Primatology.net

Thanks to Afarensis, I got my hands on Chororapithecus abyssinicus paper, “A new species of great ape from the late Miocene epoch in Ethiopia,” and I have read it. A lot of things have been clarified, such as my misunderstanding that the nine teeth were from one individual. The nine teeth are from at least three and at most six or more individuals. In all honesty, this was a stupid assumption for me to make. Other than finding the teeth inside a mandible or jaw or, it is hard to say with any confidence if any loose fossil teeth are from one individual.

For your viewing pleasure, here’s a line up of the culprits:

That said, the big thing we should be concerned about is the claim that,

“Phylogenetically, these fossils represent the first Miocene ape species to be recognized as a strong candidate for membership in the modern gorilla clade.”

The claim that these fossil teeth represent a Miocene ape is made by the ‘subtle’ similarities in size and proportions they have to a modern gorilla’s teeth. A quick disclaimer, the size of these teeth are not entirely the same to a modern gorillas… especially the molars. The various molars in this sample fall right in the largest and smallest range of modern gorilla size variation. On my other blog, Anthropology.net, I posted a fairly high resolution photograph with three of the teeth compared up to a gorilla’s jaw. In that image you can see how the overall size and form are similar.

Aside from the size, the morphology of the teeth is the other argument that supports a Miocene ape claim. The exact morphological condition is observed well below the surface, at the enamel-dentine junction, or EDJ.

You ask, “What is the enamel-dentin junction?” The EDJ is a landmark in teeth where the surface enamel, the hardest substance in body, meets dentin, the less mineralized and less brittle of the two. Unlike dentin, enamel does not contain collagen. The image to your right illustrates where enamel meets dentin. Another difference between enamel and dentin is that enamel has two types of proteins called amelogenins and enamelins, which most likely serve as a framework support.

Amelogenesis, or enamel formation, is first seen in the crown stage, which happens after the first establishment of dentin. Cells known as ameloblasts lay down amelogenins and enamelins matrix to form a partially mineralized enamel. This differentiates the two tissues in morphology. In another view, seen in image below, you see a histologial cross section of enamel (A) meeting dentin (B). Note how dentin is different, it is tubular.

Enough histology and development, talk. I can go on for days on how important teeth are in paleontology. The whole point of studying EDJ is that as a tooth forms, the growing enamel takes on the distinctive shape which was first shaped by the forming dentin. The EDJ is commonly studied in paleoprimatology, paleoanthropology, and even developmental biology and dental medicine.

Here’s a round up of articles that used EDJ to study human and primate evolution:

• Enamel thickness and the topography of the enamel-dentine junction in South African Plio-Pleistocene hominids with special reference to the Carabelli trait.
• Variation in hominoid molar enamel thickness.
• Modern human molar enamel thickness and enamel-dentine junction shape.
• The enamel-dentine junction of human and Macaca irus teeth: a light and electron microscopic study.

To study the EDJ of these nine teeth, three dimensional micro-computed tomography (micro-CT) was used for visualization. Micro-CT is usually used in medicine as a minimally invasive system. Micro-CT uses X-rays to create high resolution images. In the following excerpt you will read what was found from the mirco-CT analysis. I’ve attached figure 2 because if you are like me, you wanna see what what 3-D micro-CT scans look like, since it is such a high tech fancy pants methodology.

“In particular, the straight to weakly concave mesial protocone crest seen in the EDJ of CHO-BT 4, -BT 5 and -BT 6 is gorilla-like, and is formed by a mesiobucally located junction of the mesial protocone crest and mesial marginal ridge. Such spatial placements are best considered to be regulated by enamel-knot-related signalling patterns during early morphogenesis [23, 24], and may be one of the underlying causes of the mesiodistally elongate upper molar shape generally characteristic of folivorous primate species. In the lower molars, the most distinctive EDJ topography occurs at the trigonid crest, the structural counterpart that occludes with the upper molar mesial protocone crest. The high trigonid EDJ crest is continuous between the metaconid and protoconid cusp tips (Fig. 2). “

So only two ratios were used to measure cusp dimensions beneath the enamel cap. I don’t know why only two ratios were compared, maybe it is because the teeth were so deteriorated that only two measurements could be extracted. That’s okay though, the authors were more thorough in their cross species comparisons. In the supplemental materials, the comparison of internal cusp dimensions of Chororapithecus and gorillas was extended to chimpanzees and other apes… even Orrorin and Sahelanthropus, all with pretty large sample sizes.

With all that said, I am somewhat convinced these teeth represent Chororapithecus as an ancestor to the gorilla lineage. Why I am uncertain, is as I said earlier… the big unresolved issue… These ape-like set of teeth come from 10 million years ago.

This shakes up our understanding of primate evolution.

Check out the illustration of the stratigraphy where the fossils came out from… it is to your right. I won’t doubt where in the ground these teeth came from.

I was never a subscriber to the hypothesis that apes arose in Eurasia and migrated to Africa, and this 10 million year old African ape is a fitting blow to that hypothesis. I was taught to keep it simple. Old World monkeys gave rise to hominoids, during the Eocene, about 60 million to 34 million years ago and dryopithecines are orangutan ancestors.  The orangutan lineage was in Africa prior to the first migration of Miocene, around 23-25 million years ago of apes from Africa to Eurasia. With the exception of a 9.5 million year old maxilla, no other ape fossils have been found in Africa between 12 million and 7 million years ago. This finding is important in that it fills in that gap of the fossil record.

I was subscribed to the 4 million year old human-chimp speciation time and the orangutan-human divergence of 18 million years that was found earlier this year through sequence comparisons of genomes. In the paper, Suwa et al. challenge this, they say,

“we consider that a species split of 20 Myr ago for Pongo, 12 Myr ago for Gorilla, and 9 Myr ago for Pan are all probable estimates… We consider that the early divergence hypothesis is congruent with both fossil and molecular data…”

As you can see, these dates are not congruent. There is a 2 million year gap between what the molecular evidence tells us and the estimation made by Suwa et al for Pongo and a even larger spread for Pan. If I am to believe the genetic evidence, a 10 million year old ancestor to gorillas would not have existed. But, the teeth are convincing and look like a gorilla. Can the genetic studies have calculated the times of divergence incorrectly? Yes, it is possible if the molecular clocks they used weren’t properly calculated.

What is one to do?

A new Nature paper announces a new species of Miocene great ape, Chororapithecus abyssinicus, and both the press and the blogosphere are having a field day with this publication. From our neck of the woods, Afarensis, P.Z. Myers and John Hawks have commented on the paper and from the press Jay Kelly, Peter Andrews, and Richard Potts. No one is fully convinced.

Before, I get into the thick of it, here is a photo of the nine teeth that Suwa et al. say belong to the new Miocene great ape.

These teeth are 10 million year old. And Suwa et al. say the teeth are gorilla-like. Specifically the tooth morphology at the enamel-dentine junction is like that of a gorilla, but christened a new species name to these teeth. Hawks criticizes the findings,

“Nor is it entirely obvious that Chororapithecus is actually gorilla-like in these characters. The paper compares two ratios involving cusp dimensions measured internally beneath the enamel cap. That’s high-tech, but the ratios do not sort out gorillas from chimpanzees, don’t sort Chororapithecus from either of those apes or early hominids, and — even worse — it’s not even clear how these ratios may vary with size. Does Chororapithecus look sort-of like a gorilla on these ratios because it’s a sort-of gorilla? Or because it’s big? The enamel is relatively thicker than gorillas, like other Miocene apes and orangutans. Clearly the specimen is much less derived than gorillas, but could that be because it isn’t a gorilla?

Well, there’s the problem: there’s not too much to go on with these teeth. I think Suwa et al. laid out as good a case as there is. A 10-million-year-old gorilla can’t be expected to look just like gorillas today.”

In their defense, Suwa and crew are saying the teeth belong to a member of the gorilla family stem from similarities with teeth of modern gorillas.

Others are are criticizing this conclusion because it completely goes against what the genetic evidence has been telling us. Early this year two papers reassessed the time at which hominids diverged from the other great apes, and that was about 7 million years ago. If teeth are the safe-houses of genotype to phenotye, a common understanding in evolutionary studies, the two lines must agree. With a 10 million year old gorilla like ape and a suggestion that the split happened earlier than 10 million years ago, this just screws with the genetic findings, and further complicates the relationship between paleoanthropology and molecular evolution.

Until I read the paper and I’ll leave you with what Afarensis said,

“You would have thought paleoanthropology would have learned something from Ramapithecus. Dental gorillas don’t mean actual gorillas. Just like being a dental hominid didn’t make Ramapithecus a real hominid.”

The amount of evidence that is out there in support of chimpanzee culture is rather overwhelming if you ask me. Most primatologists will agree that these socially, intellectually, and emotionally complex great apes have unique behaviors and learning systems that begin to mimic our own cultures and social structures.

In a new Current Biology research paper, the people from the Scottish Primate Research Group along with Frans de Waal, have reported their observations where they,

“taught individual chimpanzees one of two ways to solve complex foraging tasks, and observed how the different techniques spread across two sets of three groups. The chimps had to manipulate a combination of buttons, levers or discs to extract treats from cubes….

….[then the chimps] in the two groups learned quickly how to work the devices when watching a peer who had been trained in one of the two possible sets of solutions.

Within a few days, most chimps mastered the techniques that had been “seeded” this way in their group…

…The cubes were then moved into the view of a second set of chimp groups, so they could observe their respective neighbors solving the tasks. The new groups learned the same techniques as demonstrated in the adjacent enclosure, and then passed their set of tricks on to a third group in another round of experiments….

…Next [they] want to unravel exactly how chimp culture spreads: “We need to see how status and prestige of different animals affect who learns from whom.”

An analysis of Whiten’s group’s studies already shows that the order in which individuals in each group picked up new traditions was similar for foraging tasks, but not for unrelated tasks, giving first insights into the dynamics of cultural transmission.”

Their paper is titled, “Transmission of Multiple Traditions within and between Chimpanzee Groups,” and their abstract ends with the following conclusion: parsimony suggests culture was shared with [chimpanzee and human's] common ancestor. Pretty bold statement, which has some flaws, because chimpanzee’s cultural behaviors could have evolved independently of humans just as likely as they could have evolved dependently of humans — if that makes sense.

Primatology.net has a sister site, if you don’t know already, and that’s Anthropology.net. This evening I put up a post there that may interest any one keen to primate locomotion and/or human evolution. The post is specifically on orangutan locomotion, specifically on how some researchers have observed a set of Sumatran Orangutans exhibit bipedal tendencies.

If this sounds kinda sorta familiar to this very recent post, “On the biophysics of Sumatran orangutan swaying,” it is!  The same researchers that observed orangutans cheat the system and choose limbs that help them sway the best have published a new finding on bipedalism amongst the same population.

The following post is a departure from my usual reporting on an interesting primate related tidbit of research. I’ll be posting about how I have thought about how to study primate brain evolution research. These are just ideas I have brainstormed. It is very probable that people are doing this out in their respective labs but I’m not in the know of what’s totally current. I hope you are interested in what scope of primate brain evolution research I will be discussion… I’ll be mostly taking in a functional genomic and computational biology approach, but that’s not to say more objective sciences such as psychology can’t fit into this game plan.

To start off, understanding primate brain evolution, specifically the biological mechanisms by how the primate brains have been positively selected for by size involves two complementary aspects of research. One of it is to identify the genes involved in brain growth and development, as well as their expression patterns. This is wet lab work, a whole lot of tissue sampling, mRNA isolation, cDNA synthesis and RT-PCR amplification, gene quantification and qualification and ultimately sequencing. At this level, one would need to sample multiple samples of representative primates (that have their genomes sequenced) and different developmental stages and populations.

Once these key players can be identified, the functions of these genes need to be well understood. Of course making knockout monkeys will be a costly and time consuming endeavor full of ethical issues, so I imagine having knockout neuron cultures can help understand the function of these genes better when they aren’t expressed. That’s a bit hard, neurons are awfully fickle to grown in culture. Maybe reporter constructs? Also, other non-traditional research such as sequence homology to other known proteins can help isolate potential functions based on structure.

Now once these key developmental genes have been classified, their relative importance should be noted… or in other words, one needs to organize which genes are specific to all primates and which are specific to fewer primates. Do these genes correlate with the known lineage of primates? If a unique pattern can be extracted, this will make the second aspect of research much easier and conclusive. This is the computational biology approach, using computers, statistics, and other mathematical models to identify what genes were mutated the most to yield the most growth. What genes remained fairly consistent? Can we estimate ages of coalescence or divergence, are there unique mutations to populations or species of primates… ultimately can we begin to make a phylogenetic tree of these genes and their changes throughout evolutionary time?

As I currently laid it out, these two field complement each other and if anything one is dependent on the other. Currently, I know of computational studies that seem to search high and low to find genes that have been positively selected for in primates by scanning and comparing entire genomes. If a hit is found, the research then shifts backwards to estimate functions based on the sequence homology to other known genes and their functions. While that maybe a useful, quick and easy approach, it’s all sorts of wrong. It is wrong because it is the needle in the haystack method. I advise one first narrow down the list, by doing the functional genomic screens, which is arduous and tedious, but much more quantitative and thorough. That way, one can limit things down to candidate genes specific to a species, developmental stage, etc. The playing field will be much more narrow and the computations will be much more conclusive.

What do you think? Do I have it right, do I have it wrong? Not to be rubbing my ego, but I think I have a thorough plan here — one that would make the most killer dissertation ever. Do you know of any researchers doing it this way? If any one out there, who reads this blog, carries out primate brain evolution research please feel free to comment and discuss. I’m really curious to know if what I have been thinking is even right.

For you osteology buffs out there, I want to let you know about the Digital Morphology database, if you don’t already know about it. I actually didn’t know about it myself, until I read about an extinct platyrrhine, Tremacebus harringtoni, from Afarensis’ ‘know your primate‘ periodical. The Digital Morphology (DigiMorph) database currently has about 400 species listed. If you are wondering what the database specializes in, I think the name should give you a clue as well as my shout-out to all y’all osteologists… but here’s a more formal introduction from their website,

“Digital Morphology library is a dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth’s biota.”

This database is brought to you by the University of Texas at Austin, and is an excellent execution of organization and quality, structured content. I personally love this resource. I see it as a supplement to many fields.

I also personally appreciate it because I like to see biological data be shared freely. Databases like Genbank have paved the way for natural scientists and medical professionals to share genomic data and sequences. But their data is relatively more easy to share. Agreeing upon a uniform structure to share sequence data is straight-forward – a sequence is a sequence is a sequence. It’s really kinda hard to mess up sharing raw-text data.

But, databases that specialize in phenotypes or physical characteristics of living things have proved to be more challenging. Agreeing upon uniform data fields has become one of the major challenges because there is sooo much variation. If you think about, the only fields we could effectively really categorize some living things are the major distinctions between the three major domains. Secondly, is the logistical aspects of it. Many ways we could gather phenotypic data is locked away in many museums and institutions. Some have restricted access, and to overcome the bureaucratic loopholes to get access to a skeleton is almost as hard as agreeing upon a way to structure the database. Another logistical challenge is how to document the phenotype. Photographs may seem logical, but they aren’t. First come image resolution and photographic skills. These variables can ultimately affect quality control.

And that’s where the DigiMorph’s X-ray tomography comes in. Data is totally digital and uniform. It is not related to how the photographer stages the specimen nor the quality of the camera used.

So, I’m pretty sure you are wondering, after all this blabbering and cheerleading I have done, of what importance is this to you as someone interested in primatology?

Well, if you study functional anatomy, how an animal’s body form relates to its function in life, this database is for you… especially if you do not have access to a laboratory with comparative samples! For example, you can analyze the sexual dimorphisms between a male and female tufted capuchin skulls on your own computer. I’ve plucked two lateral views of each skull for you to give it a run. Ask yourselves what differences do you see between the male and female skull? If you can make these observation I think you can see how this database is pretty nifty — cuts out the hours spent with a caliper and sketching bones out in a lab that may not have what you need!

Anyways, I hope you also find DigiMorph useful. If you want to browse their primate collection, their mammals category seems to be the deepest taxonomic level to get to the monkeys, apes, tarsiers, etc.

From the paleoprimatology department comes news that a second intact cranium of Aegyptopithecus zeuxis has been found and is, ‘”extraordinarily unusual,” …mainly because it’s complete and uncrushed.’ This fossil cranium is important because tells us a lot about what was going on with primate brain evolution many million years ago.

The fossil cranium was found by Elwyn Simons, a primatologist at Duke University, and his colleagues. Aegyptopithecus zeuxis is around 30 million years old and believed to be an old world monkey. From National Geographic News,

“The completeness of the fossil skull allowed Simons and colleagues to take computerized x-rays and create a virtual model of the specimen’s tiny brain.

Based on analyses of previous fossil skulls collected at the dig site outside Cairo…, scientists had assumed the ancient monkey’s brain was larger and more advanced.

The new fossil indicates Aegyptopithecus had a relatively primitive brain compared to its descendants…

Nevertheless, the brain region responsible for vision, called the visual cortex, was large. This suggests that, like many primates, Aegyptopithecus had good vision.”

From the x-ray scan, Simons and team also found out there was a great degree of sexual dimorphism… an anatomical size phenomenon between males and females. In this situation the newly discovered fossil was a ‘female, which may have weighed about 5.5 pounds (2.5 kilograms)’ while the older Aegyptopithecus was a male, twice the size.

Dean Falk, an anthropologist that specializes in primate brain evolution, specifically hominid brain evolution, commented on the finding. She said this finding,

“”challenges “perceived truths” that large brain size was required for things like daytime activity and living in large social groups.

“[The new study] is saying you don’t have increased brain size back when you have some of these things,” she said.

In fact, Falk believes the virtual model of Aegyptopithecus’ brain, used in the new study, suggests the brain was even less advanced than the researchers propose.

However, Falk agrees that the brain model does confirm an enlarged area for vision, suggesting good eyesight was important early on for our ancestors.”

From what I am gathering this is an important conclusion that implies the primate brain expanded vision before it enlarged anywhere else. Of course more fossil primate skulls could support that or show that this feature happened in the Aegyptopithecus lineage.

The results of the x-ray analysis of Aegyptopithecus have apparently been published in PNAS, a journal notorious for letting press releases come out way before the actual publication. That being said, I don’t have a link to the actual publication as of now.

In chimpanzee communities, it pays to be close with your maternal brethren, according to a brand new publication in the latest issue of the Proceedings of the National Academy of Sciences. The large chimpanzee population at Ngogo in Kibale National Park, Uganda, was studied for this research paper both thru behavioral and molecular approaches. I’m assuming the molecular techniques were used to trace pedigrees and lineages.

The specific scope of the research was to assess the kinship relations among male chimpanzees in this population. From the abstract of paper, the research,

“show[s] that male chimpanzees clearly prefer to affiliate and cooperate with their maternal brothers in several behavioral contexts. Despite these results, additional analyses reveal that the impact of kinship is limited; paternal brothers do not selectively affiliate and cooperate, probably because they cannot be reliably recognized, and the majority of highly affiliative and cooperative dyads are actually unrelated or distantly related. These findings add to a growing body of research that indicates that animals cooperate with each other to obtain both direct and indirect fitness benefits and that complex cooperation can occur between kin and nonkin alike.”

What does that mean? We already knew chimpanzee social structure is highly maternal and usually dominant mother chimps raise dominant sons. Well this research adds to this, indicating that sons, or ‘princes’ if you may, establish a network to dominate hierarchy over the population they preside… sorta like a chimpanzee royalty.

I’m a bit uncertain about the statement on how paternal brothers can’t identify one another… On one level, this seems logical. Its very improbable to know “who your daddy is” in a chimpanzee troop. But, a chimpanzee intimately knows his or her mother, because she reared him or her. However chimpanzees have a very high intellectual capacity, and I’m thinking they know at some level who fathered them. I won’t be willing to bet my life savings, but it is very probable.

If you would like to read more about the article, please check it out under this title and link, “The limited impact of kinship on cooperation in wild chimpanzees.” One last note, I’m not surprised this fieldwork & molecular 1,2 combo came from the primatological powerhouse that is Max Planck Institute’s department for Evolutionary Anthropology, are you?

A new study has changed the lives of seven mandrills for the better at England’s Chester Zoo. With the help of zoo staff, Durham University researchers found that placing shrubs between the glass enclosure and the visitor’s area reduced stress levels (as seen through aberrant behaviors) and increased natural behaviors.

Examples provided:

• approaching the glass
  • 54% decrease

• climbing and eating
  • 13% increase

• playing and grooming each other
  • 16% increase

Dr. Jan de Ruiter, Department of Anthropology, Durham University:

“We initially found some levels of stress among the mandrills. Their behaviour showed signs of anxiety and social tension. Visitors can further aggravate this stress as some people interpret the mandrills’ behaviour as amusing and start mimicking them.”

“As soon as the shrubs were positioned, we noticed an immediate improvement in the welfare of the mandrills, who displayed significantly less anti social behaviour. The botanical display also adds to the visitor experience as they gain a more natural impression of the type of environment in which the mandrills would be living in the wild in Africa.”

Makes sense doesn’t it?

As for visitors further aggravating the stress… as I’m sure many of us can, I can certainly vouch for that. Spending months observing behavior in the Monkey House at the Bronx Zoo, opened my eyes to the insensitivity of some individuals who feel it is acceptable to bang on the glass enclosure, yell at the animals, and egg them on in an infinite number of ways. While shrubbery won’t stop some people from being themselves, it sounds like it’s successfully keeping the distance and making life a little calmer for the mandrills. Excellent news.

Dr. Sonya Hill, Research Officer at Chester Zoo:

“This study shows that by measuring the behaviour of animals in their habitats, whether they be in the wild or in a zoo, we can understand their needs and preferences better. In this way, researchers can ‘ask’ the animals what they want. Zoos can then provide enclosures that aim to meet these needs and maintain good animal welfare. It is important to remember that life in the wild is not stress-free either, with factors such as predation, competition for food, and disease or injury, and as we learn more about each species we can understand what behavioural strategies they use to cope with their environment.”

The effort of the researchers has been recognized by UFAW (Universities Federation for Animal Welfare) and honored with the Wild Animal Welfare Award. The money awarded will be used for further animal welfare research at Chester Zoo.

A new genus and three species of primate have been announced at last month’s annual meeting of the American Association of Physical Anthropologists, and we just got news of it via Science Daily. The announcement has come by way of Jim Westgate, a professor of earth and space sciences at Lamar University and also research associate in the Vertebrate Paleontology Laboratory, Texas Natural Science Center, University of Texas-Austin. Pretty impressive breadth of disciplines for a paleoprimatologist, no?

Westgate and his team of colleagues recovered a molar, pre-molar and incisor teeth from the new primate genus and three other new primate species. The fossils were found in a,

“42 million-year-old tropical, mangrove palm swamp deposits of the Eocene age Laredo Formation exposed in Lake Casa Blanca International State Park in Laredo.”

The primates are Omoyids, members of the extinct family Omomyidae, which resemble tarsiers in form. The binomial names for these extinct primates haven’t been formally released, but I think they will be called Paralomys. The Science Daily article describes Omoyids a bit more artistically,

“Omomyids had large eye orbits, long grasping fingers and short snouts. They weighed around one kilogram, or close to two pounds and were likely nocturnal, with large eyes for seeing better at night. Like most modern-day primates, the omomyids used their long fingers for climbing. They had small mouths, and it is likely that insects were a part of their regular diet.”

Aside from ascribing a new genus, this finding is significant because it shows how four species of primates lived on the Texas coast line about 42 million years ago. This gives us an insight to the ecosystem of that era, and how it changed upon the time the Rocky Mountains were raised.

I don’t have much else to run off of this press release, other than the information I just conveyed back to you, But Westgate was quoted to say that,

“formal name of the new genus, which means “primate of the coastal lagoons” [Paralomys], will be released at publication time.”

UPDATE: Betsy had already posted this news, a while back. I forgot to double check when I posted this, so be sure to check out what Betsy wrote as well, here.