can cause, by themselves, some diseases considered polygenic.”
The new genomic catalog outlined in this series of studies has halved the number of genomic innovations that were believed to be exclusively human. This observation facilitates the identification of those mutations not shared with primates that consequently may be unique to human evolution and the characteristics that make us human.
“These studies bring comparative genomics to new heights, and we can predict the impact on both understanding of human biology and on practical clinical diagnostic issues,” said Dr. Richard Gibbs, founding director of the Human Genome Sequencing Center and Wofford Cain Chair and Professor of Molecular and Human Genetics at Baylor.
Other Baylor contributors to this work include R. Alan Harris, Muthuswamy Raveendran, Marie-Claude Gingras, Sejal Salvi and Harshavardhan Doddapaneni. For a full list of authors and funding for this work, see the publications.
A global catalog of whole-genome diversity from 233 primate species
ARTICLE PUBLICATION DATE
2-Jun-2023
The Primate Genome Project unlocks hidden secrets of primate evolution
Comparative genomic analyses of 50 primate genomes reveal crucial genetic mechanisms of primate speciation, phenotypic adaptability, and social system evolution
IMAGE: FIGURE 1. GENOMIC PHYLOGENY OF PRIMATES. CREDIT: DONG-DONG WU.view more
CREDIT: CREDIT: DONG-DONG WU.
Co-led by Guojie Zhang from Centre for Evolutionary & Organismal Biology at Zhejiang University, Dong-Dong Wu at Kunming Institute of Zoology, Xiao-Guang Qi at Northwest University, Li Yu at Yunnan University, Mikkel Heide Schierup at Aarhus University, and Yang Zhou at BGI-Research, the Primate Genome Consortium reported a series of publications from its first phase program which includes high quality reference genomes from 50 primate species of which 27 were sequenced for the first time. These studies provide new insights on the speciation process, genomic diversity, social evolution, sex chromosomes, and the evolution of the brain and other biological traits.
Large-scale phylogenomic studies reveal the genetic mechanisms underlying the evolutionary history and phenotypic innovations in primates
The comparative analysis of primate genomes within a phylogenetic context is crucial for understanding the evolution of the human genetic architecture and the inter-species genomic differences associated with primate diversification. Previous studies of primate genomes have focused mainly on primate species closely related to humans and were constrained by the lack of broader phylogenetic coverage.
“Although there are more than 500 primate species worldwide, currently, only 23 representative non-human primates species have had their genomes published, leaving 72% of genera remain unsequenced, which creates significant knowledge gaps in understanding their evolutionary history” Dong-Dong Wu states.
To address this gap, they performed high-quality genome sequencing using long-read sequencing technologies on 27 primate species, including basal lineages that had not been fully sequenced before. Combining this with previously published primate genomes, the project conducted phylogenomic studies of 50 primate species representing 38 genera and 14 families to gain new insights into their genomic and phenotypic evolution.
“Based on full genome data, we have generated a highly resolved phylogeny and estimated the emergence of crown Primates between 64.95 and 68.29 million years ago overlapping the Cretaceous/Tertiary boundary”, Dong-Dong Wu states.
The study reported detailed genomic rearrangements across primate lineages and identified thousands of candidate genes that have underwent adaptive natural selection at different ancestral branches of the phylogeny. This includes genes that are important for the development of the nervous, skeletal, digestive, and sensory systems, all of which are likely to have contributed to evolutionary innovations and adaptations of primates.
“It is surprising to see that so many genomic changes involving brain-related genes occurred in the common ancestor of the Simian group which includes New-world monkey, Old-world monkey, and great apes”, states Guojie Zhang, “These genomic innovations evolving deep in time at this ancestral node might have paved the way for the further evolution of human unique traits”.
Pervasive incomplete lineage sorting illuminates speciation and selection in primates
Although it has been well-recognized that chimpanzees and bonobos are the most closely related species to humans, 15% of our genome is closer to another great ape, the gorilla. This is primarily due to the special evolutionary event called incomplete-lineage sorting (ILS), where the ancestral genetic polymorphism randomly sorts into the descendent species. The study investigated the speciation events during the primate evolution and found ILS occurred frequently in all 29 major ancestral nodes across primates with some nodes having over 50% of genome affected by ILS.
"The genetic diversification process does not follow a bifurcation tree-like topology as we normally know for speciation process, it is more like a complicated net“, Guojie Zhang said. ”It is important to investigate the evolutionary process of each individual gene, which could also affect the evolution of phenotypes across species”.
Incomplete lineage sorting (ILS) exhibits extensive variation along the genome, primarily driven by recombination. “We observed that ILS is reduced more on the X chromosome than autosomes compared to what would be expected under neutral evolution, suggesting a higher impact of natural selection on the X chromosome during primate evolution”, Mikkel Heide Schierup states.
The study exploits ILS to perform molecular dating of speciation events solely based on genome data, without fossil calibration, and found the new dating results were highly consistent with the dating with the fossil record. “This suggests that molecular dating provides an accurate estimate of speciation time even without the fossil records”, says the first author of this paper, Iker Rivas-González.
Hybridization into species events
Hybridization is increasingly recognized as an important evolutionary force for generating species and phenotypic diversity in plants and animals. This is especially common in lineages that can tolerate whole genome duplication and increased levels of ploidy. However, speciation by hybridization has been rarely reported in mammals.
Utilizing full genome data, the team discovered that the gray snub-nosed monkey Rhinopithecusbrelichi was a descendent species from the hybridization between the morphologically differentiated species, the golden snub-nosed monkey R. roxellana and the common ancestor of black-white snub-nosed monkey R. bieti and the black snub- nosed monkey R. strykeri.
“To our knowledge, this is the first time that a hybrid speciation event is recorded in primates”, stated by Li Yu.
This study further identifies key genes in R. brelichi that derived from each parental lineages which may have contributed to the mosaic coat coloration in this species, and likely promoted premating reproductive isolation of the hybrid species from the parental lineages.
Multidisciplinary intersection reveals the genetic mechanisms of social complexity in Asian langurs
Primates have very diverse social systems, however the biological mechanisms underlying social evolution remain poorly known. The classical socioecological model hypothesized that the diversity of social systems evolved as a response to the environmental changes.
The study used Asian colobine monkeys as model system, as this group of species underwent a staged social evolution process from a one-male, multi-female unit to complex multi-level social forms. They have re-constructed the speciation process of this group using the full genome data and found a strong correlation between the environmental temperature and group size of the species. The primate species living in colder environments tend to live in larger groups. The ancient ice ages drove the social evolution of these primates, promoting the aggregation of spreading northern odd-nosed monkey species into nested multi-level social forms.
During this transition, odd-nosed monkeys exhibited positive selection in many genes related to cold adaptation and the nervous system. “The snub-nosed monkeys seem to have a longer mother-infant bond, which probably increased infant survival in cold environments, The DA/OXT receptors are important neurohormones in mediating social bonding. This signal pathway has been enhanced in odd-nosed monkey and promoted the social affiliation, cohesion and cooperation among adults of this species” Xiao-guang Qi states.
Figure 3. Gray snub-nosed monkey (Rhinopithecus brelichi). Credit: Gui-Yun Li
CREDIT
Credit: Gui-Yun Li
Figure 4 The hybrid origin of gray snub-nosed monkey. Credit: Li Yu
CREDIT
Credit: Li Yu
Figure 4. Cold promotes the social evolution of the Asian langurs. Credit: Xiao-Guang Qi.
Rivas-González I, Rousselle M, Li F, et al. 2023. Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science. https://doi.org/10.1126/science.abn4409
Qi X-G, Wu J, Zhao L, et al. 2023. Adaptations to a cold climate promoted social evolution in Asian colobine primates. Science. https://doi.org/10.1126/science.abl8621
Sørensen E, Harris R, et al. 2023. Genome-wide coancestry reveals details of ancient and recent male-driven reticulation in baboon. Science. https://doi.org/10.1126/science.abn8153
Zhang B-L, Chen W, et al. 2023. Comparative genomics reveals the hybrid origin of a macaque group. Science Advances.https://doi.org/10.1126/sciadv.add3580
Bi X-P, Zhou L, et al. 2023. Lineage-specific accelerated sequences underlying primate evolution. Science Advances.https://doi.org/10.1126/sciadv.adc9507
Zhou Y, Zhan X-Y, et al. 2023. Eighty million years of rapid evolution of the primate Y chromosomes. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-022-01974-x
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A new investigation led by Tomà s Marquès-Bonet, an ICREA researcher at the IBE (CSIC-UPF) and a professor of Genetics at the Department of Medicine and Life Sciences (MELIS) at Pompeu Fabra University (UPF), Kyle Farh (Illumina), and Jeffrey Rogers (Baylor College of Medicine), combines the genome sequencing of over 800 individuals from 233 primate species, covering nearly half of all existing primate species on Earth, through the study of fossil remains, multiplying by four the number of primate genomes available to date. The study provides new information about primates’ genetic diversity and phylogeny, which is important for understanding and conserving the biodiversity of the closest species to our own.
By comparing the genomes of 809 nonhuman primate individuals from 233 species to the human genome, the research has identified 4.3 million common missense mutations that affect the composition of amino acids and can alter the function of proteins, leading to many human diseases.
Rare missense mutations can raise the risk of disease
One of the limitations of human and clinical genetics is the current inability to detect, among hundreds of thousands of mutations, the ones that cause diseases. Currently, the genetic causes of many common diseases, such as diabetes and heart disease, are unknown, due either to the lack of genetic information or to the large number of genetic factors involved. Some diseases are thought to originate when a set of genetic variations or mutations with a “mild” effect act together to cause a disease of polygenic origin, like diabetes or cancer.
“6% of the 4.3 million missense mutations identified are abundant in primates and are therefore considered “potentially benign” in human disease, given that their presence is tolerated in these animals”, states Kyle Farh, vice president of Artificial Intelligence at Illumina.
The identification of disease-causing mutations has been achieved thanks to the PrimateAI-3D deep learning algorithm. PrimateAI-3D is an artificial intelligence (AI) algorithm developed by Illumina, the world’s leading company in DNA sequencing, and is a kind of ChatGPT for genetics that uses genome sequences instead of human language.
New insights into primate evolution and human uniqueness
The publication of this project includes the most complete catalogue of primate genomic information produced so far, covering nearly half of all existing primate species on Earth. It contains information of primates from Asia, America, Africa, and Madagascar.
According to Tomàs Marquès-Bonet, "Humans are primates. The study of hundreds of nonhuman primate genomes, given their phylogenetic position, is very valuable for human evolutionary studies, to better understand the human genome and the bases of our singularity, including the bases of human diseases, and for their future conservation".
These studies have also indicated that the genetics of primates does not always match their taxonomy. We found several cases in which relationships among primate species are best described as complex and network-like rather than simple branching trees.
Another study delves deeper into the evolution of baboon species, a large and diverse group of monkeys, showing that there have been several episodes of hybridization and gene flow among species that were not previously recognized. In addition, we found that yellow baboons from western Tanzania are the first nonhuman primate to have received genetic input from three different lineages. “These results suggest that the population genetic structure and history of introgression among baboon lineages is more complex than was previously thought, and that shows that the baboons are a good model for the evolution of humans, Neanderthals and Denisovans”, says Jeffrey Rogers, an associate professor at the Human Genome Sequencing Center and Dept. of Molecular and Human Genetics at Baylor College of Medicine, who co-led this study.
“Our studies provide clues as to which species are in most dire need of conservation efforts, and could help to identify the most effective strategies to preserve them.”, Lukas Kuderna, first author of one of the studies, asserts.
Lastly, the new genomic catalogue has halved the number of genomic innovations that were believed to be exclusively human. This observation facilitates the identification of mutations that are not shared with primates that may consequently be unique to human evolution and the characteristics that make us human.
White-fronted Capuchin (Cebus unicolor) near Manaus, Brazil.
AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)
Given primates are threatened, in many cases, by factors including climate change, habitat loss, and illegal trading and hunting, the need for a more complete understanding of primate genetic diversity is urgent. Characterizing primate variation not only allows us to better understand and conserve these species in the wild, but it also helps us to better understand ourselves.
In a special issue of Science, including two related studies from Science Advances, ten papers provide new insights into primate genomes, far exceeding past genomic analyses of primate species. In one study – results from which provide the foundation for several additional studies in the special issue – Lukas Kuderna and team present whole genome data from 233 primate species representing 86% of the primate genera and all 16 families. They used this dataset to estimate the human-chimpanzee divergence as between 9.0 and 6.9 Ma – slightly older than other recent analyses. The authors also explored the association between genomic variation and variables including climate and sociality. Kuderna et al. further studied whether genetic diversity estimates are correlated with extinction risk in primates, a subject of previous debate. “Despite our broad sampling,” the authors write, “we find no global relationship between numerically coded International Union for Conservation of Nature extinction risk categories and estimated heterozygosity.” Finally, the authors used the data to generate a better picture of the mutations that arose in the human lineage and have not emerged elsewhere in primates.
Despite the importance of nonhuman primates, reference genomes have been sequenced in <10% of species, which both impedes research and hampers conservation efforts. Yong Shao and colleagues, in another study in the special issue, present high-quality reference genomes for 27 primate species, adding to available resources. Of particular interest, they report a previously unreported increase in the rate of genomic change in the Simiiformes common ancestor that may have played a role in the later diversification of Simiiformes and the evolution of humans.
A study by Iker Rivas-González and team addresses questions around the process of speciation among populations, focusing specifically on the way some regions of the genome will not show evidence of difference for a long time after ecological speciation has occurred. This process is called incomplete lineage sorting. By accounting for incomplete lineage sorting across primates, Rivas-González et al. were able to produce a primate phylogeny that agrees with fossil estimates, unlike past attempts.
A study by Hong Wu and colleagues focuses on hybridization in mammalian evolution, the role for which is rarely examined. The authors studied the genome sequences from a group of monkey species in the Rhinopithecus genus and found clear evidence that the gray snub nosed monkey is derived from hybridization between the golden snub nosed monkey and the ancestor of two extant Rhinopithecus species. Further, they report the unusual coat color seen in the gray snub nose is due to this mixing. One group of species that has been identified as having a history of hybridization is that containing the genus Papio, the baboons. Erik Sørensen and colleagues used whole genome sequencing to reveal the evolutionary history of overlapping baboon species and found evidence of repeated admixture. “We describe the first example of a baboon population with a genetic composition that is derived from three distinct lineages,” they write. Also focused on hybridization in primates, Bao-Lin Zhang and team, in Science Advances, compared reference genomes of 12 macaque species that together cover all the known macaque groups. Their comparative phylogenomic analysis uncovered an ancient hybrid origin of a macaque lineage. “Our study provides both a strategy and a pipeline of genome analyses to identify hybrid speciation, which should pave the way for the identification and exploration of further such events in the future,” write Zhang et al.
