Primatology.net

The orangutan genome has been sequenced and published in today’s Nature. The paper, “Comparative and demographic analysis of orang-utan genomes,” is open access for you to read for yourself. I’ll be highlighting some of the high points in this post. Devin Locke, a structural geneticist at Washington University School of Medicine in St. Louis, Missouri, headed the sequencing of six Sumatran and five Bornean orangutans. As you may know Pongo abelii, or the Sumatran orangutan, is a separate species from Bornean orangutans — Pongo pygmaeus.

One remarkable finding of the study is the estimated divergence between the Sumatran and Bornean species. The team calculated the two species diverged 400,000 years ago. We know that land bridge between Indonesia’s Sumatra and Borneo split at least 21,000 years ago but until now we’ve never known at what time the two speciated.

Compared to the two other great apes whose genomes have been sequenced, humans and chimps, the orangutan genome has changed much less. We’re still waiting on the gorilla genome to be finished. Oangutans originated some 12 million to 16 million years ago. Theoretically, orangutans have had more time to accumulate  genetic variation compared to humans and chimpanzees, which split into their own lineages 5 million to 6 million years ago. One would expect at least twice as much variation in the orangutan genome. However, in the study, a comparison of the three genomes shows that humans and chimpanzees have lost or gained new genes at twice the rate of orangutans.

Why’s that?

The paper explains that orangutan genomes have much fewer active retrotransposons than human and chimp genomes. Retrotransposons, or Alu elements, are essentially jumping genes, that replicate, and amplify then insert into different parts of the genome. The initial 2001 draft of the human genome reported that around 42% of the human genome is made up of retrotransposons. The authors of the orangutan paper illustrate that the human genome has ~5,000 Alu elements, whereas the orangutan genome has 250. This is significantly different. The authors write,

“Reduced Alu retroposition potentially limited the effect of a wide variety of repeat-driven mutational mechanisms in the orang-utan lineage that played a major role in restructuring other primate genomes.”

Personally, and this is my thinking here nothing the authors say — a common source of many human retrotransposons are to prehistoric viruses that integrated into our ancestral DNA. Viruses are communicable. Orangutans are the most solitary Great apes. I suspect they would have much less exposure to viruses because of their social structure, and thus much less chance of insertion of retrotransposon. Again, this is a hypothesis of mine, and I could be very wrong to think this.

Comparison of Orangutan to Great Ape Alu sequences

One last finding, I want to bring up was published in another paper released by the same team, but in the journal Genome Research. In the paper, “Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection,” coauthors of the previous study write that there are many similarities to the human and orangutan genome, much more similar than human to chimp, in fact. They suspect that could be because humans split from a common ancestor with chimps, of which both species had the same ancestral orangutan DNA. What remains curious is that humans and chimpanzees have evolved separately for millions of years. In the process, chimps for mysterious reasons lost some orangutan DNA that humans retained.

As often in sciences, many more questions arise from studies like these but I am excited that the age of genomics is shedding more light on our fellow primates!

Locke, D., Hillier, L., Warren, W., Worley, K., Nazareth, L., Muzny, D., Yang, S., Wang, Z., Chinwalla, A., Minx, P., Mitreva, M., Cook, L., Delehaunty, K., Fronick, C., Schmidt, H., Fulton, L., Fulton, R., Nelson, J., Magrini, V., Pohl, C., Graves, T., Markovic, C., Cree, A., Dinh, H., Hume, J., Kovar, C., Fowler, G., Lunter, G., Meader, S., Heger, A., Ponting, C., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J., Eichler, E., White, S., Searle, S., Vilella, A., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darré, F., Farré, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Valle, G., Purgato, S., Rocchi, M., Konkel, M., Walker, J., Ullmer, B., Batzer, M., Smit, A., Hubley, R., Casola, C., Schrider, D., Hahn, M., Quesada, V., Puente, X., Ordoñez, G., López-Otín, C., Vinar, T., Brejova, B., Ratan, A., Harris, R., Miller, W., Kosiol, C., Lawson, H., Taliwal, V., Martins, A., Siepel, A., RoyChoudhury, A., Ma, X., Degenhardt, J., Bustamante, C., Gutenkunst, R., Mailund, T., Dutheil, J., Hobolth, A., Schierup, M., Ryder, O., Yoshinaga, Y., de Jong, P., Weinstock, G., Rogers, J., Mardis, E., Gibbs, R., & Wilson, R. (2011). Comparative and demographic analysis of orang-utan genomes Nature, 469 (7331), 529-533 DOI: 10.1038/nature09687

Hobolth, A., Dutheil, J., Hawks, J., Schierup, M., & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection Genome Research DOI: 10.1101/gr.114751.110

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.

Science just published a whole slew of papers, posters, news articles, and the like on the Rhesus Macaque because the macaque genome, the first monkey genome to be sequenced, has been unveiled today.

I haven’t read all of the content in this special issue, but from what I have skimmed so far it’s all focused on the genome, of course, but also mobile DNA, genetic relations between two macaque populations, the roles of macaques in biomedical research etc. Rhesus macaques have been used as a model organism in biology for quite sometime, and this special edition of Science pays homage to this magnificent Old World monkey.

I’ve rounded up the links, if you’d like to click around and read some more about these monkeys:

• A Barrel of Monkey Genes
• Boom Time for Monkey Research
• Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
• Mobile DNA in Old World Monkeys: A Glimpse Through the Rhesus Macaque Genome
• Poster: The Macaque Genome
• Evolutionary Formation of New Centromeres in Macaque
• Demographic Histories and Patterns of Linkage Disequilibrium in Chinese and Indian Rhesus Macaques

If you can’t check out all the content, I understand. I’ll be upset, but I’ll get over it. At the very minimum, you should check out the interactive poster that aids in

“exploration, as well as embedded video featuring seven scientists discussing the importance of the macaque and its genome sequence in studies of biomedicine and evolution. We have also created an accompanying teaching resource, including a lesson plan aimed at teachers of advanced high school life science students, for exploring what a comparison of the macaque and human genomes can tell us about human biology and evolution. These items are free to all site visitors.”

I’ve included a screenshot of to wet your monkey lovin’ appetite:

A new statistical calculation called the hidden Markov model has been applied to four regions of the human, chimpanzee and gorilla genomes as reported in the PLoS Genetics journal.

But, before I jump into a discussion of the implications of this paper, let me explain to those unfamiliar with the hidden Markov model that it was,

“developed in the 1960s and originally applied to speech recognition.”

The calculation takes observable sequences, such as DNA from several genomes in this case, and seeks to fish out hidden parameters. It does this by isolating common genetic patterns from outliers throughout the genomes being compared. Of which the amount of difference and similarities can help calibrate a molecular clock. If you are curious about this statistical test, please check out Wikipedia’s entry on hidden Markov models.

In the paper, “Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model,” the authors analyze the results from these hidden Markov model calculations and claim their findings shifts the gap between human-chimpanzee divergence from 5-7 million years ago to around about 4 million years ago. Furthermore, they claim they have evidence that,

“it took only 400,000 years for humans to become a separate species from the common chimp-human ancestor.”

The abstract, if you care,

“The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.”

You maybe asking, how did they do this? Molecular clocks, friends, which I briefly mentioned above. Molecular clocks are effectively patterns in mutations in genomes that we expect to stay fairly consistent throughout evolutionary time. Previous molecular clocks, as reported on Time Tree, average for the time of nuclear divergence between human and chimpanzee lineages to be around 5.56 million years ago. The new hidden Markov model recalibrates, narrowing several parameters such as the time at which humans diverged from other ape lineages.

The following figures from the paper best portrary the results. You will see errors above the points plotted, and those are associated with the estimatation calculated via hiden Markov model. On the x-axis targets 1 refers to Chromosome 7, targets 106 to Chromosome 20, targets 121 to Chromosome 2, and 122 to Chromosome 20. The first is a population genetics parameter for time of divergence and the second time of speciation.

Note how a, or human chromosomes, sampled, consistently stays around 4mya.

Note how t1, or human chromosomes, compared, stays around 4mya, too. While the error bars are large, the study is pretty convincing. This study is also interesting.

It shows us that up until 4 million years ago, there was a lot of genetic introgression but a complete cessation of gene flow occurred abruptly. As John Lynch, from Stranger Fruit, points out,

“The age of 4.1 million years would apparently put the split during the time of such taxa as Australopithecus anamensis, A. afarensis and Kenyanthropus platyops. It will be interesting to see how this affects our current understanding of hominid evolution.”

Some news reports about this paper:

• Chimps, humans split only 4 million years ago
• Study moves chimp-human split to 4 million years ago

Professor of Bioanthropology, Dr. Colin Groves, of the Australian National University’s Department of Anthropology has spent sometime studying a population of gray-cheeked mangabey (Lophocebus albigena). And his time spent studying this population has not been in vain. He actually found a novel trait in the skulls of this population of mangabeys, unique enough to be soon be designated as a new species, the Ugandan gray-cheeked mangabey (Lophocebus ugandae), as reported here.
I don’t have a picture of this new species to share you (to the right is a image of a regular gray-cheeked mangabey), nor do I have a publication where Groves documented his findings. Curiously, he,

“had not thought it a priority to publish it – [he has] so many other things to be getting on with.”

But he did present his findings at the International Primatological Society Congress in Entebbe last year and said he will now publish his findings because the forest this new species inhabits, the Mabira Forest, is threatened

“and the loss of this population would probably mean the loss of about a quarter of the total population of what now turns out to be an endemic species.”

Which is commendable. But that statement makes me wonder if the Mabira deforestation pressure not been around, would Groves ever publish his findings?

Furthermore to complicate the validity of this news species, Groves spoke candidly of his method that he used to speciate the new Ugandan mangabey. He calls his method ‘multivariate analyses’ which means to me one relies on two or more variable traits…. but all he shares with the news is one skull measurements! He intends to expand his study, using multivariate analysis to clarify whether other recognized subspecies of Lophocebus albigena can be broken to species level (osmani, johnstoni), which I think is a bit shakey.

I would much rather people sample DNA and use genetic analysis to define a species of primates. And in this case it is possible to do so. Genetic analysis is far more quantitative, definitive, and reliable than measuring skulls (which is a highly variable phenotype between sexes, ages, and environmental/health pressures of primates).

Part of the blogosphere that normally I keep under my radar has been carrying a lively discussion about a new paper from the Proceedings of the Royal Society of London on domestic violence among chimpanzees in the wild. The paper is aptly titled, “Male coercion and the costs of promiscuous mating for female chimpanzees” but most of your attention should focus on Shelly Batts’ post, “Domestic Violence in Chimps.” If you want, here’s the abstract to give you a sense on what the authors accomplished in their study,

“For reasons that are not yet clear, male aggression against females occurs frequently among primates with promiscuous mating systems. Here, we test the sexual coercion hypothesis that male aggression functions to constrain female mate choice. We use 10 years of behavioural and endocrine data from a community of wild chimpanzees (Pan troglodytes schweinfurthii) to show that sexual coercion is the probable primary function of male aggression against females. Specifically, we show that male aggression is targetedd towards the most fecund females, is associated with high male mating success and is costly for the victims. Such aggression can be viewed as a counter-strategy to female attempts at paternity confusion, and a cost of multi-male mating.”

Shelly does a good job summarizing the basis of the paper, which tries to give some evolutionary/reproductive success clarification for why male chimps beat up female chimps. She writes,

“during estrus, the competition for access to these few fertile females is intense. The leading theory, albeit a shaky one, is that the physical abuse is punishment for female chimps’ promiscuity. By bullying them, they are discouraged from seeking other males, making it more likely that resulting offspring is his. Another explanation is simply that the violence is the result of disputes over food resources.”

That’s what this paper tries to tackle and ends there, however as people read the paper or third hand reports of the paper they get a distorted sense of what was originally published. They quickly anthropomorphize this behavior.

Some of the comments at Shelly’s post show me how quick to interpret people are over an observed behavior. While some of the comments are really insightful, some of them are not so much, and some of them have moments of brilliance confounded with a truly reactionary comment. Take this one for example, it comes from feminazi… so you can see where this is going. At first feminazi starts out with an astute observation,

“Males have always possessed the desire to control female reproduction and they use violence or the fear of violence as a control mechanism. “

Then feminazi goes off the deep end with,

“Perhaps if male chimps could develope an artifical womb and make their own children would they finally stop trying to control females’s lives. But then they’d probably just sell the baby female chimps to other males and abuse them… Males suck. Truth hurts. Deal.”

In contrast, Joy Spoiler’s comment is excellent. It really gives me a sense this person can separate an observed behavior and its implications on a larger scale. Here’s what he/she wrote,

“…I’m really tired of science as victim narrative in anthropology. Scientists make distinctions between things that are different. Phrases like “domestic violence in chimps” are anthropomorphic fallacies and inappropriate value judgements that confuse people who aren’t trained to make such distinctions.”

Shelly’s not to blame she left the interpretation out of her post. And I don’t know who really is in this matter. Could feminazi and crew have read another report upon which they jumped to their irrational, outlandish conclusions? Perhaps. There’s a news article on this study over at Science Magazine by John Bohannon that perpetuates some of the misconceptions. John writes naively that chimps don’t “believe in monogamy.” That’s not the case John, it is hard to argue that chimps believe in a set lifestyle that we decide upon and to phrase the comment like that you subjugate people to start thinking as if chimps think the ways we do, and live the ways we do.

Chimps do not. They are one of our closest evolutionary relatives, we share a common ancestor with chimps… we have some similarities as far as social structure, behavior, morphology, and genetics for example. But we are different. We can’t take those similarities and apply them to the same situations that occur in our lives. We need to stop jumping to conclusions. Bonobos, a great ape similar to chimpanzees (actually more similar to us than we are to regular chimpanzees) do not have this ‘domestic violence’ in their society. What about that, how does this change feminazi and other reactionary comments?

What we need to understand is that chimps live in a completely different socio-cultural context from us. We need to drop this bias quickly if we want to study chimpanzees and other organisms in the context they live in… and not in the context we live in or see them living in.

If you’re interested in paleoprimatology and phylogeny at all, a new paper in PNAS titled, “New Paleocene skeletons and the relationship of plesiadapiforms to crown-clade primates” has just come out. If you don’t know Plesiadapiforms are archaic primates who lived in the Paleocene. The study focuses mostly on the initial divergence of primates, and uses some new Paleocene plesiadapiform skeletons for their analyses. And the authors conclude that these plesiadapiforms fall in line with Euprimates and indicate that the divergence of Primates from other euarchontans happened right around the Cretaceous/Tertiary boundary or 65 million years ago. Here’s the abstract where I got these conclusions from, once I’m at school, I’ll print off the article and read it in my free time,

“Plesiadapiforms are central to studies of the origin and evolution of primates and other euarchontan mammals (tree shrews and flying lemurs). We report results from a comprehensive cladistic analysis using cranial, postcranial, and dental evidence including data from recently discovered Paleocene plesiadapiform skeletons (Ignacius clarkforkensis sp. nov.; Dryomomys szalayi, gen. et sp. nov.), and the most plesiomorphic extant tree shrew, Ptilocercus lowii. Our results, based on the fossil record, unambiguously place plesiadapiforms with Euprimates and indicate that the divergence of Primates (sensu lato) from other euarchontans likely occurred before or just after the Cretaceous/Tertiary boundary (65 Mya), notably later than logistical model and molecular estimates. Anatomical features associated with specialized pedal grasping (including a nail on the hallux) and a petrosal bulla likely evolved in the common ancestor of Plesiadapoidea and Euprimates (Euprimateformes) by 62 Mya in either Asia or North America. Our results are consistent with those from recent molecular analyses that group Dermoptera with Scandentia. We find no evidence to support the hypothesis that any plesiadapiforms were mitten-gliders or closely related to Dermoptera.”

Check out some other resources on Plesiadapiforms and primate evolution here:

• Fossil Remains: The Plesiadapiformes and the Origins of the Primate Order
• Primate Taxonomy, Plesiadapiforms, and Approaches to Primate Origins

I’ve cross posted this over at Anthropology.net, just in case.

John Hawks expands on a paper that I introduced several months ago. The paper has been online for a while but has appeared in the January 2007 edition of the Journal of Human Evolution, it is titled, “Variation in brain size and ecology in Pongo.” Hawks briefly criticizes a flaw in the experimental setup of the paper, specifically about comparing the brain sizes between populations of orangs,

“Well, not exactly, since a relatively faster development might still be slowed in the resource-stress environment. The real test would be to compare the two subspecies in captivity where they presumably have similar (and sufficient) diets.”

He continues on a discussion about his thoughts about how,

“high diet quality under resource stress requires a larger (i.e. smarter) brain, while a sacrifice of diet quality with dependence on low-energy fallback foods selects for a smaller (i.e., lower energy cost) brain.”

And ties it to the Homo floresiensis debacle. It’s a quick and interesting read about how environment influences bodies, population, and ultimately evolution of primates.

Today’s interesting press release from the University of St Andrews calls attention to a paper on the singing behavior of gibbons as a mechanism to ward off predators in addition to mating practices. Esther Clarke, Klaus Zuberbuhler, both of the University of St Andrews and Ulrich Reichard, of the Max Planck Institute observed the singing behavior of white-handed gibbons in Khao Yai National Park, Thailand. The experimenters said:

“We are interested in gibbon songs because, apart from human speech, these vocalizations provide a remarkable case of acoustic sophistication and versatility in primate communication. Our study has demonstrated that gibbons not only use unique songs as a response to predators, but that fellow gibbons understand them.

This work is a really good indicator that non-human primates are able to use combinations of calls given in other contexts to relay new, and in this case, potentially life-saving information to one another. This type of referential communication is commonplace in human language, but has yet to be widely demonstrated in some of our closest living relatives – the apes.

Not unlike humans, gibbons assemble a finite number of call units into more complex structures to convey different messages, and our data show that distant individuals are able to distinguish between different song types and understand what they mean. This study offers the first evidence of a functionally referential communication system in a free-ranging ape species.

Finding this ability among ape species, especially gibbons who in a sense bridge the evolutionary gap between great apes and monkeys, could shed light on when this ability developed in the primate lineage.”

Here’s the paper.