Chimp-Human Pseudogene

"Science and the Sacred" is pleased to feature essays from various guest voices in the science-and-religion dialogue. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation.

Today's post was written by Dennis Venema and Darrel Falk.

In our previous post, we likened comparing genomes of related organisms to reading alternative history novels. We noted that before two species diverge, they share the same “backstory” but then go on to accumulate changes after separation.

One interesting feature of looking at genomes is that often we can find the mutated remains of once-functional genes. These are called pseudogenes, or “false genes.” Pseudogenes might be part of a shared backstory for two species, or they might crop up independently after two species go their separate ways. Either way, they are easy to spot at the molecular level because they retain a lot of similarity. For example, here are the DNA sequences for the start of one particular gene1 in several species (for our purposes, its function is not important).

 
 
 
As you examine the sequence of letters above, note that DNA contains a four letter code. This string of “letters” is made up of the molecules adenine, guanine, cytosine, and thymine strung together within the large super-molecule, DNA. Our cells read the encoded instructions and, interpreting the code, build each of the different proteins required for the maintenance of life.

Note that the instructions have changed a little since these five species had a common “backstory” (ancestor). Despite the changes, for the dog, mouse and chicken, the protein is fully functional. This is not so, however, for the chimp and human. The “dot” (highlighted by the red arrow) means that one single letter of the instructions has been deleted. This change would be like finding this sentence in the first edition of a book:

THE BIG RAT HIT THE RED MAT.
But, in the second edition of the same book, we find this instead:

THE BIG RAT HTT HER EDM AT
The sentence has no meaning anymore, but, as we compared the first and second versions of the book, we would be able to tell exactly what had happened: the letter “I” had been deleted from the sentence, and everything following would be messed up. A single deletion throws off the whole code from that point on. Thus, for chimps and humans, the instructions become gibberish, and the protein molecules produced according to that gene’s instructions are now badly mangled and unable to function.

As you go back and examine sequence in the human/chimp pseudogene, notice how both species carry the exact same deletion. This suggests that the occurrence of this single deletion occurred in one individual, a common ancestor with whom both species have a shared backstory.

Let’s return to our book analogy. Presumably all copies of the second edition had the exact same non-functional sentence about the BIG RAT. If someone was to examine two second edition copies of the book, each of which were missing that same letter, “I,” it would be unthinkable to propose that the exact same mistake occurred independently in the printing of each of the two books. Similarly, it would be incorrect to propose that the new incoherent sentence had some important meaning which literary scholars will discover some day. We would know, plain and simple, that a mistake had occurred. Anything other than that would be highly contrived.

Today both chimps and humans carry the exact same mutation because they both have the same backstory. However, it is even more poignant than that. There are 20,000 pseudogenes in the human genome. Each has its own unique backstory. Each can be traced out in the same manner we have just done for this one.
The hypothesis of common ancestry makes precise predictions about how pseudogenes will be distributed in related species. Once a gene has been mutated into a pseudogene in a certain species, that pseudogene with its specific inactivating mutation will be passed on to all descendents of that species.

The figure below demonstrates this for a specific pseudogene, which we will term pseudogene “y.” Note that in a very specific individual at a very specific time, gene “y” underwent a change in its code—it mutated. That altered code was passed on to the subsequent generations and ended up in two daughter species, Species A and Species B.

 
 
 
 
 
 
 
 
 
 
 
Now consider a second gene, which we call “x.” It also underwent a mutation, but did so earlier in the lineage. Let’s call the new mutated form of this gene pseudogene “x.” This is shown in the next figure. Since this mutation occurred earlier in the lineage in an organism that was a common ancestor to Species A, B, and C, all three of these species carry the abnormal, non-functional version of “x.” The lineage to species D, however, had already broken away. It does not carry the mutated version of “x.”

 
 
 
 
 
 
 
 
 
 
Finally, consider another gene, which we’ll call “z.” This gene is perfectly functional in Species A, B, and D. However, when you examine its code in Species C, guess what? It carries a non-functional pseudogene. What do you think has happened here? This is a recent change, so recent that it occurred in an individual whose ancestors only went on to become Species C. Here is a summary figure which illustrates the time at which each of the three mutations occurred and the ramifications of each change.  

In this example, since gene “x” is mutated to a pseudogene in the common ancestor of species A, B and C, we would expect to find this pseudogene, with the same exact inactivating mutation, in these three species. Similarly, the pseudogene version of gene “y” with exactly the same code-change should be found only in species A and B. Finally, there are many cases in which a pseudogene is found only within one species, or, at most, a couple of closely related sister species. Pseudogene “z” is our example of that.

If life really does have a backstory of this sort, then you can see the power of this technique for tracing the lineage. It allows us to trace the history of life, species by species. Interestingly though, there have long been other—non-genetic—ways of tracing life’s history. Biologists have been using these alternative methods for many decades. For example, by examining fossils (paleontology) and tracing changes in body structure (comparative anatomy), the history of life had already been pretty much worked out before DNA sequencing data ever came into the picture.

For the most part, the data which are emerging from DNA sequencing projects simply verify that which biologists have known for years through these other methods of exploring life’s history. Still, the results are extremely gratifying in their consistency. In science, one looks for corroborating evidence. If the DNA data had suggested totally different lineages, then there would have been good reason to doubt the common descent hypothesis. Such is not the case though. The supporting data keep piling up; there is no longer any doubt.
Remember how science works. If there are multiple lines of evidence—each internally consistent with the central overarching principle—a consensus is reached. The theory is judged to be correct and the scientists move on to further explore its ramifications.

If the theory of common descent is true, then it also makes predictions about what we would not expect to find at the genetic level. We go on to explore this topic in our next post.
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Why do Chimpanzees and Bonobos have different social traits?

It's been a puzzle why our two closest living primate relatives, chimpanzees and bonobos, have widely different social traits, despite belonging to the same genus. Now, a comparative analysis of their brains shows neuroanatomical differences that may be responsible for these behaviors, from the aggression more typical of chimpanzees to the social tolerance of bonobos.


"What's remarkable is that the data appears to match what we know about the human brain and behavior," says Emory anthropologist James Rilling, who led the analysis. "The neural circuitry that mediates anxiety, empathy and the inhibition of aggression in humans is better developed in bonobos than in chimpanzees."

The journal of Social Cognitive and Affective Neuroscience published the results April 5, the most comprehensive comparative analysis to date of the neural systems of chimpanzees and bonobos.

"By contributing to our basic understanding of how brain anatomy relates to social behavior, this study may provide clues to the brain dysfunction underlying human social behavioral disorders like psychopathy and autism," Rilling says.

Chimpanzees and bonobos diverged from a common ancestor with humans about six million years ago, and from each other just one-to-two million years ago. Despite this relatively brief separation in evolutionary terms, the two species exhibit significant differences in social behavior. Compared with chimpanzees, bonobos are more anxious, less aggressive, more socially tolerant, more playful, more sexual and perhaps more empathic.

"Chimpanzees tend to resolve conflict by using aggression, while bonobos are more likely to use behavioral mechanisms like sex and play to diffuse tension," Rilling says. "The social behaviors of the two species mirror individual differences within the human population."

Rilling heads Emory's Laboratory for Darwinian Neuroscience, a leader in the use of non-invasive neuro-imaging technology to compare the neurobiology of humans and other primates. The lab draws on resources of Emory's Yerkes National Primate Research Center.

"In addition to exploring links between neuroanatomy and different social behaviors, we're mapping the underlying biology for how species evolve and differentiate," Rilling says.

A range of imaging and analytical techniques were used in the chimpanzee-bonobo study. Voxel-based morphometry compared the gray matter in standard structural scans of the brains. Diffusion tensor imaging (DTI) captured the white matter connections, to compare the fiber tracts that "wire" the brain.

The results showed that bonobos have more developed circuitry for key nodes within the limbic system, the so-called emotional part of the brain, including the amygdala, the hypothalamus and the anterior insula. The anterior insula and the amygdala are both implicated in human empathy.

"We also found that the pathway connecting the amygdala and the prefrontal cortex is larger in bonobos than chimpanzees," Rilling says. "When our amygdala senses that our actions are causing someone else distress, we may use that pathway to adjust our behavior in a prosocial direction."

Chimpanzees have better developed visual system pathways, according to the analysis. Previous research has suggested that those pathways are important for tool use, a skill which chimpanzees appear better at than bonobos.

Provided by Emory University (news : web)
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Humans have more sophisticated brains than Primates because of chemicals

Evolution of cognition might be down to brain chemistry”, Andy Coghlan reports, (New Scientist, 28 March 2011):

Philipp Khaitovich of the Partner Institute for Computational Biology in Shanghai, China, and colleagues analysed brain tissue from deceased humans, chimpanzees and rhesus macaques to study the concentrations of 100 chemicals linked with metabolism.

In the human prefrontal cortex, the levels of 24 of these were drastically different from levels in the corresponding brain regions of the other primates. In the cerebellum, however, there were far fewer differences between humans and the other animals, with just six chemicals showing different concentrations.

This suggests that, since our lineage split off from other primates, the evolution of metabolism in the thinking and learning parts of our brains has gone much further than in our “primitive” cerebellum.

I wonder if “‘primitive’ cerebellum” will go the way of “junk” DNA?

The authors may think (they don’t say so directly) that differing brain chemistry is a cause of higher order thinking. It could just as easily be interpreted as a platform for higher order thinking, or even as a consequence of it.
Excerpt: If the error structures of the archaic DNA and one of the modern human DNA samples are similar to each other for one of many reasons, the ABBA-BABA test could report admixture when it did not in fact occur. Even a very small proportion of shared errors could cause a strong effect on the ABBA-BABA statistic. For example, small effects that we typically tend to ignore, such as shared contamination of reagents between the samples, could cause artifactual evidence of admixture.

In this podcast Dr. Patricia Fanning examines the evolutionary claim that humans evolved more sophisticated brains as a result of chemicals other primates did not have.
Story Credit here and video

Chimpanzee Study Sheds Light on Natural History of HIV

ALBANY, N.Y. (March 16, 2011) -- A University at Albany scientist's research in African chimpanzee populations may provide new insights into the natural history of simian immunodeficiency virus (SIVcpz), and the origins of HIV-AIDS.

In the cover article of the March 22nd issue of the Proceedings of the National Academy of Sciences, research by UAlbany biologist Mary Katherine Gonder and colleagues examines genetic data from one of the largest samples of chimpanzees to date. The sample originated from the west African nation of Cameroon, home to two chimpanzee subspecies: the central African chimpanzee (Pan troglodytes troglodytes) and the Nigeria-Cameroon chimpanzee (P. t. ellioti) which occupies the Gulf of Guinea biodiversity hotspot in Nigeria and Cameroon.

The study showed that the Nigeria-Cameroon chimpanzee constitutes a population exhibiting reproductive and genetic distinctiveness that clearly separates it from other chimpanzee subspecies.

Cameroon, said Gonder, is important in understanding the natural history of HIV-AIDS. Simian immunodeficiency virus found in central African chimpanzees from southern Cameroon is the likely progenitor of HIV-1 groups M and N. However, SIVcpz does not appear to occur naturally in the Nigeria-Cameroon chimpanzee, although the current sample of chimpanzees from this region tested to date remains small. The reasons the Nigeria-Cameron chimpanzee is not naturally infected with SIVcpz remain unclear, but could be explained by a lack of breeding between Nigeria-Cameroon chimpanzees and central African chimpanzees, extinctions of local chimpanzee communities from a simian AIDS-like syndrome associated with SIVcpz infection, natural resistance to SIVcpz infection, or combinations of these factors.

The research has broad implications for many branches of science and conservation practice. The research found that central and east Africa chimpanzees share most of their genetic history, despite having been thought by scientists, for nearly 100 years, to be very different from each other. According to the research, central and east African chimpanzees have stopped exchanging genes only relatively recently.

"What is revealing," said Gonder, "is how different the Nigeria-Cameroon chimpanzee is from all other chimpanzees. This forced us to reexamine and to reinterpret how chimpanzee populations are structured in other regions of Africa. Overall, our study provides a new model for interpreting chimpanzee population structure, which may have implications for understanding why SIVcpz occurs at a high prevalence in chimpanzees across equatorial Africa but is absent in Nigeria-Cameroon chimpanzees."
Gonder's research is supported by a grant from the National Science Foundation.
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"Are there functional, highly conserved genetic elements in the chimpanzee genome that are completely missing in humans?'"

Humans are clearly different from chimpanzees. The question is, why? According to researchers at the Stanford University School of Medicine, it may boil down in part to what we don't have, rather than what we do. The loss of snippets of regulatory DNA, the scientists found, could be the reason why, for example, humans lack the penile spines found in many other mammals, and also why specific regions of our brains are larger than those of our closest relatives.

Understanding these and other differences may help us learn what it means to be human. But it took the recent advent of whole-genome sequencing of several species and an open-minded, combined computational and experimental approach to reveal the particular two-steps-forward, one-step-back evolutionary dance that set us apart from other primates millions of years ago.

"Rather than looking for species-specific differences in specific genes or genomic regions that exist in humans, we asked, 'Are there functional, highly conserved genetic elements in the chimpanzee genome that are completely missing in humans?'" said Gill Bejerano, PhD, assistant professor of developmental biology and of computer science. "We found several hundred locations that, as far as we could see, are absent in our species alone." Until now, many evolutionary geneticists focused on differences among genes, rather than the regulatory regions outside the genes.

Losing small pieces of regulatory DNA, rather than the genes they control, means that the related changes are likely to be subtle: Although the location or the timing of the expression of the gene within the body may change, the gene product itself remains functional. The distinction leads to viable differences among individuals that can eventually lead to the development of new traits and species.
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New study claims man lost the penile spines of other primates during evolution

Scientists believe men once had small spines on their genitalia such as those found in chimpanzees, cats and mice.

Analysis of the genomes of humans, chimpanzees and macaques indicates that a DNA sequence thought to play a role in the production of these spines have been deleted in humans, but has been preserved in other primates.
It suggests another genetic deletion may have led to the expansion of specific regions of the human brain.
The study is in the journal Nature.

We're trying to find the molecular basis of being human”
David Kingsley
Stanford University

The researchers at Stanford, Georgia and Pennsylvania State universities in the US wanted to trace evolutionary changes in human DNA.
They compared the human genome with those of the chimpanzee and macaque, and came up with 510 stretches of DNA that have been conserved in our primate relatives but deleted in humans.

Nearly all these DNA regions appear to play a regulatory role in the function of nearby genes.

The researchers then focused on two deletions, linking one to penile spines and another to the growth of specific areas of the brain.

They then tested the effects of the deleted sequences in human skin and neural tissue, and found further evidence to support their claims.

"We're trying to find the molecular basis of being human," said Professor David Kingsley of Stanford University, one of the authors of the study.

"That's a really ambitious goal; but we live at this unique time where we have the complete genome sequence of ourselves and our closest relatives, so you can systematically go through and find all the ways that we differ from other organisms."

Arms race

Penile spines are barb-like structures found in many mammals. Their role remains under debate, and they may play different roles in different species.

They may increase stimulation for the male during mating. They might also play a part in inducing female ovulation in a small number of species, but there is evidence that they can cause damage to the female too.

Then there is the suggestion that they might have evolved to remove "mating plugs" - material that some male species deposit in the female genital tract to block other males' attempts to fertilise the same female.

"It's been proposed these structures can help remove the copulatory plugs left by other males; so in some mammals with multi-male mating systems, there's quite a little arms race going on for fertilisation," said Professor Kingsley.

The researchers believe the loss of these spines in humans may be related to changes in human courtship.

The loss of spines, they say, would result in less sensitivity and longer copulation, and may be associated with stronger pair-bonding in humans and greater paternal care for human offspring.

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Missouri is trying to pass a law to stop the breeding of Primates..... YEAH!!!!! Good bye Connie Casey Braun

Readers!!! This has made my year!!!! Everyday I do research on articles about Primates, and for the most part it is all bad or very sad news, but not today!!! This is something to hope for and will change the world of primates as we know it.

Connie Casey Braun of the Missouri Primate foundation (there's that word again that makes me laugh... foundation haha) is the largest breeder in the US and then there is another chimpanzee breeder in Missouri that recently bought out the breeder chimps from the Glasses in Texas. if these 2 breeding facilities have to have all of the chimps fixed that will be the end of pet chimps, pets in the entertainment business, chimp attacks, babies being ripped off their moms screaming. this my dear readers would be a miracle, I will keep my fingers crossed for this law to go through. KUDOS to the St Louis Zoo!!!!!

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JEFFERSON CITY — A chimpanzee named Travis mauled a woman and left her face unrecognizable when he escaped his home in Stamford, Conn., and attacked Charla Nash, a close friend of his owner on Feb. 16, 2009. A year later, another chimpanzee, Sueko, also escaped from his home in Kansas City, and attacked a police car. Both Travis and Sueko came from Jefferson County, Mo.

The Senate Agriculture Committee debated a bill that would require owners to obtain permits for and neuter their primates incited passionate testimonies from several Missouri primate breeders.

Sen. Joseph Keaveny, D-St. Louis City, sponsored the bill after Eric Miller, veterinarian and senior vice president at the Saint Louis Zoo, requested these large and exotic animals be regulated.
"Missouri is one of the few states with no (statewide) regulation of large and exotic animals," Miller said. "It's a national standard Missouri is working on catching up to."

Currently, Missouri regulates these primates on a county-by-county basis. Some counties in Missouri don't have primate requirements; others require primate owners to register their pets with the county sheriff. Owners must give the sheriff's office their address, a description of their primate and a description of the primate's living conditions.

If the bill passes, the Missouri Department of Agriculture would issue the statewide permits to primate owners, however, they have not yet taken a position for or against the bill.

More than 25 people attended a March 3 committee hearing to speak against the bill. Miller, the only proponent who spoke in favor of the bill, testified on behalf of the Saint Louis Zoo.

Suzanne Windsor, a U.S. Department of Agriculture-licensed exhibitor of primates, opposed the bill.

"It's an all out ban," Windsor said. "They are trying to go above and beyond what the state is supposed to be doing by going above and beyond federal regulations."

Her main concern was the bill's requirement to spay and neuter — both of which are high-risk surgeries for a primate, whose reproductive system resembles a human's. She said it would result in the gradual phase-out of Missouri primate breeding.
"For people that are USDA-licensed to breed and sell, it causes unnecessary surgeries on primates that could cause their deaths," Windsor said. "If you have a 22-year-old primate that's never been spayed, there's a good chance she could never come off that table [alive]."

Keaveny said he is looking into changes to the bill to appease the opposition. He said he has received several suggestions from a veterinarian to help the bill pass next year.

"We are open to making those [necessary] adjustments," he said.

The bill would exempt zoos, nonprofit organizations, animal control and law enforcement, circuses, educational institutions and exhibits, animal sanctuaries and veterinarians.

Currently, 15 states have a permit system for owning primates and 20 states have outlawed some, if not all, primate ownership. States that don't have regulations include Missouri border states Kansas and Nebraska.

A violation of the act would result in a class A misdemeanor charge unless the person intentionally releases a non-human primate, which would result in a class D felony.
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Chimpanzees can figure out what others are thinking

Chimpanzees apparently can figure out what others are thinking, a mental ability seen nowhere else in the animal kingdom so far except for in humans, scientists find.

This discovery may shed light on how advanced the mind of the last common ancestor of humans and chimps might have been.

In recent years, research has revealed just how much chimpanzees — humanity's closest living relatives — have in common with us. They can hunt with spears, play with improvised dolls and mourn their dead.

Past research also showed that chimps can figure out what others know. For instance, subordinate chimpanzees ordinarily let more dominant members get at food first, but they will eat items if they know that others cannot see them.

It was an open question as to whether chimps' mental capabilities might go beyond knowing what others might know to what others might think. Now scientists find they might possess this advanced mental ability.

The researchers tested 12 juvenile and teenage chimpanzees housed at the Wolfgang Köhler Primate Research Center. First the apes watched while a single piece of food, such as a banana slice, was hidden under one of two boards placed on a table. If food was tucked under one board, that board would visibly not lie flat on the table, since the good under it propped it up at a slant; if it was concealed under the other, that board would remain flat, because there was a hole in the table under that board.

The table (which held the boards) was then temporarily hidden from view. Sometimes another chimp was then given a chance to look for a snack at the table. The table was then shown again to the first set of apes.

Normally, the apes that saw the food get hidden went for the slanted board after they were again shown the table. However, if they knew that competitors had been given a chance at that table, they went after the other board. In other words, they avoided the option they would have normally chosen themselves on the assumption that the competitor had already done so and remembered which board was which.

"When a cognitive ability like this can be shown in our closest living relative — and, to our current knowledge, in no other non-human species — it can be argued that the last common ancestor might also have shared this ability," researcher Martin Schmelz, a primatologist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, told LiveScience. "The more we know about the differences and similarities of humans and chimpanzees, the clearer our picture of the last common ancestor can become."

The scientists detailed their findings online Jan. 31 in the Proceedings of the National Academy of Sciences.
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Awesome Video of how intelligent Chimpanzees are

How does a chimpanzee see the world? A research project at Edinburgh Zoo is designed to answer just that question in an innovative new way – by training chimps to use video touch screens and giving them a special chimp-proof camera.

How will they react to tools which in evolutionary terms are a few million years ahead of them?

As chimp specialist Betsy Herrelko finds out, trying to communicate with chimps using video technology has its trials and tribulations as power struggles, bites and fights get in the way of the hairy chimp directors.

However, by the end of the programme we are privileged to see the world’s first film shot by chimpanzees.
Story Credit here and an awesome video

Where is Ham the Chimpanzee used by NASA now?

This was just a horrible thing to do. Gosh they couldn't get any human volunteers for this?

Ham the Chimp, astronaut (July 1956 – January 19, 1983)
The first primate launched in space, Ham was also the first African astronaut, having been born in Cameroon. The only African human to have been in space was South African “space tourist” Mark Shuttleworth, in 2002.

Ham was only given his name upon successful completion of his 17-minute journey into space, as NASA didn’t want any potential dead animals in space to have a cutesy name. Although officially known as “Chimp 65” during his mission, he was informally known by his handlers as “Chop Chop Chang”.

Upon his death, Ham’s flesh tissue was removed from his body by being placed in a tank of dermestid beetles. His skeleton is currently on show at the National Museum of Health and Medicine, alongside a display of the skeletons of American Civil War soldiers.
Dom Passantino
Story Credit here

Chimpanzee and Bonobo education

"Panina" redirects here. For the Russian surname Panina, see Panin (disambiguation).
Chimpanzee, sometimes colloquially chimp, is the common name for the two extant species of ape in the genus Pan. The Congo River forms the boundary between the native habitat of the two species:[2]
Common Chimpanzee, Pan troglodytes (West and Central Africa)
Bonobo, Pan paniscus (forests of the Democratic Republic of the Congo)

Chimpanzees are members of the Hominidae family, along with gorillas, humans, and orangutans. Chimpanzees split from human evolution about 6 million years ago and the two chimpanzee species are the closest living relatives to humans, all being members of the Hominini tribe (along with extinct species of Hominina subtribe). Chimpanzees are the only known members of the Panina subtribe. The two Pan species split only about one million years ago.

Common Chimpanzee (Pan troglodytes)
Scientific classification
Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Primates
Family: Hominidae
Subfamily: Homininae
Tribe: Hominini
Subtribe: Panina
Genus: Pan
Oken, 1816
Type species
Pan troglodytes (Common Chimpanzee)
Pan paniscus (Bonobo)

Species
Pan troglodytes
Pan paniscus

Distribution of Pan troglodytes (Common Chimpanzee) and Pan paniscus (Bonobo, in red).

The taxonomic relationships of Hominoidea
Evolutionary relationship:
History of hominoid taxonomy

The taxonomic relationships of HominoideaThe genus Pan is considered to be part of the subfamily Homininae to which humans also belong. These two species are the closest living evolutionary relatives to humans, sharing a common ancestor with humans six million years ago.[3] Research by Mary-Claire King in 1973 found 99% identical DNA between human beings and chimpanzees,[4] although research since has modified that finding to about 94%[5] commonality, with some of the difference occurring in non-coding DNA. It has been proposed that troglodytes and paniscus belong with sapiens in the genus Homo, rather than in Pan. One of the arguments for this is that other species have been reclassified to belong to the same genus on the basis of less genetic similarity than that between humans and chimpanzees.

Fossils
A lot of human fossils have been found, but chimpanzee fossils were not described until 2005. Existing chimpanzee populations in West and Central Africa do not overlap with the major human fossil sites in East Africa. However, chimpanzee fossils have now been reported from Kenya. This would indicate that both humans and members of the Pan clade were present in the East African Rift Valley during the Middle Pleistocene.[6]

Anatomy and physiology
The male common chimp is up to 1.7 metres (5.6 ft) high when standing, and weighs as much as 70 kilograms (150 lb); the female is somewhat smaller. The common chimp’s long arms, when extended, have a span one and a half times as long as the body’s height and a chimpanzee's arms are longer than its legs.[7] The bonobo is a little shorter and thinner than the common chimpanzee but has longer limbs. Both species use their long, powerful arms for climbing in trees. On the ground, chimpanzees usually walk on all fours using their knuckles for support with their hands clenched, a form of locomotion called knuckle-walking. Chimpanzee feet are better suited for walking than are those of the orangutan because the chimp’s soles are broader and the toes shorter. Both the common chimpanzee and bonobo can walk upright on two legs when carrying objects with their hands and arms. The Bonobo has proportionately longer upper limbs and tends to walk upright more often than the Common Chimpanzee. The coat is dark; the face, fingers, palms of the hands, and soles of the feet are hairless; and the chimp has no tail. The exposed skin of the face, hands and feet varies from pink to very dark in both species, but is generally lighter in younger individuals, darkening as maturity is reached. A University of Chicago Medical Centre study has found significant genetic differences between chimpanzee populations.[8] A bony shelf over the eyes gives the forehead a receding appearance, and the nose is flat. Although the jaws protrude, the lips are thrust out only when a chimp pouts. The brain of a chimpanzee is about half the size of the human brain.[9]

Chimpanzee testicles are unusually large for their body size, with a combined weight of about 4 ounces (110 g) compared to a gorilla's 1 ounce (28 g) or a human's 1.5 ounces (43 g). This is generally attributed to sperm competition due to the polyandrous nature of chimpanzee mating behavior.[10] Chimpanzees reach puberty at an age of between 8 and 10 years and rarely live past the age of 40 in the wild, but have been known to reach the age of more than 60 in captivity.

Bonobo


Behaviors

BonoboAnatomical differences between the Common Chimpanzee and the Bonobo are slight, but in sexual and social behaviour there are marked differences. The Common Chimpanzee has an omnivorous diet, a troop hunting culture based on beta males led by an alpha male, and highly complex social relationships. The Bonobo, on the other hand, has a mostly frugivorous diet and an egalitarian, nonviolent, matriarchal, sexually receptive behaviour.[11] Bonobos are well known to have frequent sex, with bisexuality the norm for both males and females, and also to use sex to help prevent and resolve conflicts. Different groups of chimpanzees also have different cultural behaviour with preferences for types of tools.[12] The Common Chimpanzee tends to display higher levels of aggression than the Bonobo.[13]

Social structure
Chimpanzees live in large multi-male and multi-female social groups called communities. Within a community there is a definite social hierarchy which is dictated by the position of an individual and the influence the individual has on others. Chimpanzees live in a leaner hierarchy in which more than one individual may be dominant enough to dominate other members of lower rank. Typically there is a dominant male referred to as the Alpha male. The Alpha male is the highest-ranking male who controls the group and maintains order during any disputes. In chimpanzee society the 'dominant male' does not always have to be the largest or strongest male but rather the most manipulative and political male who can influence the goings on within a group. Male chimpanzees typically attain dominance through cultivating allies who will provide support for that individual in case of future ambitions for power. Its within a male chimpanzee's character to display in an attempt to show strength and recognition from others which may be fundamental to holding on to status. The alpha male will regularly display by making their normally slim coats puffed up to increase view size and charge to look as threatening and as powerful as possible to intimidate other members in an attempt to hold on to power and maintain authority. Lower-ranking chimpanzees will show respect by making submissive gestures in body language or reaching out their hand while grunting. Female chimpanzees will show deference to the alpha male by presenting their hind-quarters.

Female chimpanzees also have a hierarchy which is influenced by the position of a female individual within a group. In some chimpanzee communities, the young females may inherit high status from a high-ranking mother. The females will also form allies to dominate lower-ranking females. In contrast to males who have a main purpose of acquiring dominant status for access to mating privileges and sometimes violent domination of subordinates, females acquire dominant status for access to resources such as food. High-ranking females will often get first access to resources. In general, both genders acquire dominant status to improve social standing within a group.

Its often the females who choose the alpha male. For a male chimpanzee to win the alpha status he must gain acceptance from the females in the community as they are the ones who actually dictate the way the lifestyles are set up (the females are the ones who ensure the survival of the next generation; they have to make sure that their group is going to places that supply them with enough food). There are cases where a group of dominant females will oust an alpha male who is not to their preference and rather back up the other male who they see potential of leading the group as a successful alpha male.

Intelligence
Diagram of brain. Topography of the main groups of foci in the motor field of ChimpanzeeChimpanzees make tools and use them to acquire foods and for social displays; they have sophisticated hunting strategies requiring cooperation, influence and rank; they are status conscious, manipulative and capable of deception; they can learn to use symbols and understand aspects of human language including some relational syntax, concepts of number and numerical sequence;[14] and they are capable of spontaneous planning for a future state or event.[15]

Diagram of brain. Topography of the main groups of foci in the motor field of Chimpanzee

Tool use
One of the most significant discoveries was in October 1960 when Jane Goodall observed the use of tools among chimpanzees. Recent research indicates that chimpanzee stone tool use dates to at least 4,300 years ago.[16] Chimpanzee tool usage includes digging into termite mounds with a large stick tool, and then using a small stick that has been altered to "fish" the termites out.[17] A recent study revealed the use of such advanced tools as spears, with which Common Chimpanzees in Senegal sharpen with their teeth and use to spear Senegal Bushbabies out of small holes in trees.[18][19] Before the discovery of tool use in chimps, it was believed that humans were the only species to make and use tools, but several other tool-using species are now known.[20][21]

Empathy
Chimpanzee mother and babyRecent studies have shown that chimpanzees engage in apparently altruistic behaviour within groups,[22][23] but are indifferent to the welfare of unrelated group members.[24]

Chimpanzee mother and baby

Evidence for "chimpanzee spirituality" includes display of mourning, "incipient romantic love", "rain dance", appreciation of natural beauty such as a sunset over a lake, curiosity and respect towards wildlife (such as the python, which is neither a threat nor a food source to chimpanzees), empathy toward other species (such as feeding turtles) and even "animism" or "pretend play" in chimps cradling and grooming rocks or sticks.[25]

Communication
Chimps communicate in a manner similar to human non-verbal communication, using vocalizations, hand gestures, and facial expressions. Research into the chimpanzee brain has revealed that chimp communication activates an area of the chimp brain that is in the same position as Broca's area, the language center in the human brain.[26]

Studies of language

Side profile of a Chimpanzee

Scientists have long been fascinated with the studies of language, believing it to be a unique human cognitive ability. To test this hypothesis, scientists have attempted to teach human language to several species of great apes. One early attempt by Allen and Beatrice Gardner in the 1960s involved spending 51 months teaching American Sign Language to a chimpanzee named Washoe. The Gardners reported that Washoe learned 151 signs, and that she had spontaneously taught them to other chimpanzees.[27] Over a longer period of time, Washoe learned over 800 signs.[28]

There is ongoing debate among some scientists, notably Noam Chomsky and David Premack, about non-human great apes' ability to learn language. Since the early reports on Washoe, numerous other studies have been conducted with varying levels of success,[29] including one involving a chimpanzee named, in parody, Nim Chimpsky, trained by Herbert Terrace of Columbia University. Although his initial reports were quite positive, in November 1979, Terrace and his team re-evaluated the videotapes of Nim with his trainers, analyzing them frame by frame for signs as well as for exact context (what was happening both before and after Nim’s signs). In the re-analysis, Terrace concluded that Nim’s utterances could be explained merely as prompting on the part of the experimenters, as well as mistakes in reporting the data. “Much of the apes’ behavior is pure drill,” he said. “Language still stands as an important definition of the human species.” In this reversal, Terrace now argued that Nim’s use of ASL was not like human language acquisition. Nim never initiated conversations himself, rarely introduced new words, and simply imitated what the humans did. Nim’s sentences also did not grow in length, unlike human children whose vocabulary and sentence length show a strong positive correlation.[30]

Memory
A 30-year study at Kyoto University’s Primate Research Institute has shown that chimps are able to learn to recognize the numbers 1-9 and their values. The chimps further show an aptitude for photographic memory, demonstrated in experiments in which the jumbled digits 1-9 are flashed onto a computer screen for less than a quarter of a second, after which the chimp, Ayumu, is able to correctly and quickly point to the positions where they appeared in ascending order. The same experiment was failed by world memory champion Ben Pridmore on most attempts.[31]

Laughter in apes
Young chimpanzees playingLaughter might not be confined or unique to humans. The differences between chimpanzee and human laughter may be the result of adaptations that have evolved to enable human speech. Self-awareness of one's situation as seen in the mirror test, or the ability to identify with another's predicament (see mirror neurons), are prerequisites for laughter, so animals may be laughing in the same way that humans do.

Young chimpanzees playing

Chimpanzees, gorillas, and orangutans show laughterlike vocalizations in response to physical contact, such as wrestling, play chasing, or tickling. This is documented in wild and captive chimpanzees. Common Chimpanzee laughter is not readily recognizable to humans as such, because it is generated by alternating inhalations and exhalations that sound more like breathing and panting. There are instances in which non-human primates have been reported to have expressed joy. One study analyzed and recorded sounds made by human babies and Bonobos when tickled. It found that although the Bonobo's laugh was a higher frequency, the laugh followed a pattern similar to that of human babies and included similar facial expressions. Humans and chimpanzees share similar ticklish areas of the body, such as the armpits and belly. The enjoyment of tickling in chimpanzees does not diminish with age.[32]
Aggression

Male chimpanzees in Mahale National Park, Tanzania
Common Chimpanzees, particularly males, can be very aggressive. They are highly territorial and are known to kill other chimps.[33] Chimpanzees also engage in targeted hunting of lower order primates such as the red colobus[34] and bush babies,[35][36] and use the meat from these kills as a "social tool" within their community.[37] In February 2009, after an incident in which a pet chimp named Travis attacked and mutilated a woman in Stamford, Connecticut, the U.S. House of Representatives approved a primate pet ban in the United States.[38]

Interactions with humans
History
Gregoire: 62-year-old chimpanzeeAfricans have had contact with chimpanzees for millennia. Chimpanzees have been kept as pets for centuries in a few African villages, especially in the Democratic Republic of Congo. In Virunga National Park in the east of the country the park authorities regularly confiscate chimpanzees from people who are keeping them as pets.[39] The first recorded contact of Europeans with chimps took place in present-day Angola during the 17th century. The diary of Portuguese explorer Duarte Pacheco Pereira (1506), preserved in the Portuguese National Archive (Torre do Tombo), is probably the first European document to acknowledge that chimpanzees built their own rudimentary tools.

Male chimpanzees in Mahale National Park, Tanzania
The first use of the name "chimpanzee", however, did not occur until 1738. The name is derived from a Tshiluba language term "kivili-chimpenze", which is the local name for the animal and translates loosely as "mockman" or possibly just "ape". The colloquialism "chimp" was most likely coined some time in the late 1870s.[40] Biologists applied Pan as the genus name of the animal. Chimps as well as other apes had also been purported to have been known to Western writers in ancient times, but mainly as myths and legends on the edge of European and Arab societal consciousness, mainly through fragmented and sketchy accounts of European adventurers. Apes are mentioned variously by Aristotle, as well as the English Bible, where they are described as having been collected by Solomon. (1 Kings 10:22. However the Hebrew word, qőf, may mean a monkey.) Apes are mentioned in the Qur'an (7:166), where God tells Israelites who transgressed Shabbat "Be ye apes".
The first of these early transcontinental chimpanzees came from Angola and were presented as a gift to Frederick Henry, Prince of Orange in 1640, and were followed by a few of its brethren over the next several years. Scientists described these first chimpanzees as "pygmies", and noted the animals' distinct similarities to humans. The next two decades would see a number of the creatures imported into Europe, mainly acquired by various zoological gardens as entertainment for visitors.

Hugo Rheinhold's Affe mit Schädel ("Ape with skull") is an example of how chimps were viewed at the end of the 19th century
Hugo Rheinhold's Affe mit Schädel ("Ape with skull") is an example of how chimps were viewed at the end of the 19th century.Darwin's theory of natural selection (published in 1859) spurred scientific interest in chimpanzees, as in much of life science, leading eventually to numerous studies of the animals in the wild and captivity. The observers of chimpanzees at the time were mainly interested in behaviour as it related to that of humans. This was less strictly and disinterestedly scientific than it might sound, with much attention being focused on whether or not the animals had traits that could be considered 'good'; the intelligence of chimpanzees was often significantly exaggerated, as immortalized in Hugo Rheinhold's Affe mit Schädel (see image, left). By the end of the 19th century chimpanzees remained very much a mystery to humans, with very little factual scientific information available.

Chimpanzee at the Los Angeles Zoo

The 20th century saw a new age of scientific research into chimpanzee behaviour. Before 1960, almost nothing was known about chimpanzee behaviour in their natural habitat. In July of that year, Jane Goodall set out to Tanzania's Gombe forest to live among the chimpanzees, where she primarily studied the members of the Kasakela chimpanzee community. Her discovery that chimpanzees made and used tools was groundbreaking, as humans were previously believed to be the only species to do so. The most progressive early studies on chimpanzees were spearheaded primarily by Wolfgang Köhler and Robert Yerkes, both of whom were renowned psychologists. Both men and their colleagues established laboratory studies of chimpanzees focused specifically on learning about the intellectual abilities of chimpanzees, particularly problem-solving. This typically involved basic, practical tests on laboratory chimpanzees, which required a fairly high intellectual capacity (such as how to solve the problem of acquiring an out-of-reach banana). Notably, Yerkes also made extensive observations of chimpanzees in the wild which added tremendously to the scientific understanding of chimpanzees and their behaviour. Yerkes studied chimpanzees until World War II, while Köhler concluded five years of study and published his famous Mentality of Apes in 1925 (which is coincidentally when Yerkes began his analyses), eventually concluding that "chimpanzees manifest intelligent behaviour of the general kind familiar in human beings ... a type of behaviour which counts as specifically human" (1925).[41]

The August 2008 issue of the American Journal of Primatology reported results of a year-long study of chimpanzees in Tanzania’s Mahale Mountains National Park which produced evidence that chimpanzees are becoming sick from viral infectious diseases they have likely contracted from humans. Molecular, microscopic and epidemiological investigations demonstrated that the chimpanzees living at Mahale Mountains National Park have been suffering from a respiratory disease that is likely caused by a variant of a human paramyxovirus.[42]
Studies

Enos the space chimp before being inserted into the Mercury-Atlas 5 capsule in 1961.As of November 2007, there were 1,300 chimpanzees housed in 10 U.S. laboratories (out of 3,000 great apes living in captivity there), either wild-caught, or acquired from circuses, animal trainers, or zoos.[43] Most of the labs either conduct or make the chimps available for invasive research,[44] defined as "inoculation with an infectious agent, surgery or biopsy conducted for the sake of research and not for the sake of the chimpanzee, and/or drug testing".[45] Two federally-funded laboratories use chimps: Yerkes National Primate Research Laboratory at Emory University in Atlanta, Georgia, and the Southwest National Primate Center in San Antonio, Texas.[46] Five hundred chimps have been retired from laboratory use in the U.S. and live in sanctuaries in the U.S. or Canada.[44]
Chimpanzees used in biomedical research tend to be used repeatedly over decades, rather than used and killed as with most laboratory animals. Some individual chimps currently in U.S. laboratories have been used in experiments for over 40 years.[47] According to Project R&R, a campaign to release chimps held in U.S. labs—run by the New England Anti-Vivisection Society in conjunction with Jane Goodall and other primate researchers—the oldest known chimp in a U.S. lab is Wenka, who was born in a laboratory in Florida on May 21, 1954.[48] She was removed from her mother on the day of birth to be used in a vision experiment that lasted 17 months, then sold as a pet to a family in North Carolina. She was returned to the Yerkes National Primate Research Center in 1957 when she became too big to handle. Since then, she has given birth six times, and has been used in research into alcohol use, oral contraceptives, ageing, and cognitive studies.[49]

With the publication of the chimpanzee genome, there are reportedly plans to increase the use of chimps in labs, with some scientists arguing that the federal moratorium on breeding chimps for research should be lifted.[46][50] A five-year moratorium was imposed by the U.S. National Institutes of Health (NIH) in 1996, because too many chimps had been bred for HIV research, and it has been extended annually since 2001.[46]

Other researchers argue that chimps are unique animals and either should not be used in research, or should be treated differently. Pascal Gagneux, an evolutionary biologist and primate expert at the University of California, San Diego, argues that, given chimpanzees' sense of self, tool use, and genetic similarity to human beings, studies using chimps should follow the ethical guidelines that are used for human subjects unable to give consent.[46] Also, a recent study suggests that chimpanzees which are retired from labs exhibit a form of posttraumatic stress disorder.[51] Stuart Zola, director of the Yerkes National Primate Research Laboratory, disagrees. He told National Geographic: "I don't think we should make a distinction between our obligation to treat humanely any species, whether it's a rat or a monkey or a chimpanzee. No matter how much we may wish it, chimps are not human."[46]

An increasing number of governments are enacting a Great Ape research ban forbidding the use of chimpanzees and other great apes in research or toxicology testing.[52] As of 2006, Austria, New Zealand, the Netherlands, Sweden, and the UK had introduced such bans.[53]

In popular culture
Chimpanzees have been commonly stereotyped in popular culture, where they are most often cast in standardized roles[54] as childlike companions, sidekicks or clowns.[55] They are especially suited for the latter role on account of their prominent facial features, long limbs and fast movements, which humans often find amusing.[55] Accordingly, entertainment acts featuring chimpanzees dressed up as humans have been traditional staples of circuses and stage shows.[55]

In the age of television, a new genre of chimp act emerged in the United States: series whose cast consisted entirely of chimpanzees dressed as humans and "speaking" lines dubbed by human actors.[54] These shows, examples of which include Lancelot Link, Secret Chimp in the 1970s or The Chimp Channel in the 1990s, relied on the novelty of their ape cast to make their timeworn, low comedy gags funny.[54] Their chimpanzee "actors" were as interchangeable as the apes in a circus act, being amusing as chimpanzees and not as individuals.[54] Animal rights group, PETA, has urged advertisers against the use of chimpanzees in television and commercials, citing animal abuse.[56]

When chimpanzees appear in other TV shows, they generally do so as comic relief sidekicks to humans. In that role, for instance, J. Fred Muggs appeared with Today Show host Dave Garroway in the 1950s, Judy on Daktari in the 1960s or Darwin on The Wild Thornberrys in the 1990s.[54] In contrast to the fictional depictions of other animals, such as dogs (as in Lassie), dolphins (Flipper), horses (The Black Stallion) or even other great apes (King Kong), chimpanzee characters and actions are rarely relevant to the plot.[54]

Portrayals in science fictionThe rare depictions of chimpanzees as individuals rather than stock characters, and as central rather than incidental to the plot[54] are generally found in works of science fiction. Robert A. Heinlein's short story "Jerry Was a Man" (1947) centers on a genetically enhanced chimpanzee suing for better treatment. The 1972 film Conquest of the Planet of the Apes, set in the near future, portrays a revolt of enslaved apes led by the only talking chimpanzee, Caesar, against their human masters.[54] Another short story "The Pope of the Chimps" by Robert Silverberg, set in the present day, shows the development of the first signs of religiosity in a group of chimpanzees, much to the surprise of the humans observing them. David Brin's Uplift novels present a future in which humans have "uplifted" chimpanzees (and certain other species) with human-level sapience.
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Human/Chimp Similarities are undermined by new Chromosome Research

A recent high-profile article in the journal Nature released the results of a study with implications that shocked the scientific community because they contradict long-held claims of human-chimp DNA similarity.1 A previous Acts & Facts article showed that much of the research surrounding the often touted claims of 98 percent (or higher) DNA similarity between chimps and humans has been based on flawed and biased research.2 The problem is that the similarity has been uncertain because no one has performed an unbiased and comprehensive DNA similarity study until now. And the results are not good news for the story of human evolution.

One of the main deficiencies with the original chimpanzee genome sequence published in 20053 was that it was a draft sequence and only represented a 3.6-fold random coverage of the 21 chimpanzee autosomes, and a 1.8-fold redundancy of the X and Y sex chromosomes. In a draft coverage, very small fragments of the genome are sequenced in millions of individual reactions using high-throughput robotics equipment. This produces individual sequence fragments of about 500 to 1,200 bases in length. Based on overlapping reads, these individual sequences are assembled into contiguous clusters of sequence called sequencing contigs. In the case of a chimpanzee, an organism with a genome size of about 3 billion bases, a 3.6-fold coverage means that approximately 10.8 billion bases of DNA were sequenced (3.6 x 3.0). The result is a data set consisting of thousands of random sequencing contigs, or islands of contiguous sequence that need to be oriented and placed in position on their respective chromosomes.
In the 2005 chimpanzee genome project and resulting Nature journal publication, the sequence contigs4 were not assembled and oriented based on a map of the chimpanzee genome, but rather on a map of the human genome. Given the fact that the chimpanzee genome is at least 10 percent larger5 overall than the human genome, this method of assembly was not only biased toward an evolutionary presupposition of human-chimp similarity, but was also inherently flawed.
The title of the recent journal article accurately sums up the research findings: "Chimpanzee and Human Y Chromosomes are Remarkably Divergent in Structure and Gene Content." Before getting into the details of their results, it is important to understand that for the first time, the chimpanzee DNA sequence for a chromosome was assembled and oriented based on a Y chromosome map/framework built for chimpanzee and not human. As a result, the chimpanzee DNA sequence could then be more accurately compared to the human Y chromosome because it was standing on its own merit.

The Y chromosome is found only in males and contains many genes that specify male features, as well as genetic and regulatory information that is expressed throughout the whole body. Because of the recent outcome comparing the chimp and human Y chromosomes in a more objective assessment, it is possible that major discrepancies will be revealed among the other chromosomes that are claimed to be so similar.

From a large-scale perspective, the human and chimp Y chromosomes were constructed entirely differently. On the human Y chromosome, there were found four major categories of DNA sequence that occupy specific regions. One can think of this in terms of geography. Just as a continent like Europe is divided into countries because of different people groups, so are chromosomes with different categories of DNA sequence.
Not only were the locations of DNA categories completely different between human and chimp, but so were their proportions. One sequence class, or category containing DNA with a characteristic sequence, within the chimpanzee Y chromosome had less than 10 percent similarity with the same class in the human Y chromosome, and vice versa. Another large class shared only half the similarities of the other species, and vice versa. One differed by as much as 3.3-fold (330 percent), and a class specific to human "has no counterpart in the chimpanzee MSY [male-specific Y chromosome]."1

As far as looking at specific genes, the chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps.
Under evolutionary assumptions of long and gradual genetic changes, the Y chromosome structures, layouts, genes, and other sequences should be much the same in both species, given the relatively short--according to the evolutionary timeline--six-million-year time span since chimpanzees and humans supposedly diverged from a common ancestor. Instead, the differences between the Y chromosomes are marked. R. Scott Hawley, a genetics researcher at the Stowers Institute in Kansas City who wasn't involved in the research, told the Associated Press, "That result is astounding."6

Because virtually every structural aspect of the human and chimp Y chromosomes was different, it was hard to arrive at an overall similarity estimate between the two. The researchers did postulate an overall 70 percent similarity, which did not take into account size differences or structural arrangement differences. This was done by concluding that only 70 percent of the chimp sequence could be aligned with the human sequence--not taking into account differences within the alignments.

In other words, 70 percent was a conservative estimate, especially when considering that 50 percent of the human genes were missing from the chimp, and that the regions that did have some similarity were located in completely different patterns. When all aspects of non-similarity--sequence categories, genes, gene families, and gene position--are taken into account, it is safe to say that the overall similarity was lower than 70 percent. The Nature article expressed the discrepancy between this data and standard evolutionary interpretations in a rather intriguing way: "Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation."1
So, the human Y chromosome looks just as different from a chimp as the other human chromosomes do from a chicken. And to explain where all these differences between humans and chimps came from, believers in big-picture evolution are forced to invent stories of major chromosomal rearrangements and rapid generation of vast amounts of many new genes, along with accompanying regulatory DNA.

However, since each respective Y chromosome appears fully integrated and interdependently stable with its host organism, the most logical inference from the Y chromosome data is that humans and chimpanzees were each specially created as distinct creatures.
New Chromosome Research Undermines Human-Chimp Similarity Claims
by Jeffrey Tomkins, Ph.D., & Brian Thomas, M.S.
References
1.Hughes, J.F. et al. 2010. Chimpanzee and human Y chromosomes are remarkably divergent in structure gene content. Nature. 463 (7280): 536-539.
2.Tomkins, J.P. 2009. Human-chimp similarities: common ancestries or flawed research? Acts & Facts. 38 (6): 12.
3.The Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 437 (7055): 69-87.
4.For the sequencing technology in use at the time, a typical DNA sequence read used four different types of DNA clone substrates and had individual read lengths from between 200 to 1,000 high-quality DNA bases. Because of repetitive blocks of sequence, these are difficult to computationally assemble into long contiguous blocks of sequence without a map or framework to orient the repetitive DNA sequence lengths.
5.Statistics on sequencing and mapping of the chimp genome are difficult to pin down even though the mapping and sequencing were largely completed by 2006. A report describing the massive effort to produce a more accurate view of the chimpanzee genome has not yet been published.
6.Borenstein, S. Men More Evolved? Y Chromosome Study Stirs Debate. Associated Press, January 13, 2010.
* Dr. Tomkins is Research Associate and Mr. Thomas is Science Writer at the Institute for Creation Research.
Cite this article: Tomkins, J. and B. Thomas. 2010. New Chromosome Research Undermines Human-Chimp Similarity Claims. Acts & Facts. 39 (4): 4-5.
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Chimpanzee Facts

Type: Mammal
Diet: Omnivore
Lifespan: Average around 45 years
Size: 1.2 - 1.7m
Weight: 32 - 60 kg
Habitat: Savannas, deciduous woodland, Montane forest, and rainforest
Range: Equatorial Africa
Scientific name: Pan troglodytes

Did you know?

•We, Homo sapiens, share 98.4% of our DNA with chimpanzees. To put this in perspective the American songbird species, the red-eyed vireos and the similar white-eyed vireos share only 97.1% of their genetic material.

•Chimpanzees have the same bones and muscles as humans with differences only in form, such as longer arms than legs. Adapted for quadrupedal movement and movement through the trees, chimpanzees have robust bodies and powerful arms. Because of their dense bones and muscle tissue, the upper body strength of a mature chimpanzee is 8-10 times that than that of humans.

•Chimpanzees are black, but older individuals may have a grey back. Both genders often have short white beards. The ears are prominent. Infants have a white tail tuft and pink to brown facial skin, which darkens by adulthood.

•Chimpanzees live in fluid social groups consisting of a core of multiple females and dominant related males, whom are highly territorial and will routinely patrol their home boundaries. Females tend to live a more solitary life than the males, often choosing to spend much of their time alone with their offspring.

•Chimpanzee infants are completely dependent on their mothers until about five years of age. When males are between the ages of 8-12 years, or adolescence, they will increase their independence and spend more time in the company of adult males. Females tend to remain close to their mothers during adolescence, becoming mature at age 11 but only beginning to breed at age 13-14. On average females will have about three offspring during their lifetime.

•Chimpanzees travel mostly on the ground but will mostly feed in trees during the day and make a new nest every night in the forest canopy to sleep.

•Their diet varies seasonally consisting mainly of fruit (~50-75%), but also leaves (~12-45%), flowers (~1-18%), seeds (~1-11%) and animal prey (~1-5%) such as grubs, termites, ants, wasps, birds and mammals including bush-pigs, duikers, rodents and even other primates. In the Ivory Coast chimpanzees will hunt together cooperatively to catch red colobus monkeys, the meat is much prized and its subsequent sharing strengthens male alliances and familial bonds.

•Chimpanzees have opposable thumbs and toes that allow for grasping, climbing, and object manipulation. Chimpanzees are very dexterous and are able to manipulate objects in their environment in order to fashion tools. These tools are usually used to obtain food sources. Sticks are used for termite fishing and ant dipping, leaf sponges to soak up water and in West Africa chimpanzees use specially chosen rocks to crack hard palm nuts, a behaviour that can take many years to perfect. Baby female chimps were recently discovered to play with sticks like human children play with dolls.

•Chimpanzees have many different vocalizations from soft grunts and lip smacks to alarm barks and screams. One of the most notable vocalizations is the pant hoot used in situations of increasing social excitement. Chimpanzees are also capable of learning basic human sign language.

•In response to our greater understanding of our close similarity to great apes in terms of their capacity for self recognition and their innate intelligence, a movement called The Great Ape Project, calls for certain civil rights to be granted to all great apes including the rights to life, liberty and freedom from torture.

•Chimpanzees are classified as endangered in the wild. Aside from habitat loss they are hunted for bushmeat and infants taken for sale into the pet trade. Over 1000 chimpanzees are still being kept and used in biomedical labs for research.
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Characterization of a new simian immunodeficiency virus strain in a naturally infected Pan troglodytes troglodytes chimpanzee with AIDS related symptoms

Data on the evolution of natural SIV infection in chimpanzees (SIVcpz) and on the impact of SIV on local ape populations are only available for Eastern African chimpanzee subspecies (Pan troglodytes schweinfurthii), and no data exist for Central chimpanzees (Pan troglodytes troglodytes), the natural reservoir of the ancestors of HIV-1 in humans. Here, we report a case of naturally-acquired SIVcpz infection in a P.t.troglodytes chimpanzee with clinical and biological data and analysis of viral evolution over the course of infection.

Results: A male chimpanzee (Cam155), 1.5 years, was seized in southern Cameroon in November 2003 and screened SIV positive during quarantine.

Clinical follow-up and biological analyses have been performed for 7 years and showed a significant decline of CD4 counts (1,380 cells/mm3 in 2004 vs 287 in 2009), a severe thrombocytopenia (130,000 cells/mm3 in 2004 vs 5,000 cells/mm3 in 2009), a weight loss of 21.8% from August 2009 to January 2010 (16 to 12.5 kg) and frequent periods of infections with diverse pathogens.DNA from PBMC, leftover from clinical follow-up samples collected in 2004 and 2009, was used to amplify overlapping fragments and sequence two full-length SIVcpzPtt-Cam155 genomes. SIVcpzPtt-Cam155 was phylogenetically related to other SIVcpzPtt from Cameroon (SIVcpzPtt-Cam13) and Gabon (SIVcpzPtt-Gab1).

Ten molecular clones 5 years apart, spanning the V1V4 gp120 env region (1,100 bp), were obtained. Analyses of the env region showed positive selection (dN-dS>0), intra-host length variation and extensive amino acid diversity between clones, greater in 2009.

Over 5 years, N-glycosylation site frequency significantly increased (p<0.0001).

Conclusions: Here, we describe for the first time the clinical history and viral evolution of a naturally SIV infected P.t.troglodytes chimpanzee. The findings show an increasing viral diversity over time and suggest clinical progression to an AIDS-like disease, showing that SIVcpz can be pathogenic in its host, as previously described in P.t.schweinfurthii.

Although studying the impact of SIV infection in wild apes is difficult, efforts should be made to better characterize the pathogenicity of the ancestors of HIV-1 in their natural host and to find out whether SIV infection also plays a role in ape population decline.

Author: Lucie EtienneEric NerrienetMatthew LeBretonGodwin Tafon BibilaYacouba FoupouapouognigniDominique RoussetAhmadou NanaCyrille DjokoUbald TamoufeAvelin AghokengEitel Mpoudi-NgoleEric DelaporteMartine PeetersNathan WolfeAhidjo Ayouba

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Project R&R's work to help stop experimenting on Chimpanzees

2011 is off to a hopeful start for 186 chimpanzees at Alamogordo Primate Facility (APF), who have been granted a reprieve from transfer to a Texas laboratory for use in invasive research.

According to a National Institutes of Health (NIH) statement issued yesterday, the transfer will be delayed “pending an Institute of Medicine [the health arm of the National Academy of Sciences] in-depth analysis to reassess the scientific need for the continued use of chimpanzees….” The report is expected to take about two years.

NEAVS/Project R&R and other national groups, including Animal Protection of New Mexico, breathed a sigh of relief at this decision, which came after months of urging the NIH to keep the chimpanzees in New Mexico. APF, a holding facility, does not conduct experiments on the premises, and the individuals now housed there have been spared from research for the past 10 years. NIH’s plan to move them to the Southwest National Primate Research Center to be readily available for invasive research provoked national opposition, including from New Mexico Governor Bill Richardson and other public figures.

Dr. Theodora Capaldo, NEAVS/Project R&R President, stated, “In the midst of national efforts to get all chimpanzees out of invasive research, this decision signals an important willingness on the part of our government to consider their policies toward chimpanzees in research at large.”

For chimpanzees like Flo, Danny, Heidi, Robbie, and the others at APF, the delay in the transfer is good fortune. Flo, the oldest chimpanzee at APF, is 53. According to Animal Protection of New Mexico, she has chronic weight loss, anemia, and cardiac arrhythmias. Flo gave birth to four children, all of whom were taken from her for research. All but one, Jojo — now 27 and also at APF — are dead.

While this halt to the transfer is promising, NEAVS/Project R&R will continue pressing NIH to permanently retire not only the Alamogordo chimpanzees but all those now held in labs. The Great Ape Protection Act, legislation which would end invasive chimpanzee research in the U.S. and release all federally-owned chimpanzees to sanctuary, had 161 cosponsors in the U.S. House of Representatives and six cosponsors in the Senate at the close of the 111th Congress.

NEAVS/Project R&R’s work, including reviews of chimpanzee use in human disease research, along with the work of millions of individuals and dozens of other animal protection groups and sanctuaries, is building steady progress for this legislation. Broad-based support for the bill comes from bipartisan legislative leadership and co-sponsorship, as well as animal protection groups, scientists, chimpanzee experts, celebrities, and the general public.
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To take action to help these Chimpanzees and to thank Dr. Francis Collins, Director of the National Institutes of Health, for this wise and humane decision and to ask that NIH support the Great Ape Protection Act that is now before Congress. Here

Comparison of Chimpanzee skulls, jaws and teeth

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natal/postnatal infant practices of wild vs. captivity-born Chimpanzees and Bonobos

I received a comment today which I would like to provide the information I have found back to the person. I hope this is helpful. I am posting the comment so that anyone else that's interested can get educated.
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To whom... For an upcomming dental school lecture I am trying to find information on natal/post-natal infant feeding practices of wild vs. captivity-born chimpanzees and bonobos and how early feeding might impact later dental, jaw and facial development. I would appreciate any references you might be able to provide. Best Regards, (name deleted), DDS

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Hope you can find something that can be useful for your lecture

Chimpanzees and Humans might have interbred

The earliest known ancestors of modern humans might have reproduced with early chimpanzees to create a hybrid species, a new genetic analysis suggests.

 
 
 
 
 
 
 
 
 
Based on the study of human and chimp genomes, the scientists believe the split between the human and chimpanzee lines occurred much more recently than previously thought — no more than 6.3 million years ago and perhaps as recently as 5.4 million years ago.

Human and chimpanzee ancestors began branching apart on the primate evolutionary tree some 9 million years ago, but there are significant gaps in the fossil record. The new analysis suggests that a full split, which scientists call speciation, wasn't achieved for nearly 4 million years and might have occurred twice. The study was published online today by the journal Nature.

Researchers from Harvard Medical School and the Broad Institute of MIT and Harvard matched sequences of the human genome to the same regions of the genetic code of chimpanzees and several other primate species. DNA is made up of sequences of chemical bases, labeled A, T, G, and C. They compared the codes, letter by letter, and noted where there was a divergence.

Based on an estimated relative mutation rate, they calculated how long it would take to accrue the mutations and determined that millions of years of genetic divergence led to an initial speciation around 6.3 million years ago. From start to finish, complete speciation spanned a much longer time range than in any other modern apes. From start to finish, complete speciation spanned a much longer time range than in any other modern apes.

"The variation is huge," said study lead author Nick Patterson of the Broad Institute. "There are regions of the genome that don't appear to be much more than 5 million years old and there are regions that appear to be 4 million years older than that. The ancestral time over which humans and chimpanzees speciated, where there's no more gene flow, covers 4 million years."

X marks the spot

The team also observed that humans and chimps are very similar on the X chromosome, sometimes referred to as the female sex chromosome. The average age of the X chromosome in humans is about 1.2 million years "younger" than the rest of the chromosomes, and the final change occurred around 5.4 million years ago.

This suggests that after the first speciation at 6.3 million years in the past, early human ancestors may have lived and reproduced with ancestral chimps to produce hybrid primates.

"This would help explain why divergence on X between humans and chimps is so low," Patterson told LiveScience.

Mixing and matching genetic information from two species doesn't always work out well, and hybrid species often have trouble reproducing. The problem generally arises from differences on the X chromosomes.
"In a situation where it's unfavorable to have one X from one species and one from the other, which happens as hybrids reproduce among themselves, you get powerful selection for the good combination," Patterson said. "The X chromosome will fix out and everyone will have the same X."

What happened

Patterson explains one possibility for how this could have happened: The initial split occurred around 6.3 million years ago. Sometime after, the descendents of the earliest known human ancestor — the 6.5 to 7.5-million-year-old "Toumai," a biped that probably didn't look much different than chimpanzee ancestors — mated with ancestral chimps and created a hybrid species.

Scientists can't say how long the hybridization carried on, but the final speciation occurred around 5.3 million years ago, possibly because the two species' genetic coded were too different to mix or the animals were simply physically unappealing to each other.
"If that occurred, they might have been compatible enough on X that it would fix out to one species or another," Patterson said. "As it happened, it fixed to chimps, but it could have gone the other way."

This is just one possible explanation for the gap in speciation time, Patterson said, and is not meant to be interpreted as the full answer. Researchers at the Broad Institute are currently working on sequencing gorilla and other primate genomes and searching for similar patterns of evolution to help better tell the whole story.
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