New bonobo genome fine tunes great ape evolution studies

Posted on May 7, 2021 by Exposing the Big Game

https://phys.org/news/2021-05-bonobo-genome-fine-tunes-great.html

MAY 5, 2021

by University of Washington School of Medicine

New bonobo genome fine tunes great ape evolution studies — Mhudiblu, a female bonobo, holds her daughter Akema. Mhudiblu’s DNA was sequenced to help construct a new, high-quality bonobo genome assembly for great ape and other hominid evolution and genetic research Credit: Claudia Philipp/Wuppertal Zoo Germany

Chimpanzees and bonobos diverged comparatively recently in great ape evolutionary history. They split into different species about 1.7 million years ago. Some of the distinctions between chimpanzee (Pan troglodytes) and bonobo (Pan paniscus) lineages have been made clearer by a recent achievement in hominid genomics.

A new bonobo genome assembly has been constructed with a multiplatform approach and without relying on reference genomes. According to the researchers on this project, more than 98% of the genes are now completely annotated and 99% of the gaps are closed.

The high quality of this assembly is allowing scientists to more accurately compare the bonobo genome to that of other great apes—the gorilla, orangutan, chimpanzee—as well as to the modern human. All these species, as well as extinct, ancient, human-like beings, are referred to as hominids.

Because chimpanzee and bonobo are also the closest living species to modern humans, comparing higher-quality genomes could help uncover genetic changes that set the human species apart.

In a May 5 Nature paper, researchers explain how they developed and analyzed the new bonobo assembly, and what juxtaposing it to other great ape genomes is revealing.

The multi-institutional project was led by Yafei Mao, of the Department of Genome Sciences at the University of Washington School of Medicine in Seattle, and Claudia R. Catacchio, of the Department of Biology at the University of Bari, Italy. The senior scientists were Evan Eichler, professor of genome sciences at the UW School of Medicine, and Mario Ventura of the University of Bari. Eichler is also a Howard Hughes Medical Institute investigator.

By comparing the bonobo genome to that of other great apes, the researchers found more than 5,571 structural variants that distinguished the bonobo and chimpanzee lineages.

The researchers explained in the paper, “We focused on genes that have been lost, changed in structure, or expanded in the last few million years of bonobo evolution.”

The great ape genome comparisons are also enabling researchers to gain new insights on what happened to the various ape genomes during and after the divergence or splitting apart into different species from a common ancestor.https://googleads.g.doubleclick.net/pagead/ads?client=ca-pub-0536483524803400&output=html&h=280&slotname=5350699939&adk=3784993980&adf=780081655&pi=t.ma~as.5350699939&w=753&fwrn=4&fwrnh=100&lmt=1620411494&rafmt=1&psa=1&format=753×280&url=https%3A%2F%2Fphys.org%2Fnews%2F2021-05-bonobo-genome-fine-tunes-great.html&flash=0&fwr=0&rpe=1&resp_fmts=3&wgl=1&uach=WyJXaW5kb3dzIiwiMTAuMCIsIng4NiIsIiIsIjkwLjAuNDQzMC45MyIsW11d&dt=1620411487959&bpp=127&bdt=8542&idt=6205&shv=r20210505&cbv=%2Fr20190131&ptt=9&saldr=aa&abxe=1&cookie=ID%3D5d55f89f953c9743%3AT%3D1620402715%3AS%3DALNI_MYdSdCvjuDL4-5hvOL9z6LcpsVrGw&correlator=7739017579624&frm=20&pv=2&ga_vid=185394846.1565457508&ga_sid=1620411494&ga_hid=1857772748&ga_fc=0&u_tz=-420&u_his=1&u_java=0&u_h=640&u_w=1139&u_ah=607&u_aw=1139&u_cd=24&u_nplug=3&u_nmime=4&adx=263&ady=2181&biw=1123&bih=538&scr_x=0&scr_y=1000&eid=42530672%2C44739521%2C21066435%2C31060840&oid=3&pvsid=1161413371341100&pem=466&eae=0&fc=896&brdim=0%2C0%2C0%2C0%2C1139%2C0%2C1139%2C607%2C1139%2C537&vis=1&rsz=%7C%7CpEebr%7C&abl=CS&pfx=0&fu=128&bc=31&ifi=1&uci=a!1&btvi=1&fsb=1&xpc=G9aGbKQEaN&p=https%3A//phys.org&dtd=6644

They were particularly interested in what is called incomplete lineage sorting. This is the less-than-perfect passing along of alleles into the separating populations as species diverge, as well as the loss of alleles or their genetic drift. Analyses of incomplete lineage sorting can help clarify gene evolution and the genetic relationships among present-day hominids.

The higher-quality bonobo genome assembly enabled the researchers to generate a higher resolution map comparing incomplete lineage sorting in hominids. They identified regions that are inconsistent with the species tree. In addition, they estimate that 2.52% of the human genome is more closely related to the bonobo genome than the chimpanzee genome, and 2.55% of the human genome is more closely related to the chimpanzee genome than the bonobo genome.

The total proportion based on incomplete lineage sorting analysis (5.07%) is almost double earlier estimates (3.1%).

“We predict a greater fraction of the human genome is genetically closer to chimpanzees and bonobos compared to previous studies,” the researchers note.

The researchers took their incomplete lineage sorting analysis back 15 million years to include genome data from orangutan and gorilla. This increased the incomplete lineage sorting estimates for the hominid genomes to more than 36.5%, which is only slightly more than earlier predictions.

Surprisingly, more than a quarter of these regions are distributed non-randomly, have elevated rates of amino acid replacement, and are enriched for particular genes with related functions such as immunity. This suggests that incomplete lineage sorting might work to increase diversity for specific regions.

The new bonobo genome assembly is named for the female great ape whose DNA was sequenced, Mhudiblu, a current resident of the Wuppertal Zoo in Germany. The researchers estimate that sequence accuracy of the new assembly is about 99.97% to 99.99%, and closes about 99.5% of the 108,390 gaps in the previous bonobo assembly.

The bonobo is one of the last great ape genomes to be sequenced with more advanced long-read genome sequence technologies, the researchers noted.

“Its sequence will facilitate more systematic comparisons between human, chimpanzee, gorilla and orangutan without the limitations of technological differences in sequencing and assembly of the original reference,” according to the researchers.

Explo

MAY 5, 2021

New bonobo genome fine tunes great ape evolution studies

by University of Washington School of Medicine

Because chimpanzee and bonobo are also the closest living species to modern humans, comparing higher-quality genomes could help uncover genetic changes that set the human species apart.

In a May 5 Nature paper, researchers explain how they developed and analyzed the new bonobo assembly, and what juxtaposing it to other great ape genomes is revealing.

By comparing the bonobo genome to that of other great apes, the researchers found more than 5,571 structural variants that distinguished the bonobo and chimpanzee lineages.

The researchers explained in the paper, “We focused on genes that have been lost, changed in structure, or expanded in the last few million years of bonobo evolution.”

The total proportion based on incomplete lineage sorting analysis (5.07%) is almost double earlier estimates (3.1%).

“We predict a greater fraction of the human genome is genetically closer to chimpanzees and bonobos compared to previous studies,” the researchers note.

The bonobo is one of the last great ape genomes to be sequenced with more advanced long-read genome sequence technologies, the researchers noted.

Explore furtherBonobo and chimpanzee gestures share many meanings

MAY 5, 2021

New bonobo genome fine tunes great ape evolution studies

by University of Washington School of Medicine

Because chimpanzee and bonobo are also the closest living species to modern humans, comparing higher-quality genomes could help uncover genetic changes that set the human species apart.

In a May 5 Nature paper, researchers explain how they developed and analyzed the new bonobo assembly, and what juxtaposing it to other great ape genomes is revealing.

By comparing the bonobo genome to that of other great apes, the researchers found more than 5,571 structural variants that distinguished the bonobo and chimpanzee lineages.

The researchers explained in the paper, “We focused on genes that have been lost, changed in structure, or expanded in the last few million years of bonobo evolution.”

The total proportion based on incomplete lineage sorting analysis (5.07%) is almost double earlier estimates (3.1%).

“We predict a greater fraction of the human genome is genetically closer to chimpanzees and bonobos compared to previous studies,” the researchers note.

The bonobo is one of the last great ape genomes to be sequenced with more advanced long-read genome sequence technologies, the researchers noted.

Explore furtherBonobo and chimpanzee gestures share many meanings

re furtherBonobo and chimpanzee gestures share many meanings

Saving Endangered Bonobos Teaches A Lesson In Empathy

Posted on April 3, 2021 by Exposing the Big Game

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April 3, 20217:05 AM ET

https://www.npr.org/sections/health-shots/2021/04/03/983473068/saving-endangered-bonobos-teaches-a-lesson-in-empathy

JON HAMILTON

A trio of young bonobos play under the watchful eyes of their caregivers..Ley Uwera for NPR

At an animal sanctuary in the Congo, several dozen Congolese schoolchildren are getting a crash course in bonobos.

These gentle, endangered apes, who resemble chimpanzees, are “our closest cousins,” educator Blaise Mbwaki tells the students in French. “They have a human character, and they are Congolese.”

“So if you eat a bonobo,” Mbwaki says, “you are eating your cousin. It is cannibalism.”

It’s a blunt message. But Mbwaki and other staff here at the Lola ya Bonobo sanctuary think it may offer the best hope of saving this species from extinction.

Only about 20,000 wild bonobos are left, and they are found only in the central rainforests of the Democratic Republic of the Congo. So the staff at Lola are working to engage Congolese students in efforts to protect the bonobos that remain.

Bonobos share nearly 99% of their DNA with humans. And studies of the animals at Lola are helping scientists understand how humans evolved traits like empathy.

But humans haven’t shown much empathy for bonobos. As a species, we’ve hunted them for food, sold their babies as pets, and spoiled much of their natural habitat.

A male bonobo at Lola yo Bonobo sanctuary. Only about 20,000 wild bonobos are left, and they are found only in the central rainforests of the Democratic Republic of the Congo.Ley Uwera for NPR

Most of the 60 or so bonobos at Lola arrived as orphans. “Their mothers were killed in the forest for meat and hunters kept the babies to sell,” says Dr. Jonas Mukamba, the resident veterinarian at Lola.Article continues after sponsor messagehttps://0d9cecb803990edf6c50d80e8f8d0024.safeframe.googlesyndication.com/safeframe/1-0-38/html/container.html

The sanctuary’s goal is to prepare the bonobos for life in the wild. In the meantime, they live in Lola’s spacious, forested enclosures and serve as ambassadors to daily delegations of school children.

The children learn that “this animal is unique in the DRC,” says ClaudineAndré, who founded Lola ya Bonobo in 1994. “It is a treasure of nature in Congo.”

André is the daughter of a Belgian veterinarian who practiced in Kinshasa. She has spent much of her life trying to make sure bonobos have a future in the Congo.

It was the Congo river that probably gave rise to bonobo. More than a million years ago, scientists believe, some bonobo ancestors ended up on the South side of the river. That separated them from their chimpanzee relatives to the North.

Neither animal likes to swim. So over time, bonobos became a separate species, one that is smaller, gentler, and less aggressive than chimps.

GOATS AND SODA

Some Generous Apes May Help Explain The Evolution Of Human Kindness

The 10,000 plus students who have visited Lola ya Bonobo learn all this and why it matters, André says.

“Everything is connected on the planet,” she says. “So the kids have to understand that it’s not only the bonobo [at risk]. All the biodiversity is in danger.”

The children also learn to take action if they see a bonobo being kept as a pet, which is a crime in the DRC.

“Very often it’s one of these kids from the school who call us and say, “I saw a bonobo,” André says.

Today’s students have moved from the classroom to the edge of a bonobo enclosure.

Group of school children in science class visiting Lola ya Bonobo sanctuary.Ley Uwera for NPR

“Bonjour les bonobos,” Mbwaki calls out to the group of animals eyeing their human visitors. “Bonjour Elikya,” he says to one of the females.

Elikya was born here to a mother who had arrived as an orphan. Now Elikya is raising a baby of her own.

But the ultimate goal is to release bonobos like Elikya into the wild. So Lola has established a second sanctuary called Ekolo ya Bonobo hundreds of miles away.

“It’s a place where bonobos used to be,” says Dr. Raphaël Belais, a veterinarian at Lola. “But unfortunately during the wartime the hunting was going quite strong so they have no more bonobos in this piece of forest.”

It would be nice if all the bonobos at Lola could eventually go to their new home, Belais says. “Unfortunately, some of the orphans are too traumatized or too mutilated.”

Still, more than a dozen animals from Lola have been moved to Ekolo and most of them are doing well. Their future, though, will be determined by Congolese people like the students who came to Lola today.

So I ask a 10-year-old named Gaska Basili, what he learned about bonobos during the visit.

“They are like our brothers,” he replies in French.

“And what would you do if you saw a bonobo being kept illegally?” I ask.

“I would call my teacher, Papa Blaise,” he says.

Some Generous Apes May Help Explain The Evolution Of Human Kindness

Posted on March 20, 2021 by Exposing the Big Game

March 20, 20217:15 AM ET

https://www.npr.org/sections/goatsandsoda/2021/03/20/978868116/some-generous-apes-may-help-explain-the-evolution-of-human-kindness

JON HAMILTON

Esake, photographed at the Lola ya Bonobo sanctuary in the Democratic Republic of the Congo in 2019, was rescued from a hunter who killed her mom.Ley Uwera for NPR

It’s feeding time at Lola ya Bonobo, a sanctuary for bonobos in the Democratic Republic of the Congo.

“Allez,” caretaker Bernard Nsangu shouts in French as he gets ready to distribute a morning snack. The air fills with piercing shrieks as bonobos nearby tell their friends in the forest that pineapple is coming.

Soon, more than a dozen bonobos have assembled near the grassy perimeter of their enclosure.

With chimpanzees, the prospect of food can lead to aggression.

But bonobos take a different approach, says Suzy Kwetuenda, a biologist at Lola, for whom English is a third language.”As you see, there is many action of sex, many negotiation,” she tells me. “So that make peace.”

This sort of harmony is why, for more than a decade, scientists from around the world have been coming to this sanctuary just outside Kinshasa, along the banks of the Lukaya River. The researchers think bonobos may help explain how humans evolved the capacity to be nice – at least some of the time.

Same genes, different behavior

Bonobos look like smallish chimpanzees, with whom they share 99.6% of their DNA. And both of these great apes share 98.7% of their DNA with humans, making them our closest living relatives.Article continues after sponsor message

What intrigues scientists is that bonobos and chimps often behave very differently, despite their genetic similarity. What’s more, human behavior seems to incorporate aspects of both species.

For example, chimps tend to rely on cunning and competition, while bonobos emphasize cooperation and sharing. The two species also diverge when it comes to leadership, says Dr. Jonas Mukamba, the head veterinarian at Lola.

Bonobos willingly share their food with strangers and value cooperation among members of their group.Ley Uwera for NPR

“Chez bonobo,” he tells me, “it is the females who dominate and it is a female who is chief of the group.”

That’s one reason meals at Lola ya Bonobo are so peaceful, Kwetuenda tells me as we watch a group of bonobos gather for what will soon turn into a sort of polyamorous picnic.

She points to the alpha female. “This is Semendua, big mom, tough mom,” she says. “And as you can see she is in the front just to show that she is very concerned by all organization in the group.”

Semendua is smaller than many of the males around her. But if a male were to become aggressive, all the females would rally around her to chase him into the forest.

Sharing with strangers

One way that bonobos differ from other great apes is in their eagerness to share, something that has been documented in a series of experiments here at Lola.

The experiments were carried out by a team that included Kwetuenda and Brian Hare, a professor of evolutionary anthropology at Duke University. They were done in Lola’s “bonobo lab,” a building that features room-size cages and a place for scientists to observe what happens inside them.

In one experiment, the scientists put two bonobos in adjacent rooms. Then they gave one of the animals a plate of prized food, like bananas or apples, which have to be imported. The fruit plate was topped with a type of cream Kwetuenda calls “bonobo sauce.”

The bonobo with food was given a choice: eat alone, or use a special key to let in their neighbor.

“In our mind, we thought that because of nice food they would first eat,” Kwetuenda says. “But we were surprised to see that roommate is more important than favorite food.”

Later, the scientists repeated the experiment with three bonobos, one of whom was a stranger. This time, the bonobo with food usually shared with the stranger first, then invited the friend to join in.

Bonobos avoid confrontation and promote cooperation, often through sex.Ley Uwera for NPR

In another study, scientists showed that bonobos are willing to help one another obtain food even if they know they won’t get to share it. This generosity with food does not extend to tools, though.

Apparently selfless behavior may seem odd from an evolutionary perspective. But scientists believe it paved the way to the sort of large-scale cooperation that has helped Homo sapiens outlast other early humans, like Homo erectus. And this sort of cooperation has allowed our species to share new ideas, create vast nations and explore other planets.

A lab in the forest

Research at Lola ya Bonobo has produced more than 75 published studies. Scientists keep returning because the DRC is the only place on earth where these animals still live in the wild, and this sanctuary provides a unique place to study their behavior in a naturalistic setting.

Lola was founded nearly 30 years ago by Claudine André, a Belgian whose father was a veterinarian in Kinshasa. In 1991, while working at the Kinshasa Zoo, André looked into the eyes of a bonobo and, she says, “fell in love with this species.”

After Lola moved into its current home (once a summer residence for former president Mobutu Sese Seko), André began hosting scientists from countries including the U.S., Japan and Germany. Over the years, scientific research has been able to document many of the bonobo behaviors that André and the Lola staff see every day.

A trio of young bonobos play under the watchful eyes of their caregivers.Ley Uwera for NPR

For example, André has often said that bonobos are “full of empathy.” And sure enough, an Italian team found that if one bonobo yawns, others will yawn too — a behavior closely associated with empathy.

Research also support André’s belief that bonobos have a keen understanding of what’s going on in another individual’s mind, and when that individual wants to help them.

SHOTS – HEALTH NEWS

How Humans Domesticated Themselves

In their book Survival of the Friendliest, published in 2020, Brian Hare and Vanessa Woods describe an experiment in which a researcher would hide a treat under one of two upside-down cups. Then they invited several different animal species to figure out which cup hid the treat.

Chimps, despite their cleverness, just kept choosing one of the cups at random. But bonobos (and dogs) almost immediately learned to look to the scientist for a gesture indicating the right cup.

One study even found a structural difference between the brains of bonobos and chimps. The difference involved circuits controlling social and emotional behaviors.

What all the science suggests is that bonobos have evolved in a way that predisposes them to sharing, tolerance, negotiation and cooperation.

Those are all traits you can see in humans, on a good day, André says.

“Humans can be a fantastic bonobo with a big heart or a very dangerous warrior,” she says. “We are mixed.”

Lessons from a close relative

It’s been about 6 million years since the death of the last common ancestor we shared with chimps and bonobos. Since then, we humans have channeled our inner bonobo to share and cooperate on a massive scale.

But we’ve often acted more like chimps — whose murder rate in the wild is comparable to our own — when it comes to behaviors like violence against members of our own species.

Humans do not share bonobos’ assumption that every stranger is a potential friend. Studies show we may not even consider a stranger fully human if they belong to a group perceived as other and threatening.

When that happens, scientists say, we tend to suppress empathy and embrace cruelty.

Human cruelty is something Yvonne Vela Tona, a caretaker at Lola ya Bonobo, has seen up close.

Yvonne Vela Tona, one of the “mamas” at the sanctuary, looks after the young bonobo Esake.Ley Uwera for NPR

Vela Tona fled Angola more than 20 years ago to escape a civil war that would eventually kill more than 500,000 people. Since then, she’s lived in the DRC, a nation where decades of armed conflict has led to millions of deaths.

Vela Tona has raised children of her own and served as a surrogate mother to more than 20 bonobos. She’s seen both the chimp and bonobo sides of human behavior.

What people can learn from bonobos, she tells me through an interpreter, is that war and violence are not inevitable, that we, like bonobos, have the capacity to resolve conflicts through other means.

https://www.npr.org/sections/goatsandsoda/2021/03/20/978868116/some-generous-apes-may-help-explain-the-evolution-of-human-kindness

The Day the Human Race Went Vegan

Posted on July 12, 2012 by Exposing the Big Game

When we last left our intrepid Earth people, nearly seven billion of them had trifled with the idea of returning to a lifestyle of hunting—with disastrous results. Then, whether out of desperation or evolution, they decided to embrace a vision for a truly sustainable future that didn’t involve killing animals for their dinner. En masse, they laid down their weapons and vowed to live a less destructive life.

As vegans, Homo sapiens now live more peacefully with one another, like their strictly plant-eating primate cousins, the bonobos. Had early humans studied the behavior of the more familiar, omnivorous species of chimpanzee, Pan troglodytes, they could have learned a valuable lesson about the societal dangers of primates becoming predatory and saved themselves and others a lot of grief.

Pan troglodytes spend ninety percent of their time living hand to mouth, eating plants in peaceful cooperation with one another. But every so often, one of them gets a wild hair and instigates a violent hunting foray which often results in an attack on those they see as “lesser” creatures, usually monkeys. If the hunt is successful and a monkey is killed, the notion of sharing goes out the window. Like a housecat with its prey, the killer turns aggressively possessive and mayhem ensues. With loud hoots and hollers, the otherwise egalitarian chimpanzee life turns ugly, as they now have something to fight over.

The long history of Homo sapiens’ decent into carnivorousness played out the same way as their troglodyte cousins’, eventually becoming magnified to the seven billionth power.

But human beings have turned their backs on hunting and meat-eating and now live in gentle harmony with the other creatures of the Earth. Feelings of greed, selfishness and lust for power have begun to fade, as there is no longer a bone of contention—literally or figuratively.

Now there’s hope for lasting harmony among the people of the planet and nature breathes a sigh of relief.

Exposing the Big Game

Forget Hunters' Feeble Rationalizations and Trust Your Gut Feelings: Making Sport of Killing Is Not Healthy Human Behavior

Tag Archives: bonobos

New bonobo genome fine tunes great ape evolution studies

New bonobo genome fine tunes great ape evolution studies

New bonobo genome fine tunes great ape evolution studies

Saving Endangered Bonobos Teaches A Lesson In Empathy

GOATS AND SODA

Some Generous Apes May Help Explain The Evolution Of Human Kindness

Some Generous Apes May Help Explain The Evolution Of Human Kindness

SHOTS – HEALTH NEWS

How Humans Domesticated Themselves

The Day the Human Race Went Vegan